WorldWideScience

Sample records for tissue-specific congener composition

  1. Tissue-specific congener composition of organohalogen and metabolite contaminants in East Greenland polar bears (Ursus maritimus)

    Energy Technology Data Exchange (ETDEWEB)

    Gebbink, Wouter A. [National Wildlife Research Centre, Science and Technology Branch, Environment Canada, Carleton University, Ottawa, Ontario K1S 5B6 (Canada); Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6 (Canada); Sonne, Christian; Dietz, Rune; Kirkegaard, Maja; Riget, Frank F. [Department of Arctic Environment, National Environmental Research Institute, University of Aarhus, Frederiksborgvej 399, DK-4000 Roskilde (Denmark); Born, Erik W. [Greenland Institute of Natural Resources, P.O. Box 570, DK-3900 Nuuk, Greenland (Denmark); Muir, Derek C.G. [Water Science and Technology Directorate, Environment Canada, Burlington, Ontario L7R 4A6 (Canada); Letcher, Robert J. [National Wildlife Research Centre, Science and Technology Branch, Environment Canada, Carleton University, Ottawa, Ontario K1S 5B6 (Canada); Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6 (Canada)], E-mail: robert.letcher@ec.gc.ca

    2008-04-15

    Congener patterns of the major organohalogen contaminant classes of PCBs, PBDEs and their metabolites and/or by-products (OH-PCBs, MeSO{sub 2}-PCBs, OH-PBDEs and MeO-PBDEs) were examined in adipose tissue, liver, brain and blood of East Greenland polar bears (Ursus maritimus). PCB, OH-PCB, MeSO{sub 2}-PCB and PBDE congener patterns showed significant differences (p {<=} 0.05) mainly in the liver and the brain relative to the adipose tissue and the blood. OH-PBDEs and MeO-PBDEs were not detected in the brain and liver, but had different patterns in blood versus the adipose tissue. Novel OH-polybrominated biphenyls (OH-PBBs), one tri- and two tetra-brominated OH-PBBs were detected in all tissues and blood. Congener pattern differences among tissues and blood are likely due to a combination of factors, e.g., biotransformation and retention in the liver, retention in the blood and blood-brain barrier transport. Our findings suggest that different congener pattern exposures to these classes of contaminants should be considered with respect to potential target tissue-specific effects in East Greenland polar bears. - Tissues-specific (adipose tissue, liver, brain and blood) differences exist for the congener patterns of PCBs, PBDEs and their metabolites/degradation products in East Greenland polar bears.

  2. Tissue-specific congener composition of organohalogen and metabolite contaminants in East Greenland polar bears (Ursus maritimus)

    International Nuclear Information System (INIS)

    Gebbink, Wouter A.; Sonne, Christian; Dietz, Rune; Kirkegaard, Maja; Riget, Frank F.; Born, Erik W.; Muir, Derek C.G.; Letcher, Robert J.

    2008-01-01

    Congener patterns of the major organohalogen contaminant classes of PCBs, PBDEs and their metabolites and/or by-products (OH-PCBs, MeSO 2 -PCBs, OH-PBDEs and MeO-PBDEs) were examined in adipose tissue, liver, brain and blood of East Greenland polar bears (Ursus maritimus). PCB, OH-PCB, MeSO 2 -PCB and PBDE congener patterns showed significant differences (p ≤ 0.05) mainly in the liver and the brain relative to the adipose tissue and the blood. OH-PBDEs and MeO-PBDEs were not detected in the brain and liver, but had different patterns in blood versus the adipose tissue. Novel OH-polybrominated biphenyls (OH-PBBs), one tri- and two tetra-brominated OH-PBBs were detected in all tissues and blood. Congener pattern differences among tissues and blood are likely due to a combination of factors, e.g., biotransformation and retention in the liver, retention in the blood and blood-brain barrier transport. Our findings suggest that different congener pattern exposures to these classes of contaminants should be considered with respect to potential target tissue-specific effects in East Greenland polar bears. - Tissues-specific (adipose tissue, liver, brain and blood) differences exist for the congener patterns of PCBs, PBDEs and their metabolites/degradation products in East Greenland polar bears

  3. Tissue-specific congener composition of organohalogen and metabolite contaminants in East Greenland polar bears (Ursus maritimus).

    Science.gov (United States)

    Gebbink, Wouter A; Sonne, Christian; Dietz, Rune; Kirkegaard, Maja; Riget, Frank F; Born, Erik W; Muir, Derek C G; Letcher, Robert J

    2008-04-01

    Congener patterns of the major organohalogen contaminant classes of PCBs, PBDEs and their metabolites and/or by-products (OH-PCBs, MeSO2-PCBs, OH-PBDEs and MeO-PBDEs) were examined in adipose tissue, liver, brain and blood of East Greenland polar bears (Ursus maritimus). PCB, OH-PCB, MeSO2-PCB and PBDE congener patterns showed significant differences (pCongener pattern differences among tissues and blood are likely due to a combination of factors, e.g., biotransformation and retention in the liver, retention in the blood and blood-brain barrier transport. Our findings suggest that different congener pattern exposures to these classes of contaminants should be considered with respect to potential target tissue-specific effects in East Greenland polar bears.

  4. The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions.

    Science.gov (United States)

    Johnson, Brian R; Atallah, Joel; Plachetzki, David C

    2013-08-28

    A composite biological structure, such as an insect head or abdomen, contains many internal structures with distinct functions. Composite structures are often used in RNA-seq studies, though it is unclear how expression of the same gene in different tissues and structures within the same structure affects the measurement (or even utility) of the resulting patterns of gene expression. Here we determine how complex composite tissue structure affects measures of gene expression using RNA-seq. We focus on two structures in the honey bee (the sting gland and digestive tract) both contained within one larger structure, the whole abdomen. For each of the three structures, we used RNA-seq to identify differentially expressed genes between two developmental stages, nurse bees and foragers. Based on RNA-seq for each structure-specific extraction, we found that RNA-seq with composite structures leads to many false negatives (genes strongly differentially expressed in particular structures which are not found to be differentially expressed within the composite structure). We also found a significant number of genes with one pattern of differential expression in the tissue-specific extraction, and the opposite in the composite extraction, suggesting multiple signals from such genes within the composite structure. We found these patterns for different classes of genes including transcription factors. Many RNA-seq studies currently use composite extractions, and even whole insect extractions, when tissue and structure specific extractions are possible. This is due to the logistical difficultly of micro-dissection and unawareness of the potential errors associated with composite extractions. The present study suggests that RNA-seq studies of composite structures are prone to false negatives and difficult to interpret positive signals for genes with variable patterns of local expression. In general, our results suggest that RNA-seq on large composite structures should be avoided

  5. Tissue-specific composite cell aggregates drive periodontium tissue regeneration by reconstructing a regenerative microenvironment.

    Science.gov (United States)

    Zhu, Bin; Liu, Wenjia; Zhang, Hao; Zhao, Xicong; Duan, Yan; Li, Dehua; Jin, Yan

    2017-06-01

    Periodontitis is the most common cause of periodontium destruction. Regeneration of damaged tissue is the expected treatment goal. However, the regeneration of a functional periodontal ligament (PDL) insertion remains a difficulty, due to complicated factors. Recently, periodontal ligament stem cells (PDLSCs) and bone marrow-derived mesenchymal stem cells (BMMSCs) have been shown to participate in PDL regeneration, both pathologically and physiologically. Besides, interactions affect the biofunctions of different derived cells during the regenerative process. Therefore, the purpose of this study was to discuss the different derived composite cell aggregate (CA) systems of PDLSCs and BMMSCs (iliac-derived or jaw-derived) for periodontium regeneration under regenerative microenvironment reconstruction. Our results showed although all three mono-MSC CAs were compacted and the cells arranged regularly in them, jaw-derived BMMSC (JBMMSC) CAs secreted more extracellular matrix than the others. Furthermore, PDLSC/JBMMSC compound CAs highly expressed ALP, Col-I, fibronectin, integrin-β1 and periostin, suggesting that their biofunction is more appropriate for periodontal structure regeneration. Inspiringly, PDLSC/JBMMSC compound CAs regenerated more functional PDL-like tissue insertions in both nude mice ectopic and minipig orthotopic transplantation. The results indicated that the different derived CAs of PDLSCs/JBMMSCs provided an appropriate regenerative microenvironment facilitating a more stable and regular regeneration of functional periodontium tissue. This method may provide a possible strategy to solve periodontium defects in periodontitis and powerful experimental evidence for clinical applications in the future. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  6. Palytoxin congeners.

    Science.gov (United States)

    Patocka, Jiri; Nepovimova, Eugenie; Wu, Qinghua; Kuca, Kamil

    2018-01-01

    Palytoxin, isolated from a zoanthid of the genus Palythoa, is the most potent marine toxin known. Intoxication by palytoxin leads to vasoconstriction, hemorrhage, ataxia, muscle weakness, ventricular fibrillation, pulmonary hypertension, ischemia and death. Palytoxin and its numerous derivatives (congeners) may enter the food chain and accumulate mainly in fishes and crabs, causing severe human intoxication and death following ingestion of contaminated products. Furthermore, toxic effects in individuals exposed via inhalation or skin contact to marine aerosol in coincidence with Ostreopsis blooms, have been reported. Blooms of the benthic dinoflagellate Ostreopsis cf. ovata are a concern in the Mediterranean Sea, since this species produces a wide range of palytoxin-like compounds listed among the most potent marine toxins. Thus, the formerly unsuspected broad distribution of the benthic dinoflagellate Ostreopsis spp. has recently posed a problem of risk assessment for human health. Palytoxin has a strong potential for toxicity in humans and animals, and currently this toxin is of great concern worldwide. This review summarized and discussed the pharmacology and toxicology data of palytoxin and its congeners, including their cytotoxicity, human and animal toxicities. Moreover, the risk assessment and their control strategies including prevention and treatment assays were evaluated.

  7. Food Shortage Causes Differential Effects on Body Composition and Tissue-Specific Gene Expression in Salmon Modified for Increased Growth Hormone Production.

    Science.gov (United States)

    Abernathy, Jason; Panserat, Stéphane; Welker, Thomas; Plagne-Juan, Elisabeth; Sakhrani, Dionne; Higgs, David A; Audouin, Florence; Devlin, Robert H; Overturf, Ken

    2015-12-01

    Growth hormone (GH) transgenic salmon possesses markedly increased metabolic rate, appetite, and feed conversion efficiency, as well as an increased ability to compete for food resources. Thus, the ability of GH-transgenic fish to withstand periods of food deprivation as occurs in nature is potentially different than that of nontransgenic fish. However, the physiological and genetic effects of transgenic GH production over long periods of food deprivation remain largely unknown. Here, GH-transgenic coho salmon (Oncorhynchus kisutch) and nontransgenic, wild-type coho salmon were subjected to a 3-month food deprivation trial, during which time performance characteristics related to growth were measured along with proximate compositions. To examine potential genetic effects of GH-transgenesis on long-term food deprivation, a group of genes related to muscle development and liver metabolism was selected for quantitative PCR analysis. Results showed that GH-transgenic fish lose weight at an increased rate compared to wild-type even though proximate compositions remained relatively similar between the groups. A total of nine genes related to muscle physiology (cathepsin, cee, insulin-like growth factor, myostatin, murf-1, myosin, myogenin, proteasome delta, tumor necrosis factor) and five genes related to liver metabolism (carnitine palmitoyltransferase, fatty acid synthase, glucose-6-phosphatase, glucose-6-phosphate dehydrogenase, glucokinase) were shown to be differentially regulated between GH-transgenic and wild-type coho salmon over time. These genetic and physiological responses assist in identifying differences between GH-transgenic and wild-type salmon in relation to fitness effects arising from elevated growth hormone during periods of long-term food shortage.

  8. The reconstruction and analysis of tissue specific human metabolic networks.

    Science.gov (United States)

    Hao, Tong; Ma, Hong-Wu; Zhao, Xue-Ming; Goryanin, Igor

    2012-02-01

    Human tissues have distinct biological functions. Many proteins/enzymes are known to be expressed only in specific tissues and therefore the metabolic networks in various tissues are different. Though high quality global human metabolic networks and metabolic networks for certain tissues such as liver have already been studied, a systematic study of tissue specific metabolic networks for all main tissues is still missing. In this work, we reconstruct the tissue specific metabolic networks for 15 main tissues in human based on the previously reconstructed Edinburgh Human Metabolic Network (EHMN). The tissue information is firstly obtained for enzymes from Human Protein Reference Database (HPRD) and UniprotKB databases and transfers to reactions through the enzyme-reaction relationships in EHMN. As our knowledge of tissue distribution of proteins is still very limited, we replenish the tissue information of the metabolic network based on network connectivity analysis and thorough examination of the literature. Finally, about 80% of proteins and reactions in EHMN are determined to be in at least one of the 15 tissues. To validate the quality of the tissue specific network, the brain specific metabolic network is taken as an example for functional module analysis and the results reveal that the function of the brain metabolic network is closely related with its function as the centre of the human nervous system. The tissue specific human metabolic networks are available at .

  9. Description of electrophoretic loci and tissue specific gene ...

    African Journals Online (AJOL)

    Protein electrophoresis was used to study the distributions and tissue specificity of gene expression of enzymes encoded by 42 loci in Rhinolophus clivosus and R. landeri, the genetically most divergent of the ten species of southern African horseshoe bats. No differences in gene expression were found between R.

  10. Description of electrophoretic loci and tissue specific gene ...

    African Journals Online (AJOL)

    Description of electrophoretic loci and tissue specific gene expression in the horseshoe bat genus Rhinolophus (Rhinolophidae). Sarita Maree* and W.S. Grant. Department of Genetics, University of the Witwatersrand, Johannesburg, 2050 Repubfic of South Africa. Received 9 February 1994; accepted 19 Ouober 1995.

  11. Tissue-specific tagging of endogenous loci in Drosophila melanogaster

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    Kate Koles

    2016-01-01

    Full Text Available Fluorescent protein tags have revolutionized cell and developmental biology, and in combination with binary expression systems they enable diverse tissue-specific studies of protein function. However these binary expression systems often do not recapitulate endogenous protein expression levels, localization, binding partners and/or developmental windows of gene expression. To address these limitations, we have developed a method called T-STEP (tissue-specific tagging of endogenous proteins that allows endogenous loci to be tagged in a tissue specific manner. T-STEP uses a combination of efficient CRISPR/Cas9-enhanced gene targeting and tissue-specific recombinase-mediated tag swapping to temporally and spatially label endogenous proteins. We have employed this method to GFP tag OCRL (a phosphoinositide-5-phosphatase in the endocytic pathway and Vps35 (a Parkinson's disease-implicated component of the endosomal retromer complex in diverse Drosophila tissues including neurons, glia, muscles and hemocytes. Selective tagging of endogenous proteins allows, for the first time, cell type-specific live imaging and proteomics in complex tissues.

  12. Selective estrogen receptor modulators: tissue specificity and clinical utility

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    Martinkovich S

    2014-08-01

    Full Text Available Stephen Martinkovich,* Darshan Shah,* Sonia Lobo Planey, John A ArnottDepartment of Basic Sciences, The Commonwealth Medical College, Scranton, PA, USA*These authors contributed equally to this workAbstract: Selective estrogen receptor modulators (SERMs are a diverse group of ­nonsteroidal compounds that function as agonists or antagonists for estrogen receptors (ERs in a target gene-specific and tissue-specific fashion. SERM specificity involves tissue-specific expression of ER subtypes, differential expression of co-regulatory proteins in various tissues, and varying ER conformational changes induced by ligand binding. To date, the major clinical applications of SERMs are their use in the prevention and treatment of breast cancer, the prevention of osteoporosis, and the maintenance of beneficial serum lipid profiles in postmenopausal women. However, SERMs have also been found to promote adverse effects, including thromboembolic events and, in some cases, carcinogenesis, that have proven to be obstacles in their clinical utility. In this review, we discuss the mechanisms of SERM tissue specificity and highlight the therapeutic application of well-known and emergent SERMs.Keywords: selective estrogen receptor modulators, SERMs, estrogen receptors

  13. Predicting Tissue-Specific Enhancers in the Human Genome

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    Pennacchio, Len A.; Loots, Gabriela G.; Nobrega, Marcelo A.; Ovcharenko, Ivan

    2006-07-01

    Determining how transcriptional regulatory signals areencoded in vertebrate genomes is essential for understanding the originsof multi-cellular complexity; yet the genetic code of vertebrate generegulation remains poorly understood. In an attempt to elucidate thiscode, we synergistically combined genome-wide gene expression profiling,vertebrate genome comparisons, and transcription factor binding siteanalysis to define sequence signatures characteristic of candidatetissue-specific enhancers in the human genome. We applied this strategyto microarray-based gene expression profiles from 79 human tissues andidentified 7,187 candidate enhancers that defined their flanking geneexpression, the majority of which were located outside of knownpromoters. We cross-validated this method for its ability to de novopredict tissue-specific gene expression and confirmed its reliability in57 of the 79 available human tissues, with an average precision inenhancer recognition ranging from 32 percent to 63 percent, and asensitivity of 47 percent. We used the sequence signatures identified bythis approach to assign tissue-specific predictions to ~;328,000human-mouse conserved noncoding elements in the human genome. Byoverlapping these genome-wide predictions with a large in vivo dataset ofenhancers validated in transgenic mice, we confirmed our results with a28 percent sensitivity and 50 percent precision. These results indicatethe power of combining complementary genomic datasets as an initialcomputational foray into the global view of tissue-specific generegulation in vertebrates.

  14. Predicting tissue-specific expressions based on sequence characteristics

    KAUST Repository

    Paik, Hyojung

    2011-04-30

    In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

  15. Tissue-specificity of proteoglycans expression in different cancers

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    A. V. Suhovskih

    2016-01-01

    Full Text Available Background. Proteoglycans (PGs are complex glycosylated molecules playing an important role in cell-cell and cell-matrix interactions and signaling. Expression of PGs and their expression pattern change considerably during malignant transformation of mammalian cells and tissues.Objective. The aim of our work was to investigate tissue-specificity of main PGs expression (glypican-1, perlecan, syndecan-1, aggrecan, versican, CSPG4/NG2, brevican, decorin, lumican in normal cells (fibroblasts and normal epithelial prostate cells PNT2 and in different human cancer cell lines (prostate, breast, lung, brain, kidney. Expression patterns of main PGs were determined in these cells using reverse transcription polymerase chain reaction analysis and immunocytochemical staining.Results. It was shown that fibroblasts actively expressed PGs, and PNT2 cells had lower (5–6-fold expression levels of a limited set of PG. In different cancer cell lines, overall transcriptional activities of PGs varied up to 10-fold, although their expression patterns had tissue-specific properties (for example, expression of syndecan-1 is more specific for prostate cancer cells, while perlecan is typical for lung cancer cell lines.Conclusions. Along with this, variability of the PG expression patterns in cell lines of the same tissue of origin was shown, suggesting a possible contribution of the variable PGs expression to intratumoural heterogeneity of cancer cells and their potential as perspective biomarker (s for personalised cancer diagnostics.

  16. Laminin Mediates Tissue-specific Gene Expression in Mammary Epithelia

    Energy Technology Data Exchange (ETDEWEB)

    Streuli, Charles H; Schmidhauser, Christian; Bailey, Nina; Yurchenco, Peter; Skubitz, Amy P. N.; Roskelley, Calvin; Bissell, Mina J

    1995-04-01

    Tissue-specific gene expression in mammary epithelium is dependent on the extracellular matrix as well as hormones. There is good evidence that the basement membrane provides signals for regulating beta-casein expression, and that integrins are involved in this process. Here, we demonstrate that in the presence of lactogenic hormones, laminin can direct expression of the beta-casein gene. Mouse mammary epithelial cells plated on gels of native laminin or laminin-entactin undergo functional differentiation. On tissue culture plastic, mammary cells respond to soluble basement membrane or purified laminin, but not other extracellular matrix components, by synthesizing beta-casein. In mammary cells transfected with chloramphenicol acetyl transferase reporter constructs, laminin activates transcription from the beta-casein promoter through a specific enhancer element. The inductive effect of laminin on casein expression was specifically blocked by the E3 fragment of the carboxy terminal region of the alpha 1 chain of laminin, by antisera raised against the E3 fragment, and by a peptide corresponding to a sequence within this region. Our results demonstrate that laminin can direct tissue-specific gene expression in epithelial cells through its globular domain.

  17. Tissue-specific sparse deconvolution for brain CT perfusion.

    Science.gov (United States)

    Fang, Ruogu; Jiang, Haodi; Huang, Junzhou

    2015-12-01

    Enhancing perfusion maps in low-dose computed tomography perfusion (CTP) for cerebrovascular disease diagnosis is a challenging task, especially for low-contrast tissue categories where infarct core and ischemic penumbra usually occur. Sparse perfusion deconvolution has been recently proposed to effectively improve the image quality and diagnostic accuracy of low-dose perfusion CT by extracting the complementary information from the high-dose perfusion maps to restore the low-dose using a joint spatio-temporal model. However the low-contrast tissue classes where infarct core and ischemic penumbra are likely to occur in cerebral perfusion CT tend to be over-smoothed, leading to loss of essential biomarkers. In this paper, we propose a tissue-specific sparse deconvolution approach to preserve the subtle perfusion information in the low-contrast tissue classes. We first build tissue-specific dictionaries from segmentations of high-dose perfusion maps using online dictionary learning, and then perform deconvolution-based hemodynamic parameters estimation for block-wise tissue segments on the low-dose CTP data. Extensive validation on clinical datasets of patients with cerebrovascular disease demonstrates the superior performance of our proposed method compared to state-of-art, and potentially improve diagnostic accuracy by increasing the differentiation between normal and ischemic tissues in the brain. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Repressor-mediated tissue-specific gene expression in plants

    Science.gov (United States)

    Meagher, Richard B [Athens, GA; Balish, Rebecca S [Oxford, OH; Tehryung, Kim [Athens, GA; McKinney, Elizabeth C [Athens, GA

    2009-02-17

    Plant tissue specific gene expression by way of repressor-operator complexes, has enabled outcomes including, without limitation, male sterility and engineered plants having root-specific gene expression of relevant proteins to clean environmental pollutants from soil and water. A mercury hyperaccumulation strategy requires that mercuric ion reductase coding sequence is strongly expressed. The actin promoter vector, A2pot, engineered to contain bacterial lac operator sequences, directed strong expression in all plant vegetative organs and tissues. In contrast, the expression from the A2pot construct was restricted primarily to root tissues when a modified bacterial repressor (LacIn) was coexpressed from the light-regulated rubisco small subunit promoter in above-ground tissues. Also provided are analogous repressor operator complexes for selective expression in other plant tissues, for example, to produce male sterile plants.

  19. Tissue specific metal characterization of selected fish species in Pakistan.

    Science.gov (United States)

    Ahmed, Mukhtiar; Ahmad, Taufiq; Liaquat, Muhammad; Abbasi, Kashif Sarfraz; Farid, Ibrahim Bayoumi Abdel; Jahangir, Muhammad

    2016-04-01

    Concentration of various metals, i.e., zinc (Zn), copper (Cu), lead (Pb), nickel (Ni), iron (Fe), manganese (Mn), chromium (Cr), and silver (Ag), was evaluated in five indigenous fish species (namely, silver carp, common carp, mahseer, thela fish, and rainbow trout), by using atomic absorption spectrophotometer. It is proved from this study that, overall, mahseer and rainbow trout had high amount of zinc, whereas thela fish and silver carp had high concentration of copper, chromium, silver, nickel, and lead, while common carp had highest amount of iron contents. Furthermore, a tissue-specific discrimination among various fish species was observed, where higher metal concentrations were noticed in fish liver, with decreasing concentration in other organs like skin, gills, and finally the least contents in fish muscle. Multivariate data analysis showed not only a variation in heavy metals among the tissues but also discrimination among the selected fish species.

  20. Tissue specific regulation of lipogenesis by thyroid hormone

    Energy Technology Data Exchange (ETDEWEB)

    Blennemann, B.; Freake, H. (Univ. of Connecticut, Storrs (United States))

    1990-02-26

    Thyroid hormone stimulates long chain fatty acid synthesis in rat liver by increasing the amounts of key lipogenic enzymes. Sparse and conflicting data exist concerning its action on this pathway in other tissues. The authors recently showed that, in contrast to liver, hypothyroidism stimulates lipogenesis in brown adipose tissue and have now systematically examined the effects of thyroid state on fatty acid synthesis in other rat tissues. Lipogenesis was assessed by tritiated water incorporation. Euthyroid hepatic fatty acid synthesis (16.6um H/g/h) was reduced to 30% in hypothyroid rats and increased 3 fold in hyperthyroidism. Lipogenesis was detected in euthyroid kidney and heart and these levels were also stimulated by thyroid hormone treatment. Brown adipose tissue was unique in showing increased lipogenesis in the hypothyroid state. Hyperthyroid levels were not different from euthyroid. Effects in white adipose tissue were small and inconsistent. Brain, skin and lung were all lipogenically active, but did not respond to changes in thyroid state. Low but detectable levels of fatty acid synthesis were measured in muscle, which also were non-responsive. A wide spectrum of responses to thyroid hormone are seen in different rat tissues and thus the pathway of long chain fatty acid synthesis would appear to be an excellent model for examining the tissue specific regulation of gene expression by thyroid hormone.

  1. Tissue-specific expression of type IX collagen

    International Nuclear Information System (INIS)

    Nishimura, I.; Muragaki, Y.; Ninomiya, Y.; Olsen, B.R.; Hayashi, M.

    1990-01-01

    This paper reports on the tissue-specific expression of type IX collagen, a major component of cartilage fibrils. It contains molecules with three genetically distinct subunits. The subunits form three triple-helical (CO) domains separated by non-triple-helical (NC) sequences. One of the subunits in cartilage, α1(IX), contains a large amino-terminal globular domain, NC4, while a second subunit, α2(IX), contains a covalently attached chondroitin sulfate chain. The site of attachment for this chain is located within the non-triple-helical sequence NC3, which separates the amino-terminal and central triple-helical domains of the type IX molecules. The NC3 region is 5 amino acid residues longer in the α2(IX) chain than in the α1(IX) and α3(IX) chains. This may explain why type IX molecules tend to show a sharp angle in the NC3 region, and why monoclonal antibody molecules that are specific for the stub left after chondroitinase ABC digestion of the chondroitin sulfate side chain always are located on the outside of the angle

  2. Tissue-Specific Posttranslational Modification Allows Functional Targeting of Thyrotropin

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    Keisuke Ikegami

    2014-11-01

    Full Text Available Thyroid-stimulating hormone (TSH; thyrotropin is a glycoprotein secreted from the pituitary gland. Pars distalis-derived TSH (PD-TSH stimulates the thyroid gland to produce thyroid hormones (THs, whereas pars tuberalis-derived TSH (PT-TSH acts on the hypothalamus to regulate seasonal physiology and behavior. However, it had not been clear how these two TSHs avoid functional crosstalk. Here, we show that this regulation is mediated by tissue-specific glycosylation. Although PT-TSH is released into the circulation, it does not stimulate the thyroid gland. PD-TSH is known to have sulfated biantennary N-glycans, and sulfated TSH is rapidly metabolized in the liver. In contrast, PT-TSH has sialylated multibranched N-glycans; in the circulation, it forms the macro-TSH complex with immunoglobulin or albumin, resulting in the loss of its bioactivity. Glycosylation is fundamental to a wide range of biological processes. This report demonstrates its involvement in preventing functional crosstalk of signaling molecules in the body.

  3. Tissue-specific transcriptomics in the field cricket Teleogryllus oceanicus.

    Science.gov (United States)

    Bailey, Nathan W; Veltsos, Paris; Tan, Yew-Foon; Millar, A Harvey; Ritchie, Michael G; Simmons, Leigh W

    2013-02-01

    Field crickets (family Gryllidae) frequently are used in studies of behavioral genetics, sexual selection, and sexual conflict, but there have been no studies of transcriptomic differences among different tissue types. We evaluated transcriptome variation among testis, accessory gland, and the remaining whole-body preparations from males of the field cricket, Teleogryllus oceanicus. Non-normalized cDNA libraries from each tissue were sequenced on the Roche 454 platform, and a master assembly was constructed using testis, accessory gland, and whole-body preparations. A total of 940,200 reads were assembled into 41,962 contigs, to which 36,856 singletons (reads not assembled into a contig) were added to provide a total of 78,818 sequences used in annotation analysis. A total of 59,072 sequences (75%) were unique to one of the three tissues. Testis tissue had the greatest proportion of tissue-specific sequences (62.6%), followed by general body (56.43%) and accessory gland tissue (44.16%). We tested the hypothesis that tissues expressing gene products expected to evolve rapidly as a result of sexual selection--testis and accessory gland--would yield a smaller proportion of BLASTx matches to homologous genes in the model organism Drosophila melanogaster compared with whole-body tissue. Uniquely expressed sequences in both testis and accessory gland showed a significantly lower rate of matching to annotated D. melanogaster genes compared with those from general body tissue. These results correspond with empirical evidence that genes expressed in testis and accessory gland tissue are rapidly evolving targets of selection.

  4. Tissue-specific fatty acids response to different diets in common carp (Cyprinus carpio L.).

    Science.gov (United States)

    Böhm, Markus; Schultz, Sebastian; Koussoroplis, Apostolos-Manuel; Kainz, Martin J

    2014-01-01

    Fish depend on dietary fatty acids (FA) to support their physiological condition and health. Exploring the FA distribution in common carp (Cyprinus carpio), one of the world's most consumed freshwater fish, is important to understand how and where FA of different sources are allocated. We investigated diet effects on the composition of polar and neutral lipid fatty acids (PLFA and NLFA, respectively) in eight different tissues (dorsal and ventral muscle, heart, kidney, intestine, eyes, liver and adipose tissue) of common carp. Two-year old carp were exposed to three diet sources (i.e., zooplankton, zooplankton plus supplementary feeds containing vegetable, VO, or fish oil, FO) with different FA composition. The PLFA and NLFA response was clearly tissue-specific after 210 days of feeding on different diets. PLFA were generally rich in omega-3 polyunsaturated FA and only marginally influenced by dietary FA, whereas the NLFA composition strongly reflected dietary FA profiles. However, the NLFA composition in carp tissues varied considerably at low NLFA mass ratios, suggesting that carp is able to regulate the NLFA composition and thus FA quality in its tissues when NLFA contents are low. Finally, this study shows that FO were 3X more retained than VO as NLFA particularly in muscle tissues, indicating that higher nutritional quality feeds are selectively allocated into tissues and thus available for human consumption.

  5. Tissue-specific fatty acids response to different diets in common carp (Cyprinus carpio L..

    Directory of Open Access Journals (Sweden)

    Markus Böhm

    Full Text Available Fish depend on dietary fatty acids (FA to support their physiological condition and health. Exploring the FA distribution in common carp (Cyprinus carpio, one of the world's most consumed freshwater fish, is important to understand how and where FA of different sources are allocated. We investigated diet effects on the composition of polar and neutral lipid fatty acids (PLFA and NLFA, respectively in eight different tissues (dorsal and ventral muscle, heart, kidney, intestine, eyes, liver and adipose tissue of common carp. Two-year old carp were exposed to three diet sources (i.e., zooplankton, zooplankton plus supplementary feeds containing vegetable, VO, or fish oil, FO with different FA composition. The PLFA and NLFA response was clearly tissue-specific after 210 days of feeding on different diets. PLFA were generally rich in omega-3 polyunsaturated FA and only marginally influenced by dietary FA, whereas the NLFA composition strongly reflected dietary FA profiles. However, the NLFA composition in carp tissues varied considerably at low NLFA mass ratios, suggesting that carp is able to regulate the NLFA composition and thus FA quality in its tissues when NLFA contents are low. Finally, this study shows that FO were 3X more retained than VO as NLFA particularly in muscle tissues, indicating that higher nutritional quality feeds are selectively allocated into tissues and thus available for human consumption.

  6. Diet-induced weight loss has chronic tissue-specific effects on glucocorticoid metabolism in overweight postmenopausal women.

    Science.gov (United States)

    Stomby, A; Simonyte, K; Mellberg, C; Ryberg, M; Stimson, R H; Larsson, C; Lindahl, B; Andrew, R; Walker, B R; Olsson, T

    2015-05-01

    Tissue-specific glucocorticoid metabolism is altered in obesity, and may increase cardiovascular risk. This dysregulation is normalized by short-term calorie restriction and weight loss, an effect that varies with dietary macronutrient composition. However, tissue-specific glucocorticoid metabolism has not been studied during long-term (>6 months) dietary interventions. Therefore our aim was to test whether long-term dietary interventions, either a paleolithic-type diet (PD) or a diet according to Nordic nutrition recommendations (NNR) could normalize tissue-specific glucocorticoid metabolism in overweight and obese women. Forty-nine overweight/obese postmenopausal women were randomized to a paleolithic diet or a diet according to NNR for 24 months. At baseline, 6 and 24 months anthropometric measurements, insulin sensitivity, excretion of urinary glucocorticoid metabolites in 24-hour collections, conversion of orally administered cortisone to plasma cortisol and transcript levels of 11β hydroxysteroid dehydrogenase type 1 (11βHSD1) in subcutaneous adipose tissue were studied. Both diet groups achieved significant and sustained weight loss. Weight loss with the PD was greater than on NNR diet after 6 months (Pweight loss in postmenopausal women has tissue-specific and time-dependent effects on glucocorticoid metabolism. This may alter local-tissue cortisol exposure contributing to improved metabolic function during weight loss.

  7. Congener Production in Blood Samples During Preparation and Storage

    DEFF Research Database (Denmark)

    Felby, Søren; Nielsen, Erik

    1995-01-01

    Retsmedicin, congener production, preparation, head space GC, acetone, isobutanol, storage, blood samples, n-propanol, methanol, methylethylketone......Retsmedicin, congener production, preparation, head space GC, acetone, isobutanol, storage, blood samples, n-propanol, methanol, methylethylketone...

  8. Designer rhamnolipids by reduction of congener diversity: production and characterization.

    Science.gov (United States)

    Tiso, Till; Zauter, Rabea; Tulke, Hannah; Leuchtle, Bernd; Li, Wing-Jin; Behrens, Beate; Wittgens, Andreas; Rosenau, Frank; Hayen, Heiko; Blank, Lars Mathias

    2017-12-14

    -chemical characteristics. The approach demonstrated here is a first step towards the production of designer biosurfactants, tailor-made for specific applications by purposely adjusting the congener composition of the mixtures. Not only were we able to genetically engineer our cell factory to produce specific biosurfactant mixtures, but we also showed that the products are suited for different applications. These designer biosurfactants can be produced as part of a biorefinery from second generation carbon sources such as xylose.

  9. Volatile congeners in strong alcoholic fruit spirits

    OpenAIRE

    Kostik, Vesna; Memeti, Shaban; Bauer, Biljana

    2013-01-01

    The aim of our study was to identify and quantitatively analyze alcohol volatile congeners in different types of spirits from the domestic producers in order to evaluate their quality according to the Official Regulation. A total of 100 samples of three different types of grape brandies (lozova rakia, komova rakia and vinjak) and 30 samples of plum brandies obtained from seven domestic producers were analyzed on the content of ethanol, ethyl acetate, methanol, i-propanol, n- propanol, i-bu...

  10. Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.

    Directory of Open Access Journals (Sweden)

    Nadezda Kryuchkova-Mostacci

    2016-12-01

    Full Text Available The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.

  11. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  12. Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5'-UTR region.

    Science.gov (United States)

    Lawson, Mark J; Zhang, Liqing

    2008-01-15

    SSRs (simple sequence repeats) have been shown to have a variety of effects on an organism. In this study, we compared SSRs in housekeeping and tissue-specific genes in human and mouse, in terms of SSR types and distributions in different regions including 5'-UTRs, introns, coding exons, 3'-UTRs, and upstream regions. Among all these regions, SSRs in the 5'-UTR show the most distinction between housekeeping genes and tissue-specific genes in both densities and repeat types. Specifically, SSR densities in 5'-UTRs in housekeeping genes are about 1.7 times higher than those in tissue-specific genes, in contrast to the 0.8-1.2 times differences between the two classes of genes in other regions. Tri-SSRs in 5'-UTRs of housekeeping genes are more GC rich than those of tissue-specific genes and CGG, the dominant type of tri-SSR in 5'-UTR, accounts for 74-79% of the tri-SSRs in housekeeping genes, as compared to 42-57% in tissue-specific genes. 75% of the tri-SSRs in the 5'-UTR of housekeeping genes have 4-5 repeat units, versus the 86-90% in tissue-specific genes. Taken together, our results suggest that SSRs may have an effect on gene expression and may play an important role in contributing to the different expression profiles between housekeeping and tissue-specific genes.

  13. Tissue-specific RNA expression marks distant-acting developmental enhancers.

    Directory of Open Access Journals (Sweden)

    Han Wu

    2014-09-01

    Full Text Available Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci, but the prevalence of such enhancer RNAs (eRNAs within the transcriptome, and the association of eRNA expression with tissue-specific enhancer activity in vivo remain poorly understood. Here, we investigated the expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via deep RNA sequencing. Overall, approximately 80% of validated in vivo enhancers show tissue-specific RNA expression that correlates with tissue-specific enhancer activity. Globally, we identified thousands of tissue-specifically transcribed non-coding regions (TSTRs displaying various genomic hallmarks of bona fide enhancers. In transgenic mouse reporter assays, over half of tested TSTRs functioned as enhancers with reproducible activity in the predicted tissue. Together, our results demonstrate that tissue-specific eRNA expression is a common feature of in vivo enhancers, as well as a major source of extragenic transcription, and that eRNA expression signatures can be used to predict tissue-specific enhancers independent of known epigenomic enhancer marks.

  14. Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

    Science.gov (United States)

    Amin, Viren; Harris, R. Alan; Onuchic, Vitor; Jackson, Andrew R.; Charnecki, Tim; Paithankar, Sameer; Lakshmi Subramanian, Sai; Riehle, Kevin; Coarfa, Cristian; Milosavljevic, Aleksandar

    2015-01-01

    Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes. PMID:25691256

  15. Compound-specific isotopic and congener-specific analyses of polychlorinated biphenyl in the heat medium and rice oil of the Yusho incident.

    Science.gov (United States)

    Miyawaki, Takashi; Sugihara, Mari; Hirakawa, Shusaku; Hori, Tsuguhide; Kajiwara, Jumboku; Katsuki, Susumu; Mitoma, Chikage; Furue, Masutaka

    2017-09-21

    Compound-specific isotope analysis (CSIA) can be used to examine the source and transformation processes of organic pollutants in the environment. We performed a carbon stable isotope analysis of polychlorinated biphenyl (PCB) congeners in the PCB heat-transfer medium (heat medium) and the original Kanechlor-400 (KC-400, a commercial brand of PCBs) involved in the Yusho incident. The main purpose is to investigate whether isotope fractionation occurred in the rice oil deodorization process that caused the incident. The carbon isotope ratios (δ 13 C values) of the targeted PCB congeners ranged from - 29.39 to - 27.00‰ in the heat medium and from - 28.77 to - 27.05‰ in the original KC-400. No significant differences were found in the δ 13 C values, suggesting carbon isotope fractionation did not occur for the targeted PCB congeners in the heat medium when deodorization of rice oil occurred at temperatures above 200 °C. Furthermore, we also conducted a congener-specific analysis of 64 PCB congeners found in the heat medium and rice oil contaminated by it. The total PCB congener concentrations were 503 mg/g in the heat medium and 81 μg/g in the rice oil. The concentrations of the highly chlorinated congeners were significantly lower in the heat medium than in the original KC-400, and the compositional ratios of the lowly chlorinated congeners were relatively lower in the rice oil than in the heat medium. These results suggest that the PCB congener patterns gradually changed from that of the original KC-400 in the deodorization process and subsequent contamination into the rice oil. Thus, a combination of CSIA and congener-specific analysis is a new approach for investigating the changing PCB congener profiles in samples from the Yusho incident.

  16. MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes.

    Science.gov (United States)

    Bastiani, Michele; Liu, Libin; Hill, Michelle M; Jedrychowski, Mark P; Nixon, Susan J; Lo, Harriet P; Abankwa, Daniel; Luetterforst, Robert; Fernandez-Rojo, Manuel; Breen, Michael R; Gygi, Steven P; Vinten, Jorgen; Walser, Piers J; North, Kathryn N; Hancock, John F; Pilch, Paul F; Parton, Robert G

    2009-06-29

    Polymerase I and transcript release factor (PTRF)/Cavin is a cytoplasmic protein whose expression is obligatory for caveola formation. Using biochemistry and fluorescence resonance energy transfer-based approaches, we now show that a family of related proteins, PTRF/Cavin-1, serum deprivation response (SDR)/Cavin-2, SDR-related gene product that binds to C kinase (SRBC)/Cavin-3, and muscle-restricted coiled-coil protein (MURC)/Cavin-4, forms a multiprotein complex that associates with caveolae. This complex can constitutively assemble in the cytosol and associate with caveolin at plasma membrane caveolae. Cavin-1, but not other cavins, can induce caveola formation in a heterologous system and is required for the recruitment of the cavin complex to caveolae. The tissue-restricted expression of cavins suggests that caveolae may perform tissue-specific functions regulated by the composition of the cavin complex. Cavin-4 is expressed predominantly in muscle, and its distribution is perturbed in human muscle disease associated with Caveolin-3 dysfunction, identifying Cavin-4 as a novel muscle disease candidate caveolar protein.

  17. A minimal set of tissue-specific hypomethylated CpGs constitute epigenetic signatures of developmental programming.

    Directory of Open Access Journals (Sweden)

    Alejandro Colaneri

    Full Text Available Cell specific states of the chromatin are programmed during mammalian development. Dynamic DNA methylation across the developing embryo guides a program of repression, switching off genes in most cell types. Thus, the majority of the tissue specific differentially methylated sites (TS-DMS must be un-methylated CpGs.Comparison of expanded Methyl Sensitive Cut Counting data (eMSCC among four tissues (liver, testes, brain and kidney from three C57BL/6J mice, identified 138,052 differentially methylated sites of which 23,270 contain CpGs un-methylated in only one tissue (TS-DMS. Most of these CpGs were located in intergenic regions, outside of promoters, CpG islands or their shores, and up to 20% of them overlapped reported active enhancers. Indeed, tissue-specific enhancers were up to 30 fold enriched in TS-DMS. Testis showed the highest number of TS-DMS, but paradoxically their associated genes do not appear to be specific to the germ cell functions, but rather are involved in organism development. In the other tissues the differentially methylated genes are associated with tissue-specific physiological or anatomical functions. The identified sets of TS-DMS quantify epigenetic distances between tissues, generated during development. We applied this concept to measure the extent of reprogramming in the liver of mice exposed to in utero or early postnatal nutritional stress. Different protocols of food restriction reprogrammed the liver methylome in different but reproducible ways.Thus, each identified set of differentially methylated sites constituted an epigenetic signature that traced the developmental programing or the early nutritional reprogramming of each exposed mouse. We propose that our approach has the potential to outline a number of disease-associated epigenetic states. The composition of differentially methylated CpGs may vary with each situation, behaving as a composite variable, which can be used as a pre-symptomatic marker for

  18. Functional Enhancers As Master Regulators of Tissue-Specific Gene Regulation and Cancer Development

    Science.gov (United States)

    Ko, Je Yeong; Oh, Sumin; Yoo, Kyung Hyun

    2017-01-01

    Tissue-specific transcription is critical for normal development, and abnormalities causing undesirable gene expression may lead to diseases such as cancer. Such highly organized transcription is controlled by enhancers with specific DNA sequences recognized by transcription factors. Enhancers are associated with chromatin modifications that are distinct epigenetic features in a tissue-specific manner. Recently, super-enhancers comprising enhancer clusters co-occupied by lineage-specific factors have been identified in diverse cell types such as adipocytes, hair follicle stem cells, and mammary epithelial cells. In addition, noncoding RNAs, named eRNAs, are synthesized at super-enhancer regions before their target genes are transcribed. Many functional studies revealed that super-enhancers and eRNAs are essential for the regulation of tissue-specific gene expression. In this review, we summarize recent findings concerning enhancer function in tissue-specific gene regulation and cancer development. PMID:28359147

  19. TiGER: a database for tissue-specific gene expression and regulation.

    Science.gov (United States)

    Liu, Xiong; Yu, Xueping; Zack, Donald J; Zhu, Heng; Qian, Jiang

    2008-06-09

    Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

  20. TiGER: A database for tissue-specific gene expression and regulation

    Directory of Open Access Journals (Sweden)

    Zack Donald J

    2008-06-01

    Full Text Available Abstract Background Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. Results The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation. The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. Conclusion We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

  1. On enumeration of congeners of common persistent organic pollutants

    International Nuclear Information System (INIS)

    Haranczyk, Maciej; Puzyn, Tomasz; Ng, Esmond G.

    2010-01-01

    Congeners are molecules based on the same carbon skeleton but different by the number of substituents and/or a substitution pattern. Various Persistent Organic Pollutants (POPs) exist in the environment as families of halogen substituted congeners and/or their hydroxyl and methoxy substituted derivatives. Numbers of possible congeners resulting from substitution of a parent POP molecule with only one type of chemical group are generally available. At the same time, numbers of mixed-substituent congeners have not been counted and presented yet, although there is an increasing interest in such as is the increasing number of research articles presenting results on already identified Cl-/Br-mixed type congeners and/or their HO-/CH 3 O-mixed metabolites. We have enumerated and counted possible mixed-substituent congeners of common POPs. This article presents the obtained numbers for congener families of benzene, naphthalene, biphenyl, diphenyl ether, dibenzo-p-dioxin, dibenzofuran, anthracene, pyrene and others and obtained by substitution of up to five chemical group types. - This article presents the results of enumeration of congeners of common organic pollutants obtained by substitution of up to five chemical group types.

  2. Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks.

    Science.gov (United States)

    Li, Pengping; Hua, Xu; Zhang, Zhen; Li, Jie; Wang, Jin

    2013-10-31

    Transcription factors (TFs) and miRNAs are essential for the regulation of gene expression; however, the global view of human gene regulatory networks remains poorly understood. For example, how is the expression of so many genes regulated by limited cohorts of regulators and how are genes differentially expressed in different tissues despite the genetic code being the same in all tissues? We analyzed the network properties of housekeeping and tissue-specific genes in gene regulatory networks from seven human tissues. Our results show that different classes of genes behave quite differently in these networks. Tissue-specific miRNAs show a higher average target number compared with non-tissue specific miRNAs, which indicates that tissue-specific miRNAs tend to regulate different sets of targets. Tissue-specific TFs exhibit higher in-degree, out-degree, cluster coefficient and betweenness values, indicating that they occupy central positions in the regulatory network and that they transfer genetic information from upstream genes to downstream genes more quickly than other TFs. Housekeeping TFs tend to have higher cluster coefficients compared with other genes that are neither housekeeping nor tissue specific, indicating that housekeeping TFs tend to regulate their targets synergistically. Several topological properties of disease-associated miRNAs and genes were found to be significantly different from those of non-disease-associated miRNAs and genes. Tissue-specific miRNAs, TFs and disease genes have particular topological properties within the transcriptional regulatory networks of the seven human tissues examined. The tendency of tissue-specific miRNAs to regulate different sets of genes shows that a particular tissue-specific miRNA and its target gene set may form a regulatory module to execute particular functions in the process of tissue differentiation. The regulatory patterns of tissue-specific TFs reflect their vital role in regulatory networks and their

  3. Effect of polybrominated diphenyl ether congeners on placental cytokine production.

    Science.gov (United States)

    Arita, Yuko; Yeh, Corinne; Thoma, Theodosia; Getahun, Darios; Menon, Ramkumar; Peltier, Morgan R

    2018-02-01

    Polybrominated diphenyl ethers (PBDEs) are pollutants that may increase the risk of preterm birth. In previous studies, we found that a mixture of PBDEs altered the expression of biomarkers for preterm birth by the placenta. However, there are 209 different PBDE congeners with different tissue distributions. How these different congeners may alter the production of immunomodulators by the placenta that help to maintain the survival of the fetal allograft is unclear. Therefore, we compared the effects 5 common congeners on basal and bacteria-stimulated cytokine production by the placenta. Placental explant cultures were incubated with 20 μM of PBDE congeners 47, 99, 100, 153, 209 or vehicle in the presence and absence of Escherichia coli for 20 h. Conditioned medium was harvested and concentrations of IL-1β, TNF-α, IL-6, sgp130, HO-1, IL-10, BDNF, and 8-IsoP quantified. For unstimulated cultures, all congeners, except for PBDE-47, reduced the production of IL-1β and IL-6 production was enhanced by PBDE-153. BDNF concentrations tended to be reduced by most PBDE congeners and IL-10 production was enhanced by PBDE-99, -153, and -209. 8-IsoP production was enhanced by PBDE-153, but not the other congeners. For bacteria-stimulated cultures, PBDE-47 increased IL-1β production and PBDE-47, -153, and -209 tended to reduce TNF-α production. IL-6 production was enhanced by all PBDEs except 153. IL-10 production was enhanced by all congeners except for PBDE-47. All congeners significantly enhanced BDNF and 8-IsoP. These results suggest that PBDEs can alter the expression of placental biomarkers in a congener and infection-dependent manner. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Individual Polychlorinated Biphenyl (PCB) Congeners Produce Tissue- and Gene-Specific Effects on Thyroid Hormone Signaling during Development

    Science.gov (United States)

    Giera, Stefanie; Bansal, Ruby; Ortiz-Toro, Theresa M.; Taub, Daniel G.

    2011-01-01

    Polychlorinated biphenyls (PCB) are industrial chemicals linked to developmental deficits that may be caused in part by disrupting thyroid hormone (TH) action by either reducing serum TH or interacting directly with the TH receptor (TR). Individual PCB congeners can activate the TR in vitro when the metabolic enzyme cytochrome P4501A1 (CYP1A1) is induced, suggesting that specific PCB metabolites act as TR agonists. To test this hypothesis in vivo, we compared two combinations of PCB congeners that either activate the TR (PCB 105 and 118) or not (PCB 138 and 153) in the presence or absence of a PCB congener (PCB 126) that induces CYP1A1 in vitro. Aroclor 1254 was used as a positive control, and a group treated with propylthiouracil was included to characterize the effects of low serum TH. We monitored the effects on TH signaling in several peripheral tissues by measuring the mRNA expression of well-known TH-response genes in these tissues. Aroclor 1254 and its component PCB 105/118/126 reduced total T4 to the same extent as that of propylthiouracil but increased the expression of some TH target genes in liver. This effect was strongly correlated with CYP1A1 expression supporting the hypothesis that metabolism is necessary. Effects were gene and tissue specific, indicating that tissue-specific metabolism is an important component of PCB disruption of TH action and that PCB metabolites interact in complex ways with the TR. These are essential mechanisms to consider when evaluating the health risks of contaminant exposures, for both PCB and other polycyclic compounds known to interact with nuclear hormone receptors. PMID:21540284

  5. Elimination Rates of Dioxin Congeners in Former Chlorophenol Workers from Midland, Michigan

    Science.gov (United States)

    Collins, James J.; Bodner, Kenneth M.; Wilken, Michael; Bodnar, Catherine M.

    2012-01-01

    Background: Exposure reconstructions and risk assessments for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other dioxins rely on estimates of elimination rates. Limited data are available on elimination rates for congeners other than TCDD. Objectives: We estimated apparent elimination rates using a simple first-order one-compartment model for selected dioxin congeners based on repeated blood sampling in a previously studied population. Methods: Blood samples collected from 56 former chlorophenol workers in 2004–2005 and again in 2010 were analyzed for dioxin congeners. We calculated the apparent elimination half-life in each individual for each dioxin congener and examined factors potentially influencing elimination rates and the impact of estimated ongoing background exposures on rate estimates. Results: Mean concentrations of all dioxin congeners in the sampled participants declined between sampling times. Median apparent half-lives of elimination based on changes in estimated mass in the body were generally consistent with previous estimates and ranged from 6.8 years (1,2,3,7,8,9-hexachlorodibenzo-p-dioxin) to 11.6 years (pentachlorodibenzo-p-dioxin), with a composite half-life of 9.3 years for TCDD toxic equivalents. None of the factors examined, including age, smoking status, body mass index or change in body mass index, initial measured concentration, or chloracne diagnosis, was consistently associated with the estimated elimination rates in this population. Inclusion of plausible estimates of ongoing background exposures decreased apparent half-lives by approximately 10%. Available concentration-dependent toxicokinetic models for TCDD underpredicted observed elimination rates for concentrations dioxin compounds. PMID:23063871

  6. A comprehensive functional analysis of tissue specificity of human gene expression

    Directory of Open Access Journals (Sweden)

    Guryanov Alexey

    2008-11-01

    Full Text Available Abstract Background In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed ('housekeeping' genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues. Results We measured whole genome expression in 31 human tissues, identifying 2374 housekeeping genes expressed in all tissues, and genes uniquely expressed in each tissue. Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism. Network topology of the housekeeping network was characterized by higher connectivity and shorter paths between the proteins than the global network. Ontology enrichment scoring and network topology of tissue-specific genes were consistent with each tissue's function and expression patterns clustered together in accordance with tissue origin. Tissue-specific genes were twice as likely as housekeeping genes to be drug targets, allowing the identification of tissue 'signature networks' that will facilitate the discovery of new therapeutic targets and biomarkers of tissue-targeted diseases. Conclusion A comprehensive functional analysis of housekeeping and tissue-specific genes showed that the biological function of housekeeping and tissue-specific genes was consistent with tissue origin. Network analysis revealed that tissue-specific networks have distinct network properties related to each tissue's function. Tissue 'signature networks' promise to be a rich source of targets and biomarkers for disease treatment and diagnosis.

  7. Tissue-specific extracellular matrix coatings for the promotion of cell proliferation and maintenance of cell phenotype.

    Science.gov (United States)

    Zhang, Yuanyuan; He, Yujiang; Bharadwaj, Shantaram; Hammam, Nevin; Carnagey, Kristen; Myers, Regina; Atala, Anthony; Van Dyke, Mark

    2009-08-01

    Recent studies have shown that extracellular matrix (ECM) substitutes can have a dramatic impact on cell growth, differentiation and function. However, these ECMs are often applied generically and have yet to be developed for specific cell types. In this study, we developed tissue-specific ECM-based coating substrates for skin, skeletal muscle and liver cell cultures. Cellular components were removed from adult skin, skeletal muscle, and liver tissues, and the resulting acellular matrices were homogenized and dissolved. The ECM solutions were used to coat culture dishes. Tissue matched and non-tissue matched cell types were grown on these coatings to assess adhesion, proliferation, maintenance of phenotype and cell function at several time points. Each cell type showed better proliferation and differentiation in cultures containing ECM from their tissue of origin. Although subtle compositional differences in the three ECM types were not investigated in this study, these results suggest that tissue-specific ECMs provide a culture microenvironment that is similar to the in vivo environment when used as coating substrates, and this new culture technique has the potential for use in drug development and the development of cell-based therapies.

  8. Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

    Directory of Open Access Journals (Sweden)

    Chen Xiaoyu

    2007-12-01

    Full Text Available Abstract Background In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression. Results We develop a Bayesian network approach for identifying cis-regulatory modules likely to regulate tissue-specific expression. The network integrates predicted transcription factor binding site information, transcription factor expression data, and target gene expression data. At its core is a regression tree modeling the effect of combinations of transcription factors bound to a module. A new unsupervised EM-like algorithm is developed to learn the parameters of the network, including the regression tree structure. Conclusion Our approach is shown to accurately identify known human liver and erythroid-specific modules. When applied to the prediction of tissue-specific modules in 10 different tissues, the network predicts a number of important transcription factor combinations whose concerted binding is associated to specific expression.

  9. Levels of toxaphene congeners in fish from Danish waters

    DEFF Research Database (Denmark)

    Fromberg, Arvid; Cederberg, Tommy Licht; Hilbert, G.

    2000-01-01

    The levels of toxaphene congeners, in addition to PCB congeners and organochlorine pesticides, were determined in various fish samples from different Danish waters. While PCB-153 and p,p'-DDE show different levels depending on the fishing area, with highest levels in fish from the Western Baltic...... Sea, toxaphene was detected in all the samples investigated at a more constant level. The distribution of the three toxaphene congeners Parlar #26, #50 and #62 depends on the fishing area, with the Western Baltic Sea being different from the other waters by having almost equal levels of toxaphene...

  10. Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing

    Directory of Open Access Journals (Sweden)

    Vingron Martin

    2004-09-01

    Full Text Available Abstract Background Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also allow to approximate the expression pattern of the related transcripts. However, the limited number of tissues represented in the EST data as well as the different cDNA construction protocols may influence the predictive capacity of ESTs to unravel tissue-specifically expressed transcripts. Methods We predict tissue and tumor specific splice isoforms based on the genomic mapping (SpliceNest of the EST consensus sequences and library annotation provided in the GeneNest database. We further ascertain the potentially rare tissue specific transcripts as the ones represented only by ESTs derived from normalized libraries. A subset of the predicted tissue and tumor specific isoforms are then validated via RT-PCR experiments over a spectrum of 40 tissue types. Results Our strategy revealed 427 genes with at least one tissue specific transcript as well as 1120 genes showing tumor specific isoforms. While our experimental evaluation of computationally predicted tissue-specific isoforms revealed a high success rate in confirming the expression of these isoforms in the respective tissue, the strategy frequently failed to detect the expected restricted expression pattern. The analysis of putative lowly expressed transcripts using normalized cDNA libraries suggests that our ability to detect tissue-specific isoforms strongly depends on the expression level of the respective transcript as well as on the sensitivity of the experimental methods. Especially splice isoforms predicted to be disease-specific tend to represent transcripts that are expressed in a set of healthy tissues rather than novel isoforms. Conclusions We propose to combine the computational prediction of alternative splice isoforms with experimental validation for

  11. Infection-dependent phenotypes in MHC-congenic mice are not due to MHC: can we trust congenic animals?

    Directory of Open Access Journals (Sweden)

    Wilkinson Maureen

    2004-07-01

    Full Text Available Abstract Background Congenic strains of mice are assumed to differ only at a single gene or region of the genome. These mice have great importance in evaluating the function of genes. However, their utility depends on the maintenance of this true congenic nature. Although, accumulating evidence suggests that congenic strains suffer genetic divergence that could compromise interpretation of experimental results, this problem is usually ignored. During coinfection studies with Salmonella typhimurium and Theiler's murine encephalomyelitis virus (TMEV in major histocompatibility complex (MHC-congenic mice, we conducted the proper F2 controls and discovered significant differences between these F2 animals and MHC-genotype-matched P0 and F1 animals in weight gain and pathogen load. To systematically evaluate the apparent non-MHC differences in these mice, we infected all three generations (P0, F1 and F2 for 5 MHC genotypes (b/b, b/q and q/q as well as d/d, d/q, and q/q with Salmonella and TMEV. Results Infected P0 MHC q/q congenic homozygotes lost significantly more weight (p = 0.02 and had significantly higher Salmonella (p 2 q/q homozygotes. Neither weight nor pathogen load differences were present in sham-infected controls. Conclusions These data suggest that these strains differ for genes other than those in the MHC congenic region. The most likely explanation is that deleterious recessive mutations affecting response to infection have accumulated in the more than 40 years that this B10.Q-H-2q MHC-congenic strain has been separated from its B10-H-2b parental strain. During typical experiments with congenic strains, the phenotypes of these accumulated mutations will be falsely ascribed to the congenic gene(s. This problem likely affects any strains separated for appreciable time and while usually ignored, can be avoided with the use of F2 segregants.

  12. Spatial trends of polybrominated diphenyl ether (PBDE) congeners

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Spatial trends of polybrominated diphenyl ether (PBDE) congeners were analyzed in young of the year bluefish collected along the U.S. Atlantic coastline from...

  13. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

    DEFF Research Database (Denmark)

    Lundby, Alicia; Rossin, Elizabeth J.; Steffensen, Annette B.

    2014-01-01

    Genome-wide association studies (GWAS) have identified thousands of loci associated with complex traits, but it is challenging to pinpoint causal genes in these loci and to exploit subtle association signals. We used tissue-specific quantitative interaction proteomics to map a network of five gen...

  14. Tissue-specific alterations in thyroid hormone homeostasis in combined Mct10 and Mct8 deficiency

    NARCIS (Netherlands)

    J. Müller (Julia); S. Mayerl (Steffen); T.J. Visser (Theo); V.M. Darras (Veerle); A. Boelen (Anita); L. Frappart (Lucien); L. Mariotta (Luca); F. Verrey; H. Heuer (Heike)

    2014-01-01

    textabstractThe monocarboxylate transporter Mct10 (Slc16a10; T-type amino acid transporter) facilitates the cellular transport of thyroid hormone (TH) and shows an overlapping expression with the wellestablished TH transporter Mct8. Because Mct8 deficiency is associated with distinct tissue-specific

  15. Tissue-specific alterations in thyroid hormone homeostasis in combined Mct10 and Mct8 deficiency

    NARCIS (Netherlands)

    Müller, Julia; Mayerl, Steffen; Visser, Theo J.; Darras, Veerle M.; Boelen, Anita; Frappart, Lucien; Mariotta, Luca; Verrey, Francois; Heuer, Heike

    2014-01-01

    The monocarboxylate transporter Mct10 (Slc16a10; T-type amino acid transporter) facilitates the cellular transport of thyroid hormone (TH) and shows an overlapping expression with the well-established TH transporter Mct8. Because Mct8 deficiency is associated with distinct tissue-specific

  16. Tissue Specific Roles of Dynein Light Chain 1 in Regulating Germ Cell Apoptosis in Ceanorhabditis elegans

    DEFF Research Database (Denmark)

    Morthorst, Tine Hørning

    2015-01-01

    in the etiology of many diseases, including cancer, neurodegenerative, cardiovascular and autoimmune diseases. Several of the first genes found to regulate apoptosis were discovered in the nematode Caenorhabditis elegans. In this project, two different and tissue specific roles of C. elegans dynein light chain 1...

  17. Scaffolding in tissue engineering: general approaches and tissue-specific considerations.

    Science.gov (United States)

    Chan, B P; Leong, K W

    2008-12-01

    Scaffolds represent important components for tissue engineering. However, researchers often encounter an enormous variety of choices when selecting scaffolds for tissue engineering. This paper aims to review the functions of scaffolds and the major scaffolding approaches as important guidelines for selecting scaffolds and discuss the tissue-specific considerations for scaffolding, using intervertebral disc as an example.

  18. Tissue-specific and substrate-specific mitochondrial bioenergetics in feline cardiac and skeletal muscles

    DEFF Research Database (Denmark)

    Christiansen, Liselotte Bruun; Dela, Flemming; Koch, Jørgen

    2015-01-01

    No studies have investigated the mitochondrial function in permeabilized muscle fiber from cats. The aim of this study was to investigate tissue-specific and substrate-specific characteristics of mitochondrial oxidative phosphorylation (OXPHOS) capacity in feline permeabilized oxidative muscle fi...

  19. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

    NARCIS (Netherlands)

    Lundby, Alicia; Rossin, Elizabeth J.; Steffensen, Annette B.; Acha, Moshe Ray; Newton-Cheh, Christopher; Pfeufer, Arne; Lyneh, Stacey N.; Olesen, Soren-Peter; Brunak, Soren; Ellinor, Patrick T.; Jukema, J. Wouter; Trompet, Stella; Ford, Ian; Macfarlane, Peter W.; Krijthe, Bouwe P.; Hofman, Albert; Uitterlinden, Andre G.; Stricker, Bruno H.; Nathoe, Hendrik M.; Spiering, Wilko; Daly, Mark J.; Asselbergs, Ikea W.; van der Harst, Pim; Milan, David J.; de Bakker, Paul I. W.; Lage, Kasper; Olsen, Jesper V.

    Genome-wide association studies (GWAS) have identified thousands of loci associated with complex traits, but it is challenging to pinpoint causal genes in these loci and to exploit subtle association signals. We used tissue-specific quantitative interaction proteomics to map a network of five genes

  20. PCBs levels and indicator congeners in children's and adolescents' hair

    International Nuclear Information System (INIS)

    Liang, Baocui; Liu, Xinhui; Hou, Jing; Liang, Gang; Gong, Wenwen; Xu, Diandou; Zhang, Li

    2014-01-01

    Thirty polychlorinated biphenyl (PCB) congeners were determined in the hair samples collected from children (4–12) and adolescents (13–18) of Changchun city, Northeastern China. The mean concentrations of total PCBs and dioxin-like PCBs (dl-PCBs) in the adolescents' hair samples were 161.0 ng g −1 and 61.7 ng g −1 , which were relatively higher than 43.7 ng g −1 and 14.6 ng g −1 in the children's ones. Considering gender difference, the mean concentrations in the girls' hair samples were approximately two times higher than those in the boys' ones for most PCB congeners. The pentachlorinated biphenyl was the dominant homologue. It was found that the levels of total PCBs and dl-PCBs were highly correlated with PCB 118 level in the children's hair samples, and with PCB 114 level in the adolescents' ones. The result demonstrated that the two PCB congeners could be applied as the indicators to evaluate the concentrations of total PCBs and dl-PCBs in children's and adolescents' hair, respectively. -- Highlights: • PCBs levels for most congeners were higher in the adolescents' hair samples. • The mean PCBs were approximately 2 times higher for girls except few congeners. • Pentachlorinated biphenyl was the dominant homologue in the both hair samples. • PCB 118 and PCB 114 were the indicators for total PCBs and total dl-PCBs. -- The PCBs levels can be predicted conveniently by the congener-specific analysis

  1. Transgenic zebrafish reveal tissue-specific differences in estrogen signaling in response to environmental water samples

    Science.gov (United States)

    Gorelick, Daniel A.; Iwanowicz, Luke R.; Hung, Alice L.; Blazer, Vicki; Halpern, Marnie E.

    2014-01-01

    Background: Environmental endocrine disruptors (EED) are exogenous chemicals that mimic endogenous hormones, such as estrogens. Previous studies using a zebrafish transgenic reporter demonstrated that the EEDs bisphenol A and genistein preferentially activate estrogen receptors (ER) in the larval heart compared to the liver. However, it was not known whether the transgenic zebrafish reporter was sensitive enough to detect estrogens from environmental samples, whether environmental estrogens would exhibit similar tissue-specific effects as BPA and genistein or why some compounds preferentially target receptors in the heart. Methods: We tested surface water samples using a transgenic zebrafish reporter with tandem estrogen response elements driving green fluorescent protein expression (5xERE:GFP). Reporter activation was colocalized with tissue-specific expression of estrogen receptor genes by RNA in situ hybridization. Results: Selective patterns of ER activation were observed in transgenic fish exposed to river water samples from the Mid-Atlantic United States, with several samples preferentially activating receptors in embryonic and larval heart valves. We discovered that tissue-specificity in ER activation is due to differences in the expression of estrogen receptor subtypes. ERα is expressed in developing heart valves but not in the liver, whereas ERβ2 has the opposite profile. Accordingly, subtype-specific ER agonists activate the reporter in either the heart valves or the liver. Conclusion: The use of 5xERE:GFP transgenic zebrafish has revealed an unexpected tissue-specific difference in the response to environmentally relevant estrogenic compounds. Exposure to estrogenic EEDs in utero is associated with adverse health effects, with the potentially unanticipated consequence of targeting developing heart valves.

  2. Tissue-Specific Peroxisome Proliferator Activated Receptor Gamma Expression and Metabolic Effects of Telmisartan

    Czech Academy of Sciences Publication Activity Database

    Zídek, Václav; Mlejnek, Petr; Šimáková, Miroslava; Šilhavý, Jan; Landa, Vladimír; Kazdová, L.; Pravenec, Michal; Kurtz, T. W.

    2013-01-01

    Roč. 26, č. 6 (2013), s. 829-835 ISSN 0895-7061 R&D Projects: GA ČR(CZ) GAP303/10/0505; GA MŠk(CZ) LH11049; GA MŠk(CZ) LL1204; GA MŠk(CZ) 7E10067 Institutional support: RVO:67985823 Keywords : telmisartan * metabolic effects * tissue-specific Pparg knockout mice Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition Impact factor: 3.402, year: 2013

  3. Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea

    OpenAIRE

    Garg, Rohini; Jain, Mukesh

    2011-01-01

    Chickpea is a very important crop legume plant, which provides a protein-rich supplement to cereal-based diets and has the ability to fix atmospheric nitrogen. Despite its economic importance, the functional genomic resources for chickpea are very limited. Recently, we reported the complete transcriptome of chickpea using next generation sequencing technologies. We analyzed the tissue-specific expression of chickpea transcripts based on RNA-seq data. In addition, we identified two sets of lin...

  4. Simple and high yielding method for preparing tissue specific extracellular matrix coatings for cell culture.

    Science.gov (United States)

    DeQuach, Jessica A; Mezzano, Valeria; Miglani, Amar; Lange, Stephan; Keller, Gordon M; Sheikh, Farah; Christman, Karen L

    2010-09-27

    The native extracellular matrix (ECM) consists of a highly complex, tissue-specific network of proteins and polysaccharides, which help regulate many cellular functions. Despite the complex nature of the ECM, in vitro cell-based studies traditionally assess cell behavior on single ECM component substrates, which do not adequately mimic the in vivo extracellular milieu. We present a simple approach for developing naturally derived ECM coatings for cell culture that provide important tissue-specific cues unlike traditional cell culture coatings, thereby enabling the maturation of committed C2C12 skeletal myoblast progenitors and human embryonic stem cells differentiated into cardiomyocytes. Here we show that natural muscle-specific coatings can (i) be derived from decellularized, solubilized adult porcine muscle, (ii) contain a complex mixture of ECM components including polysaccharides, (iii) adsorb onto tissue culture plastic and (iv) promote cell maturation of committed muscle progenitor and stem cells. This versatile method can create tissue-specific ECM coatings, which offer a promising platform for cell culture to more closely mimic the mature in vivo ECM microenvironment.

  5. Tantalus, a novel ASX-interacting protein with tissue-specific functions.

    Science.gov (United States)

    Dietrich, B H; Moore, J; Kyba, M; dosSantos, G; McCloskey, F; Milne, T A; Brock, H W; Krause, H M

    2001-06-15

    The Drosophila trithorax- and Polycomb-group (trxG and PcG) proteins maintain activated and repressed transcriptional states at specific target gene loci. The Additional sex combs (Asx) gene is of particular interest as it appears to function in both protein complexes and yet its effects on target genes are more restricted. A novel protein, Tantalus (TAN), was identified in a yeast two-hybrid screen for ASX-interacting proteins that might confer tissue-specific ASX functions. TAN contains consensus nuclear localization sites and binds DNA in vitro. However, its subcellular localization varies in a tissue-specific fashion. In salivary glands, TAN is predominantly nuclear and associates with 66 euchromatic sites on polytene chromosomes, more than half of which overlap with ASX. These loci do not include the homeotic genes of the ANT and BX complexes bound by other PcG and trxG proteins. Rather, tan mutant defects are restricted to sensory organs. We show that one of these defects, shared by Asx, is genetically enhanced by Asx. Taken together, the data suggest that TAN is a tissue-specific cofactor for ASX, and that its activity may be partially controlled by subcellular trafficking. Copyright 2001 Academic Press.

  6. DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

    Science.gov (United States)

    Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

    2015-10-01

    The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (pentropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. The role of the endocrine system in feeding-induced tissue-specific circadian entrainment.

    Science.gov (United States)

    Sato, Miho; Murakami, Mariko; Node, Koichi; Matsumura, Ritsuko; Akashi, Makoto

    2014-07-24

    The circadian clock is entrained to environmental cycles by external cue-mediated phase adjustment. Although the light input pathway has been well defined, the mechanism of feeding-induced phase resetting remains unclear. The tissue-specific sensitivity of peripheral entrainment to feeding suggests the involvement of multiple pathways, including humoral and neuronal signals. Previous in vitro studies with cultured cells indicate that endocrine factors may function as entrainment cues for peripheral clocks. However, blood-borne factors that are well characterized in actual feeding-induced resetting have yet to be identified. Here, we report that insulin may be involved in feeding-induced tissue-type-dependent entrainment in vivo. In ex vivo culture experiments, insulin-induced phase shift in peripheral clocks was dependent on tissue type, which was consistent with tissue-specific insulin sensitivity, and peripheral entrainment in insulin-sensitive tissues involved PI3K- and MAPK-mediated signaling pathways. These results suggest that insulin may be an immediate early factor in feeding-mediated tissue-specific entrainment. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Identification and evolutionary analysis of tissue-specific isoforms of mitochondrial complex I subunit NDUFV3.

    Science.gov (United States)

    Guerrero-Castillo, Sergio; Cabrera-Orefice, Alfredo; Huynen, Martijn A; Arnold, Susanne

    2017-03-01

    Mitochondrial complex I is the largest respiratory chain complex. Despite the enormous progress made studying its structure and function in recent years, potential regulatory roles of its accessory subunits remained largely unresolved. Complex I gene NDUFV3, which occurs in metazoa, contains an extra exon that is only present in vertebrates and thereby evolutionary even younger than the rest of the gene. Alternative splicing of this extra exon gives rise to a short NDUFV3-S and a long NDUFV3-L protein isoform. Complexome profiling revealed that the two NDUFV3 isoforms are constituents of the multi-subunit complex I. Further mass spectrometric analyses of complex I from different murine and bovine tissues showed a tissue-specific expression pattern of NDUFV3-S and NDUFV3-L. Hence, NDUFV3-S was identified as the only isoform in heart and skeletal muscle, whereas in liver, brain, and lung NDUFV3-L was expressed as the dominant isoform, together with NDUFV3-S present in all tissues analyzed. Thus, we identified NDUFV3 as the first out of 30 accessory subunits of complex I present in vertebrate- and tissue-specific isoforms. Interestingly, the tissue-specific expression pattern of NDUFV3-S and NDUFV3-L isoforms was paralleled by changes in kinetic parameters, especially the substrate affinity of complex I. This may indicate a regulatory role of the NDUFV3 isoforms in different vertebrate tissues. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  9. Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes.

    Directory of Open Access Journals (Sweden)

    Edwin Jacox

    2010-08-01

    Full Text Available Transcriptome diversity provides the key to cellular identity. One important contribution to expression diversity is the use of alternative promoters, which creates mRNA isoforms by expanding the choice of transcription initiation sites of a gene. The proximity of the basal promoter to the transcription initiation site enables prediction of a promoter's location based on the gene annotations. We show that annotation of alternative promoters regulating expression of transcripts with distinct first exons enables a novel methodology to quantify expression levels and tissue specificity of mRNA isoforms.The use of distinct alternative first exons in 3,296 genes was examined using exon-microarray data from 11 human tissues. Comparing two transcripts from each gene we found that the activity of alternative promoters (i.e., P1 and P2 was not correlated through tissue specificity or level of expression. Furthermore neither P1 nor P2 conferred any bias for tissue-specific or ubiquitous expression. Genes associated with specific diseases produced transcripts whose limited expression patterns were consistent with the tissue affected in disease. Notably, genes that were historically designated as tissue-specific or housekeeping had alternative isoforms that showed differential expression. Furthermore, only a small number of alternative promoters showed expression exclusive to a single tissue indicating that "tissue preference" provides a better description of promoter activity than tissue specificity. When compared to gene expression data in public databases, as few as 22% of the genes had detailed information for more than one isoform, whereas the remainder collapsed the expression patterns from individual transcripts into one profile.We describe a computational pipeline that uses microarray data to assess the level of expression and breadth of tissue profiles for transcripts with distinct first exons regulated by alternative promoters. We conclude that

  10. Cells determine cell density using a small protein bound to a unique tissue-specific phospholipid

    Directory of Open Access Journals (Sweden)

    Christopher J. Petzold

    2013-10-01

    bone cofactor was identified as a lipid containing a ceramide phosphate, a single chained glycerol lipid and a linker. Tendon uses a different cofactor made up of two fatty acid chains linked directly to the phosphate yielding a molecule about half the size. Moreover, adding the tendon factor/cofactor to osteosarcoma cells causes them to stop growing, which is opposite to its role with tendon cells. Thus, the cofactor is cell type specific both in composition and in the triggered response. Further support of its proposed role came from frozen sections from 5 week old mice where an antibody to the factor stained strongly at the growing ends of the tendon as predicted. In conclusion, the molecule needed for cell density signaling is a small protein bound to a unique, tissue-specific phospholipid yielding a membrane associated but diffusible molecule. Signal transduction is postulated to occur by an increased ordering of the plasma membrane as the concentration of this protein/lipid increases with cell density.

  11. Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and arabidopsis.

    Science.gov (United States)

    Mukhopadhyay, Pamela; Basak, Surajit; Ghosh, Tapash Chandra

    2008-12-01

    Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome expression data for both rice and Arabidopsis has made it possible to examine the evolutionary forces in shaping codon usage pattern in both housekeeping and tissue-specific genes in plants. In the present work, we have taken 4065 rice-Arabidopsis homologous gene pairs to study evolutionary forces responsible for codon usage divergence between housekeeping and tissue-specific genes. In both rice and Arabidopsis, it is mutational bias that regulates error minimization in highly expressed genes of both housekeeping and tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes are under strong selective constraint in plants. However, in tissue-specific genes, lowly expressed genes are under stronger selective constraint compared with highly expressed genes. We demonstrated that constraint acting on mRNA secondary structure is responsible for modulating codon usage variations in rice tissue-specific genes. Thus, different evolutionary forces must underline the evolution of synonymous codon usage of highly expressed genes of housekeeping and tissue-specific genes in rice and Arabidopsis.

  12. Identification of tissue-specific cell death using methylation patterns of circulating DNA.

    Science.gov (United States)

    Lehmann-Werman, Roni; Neiman, Daniel; Zemmour, Hai; Moss, Joshua; Magenheim, Judith; Vaknin-Dembinsky, Adi; Rubertsson, Sten; Nellgård, Bengt; Blennow, Kaj; Zetterberg, Henrik; Spalding, Kirsty; Haller, Michael J; Wasserfall, Clive H; Schatz, Desmond A; Greenbaum, Carla J; Dorrell, Craig; Grompe, Markus; Zick, Aviad; Hubert, Ayala; Maoz, Myriam; Fendrich, Volker; Bartsch, Detlef K; Golan, Talia; Ben Sasson, Shmuel A; Zamir, Gideon; Razin, Aharon; Cedar, Howard; Shapiro, A M James; Glaser, Benjamin; Shemer, Ruth; Dor, Yuval

    2016-03-29

    Minimally invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA) released from dying cells is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on differences in DNA sequences in source tissues, so that cell death cannot be identified in tissues with a normal genome. We developed a method of detecting tissue-specific cell death in humans based on tissue-specific methylation patterns in cfDNA. We interrogated tissue-specific methylome databases to identify cell type-specific DNA methylation signatures and developed a method to detect these signatures in mixed DNA samples. We isolated cfDNA from plasma or serum of donors, treated the cfDNA with bisulfite, PCR-amplified the cfDNA, and sequenced it to quantify cfDNA carrying the methylation markers of the cell type of interest. Pancreatic β-cell DNA was identified in the circulation of patients with recently diagnosed type-1 diabetes and islet-graft recipients; oligodendrocyte DNA was identified in patients with relapsing multiple sclerosis; neuronal/glial DNA was identified in patients after traumatic brain injury or cardiac arrest; and exocrine pancreas DNA was identified in patients with pancreatic cancer or pancreatitis. This proof-of-concept study demonstrates that the tissue origins of cfDNA and thus the rate of death of specific cell types can be determined in humans. The approach can be adapted to identify cfDNA derived from any cell type in the body, offering a minimally invasive window for diagnosing and monitoring a broad spectrum of human pathologies as well as providing a better understanding of normal tissue dynamics.

  13. Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings

    Directory of Open Access Journals (Sweden)

    Le Yu

    2017-12-01

    Full Text Available Salt stress is one of the most crucial factors impacting plant growth, development and reproduction. However, information regarding differences in tissue-specific gene expression patterns, which may improve a plant’s tolerance to salt stress, is limited. Here, we investigated the gene expression patterns in tissues of Populus euphratica Oliv. seedlings using RNA sequencing (RNA-Seq technology. A total of 109.3 million, 125bp paired-end clean reads were generated, and 6428, 4797, 2335 and 3358 differentially expressed genes (DEGs were identified in leaf, phloem, xylem and root tissues, respectively. While the tissue-specific DEGs under salt stress had diverse functions, “membrane transporter activity” was the most significant leaf function, whereas “oxidation–reduction process” was the most significant function in root tissue. Further analysis of the tissue-specific DEGs showed that the expression patterns or functions of gene families, such as SOS, NHX, GolS, GPX, APX, RBOHF and CBL, were diverse, suggesting that calcium signaling, reactive oxygen species (ROS and salt overly sensitive (SOS pathways are all involved in ionic homeostasis in tissues from P. euphratica seedlings. The DEGs, for example the up-regulated antioxidant genes, contribute to ROS-scavenging induced by salt stress but result in decreased Na+ concentrations in root vasculature cells and in xylem sap, while the down-regulated rbohF leads to the reverse results. These results suggest that the divergence of DEGs expression patterns contribute to maintenance of ionic and ROS homeostasis in tissues and improve plant salinity tolerance. We comprehensively analyzed the response of P. euphratica seedlings to salt stress and provide helpful genetic resources for studying plant-abiotic stress interactions.

  14. Novel strong tissue specific promoter for gene expression in human germ cells

    Directory of Open Access Journals (Sweden)

    Kuzmin Denis

    2010-08-01

    Full Text Available Abstract Background Tissue specific promoters may be utilized for a variety of applications, including programmed gene expression in cell types, tissues and organs of interest, for developing different cell culture models or for use in gene therapy. We report a novel, tissue-specific promoter that was identified and engineered from the native upstream regulatory region of the human gene NDUFV1 containing an endogenous retroviral sequence. Results Among seven established human cell lines and five primary cultures, this modified NDUFV1 upstream sequence (mNUS was active only in human undifferentiated germ-derived cells (lines Tera-1 and EP2102, where it demonstrated high promoter activity (~twice greater than that of the SV40 early promoter, and comparable to the routinely used cytomegaloviral promoter. To investigate the potential applicability of the mNUS promoter for biotechnological needs, a construct carrying a recombinant cytosine deaminase (RCD suicide gene under the control of mNUS was tested in cell lines of different tissue origin. High cytotoxic effect of RCD with a cell-death rate ~60% was observed only in germ-derived cells (Tera-1, whereas no effect was seen in a somatic, kidney-derived control cell line (HEK293. In further experiments, we tested mNUS-driven expression of a hyperactive Sleeping Beauty transposase (SB100X. The mNUS-SB100X construct mediated stable transgene insertions exclusively in germ-derived cells, thereby providing further evidence of tissue-specificity of the mNUS promoter. Conclusions We conclude that mNUS may be used as an efficient promoter for tissue-specific gene expression in human germ-derived cells in many applications. Our data also suggest that the 91 bp-long sequence located exactly upstream NDUFV1 transcriptional start site plays a crucial role in the activity of this gene promoter in vitro in the majority of tested cell types (10/12, and an important role - in the rest two cell lines.

  15. HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation.

    Directory of Open Access Journals (Sweden)

    Jeffrey B Carroll

    Full Text Available The HTT CAG expansion mutation causes Huntington's Disease and is associated with a wide range of cellular consequences, including altered metabolism. The mutant allele is expressed widely, in all tissues, but the striatum and cortex are especially vulnerable to its effects. To more fully understand this tissue-specificity, early in the disease process, we asked whether the metabolic impact of the mutant CAG expanded allele in heterozygous B6.HdhQ111/+ mice would be common across tissues, or whether tissues would have tissue-specific responses and whether such changes may be affected by diet. Specifically, we cross-sectionally examined steady state metabolite concentrations from a range of tissues (plasma, brown adipose tissue, cerebellum, striatum, liver, white adipose tissue, using an established liquid chromatography-mass spectrometry pipeline, from cohorts of 8 month old mutant and wild-type littermate mice that were fed one of two different high-fat diets. The differential response to diet highlighted a proportion of metabolites in all tissues, ranging from 3% (7/219 in the striatum to 12% (25/212 in white adipose tissue. By contrast, the mutant CAG-expanded allele primarily affected brain metabolites, with 14% (30/219 of metabolites significantly altered, compared to wild-type, in striatum and 11% (25/224 in the cerebellum. In general, diet and the CAG-expanded allele both elicited metabolite changes that were predominantly tissue-specific and non-overlapping, with evidence for mutation-by-diet interaction in peripheral tissues most affected by diet. Machine-learning approaches highlighted the accumulation of diverse lipid species as the most genotype-predictive metabolite changes in the striatum. Validation experiments in cell culture demonstrated that lipid accumulation was also a defining feature of mutant HdhQ111 striatal progenitor cells. Thus, metabolite-level responses to the CAG expansion mutation in vivo were tissue specific and

  16. Tissue specific phosphorylation of mitochondrial proteins isolated from rat liver, heart muscle, and skeletal muscle

    DEFF Research Database (Denmark)

    Bak, Steffen; León, Ileana R; Jensen, Ole Nørregaard

    2013-01-01

    of TiO2 phosphopeptide-enrichment, HILIC fractionation, and LC-MS/MS on isolated mitochondria to investigate the tissue-specific mitochondrial phosphoproteomes of rat liver, heart, and skeletal muscle. In total, we identified 899 phosphorylation sites in 354 different mitochondrial proteins including......Phosphorylation of mitochondrial proteins in a variety of biological processes is increasingly being recognized and may contribute to the differences in function and energy demands observed in mitochondria from different tissues such as liver, heart, and skeletal muscle. Here, we used a combination...

  17. De novo assembly and analysis of tissue-specific transcriptomes revealed the tissue-specific genes and profile of immunity from Strongylocentrotus intermedius.

    Science.gov (United States)

    Chen, Yadong; Chang, Yaqing; Wang, Xiuli; Qiu, Xuemei; Liu, Yang

    2015-10-01

    Strongylocentrotus intermedius is an important marine species in north China and Japan. Recent years, diseases are threating the sea urchin aquaculture industry seriously. To provide a genetic resource for S. intermedius as well as overview the immune-related genes of S. intermedius, we performed transcriptome sequencing of three cDNA libraries representing three tissues, coelomocytes, gut and peristomial membrane respectively. In total 138,421 contigs were assembled from all sequencing data. 96,764 contigs were annotated according to bioinformatics databases, including NT, nr, Swiss-Prot, KEGG, COG. 49,336 Contigs were annotated as CDS. In this study, we obtained 24,778 gene families from S. intermedius transcriptome. The gene expression analysis revealed that more genes were expressed in gut, more high expression level genes in coelomocytes when compared with other tissues. Specific expressed contigs in coelomocytes, gut, and peristomial membrane were 546, 1136, and 1012 respectively. Pathway analysis suggested 25, 17 and 36 potential specifically pathways may specific progressed in peristomial membrane, gut and coelomocytes respectively. Similarities and differences between S. intermedius and other echinoderms were analyzed. S. intermedius was more homology to Strongylocentrotus purpuratus than others sea urchin. Of 24,778 genes, 1074 genes are immune-related, immune genes were expressed with a higher level in coelomocytes than other tissues. Complement system may be the most important immune system in sea urchin. We also identified 2438 SSRs and 16,236 SNPs for S. intermedius. These results provide a transcriptome resource and foundation to study molecular mechanisms of sea urchin immune system. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Tissue-specific splicing of a ubiquitously expressed transcription factor is essential for muscle differentiation.

    Science.gov (United States)

    Sebastian, Soji; Faralli, Hervé; Yao, Zizhen; Rakopoulos, Patricia; Palii, Carmen; Cao, Yi; Singh, Kulwant; Liu, Qi-Cai; Chu, Alphonse; Aziz, Arif; Brand, Marjorie; Tapscott, Stephen J; Dilworth, F Jeffrey

    2013-06-01

    Alternate splicing contributes extensively to cellular complexity by generating protein isoforms with divergent functions. However, the role of alternate isoforms in development remains poorly understood. Mef2 transcription factors are essential transducers of cell signaling that modulate differentiation of many cell types. Among Mef2 family members, Mef2D is unique, as it undergoes tissue-specific splicing to generate a muscle-specific isoform. Since the ubiquitously expressed (Mef2Dα1) and muscle-specific (Mef2Dα2) isoforms of Mef2D are both expressed in muscle, we examined the relative contribution of each Mef2D isoform to differentiation. Using both in vitro and in vivo models, we demonstrate that Mef2D isoforms act antagonistically to modulate differentiation. While chromatin immunoprecipitation (ChIP) sequencing analysis shows that the Mef2D isoforms bind an overlapping set of genes, only Mef2Dα2 activates late muscle transcription. Mechanistically, the differential ability of Mef2D isoforms to activate transcription depends on their susceptibility to phosphorylation by protein kinase A (PKA). Phosphorylation of Mef2Dα1 by PKA provokes its association with corepressors. Conversely, exon switching allows Mef2Dα2 to escape this inhibitory phosphorylation, permitting recruitment of Ash2L for transactivation of muscle genes. Thus, our results reveal a novel mechanism in which a tissue-specific alternate splicing event has evolved that permits a ubiquitously expressed transcription factor to escape inhibitory signaling for temporal regulation of gene expression.

  19. The Prolactin Gene: A Paradigm of Tissue-Specific Gene Regulation with Complex Temporal Transcription Dynamics

    Science.gov (United States)

    Featherstone, K; White, M R H; Davis, J R E

    2012-01-01

    Transcription of numerous mammalian genes is highly pulsatile, with bursts of expression occurring with variable duration and frequency. The presence of this stochastic or ‘noisy’ expression pattern has been relatively unexplored in tissue systems. The prolactin gene provides a model of tissue-specific gene regulation resulting in pulsatile transcription dynamics in both cell lines and endocrine tissues. In most cell culture models, prolactin transcription appears to be highly variable between cells, with differences in transcription pulse duration and frequency. This apparently stochastic transcription is constrained by a transcriptional refractory period, which may be related to cycles of chromatin remodelling. We propose that prolactin transcription dynamics result from the summation of oscillatory cellular inputs and by regulation through chromatin remodelling cycles. Observations of transcription dynamics in cells within pituitary tissue show reduced transcriptional heterogeneity and can be grouped into a small number of distinct patterns. Thus, it appears that the tissue environment is able to reduce transcriptional noise to enable coordinated tissue responses to environmental change. We review the current knowledge on the complex tissue-specific regulation of the prolactin gene in pituitary and extra-pituitary sites, highlighting differences between humans and rodent experimental animal models. Within this context, we describe the transcription dynamics of prolactin gene expression and how this may relate to specific processes occurring within the cell. PMID:22420298

  20. Obesity-induces Organ and Tissue Specific Tight Junction Restructuring and Barrier Deregulation by Claudin Switching.

    Science.gov (United States)

    Ahmad, Rizwan; Rah, Bilal; Bastola, Dhundy; Dhawan, Punita; Singh, Amar B

    2017-07-11

    Obesity increases susceptibility to multiple organ disorders, however, underlying mechanisms remain unclear. The subclinical inflammation assisted by obesity-induced gut permeability may underlie obesity-associated co-morbidities. Despite eminent clinical significance of the obesity led gut barrier abnormalities, its precise molecular regulation remains unclear. It is also unknown whether barrier deregulations, similar to the gut, characterize other vital organs in obese individuals. The claudin family of proteins is integral to the tight junction (TJ), the apical cell-cell adhesion and a key regulator of the epithelial barrier. Using comprehensive physiological and biochemical analysis of intestinal and renal tissues from high-fat diet fed mice, critical for maintaining metabolic homeostasis, this study demonstrates that profound TJ-restructuring by organ and tissue-specific claudin switching characterize obese organs. Protein expression and cellular distribution were examined. In-silico analysis further highlighted potential association of select claudins, modulated by the obesity, with signaling and metabolic pathways of pathological significance. In vitro studies using Leptin or DCA-treatment suggested causal significance of obesity-induced changes in tissue microenvironment in regulating barrier deregulations in tissue-specific manner. Overall, current findings advances our understanding of the molecular undertakings of obesity associated changes that help predispose to specific diseases and also identifies novel windows of preventive and/or therapeutic interventions.

  1. Model of Tryptophan Metabolism, Readily Scalable Using Tissue-specific Gene Expression Data*

    Science.gov (United States)

    Stavrum, Anne-Kristin; Heiland, Ines; Schuster, Stefan; Puntervoll, Pål; Ziegler, Mathias

    2013-01-01

    Tryptophan is utilized in various metabolic routes including protein synthesis, serotonin, and melatonin synthesis and the kynurenine pathway. Perturbations in these pathways have been associated with neurodegenerative diseases and cancer. Here we present a comprehensive kinetic model of the complex network of human tryptophan metabolism based upon existing kinetic data for all enzymatic conversions and transporters. By integrating tissue-specific expression data, modeling tryptophan metabolism in liver and brain returned intermediate metabolite concentrations in the physiological range. Sensitivity and metabolic control analyses identified expected key enzymes to govern fluxes in the branches of the network. Combining tissue-specific models revealed a considerable impact of the kynurenine pathway in liver on the concentrations of neuroactive derivatives in the brain. Moreover, using expression data from a cancer study predicted metabolite changes that resembled the experimental observations. We conclude that the combination of the kinetic model with expression data represents a powerful diagnostic tool to predict alterations in tryptophan metabolism. The model is readily scalable to include more tissues, thereby enabling assessment of organismal tryptophan metabolism in health and disease. PMID:24129579

  2. Rice tissue-specific promoters and condition-dependent promoters for effective translational application.

    Science.gov (United States)

    Jeong, Hee-Jeong; Jung, Ki-Hong

    2015-11-01

    Rice (Oryza sativa) is one of the most important staple food crops for more than half of the world's population. The demand is increasing for food security because of population growth and environmental challenges triggered by climate changes. This scenario has led to more interest in developing crops with greater productivity and sustainability. The process of genetic transformation, a major tool for crop improvement, utilizes promoters as one of its key elements. Those promoters are generally divided into three types: constitutive, spatiotemporal, and condition-dependent. Transcriptional control of a constitutive promoter often leads to reduced plant growth, due to a negative effect of accumulated molecules during cellular functions or energy consumption. To maximize the effect of a transgene on transgenic plants, it is better to use condition-dependent or tissue-specific promoters. However, until now, those types have not been as widely applied in crop biotechnology. In this review, we introduce and discuss four groups of tissue-specific promoters (50 promoters in total) and six groups of condition-dependent promoters (27 promoters). These promoters can be utilized to fine-tune desirable agronomic traits and develop crops with tolerance to various stresses, enhanced nutritional value, and advanced productivity. © 2015 Institute of Botany, Chinese Academy of Sciences.

  3. Glucocorticoid Signaling in Health and Disease: Insights From Tissue-Specific GR Knockout Mice.

    Science.gov (United States)

    Whirledge, Shannon; DeFranco, Donald B

    2018-01-01

    Glucocorticoids are adrenally produced hormones critically involved in development, general physiology, and control of inflammation. Since their discovery, glucocorticoids have been widely used to treat a variety of inflammatory conditions. However, high doses or prolonged use leads to a number of side effects throughout the body, which preclude their clinical utility. The primary actions of glucocorticoids are mediated by the glucocorticoid receptor (GR), a transcription factor that regulates many complex signaling pathways. Although GR is nearly ubiquitous throughout the body, glucocorticoids exhibit cell- and tissue-specific effects. For example, glucocorticoids stimulate glucose production in the liver, reduce glucose uptake in the skeletal muscle, and decrease insulin secretion from the pancreatic β-cells. Mouse models represent an important approach to understanding the dynamic functions of GR signaling in normal physiology, disease, and resistance. In the absence of a viable GR null model, gene-targeting techniques utilizing promoter-driven recombination have provided an opportunity to characterize the tissue-specific actions of GR. The aim of the present review is to describe the organ systems in which GR has been conditionally deleted and summarize the functions ascribed to glucocorticoid action in those tissues. Copyright © 2018 Endocrine Society.

  4. Tissue-specific metabolic reprogramming drives nutrient flux in diabetic complications

    Science.gov (United States)

    Sas, Kelli M.; Kayampilly, Pradeep; Byun, Jaeman; Nair, Viji; Hinder, Lucy M.; Zhang, Hongyu; Lin, Chengmao; Qi, Nathan R.; Michailidis, George; Groop, Per-Henrik; Nelson, Robert G.; Darshi, Manjula; Sharma, Kumar; Schelling, Jeffrey R.; Sedor, John R.; Pop-Busui, Rodica; Weinberg, Joel M.; Soleimanpour, Scott A.; Abcouwer, Steven F.; Gardner, Thomas W.; Burant, Charles F.; Feldman, Eva L.; Kretzler, Matthias; Brosius, Frank C.

    2016-01-01

    Diabetes is associated with altered cellular metabolism, but how altered metabolism contributes to the development of diabetic complications is unknown. We used the BKS db/db diabetic mouse model to investigate changes in carbohydrate and lipid metabolism in kidney cortex, peripheral nerve, and retina. A systems approach using transcriptomics, metabolomics, and metabolic flux analysis identified tissue-specific differences, with increased glucose and fatty acid metabolism in the kidney, a moderate increase in the retina, and a decrease in the nerve. In the kidney, increased metabolism was associated with enhanced protein acetylation and mitochondrial dysfunction. To confirm these findings in human disease, we analyzed diabetic kidney transcriptomic data and urinary metabolites from a cohort of Southwestern American Indians. The urinary findings were replicated in 2 independent patient cohorts, the Finnish Diabetic Nephropathy and the Family Investigation of Nephropathy and Diabetes studies. Increased concentrations of TCA cycle metabolites in urine, but not in plasma, predicted progression of diabetic kidney disease, and there was an enrichment of pathways involved in glycolysis and fatty acid and amino acid metabolism. Our findings highlight tissue-specific changes in metabolism in complication-prone tissues in diabetes and suggest that urinary TCA cycle intermediates are potential prognostic biomarkers of diabetic kidney disease progression. PMID:27699244

  5. VISTA Enhancer Browser--A Database of Tissue-Specific HumanEnhancers

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Minovitsky, Simon; Dubchak, Inna; Pennacchio, Len A.

    2006-08-01

    Despite the known existence of distant-acting cis-regulatoryelements in the human genome, only a small fraction of these elements hasbeen identified and experimentally characterized in vivo. This paucity ofenhancer collections with defined activities has thus hinderedcomputational approaches for the genome-wide prediction of enhancers andtheir functions. To fill this void, we utilize comparative genomeanalysis to identify candidate enhancer elements in the human genomecoupled with the experimental determination of their in vivo enhanceractivity in transgenic mice (1). These data are available through theVISTA Enhancer Browser (http://enhancer.lbl.gov). This growing databasecurrently contains over 250 experimentally tested DNA fragments, of whichmore than 100 have been validated as tissue-specific enhancers. For eachpositive enhancer, we provide digital images of whole-mount embryostaining at embryonic day 11.5 and an anatomical description of thereporter gene expression pattern. Users can retrieve elements near singlegenes of interest, search for enhancers that target reporter geneexpression to a particular tissue, or download entire collections ofenhancers with a defined tissue specificity or conservation depth. Theseexperimentally validated training sets are expected to provide a basisfor a wide range of downstream computational and functional studies ofenhancer function.

  6. Understanding multicellular function and disease with human tissue-specific networks

    Science.gov (United States)

    Greene, Casey S.; Krishnan, Arjun; Wong, Aaron K.; Ricciotti, Emanuela; Zelaya, Rene A.; Himmelstein, Daniel S.; Zhang, Ran; Hartmann, Boris M.; Zaslavsky, Elena; Sealfon, Stuart C.; Chasman, Daniel I.; FitzGerald, Garret A.; Dolinski, Kara; Grosser, Tilo; Troyanskaya, Olga G.

    2016-01-01

    Tissue and cell-type identity lie at the core of human physiology and disease. Understanding the genetic underpinnings of complex tissues and individual cell lineages is crucial for developing improved diagnostics and therapeutics. We present genome-wide functional interaction networks for 144 human tissues and cell types developed using a data-driven Bayesian methodology that integrates thousands of diverse experiments spanning tissue and disease states. Tissue-specific networks predict lineage-specific responses to perturbation, reveal genes’ changing functional roles across tissues, and illuminate disease-disease relationships. We introduce NetWAS, which combines genes with nominally significant GWAS p-values and tissue-specific networks to identify disease-gene associations more accurately than GWAS alone. Our webserver, GIANT, provides an interface to human tissue networks through multi-gene queries, network visualization, analysis tools including NetWAS, and downloadable networks. GIANT enables systematic exploration of the landscape of interacting genes that shape specialized cellular functions across more than one hundred human tissues and cell types. PMID:25915600

  7. Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.

    Science.gov (United States)

    Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting

    2017-09-12

    Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns. Using a comparative epigenomics approach, we identified and compared the tissue-specific DNA methylation patterns of rat against those of mouse and human across three shared tissue types. We confirmed that tissue-specific differentially methylated regions are strongly associated with tissue-specific regulatory elements. Comparisons between species revealed that at a minimum 11-37% of tissue-specific DNA methylation patterns are conserved, a phenomenon that we define as epigenetic conservation. Conserved DNA methylation is accompanied by conservation of other epigenetic marks including histone modifications. Although a significant amount of locus-specific methylation is epigenetically conserved, the majority of tissue-specific DNA methylation is not conserved across the species and tissue types that we investigated. Examination of the genetic underpinning of epigenetic conservation suggests that primary sequence conservation is a driving force behind epigenetic conservation. In contrast, evolutionary dynamics of tissue-specific DNA methylation are best explained by the maintenance or turnover of binding sites for important transcription factors. Our study extends the limited literature of comparative epigenomics and suggests a new paradigm for epigenetic conservation without genetic conservation through analysis of transcription factor binding sites.

  8. Adipocyte dysfunction in a mouse model of polycystic ovary syndrome (PCOS: evidence of adipocyte hypertrophy and tissue-specific inflammation.

    Directory of Open Access Journals (Sweden)

    Joseph S Marino

    Full Text Available Clinical research shows an association between polycystic ovary syndrome (PCOS and chronic inflammation, a pathological state thought to contribute to insulin resistance. The underlying pathways, however, have not been defined. The purpose of this study was to characterize the inflammatory state of a novel mouse model of PCOS. Female mice lacking leptin and insulin receptors in pro-opiomelanocortin neurons (IR/LepR(POMC mice and littermate controls were evaluated for estrous cyclicity, ovarian and adipose tissue morphology, and body composition by QMR and CT scan. Tissue-specific macrophage infiltration and cytokine mRNA expression were measured, as well as circulating cytokine levels. Finally, glucose regulation during pregnancy was evaluated as a measure of risk for diabetes development. Forty-five percent of IR/LepR(POMC mice showed reduced or absent ovulation. IR/LepR(POMC mice also had increased fat mass and adipocyte hypertrophy. These traits accompanied elevations in macrophage accumulation and inflammatory cytokine production in perigonadal adipose tissue, liver, and ovary. These mice also exhibited gestational hyperglycemia as predicted. This report is the first to show the presence of inflammation in IR/LepR(POMC mice, which develop a PCOS-like phenotype. Thus, IR/LepR(POMC mice may serve as a new mouse model to clarify the involvement of adipose and liver tissue in the pathogenesis and etiology of PCOS, allowing more targeted research on the development of PCOS and potential therapeutic interventions.

  9. Lung Cancer Signature Biomarkers: tissue specific semantic similarity based clustering of Digital Differential Display (DDD data

    Directory of Open Access Journals (Sweden)

    Srivastava Mousami

    2012-11-01

    Full Text Available Abstract Background The tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used ‘Gene Ontology semantic similarity score’ to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal and disease (cancer sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability. Results Subsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95 identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1–4. Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1, chemotherapy/drug resistance biomarkers (panel 2, hypoxia regulated biomarkers (panel 3 and lung extra cellular matrix biomarkers (panel 4. Conclusions Expression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3, HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1

  10. Lung cancer signature biomarkers: tissue specific semantic similarity based clustering of digital differential display (DDD) data.

    Science.gov (United States)

    Srivastava, Mousami; Khurana, Pankaj; Sugadev, Ragumani

    2012-11-02

    The tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs) in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD) rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used 'Gene Ontology semantic similarity score' to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal) and disease (cancer) sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability. Subsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95) identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1-4). Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1), chemotherapy/drug resistance biomarkers (panel 2), hypoxia regulated biomarkers (panel 3) and lung extra cellular matrix biomarkers (panel 4). Expression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3), HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1/SAG, AIB1 and AZIN1) are significantly down regulated

  11. Foetal uptake of coplanar polychlorinated biphenyl (PCB) congeners in mice

    International Nuclear Information System (INIS)

    Darnerud, P.O.; Sinjari, T.; Joensson, C.J.

    1996-01-01

    Earlier studies have shown that the Ah-receptor binding polychlorinated biphenyl (PCB) congener 3,3',4,4'-tetrachlorobiphenyl (IUPAC number CB-77) accumulated as hydroxy and methylsulphone metabolites in late gestational mice foetuses. In the present paper the foetal accumulation potential in mice of other dioxin-like PCB congeners was studied: 3,3'4,4',4-pentachlorobiphenyl, 3,3'4,4'5,5'-hexachlorobiphenyl and 2,3,3',4,4'-pentachlorobiphenyl (IUPAC numbers CB-126, CB-169, CB-105, to some extent dioxin-like) were compared to results of CB-77 (all congeners 14 C-labelled and in equimolar doses (2.0 μmol/kg body wt.)). CB-77 resulted in the comparatively strongest foetal 14 C-accumulation, when measured in plasma or whole body homogenate four days after administration (day 17 of pregnancy); the plasma 14 C-values (calculated as pmol/g wet wt.) were 760, 130, 60 and 40 for CB-77, -126, 105 and -169, respectively, and the CB-77 derived radioactivity in the foetal compartment was 3.6% of administered dose (i.e. a considerable portion of the remaining maternal body radioactivity). Thin-layer chromatography (TLC) results, suggesting extensive CB-77 metabolism and foetal metabolite uptake, support earlier findings. The effects of CB-77 and CB-169 on foetal 7-ethoxyresorufin-O-deethylase (EROD) activities (day 17 of gestation; two days after 5 mg/kg body wt. dose (14.0-17.0 μmol/kg body wt.)) was about 20 times lower than of CB-126. In the dam, high radioactivity levels were observed int he liver and fat (highest concentrations found in CB-126 and CB-105, respectively). Strain comparison - foetal 14 C-uptake (four days after administration of CB-77) in C57BL mice was almost five times higher than in NMRI - may be correlated to earlier observed differences in EROD activities between these strains. The present results indicate that congener and strain differences exist regarding both foetal and maternal distribution patterns of coplanar PCB congeners and point out the

  12. Tissue Specific Effects of Loss of Estrogen During Menopause and Aging

    Directory of Open Access Journals (Sweden)

    Korinna eWend

    2012-02-01

    Full Text Available The roles of estrogens have been best studied in the breast, breast cancers and in the female reproductive tract. However, estrogens have important functions in almost every tissue in the body. Recent clinical trials such as the Women’s Health Initiative have highlighted both the importance of estrogens and how little we know about the molecular mechanism of estrogens in these other tissues. In this review, we illustrate the diverse functions of estrogens in the bone, adipose tissue, skin, hair, brain, skeletal muscle and cardiovascular system, and how the loss of estrogens during aging affects these tissues. Early transcriptional targets of estrogen are reviewed in each tissue. We also describe the tissue-specific effects of selective estrogen receptor modulators (SERMs used for the treatment of breast cancers and post-menopausal symptoms.

  13. Rbfox proteins regulate tissue-specific alternative splicing of Mef2D required for muscle differentiation.

    Science.gov (United States)

    Runfola, Valeria; Sebastian, Soji; Dilworth, F Jeffrey; Gabellini, Davide

    2015-02-15

    Among the Mef2 family of transcription factors, Mef2D is unique in that it undergoes tissue-specific splicing to generate an isoform that is essential for muscle differentiation. However, the mechanisms mediating this muscle-specific processing of Mef2D remain unknown. Using bioinformatics, we identified Rbfox proteins as putative modulators of Mef2D muscle-specific splicing. Accordingly, we found direct and specific Rbfox1 and Rbfox2 binding to Mef2D pre-mRNA in vivo. Gain- and loss-of-function experiments demonstrated that Rbfox1 and Rbfox2 cooperate in promoting Mef2D splicing and subsequent myogenesis. Thus, our findings reveal a new role for Rbfox proteins in regulating myogenesis through activation of essential muscle-specific splicing events. © 2015. Published by The Company of Biologists Ltd.

  14. Targeting tissue-specific metabolic signaling pathways in aging: the promise and limitations.

    Science.gov (United States)

    Hu, Fang; Liu, Feng

    2014-01-01

    It has been well established that most of the age-related diseases such as insulin resistance, type 2 diabetes, hypertension, cardiovascular disease, osteoporosis, and atherosclerosis are all closely related to metabolic dysfunction. On the other hand, interventions on metabolism such as calorie restriction or genetic manipulations of key metabolic signaling pathways such as the insulin and mTOR signaling pathways slow down the aging process and improve healthy aging. These findings raise an important question as to whether improving energy homeostasis by targeting certain metabolic signaling pathways in specific tissues could be an effective anti-aging strategy. With a more comprehensive understanding of the tissue-specific roles of distinct metabolic signaling pathways controlling energy homeostasis and the cross-talks between these pathways during aging may lead to the development of more effective therapeutic interventions not only for metabolic dysfunction but also for aging.

  15. The Mitochondrial Permeability Transition Pore Regulator Cyclophilin D Exhibits Tissue-Specific Control of Metabolic Homeostasis.

    Directory of Open Access Journals (Sweden)

    Rhianna C Laker

    Full Text Available The mitochondrial permeability transition pore (mPTP is a key regulator of mitochondrial function that has been implicated in the pathogenesis of metabolic disease. Cyclophilin D (CypD is a critical regulator that directly binds to mPTP constituents to facilitate the pore opening. We previously found that global CypD knockout mice (KO are protected from diet-induced glucose intolerance; however, the tissue-specific function of CypD and mPTP, particularly in the control of glucose homeostasis, has not been ascertained. To this end, we performed calcium retention capacity (CRC assay to compare the importance of CypD in the liver versus skeletal muscle. We found that liver mitochondria are more dependent on CypD for mPTP opening than skeletal muscle mitochondria. To ascertain the tissue-specific role of CypD in metabolic homeostasis, we generated liver-specific and muscle-specific CypD knockout mice (LKO and MKO, respectively and fed them either a chow diet or 45% high-fat diet (HFD for 14 weeks. MKO mice displayed similar body weight gain and glucose intolerance compared with wild type littermates (WT, whereas LKO mice developed greater visceral obesity, glucose intolerance and pyruvate intolerance compared with WT mice. These findings demonstrate that loss of muscle CypD is not sufficient to alter whole body glucose metabolism, while the loss of liver CypD exacerbates obesity and whole-body metabolic dysfunction in mice fed HFD.

  16. In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine.

    Science.gov (United States)

    Iurlaro, Mario; McInroy, Gordon R; Burgess, Heather E; Dean, Wendy; Raiber, Eun-Ang; Bachman, Martin; Beraldi, Dario; Balasubramanian, Shankar; Reik, Wolf

    2016-06-29

    Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair. These modified bases are stable and detectable in the genome, suggesting that they could have epigenetic functions in their own right. However, functional investigation of the genome-wide distribution of 5fC has been restricted to cell culture-based systems, while its in vivo profile remains unknown. Here, we describe the first analysis of the in vivo genome-wide profile of 5fC across a range of tissues from both wild-type and Tdg-deficient E11.5 mouse embryos. Changes in the formylation profile of cytosine upon depletion of TDG suggest TET/TDG-mediated active demethylation occurs preferentially at intron-exon boundaries and reveals a major role for TDG in shaping 5fC distribution at CpG islands. Moreover, we find that active enhancer regions specifically exhibit high levels of 5fC, resulting in characteristic tissue-diagnostic patterns, which suggest a role in embryonic development. The tissue-specific distribution of 5fC can be regulated by the collective contribution of TET-mediated oxidation and excision by TDG. The in vivo profile of 5fC during embryonic development resembles that of embryonic stem cells, sharing key features including enrichment of 5fC in enhancer and intragenic regions. Additionally, by investigating mouse embryo 5fC profiles in a tissue-specific manner, we identify targeted enrichment at active enhancers involved in tissue development.

  17. Illuminating a plant's tissue-specific metabolic diversity using computational metabolomics and information theory.

    Science.gov (United States)

    Li, Dapeng; Heiling, Sven; Baldwin, Ian T; Gaquerel, Emmanuel

    2016-11-22

    Secondary metabolite diversity is considered an important fitness determinant for plants' biotic and abiotic interactions in nature. This diversity can be examined in two dimensions. The first one considers metabolite diversity across plant species. A second way of looking at this diversity is by considering the tissue-specific localization of pathways underlying secondary metabolism within a plant. Although these cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene function and regulatory processes, they have rarely been comprehensively explored by nontargeted metabolomics. As such, important questions have remained superficially addressed. For instance, which tissues exhibit prevalent signatures of metabolic specialization? Reciprocally, which metabolites contribute most to this tissue specialization in contrast to those metabolites exhibiting housekeeping characteristics? Here, we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism, by combining tissue-wide nontargeted mass spectral data acquisition, information theory analysis, and tandem MS (MS/MS) molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 nonredundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome, and most unique metabolites of anthers and other tissues were annotated through MS/MS molecular networks. Tissue-metabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation in their quest to understand gene function.

  18. Linking salinity stress tolerance with tissue-specific Na+ sequestration in wheat roots

    Directory of Open Access Journals (Sweden)

    Honghong eWu

    2015-02-01

    Full Text Available Salinity stress tolerance is a physiologically complex trait that is conferred by the large array of interacting mechanisms. Among these, vacuolar Na+ sequestration has always been considered as one of the key components differentiating between sensitive and tolerant species and genotypes. However, vacuolar Na+ sequestration has been rarely considered in the context of the tissue-specific expression and regulation of appropriate transporters contributing to Na+ removal from the cytosol. In this work, six bread wheat varieties contrasting in their salinity tolerance (three tolerant and three sensitive were used to understand the essentiality of vacuolar Na+ sequestration between functionally different root tissues, and link it with the overall salinity stress tolerance in this species. Roots of 4-d old wheat seedlings were treated with 100 mM NaCl for 3 days, and then Na+ distribution between cytosol and vacuole was quantified by CoroNa Green fluorescent dye imaging. Our major observations were as follows: 1 salinity stress tolerance correlated positively with vacuolar Na+ sequestration ability in the mature root zone but not in the root apex; 2 Contrary to expectations, cytosolic Na+ levels in root meristem were significantly higher in salt tolerant than sensitive group, while vacuolar Na+ levels showed an opposite trend. These results are interpreted as meristem cells playing a role of the salt sensor; 3 No significant difference in the vacuolar Na+ sequestration ability was found between sensitive and tolerant group in either transition or elongation zones; 4 The overall Na+ accumulation was highest in the elongation zone, suggesting its role in osmotic adjustment and turgor maintenance required to drive root expansion growth. Overall, the reported results suggest high tissue-specificity of Na+ uptake, signalling, and sequestration in wheat root. The implications of these findings for plant breeding for salinity stress tolerance are discussed.

  19. Fractionation and current time trends of PCB congeners: evolvement of distributions 1950–2010 studied using a global atmosphere-ocean general circulation model

    Directory of Open Access Journals (Sweden)

    G. Lammel

    2012-08-01

    Full Text Available PCBs are ubiquitous environmental pollutants expected to decline in abiotic environmental media in response to decreasing primary emissions since the 1970s. A coupled atmosphere-ocean general circulation model with embedded dynamic sub-models for atmospheric aerosols and the marine biogeochemistry and air-surface exchange processes with soils, vegetation and the cryosphere is used to study the transport and fate of four PCB congeners covering a range of 3–7 chlorine atoms.

    The change of the geographic distribution of the PCB mixture reflects the sources and sinks' evolvement over time. Globally, secondary emissions (re-volatilisation from surfaces are on the long term increasingly gaining importance over primary emissions. Secondary emissions are most important for the congeners with 5–6 chlorine atoms. Correspondingly, the levels of these congeners are predicted to decrease slowest. Changes in congener mixture composition (fractionation are characterized both geographically and temporally. In high latitudes enrichment of the lighter, less persistent congeners and more delayed decreasing levels in response to decreasing emissions are found. The delivery of the contaminants to high latitudes is predicted to be more efficient than previously suggested. The results suggest furthermore that the effectiveness of emission control measures may significantly vary among substances. The trends of decline of organic contaminant levels in the abiotic environmental media do not only vary with latitude (slow in high latitudes, but do also show longitudinal gradients.

  20. Metabolite profiling of red and blue potatoes revealed cultivar and tissue specific patterns for anthocyanins and other polyphenols.

    Science.gov (United States)

    Oertel, Anne; Matros, Andrea; Hartmann, Anja; Arapitsas, Panagiotis; Dehmer, Klaus J; Martens, Stefan; Mock, Hans-Peter

    2017-08-01

    Metabolite profiling of tuber flesh and peel for selected colored potato varieties revealed cultivar and tissue specific profiles of anthocyanins and other polyphenols with variations in composition and concentration. Starchy tubers of Solanum tuberosum are a staple crop and food in many countries. Among cultivated potato varieties a huge biodiversity exists, including an increasing number of red and purple colored cultivars. This coloration relates to the accumulation of anthocyanins and is supposed to offer nutritional benefits possibly associated with the antioxidative capacity of anthocyanins. However, the anthocyanin composition and its relation to the overall polyphenol constitution in colored potato tubers have not been investigated closely. This study focuses on the phytochemical characterization of the phenolic composition of a variety of colored potato tubers, both for peel and flesh tissues. First, liquid chromatography (LC) separation coupled to UV and mass spectrometry (MS) detection of polyphenolic compounds of potato tubers from 57 cultivars was used to assign groups of potato cultivars differing in their anthocyanin and polyphenol profiles. Tissues from 19 selected cultivars were then analyzed by LC separation coupled to multiple reaction monitoring (MRM) to detect quantitative differences in anthocyanin and polyphenol composition. The measured intensities of 21 anthocyanins present in the analyzed potato cultivars and tissues could be correlated with the specific tuber coloration. Besides secondary metabolites well-known for potato tubers, the metabolic profiling led to the detection of two anthocyanins not described for potato tuber previously, which we tentatively annotated as pelargonidin feruloyl-xylosyl-glucosyl-galactoside and cyanidin 3-p-coumaroylrutinoside-5-glucoside. We detected significant correlations between some of the measured metabolites, as for example the negative correlation between the main anthocyanins of red and blue potato

  1. Predicting water solubility of congeners: Chloronaphthalenes-A case study

    Energy Technology Data Exchange (ETDEWEB)

    Puzyn, Tomasz, E-mail: puzi@qsar.eu.org [Faculty of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Mostrag, Aleksandra; Falandysz, Jerzy [Faculty of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Kholod, Yana; Leszczynski, Jerzy [NSF CREST Nanotoxicity Center, Department of Chemistry, Jackson State University, 1325 Lynch St, Jackson, MS 39217-0510 (United States)

    2009-10-30

    Since the important physicochemical data for chloronaphtalenes (PCNs) are still scarce, we have predicted water solubility (log S) of all 75 congeners with the Quantitative Structure-Property Relationship (QSPR) scheme. The values of log S, predicted by the most efficient model, varied from 0.01 to 1660 {mu}g dm{sup -3} (2.85 x 10{sup -11}-1.02 x 10{sup -5} mol dm{sup -3}), depending on the number of chlorine atoms present in the molecule and the substitution pattern. We found that the main factor determining relative differences in solubility between the congeners is the solvent accessible volume related to the cavitation process occurring in the solvent. The results are presented as a case study of QSPR modeling for those Persistent Organic Pollutants (POPs) that exist as families of congeners. By investigating the impact of (i) the way of the molecular descriptors' calculation, (ii) the size of applied database and (iii) chemometric method of modeling (Multiple Linear Regression, MLR, and/or Partial Least Squares regression, PLS) on the quality of the models we proposed general recommendations for dealing with congeners. We found that the combination of the B3LYP functional with 6-311++G(d,p) basis set was the most optimal technique of the molecular descriptors' calculation for congeners when comparing with semi-empirical PM3, ab initio Hartee-Fock (HF), and Moller-Pleset 2 (MP2) method carried out with different-size basis sets. Moreover, the model developed with a larger and more general database that includes chloronaphthalenes, polychlorinated dibezno-p-dioxins, furans and biphenyls predicted the values of log S for PCNs noticeable worse than the model calibrated only on PCNs. In the later case it was possible to obtain satisfactory results by employing even the simplest MLR method and only one molecular descriptor. The values of log S were also calculated with the WSKOWIN and COSMO-RS models as the reference techniques and then compared to our

  2. Predicting water solubility of congeners: Chloronaphthalenes-A case study

    International Nuclear Information System (INIS)

    Puzyn, Tomasz; Mostrag, Aleksandra; Falandysz, Jerzy; Kholod, Yana; Leszczynski, Jerzy

    2009-01-01

    Since the important physicochemical data for chloronaphtalenes (PCNs) are still scarce, we have predicted water solubility (log S) of all 75 congeners with the Quantitative Structure-Property Relationship (QSPR) scheme. The values of log S, predicted by the most efficient model, varied from 0.01 to 1660 μg dm -3 (2.85 x 10 -11 -1.02 x 10 -5 mol dm -3 ), depending on the number of chlorine atoms present in the molecule and the substitution pattern. We found that the main factor determining relative differences in solubility between the congeners is the solvent accessible volume related to the cavitation process occurring in the solvent. The results are presented as a case study of QSPR modeling for those Persistent Organic Pollutants (POPs) that exist as families of congeners. By investigating the impact of (i) the way of the molecular descriptors' calculation, (ii) the size of applied database and (iii) chemometric method of modeling (Multiple Linear Regression, MLR, and/or Partial Least Squares regression, PLS) on the quality of the models we proposed general recommendations for dealing with congeners. We found that the combination of the B3LYP functional with 6-311++G(d,p) basis set was the most optimal technique of the molecular descriptors' calculation for congeners when comparing with semi-empirical PM3, ab initio Hartee-Fock (HF), and Moller-Pleset 2 (MP2) method carried out with different-size basis sets. Moreover, the model developed with a larger and more general database that includes chloronaphthalenes, polychlorinated dibezno-p-dioxins, furans and biphenyls predicted the values of log S for PCNs noticeable worse than the model calibrated only on PCNs. In the later case it was possible to obtain satisfactory results by employing even the simplest MLR method and only one molecular descriptor. The values of log S were also calculated with the WSKOWIN and COSMO-RS models as the reference techniques and then compared to our results.

  3. Endometrial natural killer (NK) cells reveal a tissue-specific receptor repertoire.

    Science.gov (United States)

    Feyaerts, D; Kuret, T; van Cranenbroek, B; van der Zeeuw-Hingrez, S; van der Heijden, O W H; van der Meer, A; Joosten, I; van der Molen, R G

    2018-02-13

    Is the natural killer (NK) cell receptor repertoire of endometrial NK (eNK) cells tissue-specific? The NK cell receptor (NKR) expression profile in pre-pregnancy endometrium appears to have a unique tissue-specific phenotype, different from that found in NK cells in peripheral blood, suggesting that these cells are finely tuned towards the reception of an allogeneic fetus. NK cells are important for successful pregnancy. After implantation, NK cells encounter extravillous trophoblast cells and regulate trophoblast invasion. NK cell activity is amongst others regulated by C-type lectin heterodimer (CD94/NKG2) and killer cell immunoglobulin-like (KIR) receptors. KIR expression on decidual NK cells is affected by the presence of maternal HLA-C and biased towards KIR2D expression. However, little is known about NKR expression on eNK cells prior to pregnancy. In this study, matched peripheral and menstrual blood (a source of endometrial cells) was obtained from 25 healthy females with regular menstrual cycles. Menstrual blood was collected during the first 36 h of menstruation using a menstrual cup, a non-invasive technique to obtain endometrial cells. KIR and NKG2 receptor expression on eNK cells was characterized by 10-color flow cytometry, and compared to matched pbNK cells of the same female. KIR and HLA-C genotypes were determined by PCR-SSOP techniques. Anti-CMV IgG antibodies in plasma were measured by chemiluminescence immunoassay. KIR expression patterns of eNK cells collected from the same female do not differ over consecutive menstrual cycles. The percentage of NK cells expressing KIR2DL2/L3/S2, KIR2DL3, KIR2DL1, LILRB1 and/or NKG2A was significantly higher in eNK cells compared to pbNK cells, while no significant difference was observed for NKG2C, KIR2DL1/S1, and KIR3DL1. The NKR repertoire of eNK cells was clearly different from pbNK cells, with eNK cells co-expressing more than three NKR simultaneously. In addition, outlier analysis revealed 8 and 15 NKR

  4. Whole-organ isolation approach as a basis for tissue-specific analyses in Schistosoma mansoni.

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    Steffen Hahnel

    Full Text Available BACKGROUND: Schistosomiasis is one of the most important parasitic diseases worldwide, second only to malaria. Schistosomes exhibit an exceptional reproductive biology since the sexual maturation of the female, which includes the differentiation of the reproductive organs, is controlled by pairing. Pathogenicity originates from eggs, which cause severe inflammation in their hosts. Elucidation of processes contributing to female maturation is not only of interest to basic science but also considering novel concepts combating schistosomiasis. METHODOLOGY/PRINCIPAL FINDINGS: To get direct access to the reproductive organs, we established a novel protocol using a combined detergent/protease-treatment removing the tegument and the musculature of adult Schistosoma mansoni. All steps were monitored by scanning electron microscopy (SEM and bright-field microscopy (BF. We focused on the gonads of adult schistosomes and demonstrated that isolated and purified testes and ovaries can be used for morphological and structural studies as well as sources for RNA and protein of sufficient amounts for subsequent analyses such as RT-PCR and immunoblotting. To this end, first exemplary evidence was obtained for tissue-specific transcription within the gonads (axonemal dynein intermediate chain gene SmAxDynIC; aquaporin gene SmAQP as well as for post-transcriptional regulation (SmAQP. CONCLUSIONS/SIGNIFICANCE: The presented method provides a new way of getting access to tissue-specific material of S. mansoni. With regard to many still unanswered questions of schistosome biology, such as elucidating the molecular processes involved in schistosome reproduction, this protocol provides opportunities for, e.g., sub-transcriptomics and sub-proteomics at the organ level. This will promote the characterisation of gene-expression profiles, or more specifically to complete knowledge of signalling pathways contributing to differentiation processes, so discovering involved

  5. De novo assembly and characterization of tissue specific transcriptomes in the emerald notothen, Trematomus bernacchii.

    Science.gov (United States)

    Huth, Troy J; Place, Sean P

    2013-11-20

    The notothenioids comprise a diverse group of fishes that rapidly radiated after isolation by the Antarctic Circumpolar Current approximately 14-25 million years ago. Given that evolutionary adaptation has led to finely tuned traits with narrow physiological limits in these organisms, this system provides a unique opportunity to examine physiological trade-offs and limits of adaptive responses to environmental perturbation. As such, notothenioids have a rich history with respect to studies attempting to understand the vulnerability of polar ecosystems to the negative impacts associated with global climate change. Unfortunately, despite being a model system for understanding physiological adaptations to extreme environments, we still lack fundamental molecular tools for much of the Nototheniidae family. Specimens of the emerald notothen, Trematomus bernacchii, were acclimated for 28 days in flow-through seawater tanks maintained near ambient seawater temperatures (-1.5°C) or at +4°C. Following acclimation, tissue specific cDNA libraries for liver, gill and brain were created by pooling RNA from n = 5 individuals per temperature treatment. The tissue specific libraries were bar-coded and used for 454 pyrosequencing, which yielded over 700 thousand sequencing reads. A de novo assembly and annotation of these reads produced a functional transcriptome library of T. bernacchii containing 30,107 unigenes, 13,003 of which possessed significant homology to a known protein product. Digital gene expression analysis of these extremely cold adapted fish reinforced the loss of an inducible heat shock response and allowed the preliminary exploration into other elements of the cellular stress response. Preliminary exploration of the transcriptome of T. bernacchii under elevated temperatures enabled a semi-quantitative comparison to prior studies aimed at characterizing the thermal response of this endemic fish whose size, abundance and distribution has established it as a

  6. Chemometric comparison of polychlorinated biphenyl residues and toxicologically active polychlorinated biphenyl congeners in the eggs of Forster's Terns (Sterna fosteri)

    Science.gov (United States)

    Schwartz, Ted R.; Stalling, David L.

    1991-01-01

    The separation and characterization of complex mixtures of polychlorinated biphenyls (PCBs) is approached from the perspective of a problem in chemometrics. A technique for quantitative determination of PCB congeners is described as well as an enrichment technique designed to isolate only those congener residues which induce mixed aryl hydrocarbon hydroxylase enzyme activity. A congener-specific procedure is utilized for the determination of PCBs in whichn-alkyl trichloroacetates are used as retention index marker compounds. Retention indices are reproducible in the range of ±0.05 to ±0.7 depending on the specific congener. A laboratory data base system developed to aid in the editing and quantitation of data generated from capillary gas chromatography was employed to quantitate chromatographic data. Data base management was provided by computer programs written in VAX-DSM (Digital Standard MUMPS) for the VAX-DEC (Digital Equipment Corp.) family of computers.In the chemometric evaluation of these complex chromatographic profiles, data are viewed from a single analysis as a point in multi-dimensional space. Principal Components Analysis was used to obtain a representation of the data in a lower dimensional space. Two-and three-dimensional proections based on sample scores from the principal components models were used to visualize the behavior of Aroclor® mixtures. These models can be used to determine if new sample profiles may be represented by Aroclor profiles. Concentrations of individual congeners of a given chlorine substitution may be summed to form homologue concentration. However, the use of homologue concentrations in classification studies with environmental samples can lead to erroneous conclusions about sample similarity. Chemometric applications are discussed for evaluation of Aroclor mixture analysis and compositional description of environmental residues of PCBs in eggs of Forster's terns (Sterna fosteri) collected from colonies near Lake Poygan

  7. Tissue-specific increases in 11beta-hydroxysteroid dehydrogenase type 1 in normal weight postmenopausal women.

    Directory of Open Access Journals (Sweden)

    Therése Andersson

    Full Text Available With age and menopause there is a shift in adipose distribution from gluteo-femoral to abdominal depots in women. Associated with this redistribution of fat are increased risks of type 2 diabetes and cardiovascular disease. Glucocorticoids influence body composition, and 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1 which converts inert cortisone to active cortisol is a putative key mediator of metabolic complications in obesity. Increased 11betaHSD1 in adipose tissue may contribute to postmenopausal central obesity. We hypothesized that tissue-specific 11betaHSD1 gene expression and activity are up-regulated in the older, postmenopausal women compared to young, premenopausal women. Twenty-three pre- and 23 postmenopausal, healthy, normal weight women were recruited. The participants underwent a urine collection, a subcutaneous adipose tissue biopsy and the hepatic 11betaHSD1 activity was estimated by the serum cortisol response after an oral dose of cortisone. Urinary (5alpha-tetrahydrocortisol+5beta-tetrahydrocortisol/tetrahydrocortisone ratios were higher in postmenopausal women versus premenopausal women in luteal phase (P<0.05, indicating an increased whole-body 11betaHSD1 activity. Postmenopausal women had higher 11betaHSD1 gene expression in subcutaneous fat (P<0.05. Hepatic first pass conversion of oral cortisone to cortisol was also increased in postmenopausal women versus premenopausal women in follicular phase of the menstrual cycle (P<0.01, at 30 min post cortisone ingestion, suggesting higher hepatic 11betaHSD1 activity. In conclusion, our results indicate that postmenopausal normal weight women have increased 11betaHSD1 activity in adipose tissue and liver. This may contribute to metabolic dysfunctions with menopause and ageing in women.

  8. Transposon-mediated transgenesis, transgenic rescue, and tissue-specific gene expression in rodents and rabbits.

    Science.gov (United States)

    Katter, Katharina; Geurts, Aron M; Hoffmann, Orsolya; Mátés, Lajos; Landa, Vladimir; Hiripi, László; Moreno, Carol; Lazar, Jozef; Bashir, Sanum; Zidek, Vaclav; Popova, Elena; Jerchow, Boris; Becker, Katja; Devaraj, Anantharam; Walter, Ingrid; Grzybowksi, Michael; Corbett, Molly; Filho, Artur Rangel; Hodges, Matthew R; Bader, Michael; Ivics, Zoltán; Jacob, Howard J; Pravenec, Michal; Bosze, Zsuzsanna; Rülicke, Thomas; Izsvák, Zsuzsanna

    2013-03-01

    Germline transgenesis is an important procedure for functional investigation of biological pathways, as well as for animal biotechnology. We have established a simple, nonviral protocol in three important biomedical model organisms frequently used in physiological studies. The protocol is based on the hyperactive Sleeping Beauty transposon system, SB100X, which reproducibly promoted generation of transgenic founders at frequencies of 50-64, 14-72, and 15% in mice, rats, and rabbits, respectively. The SB100X-mediated transgene integrations are less prone to genetic mosaicism and gene silencing as compared to either the classical pronuclear injection or to lentivirus-mediated transgenesis. The method was successfully applied to a variety of transgenes and animal models, and can be used to generate founders with single-copy integrations. The transposon vector also allows the generation of transgenic lines with tissue-specific expression patterns specified by promoter elements of choice, exemplified by a rat reporter strain useful for tracking serotonergic neurons. As a proof of principle, we rescued an inborn genetic defect in the fawn-hooded hypertensive rat by SB100X transgenesis. A side-by-side comparison of the SB100X- and piggyBac-based protocols revealed that the two systems are complementary, offering new opportunities in genome manipulation.

  9. A novel CpG island set identifies tissue-specific methylation at developmental gene loci.

    Directory of Open Access Journals (Sweden)

    Robert Illingworth

    2008-01-01

    Full Text Available CpG islands (CGIs are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation, we devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcription start sites, the remainder being intra- or intergenic. Using an array representing over 17,000 CGIs, we established that 6%-8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen. Inter- and intragenic CGIs are preferentially susceptible to methylation. CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members. The findings enable a comprehensive analysis of the roles played by CGI methylation in normal and diseased human tissues.

  10. Tissue-Specific Ablation of Prkar1a Causes Schwannomas by Suppressing Neurofibromatosis Protein Production

    Directory of Open Access Journals (Sweden)

    Georgette N. Jones

    2008-11-01

    Full Text Available Signaling events leading to Schwann cell tumor initiation have been extensively characterized in the context of neurofibromatosis (NF. Similar tumors are also observed in patients with the endocrine neoplasia syndrome Carney complex, which results from inactivating mutations in PRKAR1A. Loss of PRKAR1A causes enhanced protein kinase A activity, although the pathways leading to tumorigenesis are not well characterized. Tissue-specific ablation of Prkar1a in neural crest precursor cells (TEC3KO mice causes schwannomas with nearly 80% penetrance by 10 months. These heterogeneous neoplasms were clinically characterized as genetically engineered mouse schwannomas, grades II and III. At the molecular level, analysis of the tumors revealed almost complete loss of both NF proteins, despite the fact that transcript levels were increased, implying posttranscriptional regulation. Although Erk and Akt signaling are typically enhanced in NF-associated tumors, we observed no activation of either of these pathways in TEC3KO tumors. Furthermore, the small G proteins Ras, Rac1, and RhoA are all known to be involved with NF signaling. In TEC3KO tumors, all three molecules showed modest increases in total protein, but only Rac1 showed significant activation. These data suggest that dysregulated protein kinase A activation causes tumorigenesis through pathways that overlap but are distinct from those described in NF tumorigenesis.

  11. Tissue Specificity of a Response of the Pro- and Antioxidative System After Resuscitation

    Directory of Open Access Journals (Sweden)

    A. G. Zhukova

    2005-01-01

    Full Text Available This investigation was undertaken to study the resistance of membrane structures and the level of the intracellular defense systems of the heart, brain, and liver in animals with active versus passive behavior in different periods (days 7 and 30 after resuscitation made 10 minutes following systemic circulatory arrest. All the animals in which systemic circulation had been stopped were survivors with the cession of neurological deficit. The activity of antioxidative defense enzymes, such as cata-lase and superoxide dismutase, in cardiac, cerebral, and hepatic tissues was assayed by spectrophotometry using the conventional methods. The level of stress-induced protein HSP70 was measured in the tissue cytosolic fraction by the Western blotting assay. The activity of Ca2+ transport in the myocardial sarcoplasmic reticulum was determined on an Orion EA 940 ionomer («Orion Research», USA having a Ca2+-selective electrode. The findings show a significant tissue specificity in different postresuscitative periods (days 7 and 30 and varying (protective to damaging cardiac, cerebral, and hepatic responses in active and passive animals to hypoxia.

  12. HOXA5 plays tissue-specific roles in the developing respiratory system.

    Science.gov (United States)

    Landry-Truchon, Kim; Houde, Nicolas; Boucherat, Olivier; Joncas, France-Hélène; Dasen, Jeremy S; Philippidou, Polyxeni; Mansfield, Jennifer H; Jeannotte, Lucie

    2017-10-01

    Hoxa5 is essential for development of several organs and tissues. In the respiratory system, loss of Hoxa5 function causes neonatal death due to respiratory distress. Expression of HOXA5 protein in mesenchyme of the respiratory tract and in phrenic motor neurons of the central nervous system led us to address the individual contribution of these Hoxa5 expression domains using a conditional gene targeting approach. Hoxa5 does not play a cell-autonomous role in lung epithelium, consistent with lack of HOXA5 expression in this cell layer. In contrast, ablation of Hoxa5 in mesenchyme perturbed trachea development, lung epithelial cell differentiation and lung growth. Further, deletion of Hoxa5 in motor neurons resulted in abnormal diaphragm innervation and musculature, and lung hypoplasia. It also reproduced the neonatal lethality observed in null mutants, indicating that the defective diaphragm is the main cause of impaired survival at birth. Thus, Hoxa5 possesses tissue-specific functions that differentially contribute to the morphogenesis of the respiratory tract. © 2017. Published by The Company of Biologists Ltd.

  13. Regulating expressin of cell and tissue-specific genes by modifying transcription

    Energy Technology Data Exchange (ETDEWEB)

    Beachy, Roger N. [Donald Danforth Plant Science Center, St. Louis, MO (United States); Dai, Shunhong [Donald Danforth Plant Science Center, St. Louis, MO (United States)

    2009-12-15

    Transcriptional regulation is the primary step to control gene expression, therefore function. Such regulation is achieved primarily via a combination of the activities of the promoter cis regulatory DNA elements and trans regulatory proteins that function through binding to these DNA elements. Our research supported by this program has led to the identification of rice bZIP transcription factors RF2a, RF2b and RLP1 that play key roles in regulating the activity of a vascular tissue specific promoter isolated from Rice Tungro Bacilliform Virus (RTBV) through their interactions with the Box II essential cis element located in the promoter. RF2a, RF2b and RLP1 possess multiple regulatory domains. Functional characterization reveals that those domains can activate or repress the activity of the RTBV promoter. Studies of transcriptional regulation of the RTBV promoter by this group of bZIP proteins not only provide insights about gene expression in the vascular tissue, but also insights about general mechanisms of transcription activation and repression. The knowledge gained from this research will also enable us to develop a well-described set of tools that can be used to control expression of multiple genes in transgenic plants and to improve biofuel feedstock.

  14. Lesions by tissue specific imaging characterize multiple sclerosis patients with more advanced disease.

    Science.gov (United States)

    Bagnato, Francesca; Ikonomidou, Vasiliki N; van Gelderen, Peter; Auh, Sungyoung; Hanafy, Jailan; Cantor, Fredric K; Ohayon, Joan; Richert, Nancy; Duyn, Jeff

    2011-12-01

    Cerebrospinal fluid tissue specific imaging (CSF-TSI), a newly implemented magnetic resonance imaging (MRI) technique, allows visualization of a subset of chronic black holes (cBHs) with MRI characteristics suggestive of the presence of CSF-like fluid, and representing lesions with extensive tissue destruction. To investigate the relationship between lesions in CSF-TSI and disease measures in patients with multiple sclerosis (MS). Twenty-six patients with MS were imaged at 3.0 T, obtaining T(1)-weighted (T(1)-w) and T(2)-w spin echo (SE), T(1) volumetric images and CSF-TSI images. We measured: (i) lesion volume (LV) in T(1)-w (cBH-LV) and T(2)-w SE images, and in CSF-TSI; (ii) brain parenchyma fraction (BPF). Differences between patients with and without CSF-TSI lesions were analyzed and association between clinical and MRI metrics were investigated. cBHs were seen in 92% of the patients while lesions in CSF-TSI were seen in 40%. Patients with CSF-TSI lesions were older, with longer disease duration, higher disability scores, larger cBH-LV and T(2)-LV, and lower BPF than patients without CSF-TSI lesions (≤0.047). Partial correlation analysis correcting for T(2)-LV, cBH-LV and BPF showed an association (p TSI LV and disability score. CSF-TSI lesions characterize patients with more advanced disease and probably contribute to the progress of disability.

  15. Regulating expression of cell and tissue-specific genes by modifying transcription

    Energy Technology Data Exchange (ETDEWEB)

    Beachy, Roger N; Dai, Shunhong

    2010-06-14

    Transcriptional regulation is the primary step to control gene expression, therefore function. Such regulation is achieved primarily via a combination of the activities of the promoter cis regulatory DNA elements and trans regulatory proteins that function through binding to these DNA elements. Rice bZIP transcription factors RF2a, RF2b and RLP1 play key roles in regulating the activity of a vascular tissue specific promoter isolated from Rice Tungro Bacilliform Virus (RTBV), through their interactions with the Box II essential cis element located in the promoter (Dai et al., 2006., Dai et al., 2004., Yin et al., 1997). RF2a, RF2b and RLP1 possess multiple regulatory domains. Functional characterization reveals that those domains can activate or repress the activity of the RTBV promoter. It is equally as important to recognize that these proteins control plant development by regulating differentiation and/or function of the vascular tissues. Studies of transcriptional regulation of the RTBV promoter by this group of bZIP proteins will not only provide insights about gene expression in the vascular tissue, but also insights about general mechanisms of transcription activation and repression. The knowledge gained from this research will also enable us to develop a well-described set of tools that can be used to control expression of multiple genes in transgenic plants. We have proposed characterize the function domains of RF2a, RF2b and RLP1 and explore the biological function of the transcription repressor RLP1.

  16. Intermittent fasting results in tissue-specific changes in bioenergetics and redox state.

    Science.gov (United States)

    Chausse, Bruno; Vieira-Lara, Marcel A; Sanchez, Angélica B; Medeiros, Marisa H G; Kowaltowski, Alicia J

    2015-01-01

    Intermittent fasting (IF) is a dietary intervention often used as an alternative to caloric restriction (CR) and characterized by 24 hour cycles alternating ad libitum feeding and fasting. Although the consequences of CR are well studied, the effects of IF on redox status are not. Here, we address the effects of IF on redox state markers in different tissues in order to uncover how changes in feeding frequency alter redox balance in rats. IF rats displayed lower body mass due to decreased energy conversion efficiency. Livers in IF rats presented increased mitochondrial respiratory capacity and enhanced levels of protein carbonyls. Surprisingly, IF animals also presented an increase in oxidative damage in the brain that was not related to changes in mitochondrial bioenergetics. Conversely, IF promoted a substantial protection against oxidative damage in the heart. No difference in mitochondrial bioenergetics or redox homeostasis was observed in skeletal muscles of IF animals. Overall, IF affects redox balance in a tissue-specific manner, leading to redox imbalance in the liver and brain and protection against oxidative damage in the heart.

  17. Intermittent fasting results in tissue-specific changes in bioenergetics and redox state.

    Directory of Open Access Journals (Sweden)

    Bruno Chausse

    Full Text Available Intermittent fasting (IF is a dietary intervention often used as an alternative to caloric restriction (CR and characterized by 24 hour cycles alternating ad libitum feeding and fasting. Although the consequences of CR are well studied, the effects of IF on redox status are not. Here, we address the effects of IF on redox state markers in different tissues in order to uncover how changes in feeding frequency alter redox balance in rats. IF rats displayed lower body mass due to decreased energy conversion efficiency. Livers in IF rats presented increased mitochondrial respiratory capacity and enhanced levels of protein carbonyls. Surprisingly, IF animals also presented an increase in oxidative damage in the brain that was not related to changes in mitochondrial bioenergetics. Conversely, IF promoted a substantial protection against oxidative damage in the heart. No difference in mitochondrial bioenergetics or redox homeostasis was observed in skeletal muscles of IF animals. Overall, IF affects redox balance in a tissue-specific manner, leading to redox imbalance in the liver and brain and protection against oxidative damage in the heart.

  18. Identification of a novel, tissue-specific ABCG2 promoter expressed in pediatric acute megakaryoblastic leukemia.

    Science.gov (United States)

    Campbell, Patrick K; Zong, Yang; Yang, Shengping; Zhou, Sheng; Rubnitz, Jeffrey E; Sorrentino, Brian P

    2011-10-01

    ABCG2 encodes a transporter protein that is associated with multidrug-resistant phenotypes in many cancers, including acute myeloid leukemia (AML); high levels of expression are generally associated with a poor prognosis. To better understand how expression of ABCG2 is controlled in pediatric AML, we performed a detailed analysis of the ABCG2 transcript isoforms from a variety of tissue sources, including 85 pediatric AML samples. These studies revealed a complex 5' untranslated region (UTR) with 6 novel exons and multiple splice variants. Samples from children with acute megakaryoblastic leukemia (AML FAB-M7) not associated with Down syndrome showed uniformly higher levels of ABCG2 transcripts than samples from children with other AML subtypes. A novel 5' UTR identified 90kb upstream of the exon 2 translation initiation site was expressed only in M7 AML subtypes. An associated upstream promoter fragment was shown to be selectively expressed in megakaryoblastic leukemia cells but not in human epithelial cell lines. These findings identify a new tissue-specific ABCG2 promoter that is selectively expressed in pediatric M7 AML. We also show a relatively high incidence of ABCG2 mRNA expression in non-Down associated M7 AML, which may contribute to the relatively poor prognosis of the M7 AML subtype. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Tissue-specific distribution of serine/threonine protein phosphatase 1 of Toxocara canis.

    Science.gov (United States)

    Ma, Guang Xu; Zhou, Rong Qiong; Huang, Han Cheng; Hu, Shi Jun; Lin, Jie

    2014-10-15

    Serine/threonine protein phosphatase 1 (PP1) is expressed in developing and reproductively active male Toxocara canis. To investigate the tissue-specific expression of PP1 in T. canis, the PP1 protein was expressed in Escherichia coli, and the recombinant protein was used to generate a rabbit polyclonal antiserum. Indirect fluorescence immunohistochemical analysis of adult male T. canis showed that PP1 was expressed in the germ line tissues, primarily in the testis, seminal vesicle, vas deferens, and sperm cells, indicating the potential roles of PP1 in spermatogenesis. What's more, structural predictions of PP1 in T. canis were performed. The predictions of the structure indicated that PP1 may be a potential target for antihelmintic drugs. This is the first report of the tissue distributions and structural prediction of PP1 in T. canis, which might lead to the development of novel, innovative strategies for controlling T. canis infestations. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. An immunohistochemical study on the tissue-specific localization of metallothionein in dogs.

    Science.gov (United States)

    Shimada, A; Yanagida, M; Umemura, T

    1997-01-01

    To study the tissue specificity of metallothionein (MT) expression, tissues of dogs ranging in age from 1 day to 18 years were examined immunohistochemically. Of the organs examined, liver and kidney showed the strongest immunoreactivity; a comparable intensity of MT immunolabelling was noted in the two organs in adult animals. In the central nervous system, astrocytes and ependymal cells showed MT immunoreactivity. MT labelling was shown in the sustentacular cells of the olfactory epithelium, but immunoreactivity was slight in the epithelium of the respiratory tract. Slight MT immunoreactivity was demonstrated in the epithelium of a variety of glands (sweat, uterine, mammary, olfactory, perianal and thyroid) and in parietal cells of the fundic glands of the stomach. Sporadic MT immunolabelling was demonstrated in the columnar and goblet cells of the small and large intestines, surface mucosal cells of the stomach and epithelial cells of the hair follicles. These findings may help in understanding important features of MT, such as its dynamic induction mechanism, its systemic degradation pathway and the possible biological functions.

  1. Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models.

    Science.gov (United States)

    Di Filippo, Marzia; Colombo, Riccardo; Damiani, Chiara; Pescini, Dario; Gaglio, Daniela; Vanoni, Marco; Alberghina, Lilia; Mauri, Giancarlo

    2016-06-01

    The metabolic rearrangements occurring in cancer cells can be effectively investigated with a Systems Biology approach supported by metabolic network modeling. We here present tissue-specific constraint-based core models for three different types of tumors (liver, breast and lung) that serve this purpose. The core models were extracted and manually curated from the corresponding genome-scale metabolic models in the Human Metabolic Atlas database with a focus on the pathways that are known to play a key role in cancer growth and proliferation. Along similar lines, we also reconstructed a core model from the original general human metabolic network to be used as a reference model. A comparative Flux Balance Analysis between the reference and the cancer models highlighted both a clear distinction between the two conditions and a heterogeneity within the three different cancer types in terms of metabolic flux distribution. These results emphasize the need for modeling approaches able to keep up with this tumoral heterogeneity in order to identify more suitable drug targets and develop effective treatments. According to this perspective, we identified key points able to reverse the tumoral phenotype toward the reference one or vice-versa. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit.

    Science.gov (United States)

    Opitz, Nina; Marcon, Caroline; Paschold, Anja; Malik, Waqas Ahmed; Lithio, Andrew; Brandt, Ronny; Piepho, Hans-Peter; Nettleton, Dan; Hochholdinger, Frank

    2016-02-01

    Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the cortex of the mature root zone and in the elongation zone. The most prominent functional categories among differentially expressed genes in all tissues were 'transcriptional regulation' and 'hormone metabolism', indicating global reprogramming of cellular metabolism as an adaptation to water deficit. Additionally, the most significant transcriptomic changes in the root tip were associated with cell wall reorganization, leading to continued root growth despite water deficit conditions. This study provides insight into tissue-specific water deficit responses and will be a resource for future genetic analyses and breeding strategies to develop more drought-tolerant maize cultivars. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  3. Tissue-specific concentrations and patterns of perfluoroalkyl carboxylates and sulfonates in East Greenland polar bears.

    Science.gov (United States)

    Greaves, Alana K; Letcher, Robert J; Sonne, Christian; Dietz, Rune; Born, Erik W

    2012-11-06

    Several perfluoroalkyl carboxylates (PFCAs) and perfluoroalkyl sulfonates (PFSAs) of varying chain length are bioaccumulative in biota. However, wildlife reports have focused on liver and with very little examination of other tissues, and thus there is a limited understanding of their distribution and potential effects in the mammalian body. In the present study, the comparative accumulation of C(6) to C(15) PFCAs, C(4), C(6), C(8) and C(10) PFSAs, and select precursors were examined in the liver, blood, muscle, adipose, and brain of 20 polar bears (Ursus maritimus) from Scoresby Sound, Central East Greenland. Overall, PFSA and PFCA concentrations were highest in liver followed by blood > brain > muscle ≈ adipose. Liver and blood samples contained proportionally more of the shorter/medium chain length (C(6) to C(11)) PFCAs, whereas adipose and brain samples were dominated by longer chain (C(13) to C(15)) PFCAs. PFCAs with lower lipophilicities accumulated more in the liver, whereas the brain accumulated PFCAs with higher lipophilicities. The concentration ratios (±SE) between perfluorooctane sulfonate and its precursor perfluorooctane sulfonamide varied among tissues from 9 (±1):1 (muscle) to 36 (±7):1 (liver). PFCA and PFSA patterns in polar bears indicate that the pharmacokinetics of these compounds are to some extent tissue-specific, and are the result of several factors that may include differing protein interactions throughout the body.

  4. A tissue-specific atlas of mouse protein phosphorylation and expression.

    Science.gov (United States)

    Huttlin, Edward L; Jedrychowski, Mark P; Elias, Joshua E; Goswami, Tapasree; Rad, Ramin; Beausoleil, Sean A; Villén, Judit; Haas, Wilhelm; Sowa, Mathew E; Gygi, Steven P

    2010-12-23

    Although most tissues in an organism are genetically identical, the biochemistry of each is optimized to fulfill its unique physiological roles, with important consequences for human health and disease. Each tissue's unique physiology requires tightly regulated gene and protein expression coordinated by specialized, phosphorylation-dependent intracellular signaling. To better understand the role of phosphorylation in maintenance of physiological differences among tissues, we performed proteomic and phosphoproteomic characterizations of nine mouse tissues. We identified 12,039 proteins, including 6296 phosphoproteins harboring nearly 36,000 phosphorylation sites. Comparing protein abundances and phosphorylation levels revealed specialized, interconnected phosphorylation networks within each tissue while suggesting that many proteins are regulated by phosphorylation independently of their expression. Our data suggest that the "typical" phosphoprotein is widely expressed yet displays variable, often tissue-specific phosphorylation that tunes protein activity to the specific needs of each tissue. We offer this dataset as an online resource for the biological research community. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1.

    Science.gov (United States)

    Kadauke, Stephan; Udugama, Maheshi I; Pawlicki, Jan M; Achtman, Jordan C; Jain, Deepti P; Cheng, Yong; Hardison, Ross C; Blobel, Gerd A

    2012-08-17

    Tissue-specific transcription patterns are preserved throughout cell divisions to maintain lineage fidelity. We investigated whether transcription factor GATA1 plays a role in transmitting hematopoietic gene expression programs through mitosis when transcription is transiently silenced. Live-cell imaging revealed that a fraction of GATA1 is retained focally within mitotic chromatin. ChIP-seq of highly purified mitotic cells uncovered that key hematopoietic regulatory genes are occupied by GATA1 in mitosis. The GATA1 coregulators FOG1 and TAL1 dissociate from mitotic chromatin, suggesting that GATA1 functions as platform for their postmitotic recruitment. Mitotic GATA1 target genes tend to reactivate more rapidly upon entry into G1 than genes from which GATA1 dissociates. Mitosis-specific destruction of GATA1 delays reactivation selectively of genes that retain GATA1 during mitosis. These studies suggest a requirement of mitotic "bookmarking" by GATA1 for the faithful propagation of cell-type-specific transcription programs through cell division. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Human glucagon gene promoter sequences regulating tissue-specific versus nutrient-regulated gene expression.

    Science.gov (United States)

    Nian, Min; Gu, Jun; Irwin, David M; Drucker, Daniel J

    2002-01-01

    The glucagon-like peptides (GLPs) are synthesized and secreted in a nutrient-dependent manner in rodents; however, the factors regulating human GLP-1 and GLP-2 biosynthesis remain unclear. To understand how nutrients regulate human proglucagon gene expression, we studied the expression of a human proglucagon promoter-growth hormone (GH) transgene in 1.6 human glucagon-GH transgenic mice. Fasting-refeeding significantly decreased and increased the levels of circulating mouse insulin and transgene-derived hGH (P fasting vs. refeeding) and decreased and upregulated, respectively, the levels of endogenous mouse proglucagon RNA in the ileum but not in the jejunum or colon. High-fiber feeding significantly increased the levels of glucose-stimulated circulating hGH and upregulated levels of mouse intestinal proglucagon gene expression in the jejunum, ileum, and colon (P fasting-refeeding nor a high-fiber diet upregulated the expression of the human proglucagon promoter-hGH transgene. These findings demonstrate that human proglucagon gene regulatory sequences specifying tissue-specific expression in gut endocrine cells are not sufficient for recognition of energy-derived signals regulating murine glucagon gene expression in enteroendocrine cells in vivo.

  7. Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity.

    Science.gov (United States)

    Mintz-Oron, Shira; Meir, Sagit; Malitsky, Sergey; Ruppin, Eytan; Aharoni, Asaph; Shlomi, Tomer

    2012-01-03

    Plant metabolic engineering is commonly used in the production of functional foods and quality trait improvement. However, to date, computational model-based approaches have only been scarcely used in this important endeavor, in marked contrast to their prominent success in microbial metabolic engineering. In this study we present a computational pipeline for the reconstruction of fully compartmentalized tissue-specific models of Arabidopsis thaliana on a genome scale. This reconstruction involves automatic extraction of known biochemical reactions in Arabidopsis for both primary and secondary metabolism, automatic gap-filling, and the implementation of methods for determining subcellular localization and tissue assignment of enzymes. The reconstructed tissue models are amenable for constraint-based modeling analysis, and significantly extend upon previous model reconstructions. A set of computational validations (i.e., cross-validation tests, simulations of known metabolic functionalities) and experimental validations (comparison with experimental metabolomics datasets under various compartments and tissues) strongly testify to the predictive ability of the models. The utility of the derived models was demonstrated in the prediction of measured fluxes in metabolically engineered seed strains and the design of genetic manipulations that are expected to increase vitamin E content, a significant nutrient for human health. Overall, the reconstructed tissue models are expected to lay down the foundations for computational-based rational design of plant metabolic engineering. The reconstructed compartmentalized Arabidopsis tissue models are MIRIAM-compliant and are available upon request.

  8. ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Blow, Matthew J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Ren, Bing; Rubin, Edward M.; Pennacchio, Len A.

    2009-02-01

    A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

  9. Congener-specific carbon isotope analysis of technical PCN and PCB preparations using 2DGC-IRMS

    Energy Technology Data Exchange (ETDEWEB)

    Horii, Y.; Yamashita, N. [National Institute of Advanced Industrial Science and Technology (AIST). Tsukuba (Japan); Petrick, G. [Kiel Univ. (Germany). Inst. fuer Marineforschung; Katase, T. [Nihon Univ., Fujisawa (Japan). College of Bioresource Sciences; Gamo, T. [Tokyo Univ. (Japan). Ocean Research Institute

    2004-09-15

    Carbon isotope analysis is one of the most traditional approaches used in biogeochemical research for the last few decades. The isotopic composition of 13C/12C in bulk carbon has been measured in many kinds of environmental matrixes and supposed to be a useful indicator to understand biogeochemical circulation of carbon in ecosystems. With the recent advancements in instrumental analysis, compound-specific carbon isotope analysis (CSIA) is emerging as a hot issue in the research area of source determination of natural products. However, only limited investigations have been reported to date, regarding the CSIA of manmade chemicals such as polychlorinated biphenyls (PCBs). Although a traditional approaches such as fingerprinting, to determine sources of specific anthropogenic chemicals in environment has been in use for decades, those techniques are relatively more qualitative than quantitative; therefore, development of novel and reliable method is required to enable comprehensive understanding of sources and environmental destiny of man-made chemicals, especially those that are hazardous ones. In this study, we developed a new approach of CSIA using two-dimensional gas chromatograph (2DGC) with combustion chamber (C)/ isotope ratio mass spectrometer (IRMS) and applied for ''congener-specific'' carbon isotopic analysis of PCBs and polychlorinated naphthalenes (PCNs). We clarified the need to solve the co-elution of individual chlorobiphenyl and chloronaphthalene congeners and to decrease the blank for ''congener-specific'' CSIA.

  10. Phylogenic diversity and tissue specificity of fungal endophytes associated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach.

    Science.gov (United States)

    Jin, Hui; Yang, Xiaoyan; Lu, Dengxue; Li, Chunjie; Yan, Zhiqiang; Li, Xiuzhuang; Zeng, Liming; Qin, Bo

    2015-10-01

    The fungal endophytes associated with medicinal plants have been demonstrated as a reservoir with novel natural products useful in medicine and agriculture. It is desirable to explore the species composition, diversity and tissue specificity of endophytic fungi that inhabit in different tissues of medicinal plants. In this study, a culture-independent survey of fungal diversity in the rhizosphere, leaves, stems and roots of a toxic medicinal plant, Stellera chamaejasme L., was conducted by sequence analysis of clone libraries of the partial internal transcribed spacer region. Altogether, 145 fungal OTUs (operational taxonomic units), represented by 464 sequences, were found in four samples, of these 109 OTUs (75.2 %) belonging to Ascomycota, 20 (13.8 %) to Basidiomycota, 14 (9.7 %) to Zygomycota, 1 (0.7 %) to Chytridiomycota, and 1 (0.7 %) to Glomeromycota. The richness and diversity of fungal communities were strongly influenced by plant tissue environments, and the roots are associated with a surprisingly rich endophyte community. The endophyte assemblages associated with S. chamaejasme were strongly shaped by plant tissue environments, and exhibited a certain degree of tissue specificity. Our results suggested that a wide variety of fungal assemblages inhabit in S. chamaejasme, and plant tissue environments conspicuously influence endophyte community structure.

  11. Functionalized Congeners of P2Y1 Receptor Antagonists:

    Energy Technology Data Exchange (ETDEWEB)

    de Castro, Sonia [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Maruoka, Hiroshi [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Hong, Kunlun [ORNL; Kilbey, II, S Michael [ORNL; Costanzi, Stefano [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Hechler, Béatrice [University of Strasbourg; Gachet, Christian [EFS-Alsace, Strasbourg, France; Harden, T. Kendall [University of North Carolina School of Medicine; Jacobson, Kenneth A. [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health

    2010-01-01

    The P2Y{sub 1} receptor is a prothrombotic G protein-coupled receptor (GPCR) activated by ADP. Preference for the North (N) ring conformation of the ribose moiety of adenine nucleotide 3',5'-bisphosphate antagonists of the P2Y{sub 1} receptor was established by using a ring-constrained methanocarba (a bicyclo[3.1.0]hexane) ring as a ribose substitute. A series of covalently linkable N{sup 6}-methyl-(N)-methanocarba-2'-deoxyadenosine-3',5'-bisphosphates containing extended 2-alkynyl chains was designed, and binding affinity at the human (h) P2Y{sub 1} receptor determined. The chain of these functionalized congeners contained hydrophilic moieties, a reactive substituent, or biotin, linked via an amide. Variation of the chain length and position of an intermediate amide group revealed high affinity of carboxylic congener 8 (K{sub i} 23 nM) and extended amine congener 15 (K{sub i} 132 nM), both having a 2-(1-pentynoyl) group. A biotin conjugate 18 containing an extended {epsilon}-aminocaproyl spacer chain exhibited higher affinity than a shorter biotinylated analogue. Alternatively, click coupling of terminal alkynes of homologous 2-dialkynyl nucleotide derivatives to alkyl azido groups produced triazole derivatives that bound to the P2Y{sub 1} receptor following deprotection of the bisphosphate groups. The preservation of receptor affinity of the functionalized congeners was consistent with new P2Y{sub 1} receptor modeling and ligand docking. Attempted P2Y{sub 1} antagonist conjugation to PAMAM dendrimer carriers by amide formation or palladium-catalyzed reaction between an alkyne on the dendrimer and a 2-iodopurine-derivatized nucleotide was unsuccessful. A dialkynyl intermediate containing the chain length favored in receptor binding was conjugated to an azide-derivatized dendrimer, and the conjugate inhibited ADP-promoted human platelet aggregation. This is the first example of attaching a strategically functionalized P2Y receptor

  12. Detection of neuronal tissue in meat using tissue specific DNA modifications

    Directory of Open Access Journals (Sweden)

    Harris N.

    2004-01-01

    Full Text Available A method has been developed to differentiate between non-muscle tissues such as liver, kidney and heart and that of muscle in meat samples using tissue specific DNA detection. Only muscle tissue is considered meat from the point of view of labelling (Food Labelling [Amendment] (England Regulations 2003 and Quantitative Ingredient Declaration (QUID, and also certain parts of the carcass are prohibited to be used in raw meat products (Meat Products [England] Regulations 2003. Included in the prohibited offal are brain and spinal cord. The described methodology has therefore been developed primarily to enforce labelling rules but also to contribute to the enforcement of BSE legislation on the detection of Central Nervous System (CNS tissue. The latter requires the removal of Specified Risk Material (SRM, such as bovine and ovine brain and spinal cord, from the food chain. Current methodologies for detection of CNS tissue include histological examination, analysis of cholesterol content and immunodetection. These can potentially be time consuming, less applicable to processed samples and may not be readily adapted to high throughput sample analysis. The objective of this work was therefore to develop a DNAbased detection assay that exploits the sensitivity and specificity of PCR and is potentially applicable to more highly processed food samples. For neuronal tissue, the DNA target selected was the promoter for Glial Fibrillary Acidic Protein (GFAP, a gene whose expression is restricted to astroglial cells within CNS tissue. The promoter fragments from both cattle and sheep have been isolated and key differences in the methylation patterns of certain CpG dinucleotides in the sequences from bovine and sheep brain and spinal cord and the corresponding skeletal muscle identified. These have been used to design a PCR assay exploiting Methylation Specific PCR (MSP to specifically amplify the neuronal tissue derived sequence and therefore identify the

  13. Tissue-specific transcriptome analyses provide new insights into GPCR signalling in adult Schistosoma mansoni.

    Science.gov (United States)

    Hahnel, Steffen; Wheeler, Nic; Lu, Zhigang; Wangwiwatsin, Arporn; McVeigh, Paul; Maule, Aaron; Berriman, Matthew; Day, Timothy; Ribeiro, Paula; Grevelding, Christoph G

    2018-01-01

    Schistosomes are blood-dwelling trematodes with global impact on human and animal health. Because medical treatment is currently based on a single drug, praziquantel, there is urgent need for the development of alternative control strategies. The Schistosoma mansoni genome project provides a platform to study and connect the genetic repertoire of schistosomes to specific biological functions essential for successful parasitism. G protein-coupled receptors (GPCRs) form the largest superfamily of transmembrane receptors throughout the Eumetazoan phyla, including platyhelminths. Due to their involvement in diverse biological processes, their pharmacological importance, and proven druggability, GPCRs are promising targets for new anthelmintics. However, to identify candidate receptors, a more detailed understanding of the roles of GPCR signalling in schistosome biology is essential. An updated phylogenetic analysis of the S. mansoni GPCR genome (GPCRome) is presented, facilitated by updated genome data that allowed a more precise annotation of GPCRs. Additionally, we review the current knowledge on GPCR signalling in this parasite and provide new insights into the potential roles of GPCRs in schistosome reproduction based on the findings of a recent tissue-specific transcriptomic study in paired and unpaired S. mansoni. According to the current analysis, GPCRs contribute to gonad-specific functions but also to nongonad, pairing-dependent processes. The latter may regulate gonad-unrelated functions during the multifaceted male-female interaction. Finally, we compare the schistosome GPCRome to that of another parasitic trematode, Fasciola, and discuss the importance of GPCRs to basic and applied research. Phylogenetic analyses display GPCR diversity in free-living and parasitic platyhelminths and suggest diverse functions in schistosomes. Although their roles need to be substantiated by functional studies in the future, the data support the selection of GPCR candidates

  14. Tissue-specific expression of monocarboxylate transporters during fasting in mice.

    Directory of Open Access Journals (Sweden)

    Alexandra Schutkowski

    Full Text Available Monocarboxylates such as pyruvate, lactate and ketone bodies are crucial for energy supply of all tissues, especially during energy restriction. The transport of monocarboxylates across the plasma membrane of cells is mediated by monocarboxylate transporters (MCTs. Out of 14 known mammalian MCTs, six isoforms have been functionally characterized to transport monocarboxylates and short chain fatty acids (MCT1-4, thyroid hormones (MCT8, -10 and aromatic amino acids (MCT10. Knowledge on the regulation of the different MCT isoforms is rare. In an attempt to get more insights in regulation of MCT expression upon energy deprivation, we carried out a comprehensive analysis of tissue specific expression of five MCT isoforms upon 48 h of fasting in mice. Due to the crucial role of peroxisome proliferator-activated receptor (PPAR-α as a central regulator of energy metabolism and as known regulator of MCT1 expression, we included both wildtype (WT and PPARα knockout (KO mice in our study. Liver, kidney, heart, small intestine, hypothalamus, pituitary gland and thyroid gland of the mice were analyzed. Here we show that the expression of all examined MCT isoforms was markedly altered by fasting compared to feeding. Expression of MCT1, MCT2 and MCT10 was either increased or decreased by fasting dependent on the analyzed tissue. MCT4 and MCT8 were down-regulated by fasting in all examined tissues. However, PPARα appeared to have a minor impact on MCT isoform regulation. Due to the fundamental role of MCTs in transport of energy providing metabolites and hormones involved in the regulation of energy homeostasis, we assumed that the observed fasting-induced adaptations of MCT expression seem to ensure an adequate energy supply of tissues during the fasting state. Since, MCT isoforms 1-4 are also necessary for the cellular uptake of drugs, the fasting-induced modifications of MCT expression have to be considered in future clinical care algorithms.

  15. Tissue-Specific Expression of Monocarboxylate Transporters during Fasting in Mice

    Science.gov (United States)

    Schutkowski, Alexandra; Wege, Nicole; Stangl, Gabriele I.; König, Bettina

    2014-01-01

    Monocarboxylates such as pyruvate, lactate and ketone bodies are crucial for energy supply of all tissues, especially during energy restriction. The transport of monocarboxylates across the plasma membrane of cells is mediated by monocarboxylate transporters (MCTs). Out of 14 known mammalian MCTs, six isoforms have been functionally characterized to transport monocarboxylates and short chain fatty acids (MCT1-4), thyroid hormones (MCT8, -10) and aromatic amino acids (MCT10). Knowledge on the regulation of the different MCT isoforms is rare. In an attempt to get more insights in regulation of MCT expression upon energy deprivation, we carried out a comprehensive analysis of tissue specific expression of five MCT isoforms upon 48 h of fasting in mice. Due to the crucial role of peroxisome proliferator-activated receptor (PPAR)-α as a central regulator of energy metabolism and as known regulator of MCT1 expression, we included both wildtype (WT) and PPARα knockout (KO) mice in our study. Liver, kidney, heart, small intestine, hypothalamus, pituitary gland and thyroid gland of the mice were analyzed. Here we show that the expression of all examined MCT isoforms was markedly altered by fasting compared to feeding. Expression of MCT1, MCT2 and MCT10 was either increased or decreased by fasting dependent on the analyzed tissue. MCT4 and MCT8 were down-regulated by fasting in all examined tissues. However, PPARα appeared to have a minor impact on MCT isoform regulation. Due to the fundamental role of MCTs in transport of energy providing metabolites and hormones involved in the regulation of energy homeostasis, we assumed that the observed fasting-induced adaptations of MCT expression seem to ensure an adequate energy supply of tissues during the fasting state. Since, MCT isoforms 1–4 are also necessary for the cellular uptake of drugs, the fasting-induced modifications of MCT expression have to be considered in future clinical care algorithms. PMID:25390336

  16. A tissue-specific approach to the analysis of metabolic changes in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Jürgen Hench

    Full Text Available The majority of metabolic principles are evolutionarily conserved from nematodes to humans. Caenorhabditis elegans has widely accelerated the discovery of new genes important to maintain organismic metabolic homeostasis. Various methods exist to assess the metabolic state in worms, yet they often require large animal numbers and tend to be performed as bulk analyses of whole worm homogenates, thereby largely precluding a detailed studies of metabolic changes in specific worm tissues. Here, we have adapted well-established histochemical methods for the use on C. elegans fresh frozen sections and demonstrate their validity for analyses of morphological and metabolic changes on tissue level in wild type and various mutant strains. We show how the worm presents on hematoxylin and eosin (H&E stained sections and demonstrate their usefulness in monitoring and the identification of morphological abnormalities. In addition, we demonstrate how Oil-Red-O staining on frozen worm cross-sections permits quantification of lipid storage, avoiding the artifact-prone fixation and permeabilization procedures of traditional whole-mount protocols. We also adjusted standard enzymatic stains for respiratory chain subunits (NADH, SDH, and COX to monitor metabolic states of various C. elegans tissues. In summary, the protocols presented here provide technical guidance to obtain robust, reproducible and quantifiable tissue-specific data on worm morphology as well as carbohydrate, lipid and mitochondrial energy metabolism that cannot be obtained through traditional biochemical bulk analyses of worm homogenates. Furthermore, analysis of worm cross-sections overcomes the common problem with quantification in three-dimensional whole-mount specimens.

  17. Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers.

    Science.gov (United States)

    Mohammed, Akram; Biegert, Greyson; Adamec, Jiri; Helikar, Tomáš

    2017-10-17

    Machine learning techniques for cancer prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. Recent "OMICS" studies which include a variety of cancer and normal tissue samples along with machine learning approaches have the potential to further accelerate such discovery. To demonstrate this potential, 2,175 gene expression samples from nine tissue types were obtained to identify gene sets whose expression is characteristic of each cancer class. Using random forests classification and ten-fold cross-validation, we developed nine single-tissue classifiers, two multi-tissue cancer-versus-normal classifiers, and one multi-tissue normal classifier. Given a sample of a specified tissue type, the single-tissue models classified samples as cancer or normal with a testing accuracy between 85.29% and 100%. Given a sample of non-specific tissue type, the multi-tissue bi-class model classified the sample as cancer versus normal with a testing accuracy of 97.89%. Given a sample of non-specific tissue type, the multi-tissue multi-class model classified the sample as cancer versus normal and as a specific tissue type with a testing accuracy of 97.43%. Given a normal sample of any of the nine tissue types, the multi-tissue normal model classified the sample as a particular tissue type with a testing accuracy of 97.35%. The machine learning classifiers developed in this study identify potential cancer biomarkers with sensitivity and specificity that exceed those of existing biomarkers and pointed to pathways that are critical to tissue-specific tumor development. This study demonstrates the feasibility of predicting the tissue origin of carcinoma in the context of multiple cancer classes.

  18. Snakes exhibit tissue-specific variation in cardiotonic steroid sensitivity of Na+/K+-ATPase.

    Science.gov (United States)

    Mohammadi, Shabnam; Petschenka, Georg; French, Susannah S; Mori, Akira; Savitzky, Alan H

    2018-03-01

    Toads are among several groups of organisms chemically defended with lethal concentrations of cardiotonic steroids. As a result, most predators that prey on amphibians avoid toads. However, several species of snakes have gained resistance-conferring mutations of Na + /K + -ATPase, the molecular target of cardiotonic steroids, and can feed on toads readily. Despite recent advances in our understanding of this adaptation at the genetic level, we have lacked functional evidence for how mutations of Na + /K + -ATPase account for cardiotonic steroid resistance in snake tissues. To address this issue, it is necessary to determine how the Na + /K + -ATPases of snakes react to the toxins. Some tissues might have Na + /K + -ATPases that are more susceptible than others and can thus provide clues about how the toxins influence organismal function. Here we provide a mechanistic link between observed Na + /K + -ATPase substitutions and observed resistance using actual snake Na + /K + -ATPases. We used an in vitro approach to determine the tissue-specific levels of sensitivity to cardiotonic steroids in select resistant and non-resistant snakes. We compared the sensitivities of select tissues within and between species. Our results suggest that resistant snakes contain highly resistant Na + /K + -ATPases in their heart and kidney, both of which rely heavily on the enzymes to function, whereas tissues that do not rely as heavily on Na + /K + -ATPases or might be protected from cardiotonic steroids by other means (liver, gut, and brain) contain non-resistant forms of the enzyme. This study reveals functional evidence that tissue-level target-site insensitivity to cardiotonic steroids varies not only among species but also across tissues within resistant taxa. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Tissue-specific metabolic activation and mutagenicity of 3-nitrobenzanthrone in MutaMouse.

    Science.gov (United States)

    Chen, Guosheng; Gingerich, John; Soper, Lynda; Douglas, George R; White, Paul A

    2008-10-01

    3-Nitrobenzanthrone (3-NBA) is a mutagen and suspected human carcinogen detected in diesel exhaust, airborne particulate matter, and urban soil. We investigated the tissue specific mutagenicity of 3-NBA at the lacZ locus of transgenic MutaMouse following acute single dose or 28-day repeated-dose oral administration. In the acute high dose (50 mg/kg) exposure, increased lacZ mutant frequency was observed in bone marrow and colonic epithelium, but not in liver and bladder. In the repeated-dose study, a dose-dependent increase in lacZ mutant frequency was observed in bone marrow and liver (2- and 4-fold increase above control), but not in lung or intestinal epithelium. In addition, a concentration-dependent increase in mutant frequency (8.5-fold above control) was observed for MutaMouse FE1 lung epithelial cells exposed in vitro. 1-Nitropyrene reductase, 3-NBA reductase, and acetyltransferase activities were measured in a variety of MutaMouse specimens in an effort to link metabolic activation and mutagenicity. High 3-NBA nitroreductase activities were observed in lung, liver, colon and bladder, and detectable N-acetyltransferase activities were found in all tissues except bone marrow. The relatively high 3-NBA nitroreductase activity in MutaMouse tissues, as compared with those in Salmonella TA98 and TA100, suggests that 3-NBA is readily reduced and activated in vivo. High 3-NBA nitroreductase levels in liver and colon are consistent with the elevated lacZ mutant frequency values, and previously noted inductions of hepatic DNA adducts. Despite an absence of induced lacZ mutations, the highest 3-NBA reductase activity was detected in lung. Further studies are warranted, especially following inhalation or intratracheal exposures. Published 2008 Wiley-Liss, Inc.

  20. Tissue-Specific Transcriptomics of the Exotic Invasive Insect Pest Emerald Ash Borer (Agrilus planipennis)

    Science.gov (United States)

    Mittapalli, Omprakash; Bai, Xiaodong; Bonello, Pierluigi; Herms, Daniel A.

    2010-01-01

    Background The insect midgut and fat body represent major tissue interfaces that deal with several important physiological functions including digestion, detoxification and immune response. The emerald ash borer (Agrilus planipennis), is an exotic invasive insect pest that has killed millions of ash trees (Fraxinus spp.) primarily in the Midwestern United States and Ontario, Canada. However, despite its high impact status little knowledge exists for A. planipennis at the molecular level. Methodology and Principal Findings Newer-generation Roche-454 pyrosequencing was used to obtain 126,185 reads for the midgut and 240,848 reads for the fat body, which were assembled into 25,173 and 37,661 high quality expressed sequence tags (ESTs) for the midgut and the fat body of A. planipennis larvae, respectively. Among these ESTs, 36% of the midgut and 38% of the fat body sequences showed similarity to proteins in the GenBank nr database. A high number of the midgut sequences contained chitin-binding peritrophin (248)and trypsin (98) domains; while the fat body sequences showed high occurrence of cytochrome P450s (85) and protein kinase (123) domains. Further, the midgut transcriptome of A. planipennis revealed putative microbial transcripts encoding for cell-wall degrading enzymes such as polygalacturonases and endoglucanases. A significant number of SNPs (137 in midgut and 347 in fat body) and microsatellite loci (317 in midgut and 571 in fat body) were predicted in the A. planipennis transcripts. An initial assessment of cytochrome P450s belonging to various CYP clades revealed distinct expression patterns at the tissue level. Conclusions and Significance To our knowledge this study is one of the first to illuminate tissue-specific gene expression in an invasive insect of high ecological and economic consequence. These findings will lay the foundation for future gene expression and functional studies in A. planipennis. PMID:21060843

  1. Tissue-specific gene expression in maize seeds during colonization by Aspergillus flavus and Fusarium verticillioides.

    Science.gov (United States)

    Shu, Xiaomei; Livingston, David P; Franks, Robert G; Boston, Rebecca S; Woloshuk, Charles P; Payne, Gary A

    2015-09-01

    Aspergillus flavus and Fusarium verticillioides are fungal pathogens that colonize maize kernels and produce the harmful mycotoxins aflatoxin and fumonisin, respectively. Management practice based on potential host resistance to reduce contamination by these mycotoxins has proven difficult, resulting in the need for a better understanding of the infection process by these fungi and the response of maize seeds to infection. In this study, we followed the colonization of seeds by histological methods and the transcriptional changes of two maize defence-related genes in specific seed tissues by RNA in situ hybridization. Maize kernels were inoculated with either A. flavus or F. verticillioides 21-22 days after pollination, and harvested at 4, 12, 24, 48, 72, 96 and 120 h post-inoculation. The fungi colonized all tissues of maize seed, but differed in their interactions with aleurone and germ tissues. RNA in situ hybridization showed the induction of the maize pathogenesis-related protein, maize seed (PRms) gene in the aleurone and scutellum on infection by either fungus. Transcripts of the maize sucrose synthase-encoding gene, shrunken-1 (Sh1), were observed in the embryo of non-infected kernels, but were induced on infection by each fungus in the aleurone and scutellum. By comparing histological and RNA in situ hybridization results from adjacent serial sections, we found that the transcripts of these two genes accumulated in tissue prior to the arrival of the advancing pathogens in the seeds. A knowledge of the patterns of colonization and tissue-specific gene expression in response to these fungi will be helpful in the development of resistance. © 2014 BSPP AND JOHN WILEY & SONS LTD.

  2. Tissue-Specific Gain of RTK Signalling Uncovers Selective Cell Vulnerability during Embryogenesis.

    Directory of Open Access Journals (Sweden)

    Yannan Fan

    Full Text Available The successive events that cells experience throughout development shape their intrinsic capacity to respond and integrate RTK inputs. Cellular responses to RTKs rely on different mechanisms of regulation that establish proper levels of RTK activation, define duration of RTK action, and exert quantitative/qualitative signalling outcomes. The extent to which cells are competent to deal with fluctuations in RTK signalling is incompletely understood. Here, we employ a genetic system to enhance RTK signalling in a tissue-specific manner. The chosen RTK is the hepatocyte growth factor (HGF receptor Met, an appropriate model due to its pleiotropic requirement in distinct developmental events. Ubiquitously enhanced Met in Cre/loxP-based Rosa26(stopMet knock-in context (Del-R26(Met reveals that most tissues are capable of buffering enhanced Met-RTK signalling thus avoiding perturbation of developmental programs. Nevertheless, this ubiquitous increase of Met does compromise selected programs such as myoblast migration. Using cell-type specific Cre drivers, we genetically showed that altered myoblast migration results from ectopic Met expression in limb mesenchyme rather than in migrating myoblasts themselves. qRT-PCR analyses show that ectopic Met in limbs causes molecular changes such as downregulation in the expression levels of Notum and Syndecan4, two known regulators of morphogen gradients. Molecular and functional studies revealed that ectopic Met expression in limb mesenchyme does not alter HGF expression patterns and levels, but impairs HGF bioavailability. Together, our findings show that myoblasts, in which Met is endogenously expressed, are capable of buffering increased RTK levels, and identify mesenchymal cells as a cell type vulnerable to ectopic Met-RTK signalling. These results illustrate that embryonic cells are sensitive to alterations in the spatial distribution of RTK action, yet resilient to fluctuations in signalling levels of an

  3. Tissue-specific responses to the LRPPRC founder mutation in French Canadian Leigh Syndrome.

    Science.gov (United States)

    Sasarman, Florin; Nishimura, Tamiko; Antonicka, Hana; Weraarpachai, Woranontee; Shoubridge, Eric A

    2015-01-15

    French Canadian Leigh Syndrome (LSFC) is an early-onset, progressive neurodegenerative disorder with a distinct pattern of tissue involvement. Most cases are caused by a founder missense mutation in LRPPRC. LRPPRC forms a ribonucleoprotein complex with SLIRP, another RNA-binding protein, and this stabilizes polyadenylated mitochondrial mRNAs. LSFC fibroblasts have reduced levels of LRPPRC and a specific complex IV assembly defect; however, further depletion of mutant LRPPRC results in a complete failure to assemble a functional oxidative phosphorylation system, suggesting that LRPPRC levels determine the nature of the biochemical phenotype. We tested this hypothesis in cultured muscle cells and tissues from LSFC patients. LRPPRC levels were reduced in LSFC muscle cells, resulting in combined complex I and IV deficiencies. A similar combined deficiency was observed in skeletal muscle. Complex IV was only moderately reduced in LSFC heart, but was almost undetectable in liver. Both of these tissues showed elevated levels of complexes I and III. Despite the marked biochemical differences, the steady-state levels of LRPPRC and mitochondrial mRNAs were extremely low, LRPPRC was largely detergent-insoluble, and SLIRP was undetectable in all LSFC tissues. The level of the LRPPRC/SLIRP complex appeared much reduced in control tissues by the first dimension blue-native polyacrylamide gel electrophoresis (BN-PAGE) analysis compared with fibroblasts, and even by second dimension analysis it was virtually undetectable in control heart. These results point to tissue-specific pathways for the post-transcriptional handling of mitochondrial mRNAs and suggest that the biochemical defects in LSFC reflect the differential ability of tissues to adapt to the mutation. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. Reprimo tissue-specific expression pattern is conserved between zebrafish and human.

    Directory of Open Access Journals (Sweden)

    Ricardo J Figueroa

    Full Text Available Reprimo (RPRM, a member of the RPRM gene family, is a tumor-suppressor gene involved in the regulation of the p53-mediated cell cycle arrest at G2/M. RPRM has been associated with malignant tumor progression and proposed as a potential biomarker for early cancer detection. However, the expression and role of RPRM, as well as its family, are poorly understood and their physiology is as yet unstudied. In this scenario, a model system like the zebrafish could serve to dissect the role of the RPRM family members in vivo. Phylogenetic analysis reveals that RPRM and RPRML have been differentially retained by most species throughout vertebrate evolution, yet RPRM3 has been retained only in a small group of distantly related species, including zebrafish. Herein, we characterized the spatiotemporal expression of RPRM (present in zebrafish as an infraclass duplication rprma/rprmb, RPRML and RPRM3 in the zebrafish. By whole-mount in situ hybridization (WISH and fluorescent in situ hybridization (FISH, we demonstrate that rprm (rprma/rprmb and rprml show a similar spatiotemporal expression profile during zebrafish development. At early developmental stages rprmb is expressed in somites. After one day post-fertilization, rprm (rprma/rprmb and rprml are expressed in the notochord, brain, blood vessels and digestive tube. On the other hand, rprm3 shows the most unique expression profile, being expressed only in the central nervous system (CNS. We assessed the expression patterns of RPRM gene transcripts in adult zebrafish and human RPRM protein product in tissue samples by RT-qPCR and immunohistochemistry (IHC staining, respectively. Strikingly, tissue-specific expression patterns of the RPRM transcripts and protein are conserved between zebrafish and humans. We propose the zebrafish as a powerful tool to elucidate the both physiological and pathological roles of the RPRM gene family.

  5. Exercise and type 2 diabetes mellitus: changes in tissue-specific fat distribution and cardiac function.

    Science.gov (United States)

    Jonker, Jacqueline T; de Mol, Pieter; de Vries, Suzanna T; Widya, Ralph L; Hammer, Sebastiaan; van Schinkel, Linda D; van der Meer, Rutger W; Gans, Rijk O B; Webb, Andrew G; Kan, Hermien E; de Koning, Eelco J P; Bilo, Henk J G; Lamb, Hildo J

    2013-11-01

    To prospectively assess the effects of an exercise intervention on organ-specific fat accumulation and cardiac function in type 2 diabetes mellitus. Written informed consent was obtained from all participants, and the study protocol was approved by the medical ethics committee. The study followed 12 patients with type 2 diabetes mellitus (seven men; mean age, 46 years ± 2 [standard error]) before and after 6 months of moderate-intensity exercise, followed by a high-altitude trekking expedition with exercise of long duration. Abdominal, epicardial, and paracardial fat volume were measured by using magnetic resonance (MR) imaging. Cardiac function was quantified with cardiac MR, and images were analyzed by a researcher who was supervised by a senior researcher (4 and 21 years of respective experience in cardiac MR). Hepatic, myocardial, and intramyocellular triglyceride (TG) content relative to water were measured with proton MR spectroscopy at 1.5 and 7 T. Two-tailed paired t tests were used for statistical analysis. Exercise reduced visceral abdominal fat volume from 348 mL ± 57 to 219 mL ± 33 (P Exercise decreased hepatic TG content from 6.8% ± 2.3 to 4.6% ± 1.6 (P Exercise did not change epicardial fat volume (P = .9), myocardial TG content (P = .9), intramyocellular lipid content (P = .3), or cardiac function (P = .5). A 6-month exercise intervention in type 2 diabetes mellitus decreased hepatic TG content and visceral abdominal and paracardial fat volume, which are associated with increased cardiovascular risk, but cardiac function was unaffected. Tissue-specific exercise-induced changes in body fat distribution in type 2 diabetes mellitus were demonstrated in this study. RSNA, 2013

  6. Quantifying Short-Chain Chlorinated Paraffin Congener Groups.

    Science.gov (United States)

    Yuan, Bo; Bogdal, Christian; Berger, Urs; MacLeod, Matthew; Gebbink, Wouter A; Alsberg, Tomas; de Wit, Cynthia A

    2017-09-19

    Accurate quantification of short-chain chlorinated paraffins (SCCPs) poses an exceptional challenge to analytical chemists. SCCPs are complex mixtures of chlorinated alkanes with variable chain length and chlorination level; congeners with a fixed chain length (n) and number of chlorines (m) are referred to as a "congener group" C n Cl m . Recently, we resolved individual C n Cl m by mathematically deconvolving soft ionization high-resolution mass spectra of SCCP mixtures. Here we extend the method to quantifying C n Cl m by introducing C n Cl m specific response factors (RFs) that are calculated from 17 SCCP chain-length standards with a single carbon chain length and variable chlorination level. The signal pattern of each standard is measured on APCI-QTOF-MS. RFs of each C n Cl m are obtained by pairwise optimization of the normal distribution's fit to the signal patterns of the 17 chain-length standards. The method was verified by quantifying SCCP technical mixtures and spiked environmental samples with accuracies of 82-123% and 76-109%, respectively. The absolute differences between calculated and manufacturer-reported chlorination degrees were -0.9 to 1.0%Cl for SCCP mixtures of 49-71%Cl. The quantification method has been replicated with ECNI magnetic sector MS and ECNI-Q-Orbitrap-MS. C n Cl m concentrations determined with the three instruments were highly correlated (R 2 > 0.90) with each other.

  7. Distributions of PCB congeners and homologues in white sucker and coho salmon from Lake Michigan

    Science.gov (United States)

    Stapanian, Martin A.; Madenjian, Charles P.; Batterman, Stuart A.; Chernyak, Sergei M.; Edwards, William; McIntyre, Peter B.

    2018-01-01

    We tested the hypothesis of the proportion of higher chlorinated biphenyl (PCB) congeners increasing with increasing trophic level by comparing the respective PCB homologue distributions in an omnivore, white sucker (Catostomus commersoni), and a top predator, coho salmon (Oncorhynchus kisutch), from Lake Michigan. Adult females had the same congener and homologue proportions of total PCB concentration (ΣPCB) as adult males in both species. Hexachlorinated congeners comprised the largest proportion (32%) found in white sucker, followed by heptachlorinated (21%) and octochlorinated (18%) congeners. In contrast, pentachlorinated congeners comprised the largest proportion (33%) of ΣPCB found in coho salmon, followed by hexachlorinated (26%) and tetrachlorinated (24%) congeners. Coho salmon contained significantly higher proportions of tri-, tetra-, and pentachlorinated congeners, whereas white sucker contained significantly higher proportions of hexa- through decachlorinated congeners. Our results were opposite of the hypothesis of greater degree of PCB chlorination with increasing trophic level, and supported the contention that the PCB congener proportions in fish depends mainly on diet, and does not necessarily reflect the trophic level of the fish. Our results also supported the contention that diets do not vary between the sexes in most fish populations.

  8. Inhibition of LPS-induced splenocyte proliferation by ortho-substituted polychlorinated biphenyl congeners

    International Nuclear Information System (INIS)

    Smithwick, L. Ashley; Smith, Andrew; Quensen, John F.; Stack, Allison; London, Lucille; Morris, Pamela J.

    2003-01-01

    Polychlorinated biphenyls (PCBs) are persistent environmental contaminants, and their ubiquitous nature has prompted studies of their potential health hazards. As a result of their lipophilic nature, PCBs accumulate in breast milk and subsequently affect the health of offspring of exposed individuals. Biological effects of PCBs in animals have mostly been attributed to coplanar congeners, although effects of ortho congeners also have been demonstrated. To investigate the relationship of immunotoxicity and chlorine substitution pattern, the effects of PCB congeners and mixtures of ortho and non-ortho-substituted constituents of Aroclor 1242 on splenocytes from C57B1/6 mice were examined. The immunotoxic endpoints investigated included splenocyte viability, lipopolysaccharide (LPS)-induced splenocyte proliferation, and LPS-induced antibody secretion. Congeners with multiple ortho chlorines preferentially inhibited splenocyte proliferation as compared with non- or mono-ortho-substituted congeners. However, mixtures of non- and mono-ortho-substituted congeners and multi-ortho-substituted congeners inhibited LPS-induced splenocyte proliferation and antibody secretion at similar concentrations. Exposure of splenocytes to these mixtures did not activate the aryl hydrocarbon receptor (AhR) signal transduction pathway. These results suggest individual multi-ortho-substituted congeners preferentially inhibit LPS-induced splenocyte proliferation, while congeners not exhibiting an effect individually may have additive effects in a mixture to produce an immunotoxic response through an AhR-independent pathway

  9. Conditional Tissue-Specific Foxa2 Ablation in Mouse Pancreas Causes Hyperinsulinemic Hypoglycemia: RETRACTED.

    Science.gov (United States)

    Wu, Zengbin; Fei, Aihua; Liu, Yingbin; Pan, Shuming

    The forkhead/winged helix transcription factor Foxa2 is a major upstream regulator of Pdx1, a transcription factor necessary for pancreatic development. In the present study, we conditionally knocked out Foxa2 in Pdx1-expressing domain and further analyzed the contribution of Foxa2 to α- and β-cell development and the effect of Foxa2 deletion on plasma insulin, glucagon, and glucose levels. Homozygous pdx1 Foxa2 mice and heterozygous pdx1 Foxa2 mice were generated by homologous recombination using a Foxa2 gene-targeting vector. α- and β-cell mass was examined by immunofluorescence microscopy. Plasma glucose, insulin, and plasma were measured at postnatal day 10. For pdx1 lineage tracing studies, heterozygous pdx1 Foxa2 EYFP and homozygous pdx1 Foxa2 EYFP mice were used. Our immunofluorescence analysis revealed that in the pancreas sections of the homozygous mutant mice, Foxa2 was virtually absent from non-β cells and its expression almost exclusively coincided with remnant β cells. The density of both α and β cells apparently decreased in the pancreas of the heterozygous mutant mice and in the pancreas of the homozygous mutant mice, α cells lost its predominance and β cells increased proportionally. Direct Pdx1 cell lineage tracing revealed that, on embryonic day 18.5, in the homozygous mutant mice, Pdx1 expression coincided almost exclusively with that of insulin-secreting β cells. Chemiluminescence assays revealed that heterozygous pdx1 Foxa2 mice had significantly lower insulin levels than control mice (P Foxa2 mice and control mice (P > 0.05). Chemiluminescence assays also showed that Foxa2 deletion significantly depressed plasma glucagon levels in both homozygous pdx1 Foxa2 mice and heterozygous pdx1 Foxa2 mice (P Foxa2 mice compared with control mice (P Foxa2 ablation leads to an imbalance in β/α ratio, profound hypoglucagonemia, inappropriate hyperinsulinemia, and hypoglycemia in mice. Our conditional tissue-specific Foxa2 ablation mouse model

  10. Conditional Tissue-Specific Foxa2 Ablation in Mouse Pancreas Causes Hyperinsulinemic Hypoglycemia.

    Science.gov (United States)

    Wu, Zengbin; Fei, Aihua; Liu, Yingbin; Pan, Shuming

    The forkhead/winged helix transcription factor Foxa2 is a major upstream regulator of Pdx1, a transcription factor necessary for pancreatic development. In the present study, we conditionally knocked out Foxa2 in Pdx1-expressing domain and further analyzed the contribution of Foxa2 to α- and β-cell development and the effect of Foxa2 deletion on plasma insulin, glucagon, and glucose levels. Homozygous pdx1 Foxa2 mice and heterozygous pdx1 Foxa2 mice were generated by homologous recombination using a Foxa2 gene-targeting vector. α- and β-cell mass was examined by immunofluorescence microscopy. Plasma glucose, insulin, and plasma were measured at postnatal day 10. For pdx1 lineage tracing studies, heterozygous pdx1 Foxa2 EYFP and homozygous pdx1 Foxa2 EYFP mice were used. Our immunofluorescence analysis revealed that in the pancreas sections of the homozygous mutant mice, Foxa2 was virtually absent from non-β cells and its expression almost exclusively coincided with remnant β cells. The density of both α and β cells apparently decreased in the pancreas of the heterozygous mutant mice and in the pancreas of the homozygous mutant mice, α cells lost its predominance and β cells increased proportionally. Direct Pdx1 cell lineage tracing revealed that, on embryonic day 18.5, in the homozygous mutant mice, Pdx1 expression coincided almost exclusively with that of insulin-secreting β cells. Chemiluminescence assays revealed that heterozygous pdx1 Foxa2 mice had significantly lower insulin levels than control mice (P Foxa2 mice and control mice (P > 0.05). Chemiluminescence assays also showed that Foxa2 deletion significantly depressed plasma glucagon levels in both homozygous pdx1 Foxa2 mice and heterozygous pdx1 Foxa2 mice (P Foxa2 mice compared with control mice (P Foxa2 ablation leads to an imbalance in β/α ratio, profound hypoglucagonemia, inappropriate hyperinsulinemia, and hypoglycemia in mice. Our conditional tissue-specific Foxa2 ablation mouse model

  11. Tissue specific responses to cadmium-based quantum dots in the marine mussel Mytilus galloprovincialis

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, Thiago Lopes [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Gomes, Tânia [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo (Norway); Mestre, Nélia C.; Cardoso, Cátia [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Bebianno, Maria João, E-mail: mbebian@ualg.pt [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)

    2015-12-15

    Highlights: • Mussel gills are the main target for oxidative stress induced by Cd-based QDs. • Antioxidants responses induced by Cd-based QDs and dissolved Cd are mediated by different mechanisms. • CdTe QDs are more pro-oxidant Cd form when compared to dissolved Cd. • Differential tissue response indicated nano-specific effects. - Abstract: In recent years, Cd-based quantum dots (QDs) have generated interest from the life sciences community due to their potential applications in nanomedicine, biology and electronics. However, these engineered nanomaterials can be released into the marine environment, where their environmental health hazards remain unclear. This study investigated the tissue-specific responses related to alterations in the antioxidant defense system induced by CdTe QDs, in comparison with its dissolved counterpart, using the marine mussel Mytilus galloprovincialis. Mussels were exposed to CdTe QDs and dissolved Cd for 14 days at 10 μgCd L{sup −1} and biomarkers of oxidative stress [superoxide dismutase (SOD), catalase (CAT), glutathione peroxidases (total, Se-independent and Se-dependent GPx) and glutathione-S-transferase (GST) activities] were analyzed along with Cd accumulation in the gills and digestive gland of mussels. Results show that both Cd forms changed mussels’ antioxidant responses with distinct modes of action (MoA). There were tissue- and time-dependent differences in the biochemical responses to each Cd form, wherein QDs are more pro-oxidant when compared to dissolved Cd. The gills are the main tissue affected by QDs, with effects related to the increase of SOD, GST and GPx activities, while those of dissolved Cd was associated to the increase of CAT activity, Cd accumulation and exposure time. Digestive gland is a main tissue for accumulation of both Cd forms, but changes in antioxidant enzyme activities are smaller than in gills. A multivariate analysis revealed that the antioxidant patterns are tissue dependent

  12. Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes.

    Science.gov (United States)

    Garg, Anchal; Agrawal, Lalit; Misra, Rajesh Chandra; Sharma, Shubha; Ghosh, Sumit

    2015-09-02

    Kalmegh (Andrographis paniculata) has been widely exploited in traditional medicine for the treatment of infectious diseases and health disorders. Ent-labdane-related diterpene (ent-LRD) specialized (i.e., secondary) metabolites of kalmegh such as andrographolide, neoandrographolide and 14-deoxy-11,12-didehydroandrographolide, are known for variety of pharmacological activities. However, due to the lack of genomic and transcriptomic information, underlying molecular basis of ent-LRDs biosynthesis has remained largely unknown. To identify candidate genes of the ent-LRD biosynthetic pathway, we performed comparative transcriptome analysis using leaf and root tissues that differentially accumulate ent-LRDs. De novo assembly of Illumina HiSeq2000 platform-generated paired-end sequencing reads resulted into 69,011 leaf and 64,244 root transcripts which were assembled into a total of 84,628 unique transcripts. Annotation of these transcripts to the Uniprot, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active Enzymes (CAZy) databases identified candidate transcripts of the ent-LRD biosynthetic pathway. These included transcripts that encode enzymes of the plastidial 2C-methyl-D-erythritol-4-phosphate pathway which provides C5 isoprenoid precursors for the ent-LRDs biosynthesis, geranylgeranyl diphosphate synthase, class II diterpene synthase (diTPS), cytochrome P450 monooxygenase and glycosyltransferase. Three class II diTPSs (ApCPS1, ApCPS2 and ApCPS3) that showed distinct tissue-specific expression profiles and are phylogenetically related to the dicotyledon ent-copalyl diphosphate synthases, are identified. ApCPS1, ApCPS2 and ApCPS3 encode for 832-, 817- and 797- amino acids proteins of 55-63 % identity, respectively. Spatio-temporal patterns of transcripts and ent-LRDs accumulation are consistent with the involvement of ApCPS1 in general (i.e., primary) metabolism for the biosynthesis of phytohormone gibberellin, ApCPS2 in leaf specialized ent

  13. Novel human ZAKI-4 isoforms: hormonal and tissue-specific regulation and function as calcineurin inhibitors.

    Science.gov (United States)

    Cao, Xia; Kambe, Fukushi; Miyazaki, Takashi; Sarkar, Devanand; Ohmori, Sachiko; Seo, Hisao

    2002-01-01

    We identified a thyroid hormone [3,5,3'-tri-iodothyronine (T(3))]-responsive gene, ZAKI-4, in cultured human skin fibroblasts. It belongs to a family of genes that encode proteins containing a conserved motif. The motif binds to calcineurin and inhibits its phosphatase activity. In the present study, we have demonstrated three different ZAKI-4 transcripts, alpha, beta1 and beta2, in human brain by 5'- and 3'-RACE (rapid amplification of cDNA ends). The alpha transcript was identical with the one that we originally cloned from human fibroblasts and the other two are novel. The three transcripts are generated by alternative initiation and splicing from a single gene on the short arm of chromosome 6. It is predicted that beta1 and beta2 encode an identical protein product, beta, which differs from alpha in its N-terminus. Since alpha and beta contain an identical C-terminal region harbouring the conserved motif, both isoforms are suggested to inhibit calcineurin activity. Indeed, each isoform associates with calcineurin A and inhibits its activity in a similar manner, suggesting that the difference in N-terminus of each isoform does not affect the inhibitory function on calcineurin. An examination of the expression profile of the three transcripts in 12 human tissues revealed that the alpha transcript is expressed exclusively in the brain, whereas beta transcripts are expressed ubiquitously, most abundantly in brain, heart, skeletal muscle and kidney. It was also demonstrated that human skin fibroblasts express both alpha and beta transcripts, raising the question of which transcript is up-regulated by T(3). It was revealed that T(3) markedly induced the expression of alpha isoform but not of beta. This T(3)-mediated increase in the alpha isoform was associated with a significant decrease in endogenous calcineurin activity. These results suggest that the expression of ZAKI-4 isoforms is subjected to distinct hormonal as well as tissue-specific regulation, constituting

  14. Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

    Directory of Open Access Journals (Sweden)

    Hong Lu

    Full Text Available Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown.To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage.Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small

  15. Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation.

    Science.gov (United States)

    Li, Min; Zhang, Jiayi; Liu, Qing; Wang, Jianxin; Wu, Fang-Xiang

    2014-01-01

    Predicting disease-related genes is one of the most important tasks in bioinformatics and systems biology. With the advances in high-throughput techniques, a large number of protein-protein interactions are available, which make it possible to identify disease-related genes at the network level. However, network-based identification of disease-related genes is still a challenge as the considerable false-positives are still existed in the current available protein interaction networks (PIN). Considering the fact that the majority of genetic disorders tend to manifest only in a single or a few tissues, we constructed tissue-specific networks (TSN) by integrating PIN and tissue-specific data. We further weighed the constructed tissue-specific network (WTSN) by using DNA methylation as it plays an irreplaceable role in the development of complex diseases. A PageRank-based method was developed to identify disease-related genes from the constructed networks. To validate the effectiveness of the proposed method, we constructed PIN, weighted PIN (WPIN), TSN, WTSN for colon cancer and leukemia, respectively. The experimental results on colon cancer and leukemia show that the combination of tissue-specific data and DNA methylation can help to identify disease-related genes more accurately. Moreover, the PageRank-based method was effective to predict disease-related genes on the case studies of colon cancer and leukemia. Tissue-specific data and DNA methylation are two important factors to the study of human diseases. The same method implemented on the WTSN can achieve better results compared to those being implemented on original PIN, WPIN, or TSN. The PageRank-based method outperforms degree centrality-based method for identifying disease-related genes from WTSN.

  16. Feasibility of Trace Alcohol Congener Detection and Identification Using Laser-Induced Breakdown Spectroscopy

    International Nuclear Information System (INIS)

    Zhang Jialiang; Wang Shangmin; Zhao Lixian; Liu Liying; Wang Dezhen

    2014-01-01

    In this paper, a feasible scheme is reported for the detection and identification of trace alcohol congeners that have identical elemental composition using laser-induced breakdown spectroscopy (LIBS). In the scheme, an intensive pulsed laser is used to break down trace alcohol samples and the optical emission spectra of the induced plasma are collected for the detection and identification of alcohol molecules. In order to prepare trace alcohol samples, pure ethanol or methanol is bubbled by argon carrier gas and then mixed into matrix gases. The key issue for the scheme is to constitute indices from the LIBS data of the alcohol samples. Two indices are found to be suitable for alcohol detection and identification. One is the emission intensity ratio (denoted as H/C) of the hydrogen line (653.3 nm) to the carbon line (247.9 nm) for identification and the other is the ratio of the carbon line (as C/Ar) or the hydrogen line (as H/Ar) to the argon lines (866.7 nm) for quantitative detection. The calibration experiment result shows that the index H/C is specific for alcohol congeners while almost being independent of alcohol concentration. In detail, the H/C keeps a specific constant of 34 and 23 respectively for ethanol and methanol. In the meanwhile, the C/Ar and H/Ar indices respond almost linearly to the alcohol concentration below 1300 ppm, and are therefore competent for concentration measurement. With the indices, trace alcohol concentration measurement achieves a limit of 140 ppm using a laser pulse energy of 300 mJ. (plasma technology)

  17. Serum PCB levels and congener profiles among teachers in PCB-containing schools: a pilot study

    Science.gov (United States)

    2011-01-01

    Background PCB contamination in the built environment may result from the release of PCBs from building materials. The significance of this contamination as a pathway of human exposure is not well-characterized, however. This research compared the serum PCB concentrations, and congener profiles between 18 teachers in PCB-containing schools and referent populations. Methods Blood samples from 18 teachers in PCB-containing schools were analyzed for 57 PCB congeners. Serum PCB concentrations and congener patterns were compared between the teachers, to the 2003-4 NHANES (National Health and Nutrition Examination Survey) data, and to data from 358 Greater Boston area men. Results Teachers at one school had higher levels of lighter (PCB 6-74) congeners compared to teachers from other schools. PCB congener 47 contributed substantially to these elevated levels. Older teachers (ages 50-64) from all schools had higher total (sum of 33 congeners) serum PCB concentrations than age-comparable NHANES reference values. Comparing the teachers to the referent population of men from the Greater Boston area (all under age 51), no difference in total serum PCB levels was observed between the referents and teachers up to 50 years age. However, the teachers had significantly elevated serum concentrations of lighter congeners (PCB 6-74). This difference was confirmed by comparing the congener-specific ratios between groups, and principal component analysis showed that the relative contribution of lighter congeners differed between the teachers and the referents. Conclusions These findings suggest that the teachers in the PCB-containing buildings had higher serum levels of lighter PCB congeners (PCB 6-74) than the referent populations. Examination of the patterns, as well as concentrations of individual PCB congeners in serum is essential to investigating the contributions from potential environmental sources of PCB exposure. PMID:21668970

  18. Tissue specific promoters improve the localization of radiation-inducible gene expression

    International Nuclear Information System (INIS)

    Hallahan, Dennis; Kataoka, Yasushi; Kuchibhotla, Jaya; Virudachalam, Subbu; Weichselbaum, Ralph

    1996-01-01

    expression was quantified in vascular endothelial cells from large vessel (HUVEC) and small vessels (HMEC). We found cell-type specificity of radiation-induction. The promoter region from the ELAM gene gave no expression in cells that were not of endothelial cell origin and x-ray-induction of ELAM in the endothelium required the NFkB binding cis-acting element. ELAM induction was achieved at doses as low as 1 Gy, whereas induction of other radiation inducible genes required 5 to 10 Gy. Cells transfected with the minimal promoter (plasmid pTK-CAT) demonstrated no radiation induction. Expression of the CMV-LacZ genetic construct that was used as a negative control in each transfection was not altered by x-irradiation. Moreover, intravenous administration of liposomes containing a reporter gene linked to the ELAM promoter and a transcriptional amplification system were induced specifically at sites of x-irradiation in an animal model. Conclusions: Activation of transcription of the ELAM-1 promoter by ionizing radiation is a means of activating gene therapy within the vascular endothelium and demonstrates the feasibility of treating vascular lesions with noninvasive procedures. Tissue specific promoters (e. g., ELAM-1) combined with radiation inducible gene therapy improves the localization of gene therapy expression. These results have applications in intravascular brachytherapy for the prevention of blood vessel restenosis

  19. SMRT has tissue-specific isoform profiles that include a form containing one CoRNR box

    International Nuclear Information System (INIS)

    Short, Stephen; Malartre, Marianne; Sharpe, Colin

    2005-01-01

    SMRT acts as a corepressor for a range of transcription factors. The amino-terminal part of the protein includes domains that mainly mediate transcriptional repression whilst the carboxy-terminal part includes domains that interact with nuclear receptors using up to three motifs called CoRNR boxes. The region of the SMRT primary transcript encoding the interaction domains is subject to alternative splicing that varies the inclusion of the third CoRNR box. The profile in mice includes an abundant, novel SMRT isoform that possesses just one CoRNR box. Mouse tissues therefore express SMRT isoforms containing one, two or three CoRNR boxes. In frogs, the SMRT isoform profile is tissue-specific. The mouse also shows distinct profiles generated by differential expression levels of the SMRT transcript isoforms. The formation of multiple SMRT isoforms and their tissue-specific regulation indicates a mechanism, whereby cells can define the repertoire of transcription factors regulated by SMRT

  20. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.

    Science.gov (United States)

    Fagerberg, Linn; Hallström, Björn M; Oksvold, Per; Kampf, Caroline; Djureinovic, Dijana; Odeberg, Jacob; Habuka, Masato; Tahmasebpoor, Simin; Danielsson, Angelika; Edlund, Karolina; Asplund, Anna; Sjöstedt, Evelina; Lundberg, Emma; Szigyarto, Cristina Al-Khalili; Skogs, Marie; Takanen, Jenny Ottosson; Berling, Holger; Tegel, Hanna; Mulder, Jan; Nilsson, Peter; Schwenk, Jochen M; Lindskog, Cecilia; Danielsson, Frida; Mardinoglu, Adil; Sivertsson, Asa; von Feilitzen, Kalle; Forsberg, Mattias; Zwahlen, Martin; Olsson, IngMarie; Navani, Sanjay; Huss, Mikael; Nielsen, Jens; Ponten, Fredrik; Uhlén, Mathias

    2014-02-01

    Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.

  1. Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity

    Directory of Open Access Journals (Sweden)

    Thomas Marshall

    2011-02-01

    Full Text Available Abstract Background In addition to determining static states of gene expression (high vs. low, it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before. Results We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs and other genes. Responsive genes (N = 4746, which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF and our new data for 15 organs and tissues. Non-responsive genes (N = 9562, which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters. Conclusions We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.

  2. A study of diffusion tensor imaging by tissue-specific, smoothing-compensated voxel-based analysis.

    Science.gov (United States)

    Lee, Jee Eun; Chung, Moo K; Lazar, Mariana; DuBray, Molly B; Kim, Jinsuh; Bigler, Erin D; Lainhart, Janet E; Alexander, Andrew L

    2009-02-01

    Voxel-based analysis (VBA) is commonly used for statistical analysis of image data, including the detection of significant signal differences between groups. Typically, images are co-registered and then smoothed with an isotropic Gaussian kernel to compensate for image misregistration, to improve the signal-to-noise ratio (SNR), to reduce the number of multiple comparisons, and to apply random field theory. Problems with typical implementations of VBA include poor tissue specificity from image misregistration and smoothing. In this study, we developed a new tissue-specific, smoothing-compensated (T-SPOON) method for the VBA of diffusion tensor imaging (DTI) data with improved tissue specificity and compensation for image misregistration and smoothing. When compared with conventional VBA methods, the T-SPOON method introduced substantially less errors in the normalized and smoothed DTI maps. Another confound of the conventional DTI-VBA is that it is difficult to differentiate between differences in morphometry and DTI measures that describe tissue microstructure. T-SPOON VBA decreased the effects of differential morphometry in the DTI VBA studies. T-SPOON and conventional VBA were applied to a DTI study of white matter in autism. T-SPOON VBA results were found to be more consistent with region of interest (ROI) measurements in the corpus callosum and temporal lobe regions. The T-SPOON method may be also applicable to other quantitative imaging maps such as T1 or T2 relaxometry, magnetization transfer, or PET tracer maps.

  3. EPS: an empirical Bayes approach to integrating pleiotropy and tissue-specific information for prioritizing risk genes.

    Science.gov (United States)

    Liu, Jin; Wan, Xiang; Ma, Shuangge; Yang, Can

    2016-06-15

    Researchers worldwide have generated a huge volume of genomic data, including thousands of genome-wide association studies (GWAS) and massive amounts of gene expression data from different tissues. How to perform a joint analysis of these data to gain new biological insights has become a critical step in understanding the etiology of complex diseases. Due to the polygenic architecture of complex diseases, the identification of risk genes remains challenging. Motivated by the shared risk genes found in complex diseases and tissue-specific gene expression patterns, we propose as an Empirical Bayes approach to integrating Pleiotropy and Tissue-Specific information (EPS) for prioritizing risk genes. As demonstrated by extensive simulation studies, EPS greatly improves the power of identification for disease-risk genes. EPS enables rigorous hypothesis testing of pleiotropy and tissue-specific risk gene expression patterns. All of the model parameters can be adaptively estimated from the developed expectation-maximization (EM) algorithm. We applied EPS to the bipolar disorder and schizophrenia GWAS from the Psychiatric Genomics Consortium, along with the gene expression data for multiple tissues from the Genotype-Tissue Expression project. The results of the real data analysis demonstrate many advantages of EPS. The EPS software is available on https://sites.google.com/site/liujin810822 CONTACT: eeyang@hkbu.edu.hk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Expression analysis of five tobacco EIN3 family members in relation to tissue-specific ethylene responses.

    Science.gov (United States)

    Rieu, I; Mariani, C; Weterings, K

    2003-10-01

    Ethylene induces different sets of genes in different tissues and at different stages of development. To investigate whether these differential responses are caused by differential expression of members of the EIN3 family transcription factors, five tobacco family members were isolated. They can be divided into three subgroups, which is probably due to the amphidiploid nature of tobacco. In phylogenetic analysis, each of the subgroups clustered with one of the three tomato EIL proteins and all NtEILs proved to be most homologous to Arabidopsis EIN3 and EIL1. Although organ-specific ethylene responses have been observed before, northern blot analysis showed that all NtEILs were expressed in all organs. To study differential NtEIL expression at the cellular level, in situ hybridization was used on the tobacco ovary. It was found that different ovary tissues displayed variable ethylene-induced expression of two ethylene-responsive marker genes. By contrast, no differences were found in expression level or tissue-specificity for any of the NtEILs in the ovary, before or after ethylene treatment. This indicates that the organ and tissue-specific ethylene responses are not caused by differential expression of NtEIL family members. These results support a model in which the developmental signals that regulate the tissue-specific responses are integrated with the ethylene signal downstream of a common primary ethylene-signalling pathway.

  5. Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

    Directory of Open Access Journals (Sweden)

    Girgis Hani Z

    2012-02-01

    Full Text Available Abstract Background Researchers seeking to unlock the genetic basis of human physiology and diseases have been studying gene transcription regulation. The temporal and spatial patterns of gene expression are controlled by mainly non-coding elements known as cis-regulatory modules (CRMs and epigenetic factors. CRMs modulating related genes share the regulatory signature which consists of transcription factor (TF binding sites (TFBSs. Identifying such CRMs is a challenging problem due to the prohibitive number of sequence sets that need to be analyzed. Results We formulated the challenge as a supervised classification problem even though experimentally validated CRMs were not required. Our efforts resulted in a software system named CrmMiner. The system mines for CRMs in the vicinity of related genes. CrmMiner requires two sets of sequences: a mixed set and a control set. Sequences in the vicinity of the related genes comprise the mixed set, whereas the control set includes random genomic sequences. CrmMiner assumes that a large percentage of the mixed set is made of background sequences that do not include CRMs. The system identifies pairs of closely located motifs representing vertebrate TFBSs that are enriched in the training mixed set consisting of 50% of the gene loci. In addition, CrmMiner selects a group of the enriched pairs to represent the tissue-specific regulatory signature. The mixed and the control sets are searched for candidate sequences that include any of the selected pairs. Next, an optimal Bayesian classifier is used to distinguish candidates found in the mixed set from their control counterparts. Our study proposes 62 tissue-specific regulatory signatures and putative CRMs for different human tissues and cell types. These signatures consist of assortments of ubiquitously expressed TFs and tissue-specific TFs. Under controlled settings, CrmMiner identified known CRMs in noisy sets up to 1:25 signal-to-noise ratio. CrmMiner was

  6. Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.

    Science.gov (United States)

    Girgis, Hani Z; Ovcharenko, Ivan

    2012-02-07

    Researchers seeking to unlock the genetic basis of human physiology and diseases have been studying gene transcription regulation. The temporal and spatial patterns of gene expression are controlled by mainly non-coding elements known as cis-regulatory modules (CRMs) and epigenetic factors. CRMs modulating related genes share the regulatory signature which consists of transcription factor (TF) binding sites (TFBSs). Identifying such CRMs is a challenging problem due to the prohibitive number of sequence sets that need to be analyzed. We formulated the challenge as a supervised classification problem even though experimentally validated CRMs were not required. Our efforts resulted in a software system named CrmMiner. The system mines for CRMs in the vicinity of related genes. CrmMiner requires two sets of sequences: a mixed set and a control set. Sequences in the vicinity of the related genes comprise the mixed set, whereas the control set includes random genomic sequences. CrmMiner assumes that a large percentage of the mixed set is made of background sequences that do not include CRMs. The system identifies pairs of closely located motifs representing vertebrate TFBSs that are enriched in the training mixed set consisting of 50% of the gene loci. In addition, CrmMiner selects a group of the enriched pairs to represent the tissue-specific regulatory signature. The mixed and the control sets are searched for candidate sequences that include any of the selected pairs. Next, an optimal Bayesian classifier is used to distinguish candidates found in the mixed set from their control counterparts. Our study proposes 62 tissue-specific regulatory signatures and putative CRMs for different human tissues and cell types. These signatures consist of assortments of ubiquitously expressed TFs and tissue-specific TFs. Under controlled settings, CrmMiner identified known CRMs in noisy sets up to 1:25 signal-to-noise ratio. CrmMiner was 21-75% more precise than a related CRM

  7. PCB in soils and estimated soil-air exchange fluxes of selected PCB congeners in the south of Sweden

    International Nuclear Information System (INIS)

    Backe, Cecilia; Cousins, Ian T.; Larsson, Per

    2004-01-01

    PCB concentrations were studied in different soils to determine the spatial variation over a region of approximately 11 000 km 2 . PCB congener pattern was used to illustrate the spatial differences, as shown by principal component analysis (PCA). The relationship to different soil parameters was studied. PCB concentrations in soil showed a large variation between sampling-areas with median concentrations ranging between 2.3 and 332 ng g -1 (dw). Highest concentrations were found at two sites with sandy soils, one with extremely high organic carbon content. Both sites were located on the west coast of southern Sweden. Soils with similar soil textures (i.e. sandy silt moraine) did not show any significant differences in PCB concentrations. PCB congener composition was shown to differ between sites, with congener patterns almost site-specific. PCB in air and precipitation was measured and the transfer of chemicals between the soil and air compartments was estimated. Soil-air fugacity quotient calculations showed that the PCBs in the soil consistently had a higher fugacity than the PCBs in the air, with a median quotient value of 2.7. The gaseous fluxes between soil and air were estimated using standard modelling equations and a net soil-air flux estimated by subtracting bulk deposition from gaseous soil-air fluxes. It was shown that inclusion of vertical sorbed phase transport of PCBs in the soil had a large effect on the direction of the net soil-air exchange fluxes. - Soil-air exchange of PCBs is investigated and modelled across Sweden

  8. Brown Norway chromosome 1 congenic reduces symptoms of renal disease in fatty Zucker rats.

    Directory of Open Access Journals (Sweden)

    Craig H Warden

    Full Text Available We previously reported that a congenic rat with Brown Norway (BN alleles on chromosome 1 reduces renal disease of 15-week old fatty Zucker rats (ZUC. Development of renal disease in fatty BN congenic and fatty ZUC rats from 9 through 28 weeks is now examined. Analysis of urine metabolites by (1H nuclear magnetic resonance (NMR spectroscopy revealed a significantly increased urinary loss of glucose, myo-inositol, urea, creatine, and valine in ZUC. Food intake was lower in the BN congenic rats at weeks 9-24, but they weighed significantly more at 28 weeks compared with the ZUC group. Fasting glucose was significantly higher in ZUC than congenic and adiponectin levels were significantly lower in ZUC, but there was no significant genotype effect on Insulin levels. Glucose tolerance tests exhibited no significant differences between ZUC and congenic when values were normalized to basal glucose levels. Quantitative PCR on livers revealed evidence for higher gluconeogenesis in congenics than ZUC at 9 weeks. Plasma urea nitrogen and creatinine were more than 2-fold higher in 28-week ZUC. Twelve urine protein markers of glomerular, proximal and distal tubule disease were assayed at three ages. Several proteins that indicate glomerular and proximal tubular disease increased with age in both congenic and ZUC. Epidermal growth factor (EGF level, a marker whose levels decrease with distal tubule disease, was significantly higher in congenics. Quantitative histology of 28 week old animals revealed the most significant genotype effect was for tubular dilation and intratubular protein. The congenic donor region is protective of kidney disease, and effects on Type 2 diabetes are likely limited to fasting glucose and adiponectin. The loss of urea together with a small increase of food intake in ZUC support the hypothesis that nitrogen balance is altered in ZUC from an early age.

  9. The role of tissue-specific microbiota in initial establishment success of Pacific oysters.

    Science.gov (United States)

    Lokmer, Ana; Kuenzel, Sven; Baines, John F; Wegner, Karl Mathias

    2016-03-01

    Microbiota can have positive and negative effects on hosts depending on the environmental conditions. Therefore, it is important to decipher host-microbiota-environment interactions, especially under natural conditions exerting (a)biotic stress. Here, we assess the relative importance of microbiota in different tissues of Pacific oyster for its successful establishment in a new environment. We transplanted oysters from the Southern to the Northern Wadden Sea and controlled for the effects of resident microbiota by administering antibiotics to half of the oysters. We then followed survival and composition of haemolymph, mantle, gill and gut microbiota in local and translocated oysters over 5 days. High mortality was recorded only in non-antibiotic-treated translocated oysters, where high titres of active Vibrio sp. in solid tissues indicated systemic infections. Network analyses revealed the highest connectivity and a link to seawater communities in the haemolymph microbiota. Since antibiotics decreased modularity and increased connectivity of the haemolymph-based networks, we propose that community destabilization in non-treated translocated oysters could be attributed to interactions between resident and external microbiota, which in turn facilitated passage of vibrios into solid tissues and invoked disease. These interactions of haemolymph microbiota with the external and internal environment may thus represent an important component of oyster fitness. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. Evaluating the Application of Tissue-Specific Dose Kernels Instead of Water Dose Kernels in Internal Dosimetry : A Monte Carlo Study

    NARCIS (Netherlands)

    Moghadam, Maryam Khazaee; Asl, Alireza Kamali; Geramifar, Parham; Zaidi, Habib

    2016-01-01

    Purpose: The aim of this work is to evaluate the application of tissue-specific dose kernels instead of water dose kernels to improve the accuracy of patient-specific dosimetry by taking tissue heterogeneities into consideration. Materials and Methods: Tissue-specific dose point kernels (DPKs) and

  11. Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

    KAUST Repository

    Horiuchi, Youko

    2015-12-23

    Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis-eQTLs. Expression

  12. The Identification of Congeners and Aliens by Drosophila Larvae.

    Directory of Open Access Journals (Sweden)

    Francisco Del Pino

    Full Text Available We investigated the role of Drosophila larva olfactory system in identification of congeners and aliens. We discuss the importance of these activities in larva navigation across substrates, and the implications for allocation of space and food among species of similar ecologies. Wild type larvae of cosmopolitan D. melanogaster and endemic D. pavani, which cohabit the same breeding sites, used species-specific volatiles to identify conspecifics and aliens moving toward larvae of their species. D. gaucha larvae, a sibling species of D. pavani that is ecologically isolated from D. melanogaster, did not respond to melanogaster odor cues. Similar to D. pavani larvae, the navigation of pavani female x gaucha male hybrids was influenced by conspecific and alien odors, whereas gaucha female x pavani male hybrid larvae exhibited behavior similar to the D. gaucha parent. The two sibling species exhibited substantial evolutionary divergence in processing the odor inputs necessary to identify conspecifics. Orco (Or83b mutant larvae of D. melanogaster, which exhibit a loss of sense of smell, did not distinguish conspecific from alien larvae, instead moving across the substrate. Syn97CS and rut larvae of D. melanogaster, which are unable to learn but can smell, moved across the substrate as well. The Orco (Or83b, Syn97CS and rut loci are necessary to orient navigation by D. melanogaster larvae. Individuals of the Trana strain of D. melanogaster did not respond to conspecific and alien larval volatiles and therefore navigated randomly across the substrate. By contrast, larvae of the Til-Til strain used larval volatiles to orient their movement. Natural populations of D. melanogaster may exhibit differences in identification of conspecific and alien larvae. Larval locomotion was not affected by the volatiles.

  13. Use of herbarium data to evaluate weediness in five congeners

    Science.gov (United States)

    Hanan-A., Ana M.; Vibrans, Heike; Cacho, N. Ivalú; Villaseñor, José L.; Ortiz, Enrique; Gómez-G., Vinicio A.

    2016-01-01

    It is often desirable to quantify a plant's relative weediness or synanthropy, that is, the degree to which a species associates with human-caused disturbance, in order to study and understand the biology, ecology and evolution of weeds and invasive plants. Herbarium specimens are among the most accessible and verifiable sources of data on distribution and habitat. However, the habitat distribution of species may not be reflected accurately by herbarium specimen data, due to well-known biases in plant collection. Here, we assess how well herbarium specimens reflect species' weediness, when compared with direct field surveys. We used five species of Melampodium (Asteraceae) and classified their degree of weediness with a modification of Nuorteva's synanthropy index, based on herbarium specimens. We then modelled the distribution of our focal species in Mexico using MaxEnt and identified a polygon of ∼3000 km2 in the state of Nayarit, Mexico, where there was a high probability of finding all five species. Systematic field searches in the target area documented all visible populations of four species along major and minor roads. Then we, again, classified their degree of weediness with the synanthropy index, based now on field data, and compared. We found that herbarium data were an accurate predictor of a species' weediness relative to its congeners despite the well-documented skew of herbarium data towards natural areas, which our data reflected as well. So, herbarium data can be used to classify species' weediness relative to each other, but not in absolute terms, if the specimens were correctly identified and none of the species were subject to particular collection bias. This study is the first attempt to compare herbarium and field data on this subject and may be relevant for other types of investigations based on herbarium data. Our work also highlights the usefulness of distribution models based on herbarium specimens. PMID:26672076

  14. Use of herbarium data to evaluate weediness in five congeners.

    Science.gov (United States)

    Hanan-A, Ana M; Vibrans, Heike; Cacho, N Ivalú; Villaseñor, José L; Ortiz, Enrique; Gómez-G, Vinicio A

    2015-12-15

    It is often desirable to quantify a plant's relative weediness or synanthropy, that is, the degree to which a species associates with human-caused disturbance, in order to study and understand the biology, ecology and evolution of weeds and invasive plants. Herbarium specimens are among the most accessible and verifiable sources of data on distribution and habitat. However, the habitat distribution of species may not be reflected accurately by herbarium specimen data, due to well-known biases in plant collection. Here, we assess how well herbarium specimens reflect species' weediness, when compared with direct field surveys. We used five species of Melampodium (Asteraceae) and classified their degree of weediness with a modification of Nuorteva's synanthropy index, based on herbarium specimens. We then modelled the distribution of our focal species in Mexico using MaxEnt and identified a polygon of ∼3000 km(2) in the state of Nayarit, Mexico, where there was a high probability of finding all five species. Systematic field searches in the target area documented all visible populations of four species along major and minor roads. Then we, again, classified their degree of weediness with the synanthropy index, based now on field data, and compared. We found that herbarium data were an accurate predictor of a species' weediness relative to its congeners despite the well-documented skew of herbarium data towards natural areas, which our data reflected as well. So, herbarium data can be used to classify species' weediness relative to each other, but not in absolute terms, if the specimens were correctly identified and none of the species were subject to particular collection bias. This study is the first attempt to compare herbarium and field data on this subject and may be relevant for other types of investigations based on herbarium data. Our work also highlights the usefulness of distribution models based on herbarium specimens. Published by Oxford University Press

  15. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Je-Hyuk Lee

    2009-11-01

    Full Text Available Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.

  16. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

    Science.gov (United States)

    Lee, Je-Hyuk; Park, In-Hyun; Gao, Yuan; Li, Jin Billy; Li, Zhe; Daley, George Q; Zhang, Kun; Church, George M

    2009-11-01

    Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.

  17. Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1.

    Science.gov (United States)

    Zhang, Huiming; Kim, Mi-Seong; Sun, Yan; Dowd, Scot E; Shi, Huazhong; Paré, Paul W

    2008-06-01

    Elevated sodium (Na(+)) decreases plant growth and, thereby, agricultural productivity. The ion transporter high-affinity K(+) transporter (HKT)1 controls Na(+) import in roots, yet dysfunction or overexpression of HKT1 fails to increase salt tolerance, raising questions as to HKT1's role in regulating Na(+) homeostasis. Here, we report that tissue-specific regulation of HKT1 by the soil bacterium Bacillus subtilis GB03 confers salt tolerance in Arabidopsis thaliana. Under salt stress (100 mM NaCl), GB03 concurrently down- and upregulates HKT1 expression in roots and shoots, respectively, resulting in lower Na(+) accumulation throughout the plant compared with controls. Consistent with HKT1 participation in GB03-induced salt tolerance, GB03 fails to rescue salt-stressed athkt1 mutants from stunted foliar growth and elevated total Na(+) whereas salt-stressed Na(+) export mutants sos3 show GB03-induced salt tolerance with enhanced shoot and root growth as well as reduced total Na(+). These results demonstrate that tissue-specific regulation of HKT1 is critical for managing Na(+) homeostasis in salt-stressed plants, as well as underscore the breadth and sophistication of plant-microbe interactions.

  18. Tissue-Specific Contributions of Paternally Expressed Gene 3 in Lactation and Maternal Care of Mus musculus.

    Directory of Open Access Journals (Sweden)

    Wesley D Frey

    Full Text Available Paternally Expressed Gene 3 (Peg3 is an imprinted gene that controls milk letdown and maternal-caring behaviors. In this study, a conditional knockout allele has been developed in Mus musculus to further characterize these known functions of Peg3 in a tissue-specific manner. The mutant line was first crossed with a germline Cre. The progeny of this cross displayed growth retardation phenotypes. This is consistent with those seen in the previous mutant lines of Peg3, confirming the usefulness of the new mutant allele. The mutant line was subsequently crossed individually with MMTV- and Nkx2.1-Cre lines to test Peg3's roles in the mammary gland and hypothalamus, respectively. According to the results, the milk letdown process was impaired in the nursing females with the Peg3 mutation in the mammary gland, but not in the hypothalamus. This suggests that Peg3's roles in the milk letdown process are more critical in the mammary gland than in the hypothalamus. In contrast, one of the maternal-caring behaviors, nest-building, was interrupted in the females with the mutation in both MMTV- and Nkx2.1-driven lines. Overall, this is the first study to introduce a conditional knockout allele of Peg3 and to further dissect its contribution to mammalian reproduction in a tissue-specific manner.

  19. Aire deficient mice do not develop the same profile of tissue-specific autoantibodies as APECED patients.

    Science.gov (United States)

    Pöntynen, Nora; Miettinen, Aaro; Arstila, T Petteri; Kämpe, Olle; Alimohammadi, Mohammad; Vaarala, Outi; Peltonen, Leena; Ulmanen, Ismo

    2006-09-01

    Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED, or APS1), is a monogenic autoimmune disease caused by mutations in the autoimmune regulator (AIRE) gene. The three main components of APECED are chronic mucocuteaneous candidiasis, hypoparathyroidism and adrenocortical insufficiency. However, several additional endocrine or other autoimmune disease components, or ectodermal dystrophies form the individually variable clinical picture of APECED. An important feature of APECED is a spectrum of well-characterized circulating autoantibodies, reacting against tissue-specific autoantigens. Aire deficient mice develop some characteristics of APECED phenotype. In order to investigate whether the Aire deficient mice produce autoantibodies similar to human APECED, we studied the reactivity of Aire mouse sera against mouse homologues of 11 human APECED antigens. None of the APECED antigens indicated elevated reactivity in the Aire knock-out mouse sera, implying the absence of APECED associated autoantibodies in Aire deficient mice. These findings were supported by the failure of the autoantigens to activate mouse T-cells. Furthermore, Aire knock-out mice did not express increased levels of anti-nuclear antibodies compared to wt mice. This study indicates that spontaneous induction of tissue-specific autoantibodies similar to APECED does not occur in the rodent model suggesting differences in the immunopathogenic mechanisms between mice and men. Copyright 2006 Elsevier Ltd.

  20. p63 regulates Satb1 to control tissue-specific chromatin remodeling during development of the epidermis

    Science.gov (United States)

    Fessing, Michael Y.; Mardaryev, Andrei N.; Gdula, Michal R.; Sharov, Andrey A.; Sharova, Tatyana Y.; Rapisarda, Valentina; Gordon, Konstantin B.; Smorodchenko, Anna D.; Poterlowicz, Krzysztof; Ferone, Giustina; Kohwi, Yoshinori; Missero, Caterina

    2011-01-01

    During development, multipotent progenitor cells establish tissue-specific programs of gene expression. In this paper, we show that p63 transcription factor, a master regulator of epidermal morphogenesis, executes its function in part by directly regulating expression of the genome organizer Satb1 in progenitor cells. p63 binds to a proximal regulatory region of the Satb1 gene, and p63 ablation results in marked reduction in the Satb1 expression levels in the epidermis. Satb1−/− mice show impaired epidermal morphology. In Satb1-null epidermis, chromatin architecture of the epidermal differentiation complex locus containing genes associated with epidermal differentiation is altered primarily at its central domain, where Satb1 binding was confirmed by chromatin immunoprecipitation–on-chip analysis. Furthermore, genes within this domain fail to be properly activated upon terminal differentiation. Satb1 expression in p63+/− skin explants treated with p63 small interfering ribonucleic acid partially restored the epidermal phenotype of p63-deficient mice. These data provide a novel mechanism by which Satb1, a direct downstream target of p63, contributes in epidermal morphogenesis via establishing tissue-specific chromatin organization and gene expression in epidermal progenitor cells. PMID:21930775

  1. Yki/YAP, Sd/TEAD and Hth/MEIS control tissue specification in the Drosophila eye disc epithelium.

    Science.gov (United States)

    Zhang, Tianyi; Zhou, Qingxiang; Pignoni, Francesca

    2011-01-01

    During animal development, accurate control of tissue specification and growth are critical to generate organisms of reproducible shape and size. The eye-antennal disc epithelium of Drosophila is a powerful model system to identify the signaling pathway and transcription factors that mediate and coordinate these processes. We show here that the Yorkie (Yki) pathway plays a major role in tissue specification within the developing fly eye disc epithelium at a time when organ primordia and regional identity domains are specified. RNAi-mediated inactivation of Yki, or its partner Scalloped (Sd), or increased activity of the upstream negative regulators of Yki cause a dramatic reorganization of the eye disc fate map leading to specification of the entire disc epithelium into retina. On the contrary, constitutive expression of Yki suppresses eye formation in a Sd-dependent fashion. We also show that knockdown of the transcription factor Homothorax (Hth), known to partner Yki in some developmental contexts, also induces an ectopic retina domain, that Yki and Scalloped regulate Hth expression, and that the gain-of-function activity of Yki is partially dependent on Hth. Our results support a critical role for Yki- and its partners Sd and Hth--in shaping the fate map of the eye epithelium independently of its universal role as a regulator of proliferation and survival.

  2. Yki/YAP, Sd/TEAD and Hth/MEIS control tissue specification in the Drosophila eye disc epithelium.

    Directory of Open Access Journals (Sweden)

    Tianyi Zhang

    Full Text Available During animal development, accurate control of tissue specification and growth are critical to generate organisms of reproducible shape and size. The eye-antennal disc epithelium of Drosophila is a powerful model system to identify the signaling pathway and transcription factors that mediate and coordinate these processes. We show here that the Yorkie (Yki pathway plays a major role in tissue specification within the developing fly eye disc epithelium at a time when organ primordia and regional identity domains are specified. RNAi-mediated inactivation of Yki, or its partner Scalloped (Sd, or increased activity of the upstream negative regulators of Yki cause a dramatic reorganization of the eye disc fate map leading to specification of the entire disc epithelium into retina. On the contrary, constitutive expression of Yki suppresses eye formation in a Sd-dependent fashion. We also show that knockdown of the transcription factor Homothorax (Hth, known to partner Yki in some developmental contexts, also induces an ectopic retina domain, that Yki and Scalloped regulate Hth expression, and that the gain-of-function activity of Yki is partially dependent on Hth. Our results support a critical role for Yki- and its partners Sd and Hth--in shaping the fate map of the eye epithelium independently of its universal role as a regulator of proliferation and survival.

  3. Intramyocardial Injection of siRNAs Can Efficiently Establish Myocardial Tissue-Specific Renalase Knockdown Mouse Model.

    Science.gov (United States)

    Huang, Kun; Liu, Ju; Zhang, Hui; Wang, Jiliang; Li, Huili

    2016-01-01

    Ischaemia/reperfusion (I/R) injury will cause additional death of cardiomyocytes in ischaemic heart disease. Recent studies revealed that renalase was involved in the I/R injury. So, the myocardial tissue-specific knockdown mouse models were needed for the investigations of renalase. To establish the mouse models, intramyocardial injection of siRNAs targeting renalase was performed in mice. The wild distribution and high transfection efficiency of the siRNAs were approved. And the renalase expression was efficiently suppressed in myocardial tissue. Compared with the high cost, time consumption, and genetic compensation risk of the Cre/loxP technology, RNA interference (RNAi) technology is much cheaper and less time-consuming. Among the RNAi technologies, injection of siRNAs is safer than virus. And considering the properties of the I/R injury mouse models, the efficiency and durability of injection with siRNAs are acceptable for the studies. Altogether, intramyocardial injection of siRNAs targeting renalase is an economical, safe, and efficient method to establish myocardial tissue-specific renalase knockdown mouse models.

  4. Tissue Discrimination by Uncorrected Autofluorescence Spectra: A Proof-of-Principle Study for Tissue-Specific Laser Surgery

    Directory of Open Access Journals (Sweden)

    Katja Tangermann-Gerk

    2013-10-01

    Full Text Available Laser surgery provides a number of advantages over conventional surgery. However, it implies large risks for sensitive tissue structures due to its characteristic non-tissue-specific ablation. The present study investigates the discrimination of nine different ex vivo tissue types by using uncorrected (raw autofluorescence spectra for the development of a remote feedback control system for tissue-selective laser surgery. Autofluorescence spectra (excitation wavelength 377 ± 50 nm were measured from nine different ex vivo tissue types, obtained from 15 domestic pig cadavers. For data analysis, a wavelength range between 450 nm and 650 nm was investigated. Principal Component Analysis (PCA and Quadratic Discriminant Analysis (QDA were used to discriminate the tissue types. ROC analysis showed that PCA, followed by QDA, could differentiate all investigated tissue types with AUC results between 1.00 and 0.97. Sensitivity reached values between 93% and 100% and specificity values between 94% and 100%. This ex vivo study shows a high differentiation potential for physiological tissue types when performing autofluorescence spectroscopy followed by PCA and QDA. The uncorrected autofluorescence spectra are suitable for reliable tissue discrimination and have a high potential to meet the challenges necessary for an optical feedback system for tissue-specific laser surgery.

  5. Production of WTC.ZI-zi rat congenic strain and its pathological and genetic analyses.

    Science.gov (United States)

    Kuramoto, T; Yamasaki, K; Kondo, A; Nakajima, K; Yamada, M; Serikawa, T

    1998-04-01

    A new rat congenic strain, WTC.ZI-zi, was produced after eleven generations of backcrossing between ZI strain as a donor strain and WTC strain as an inbred partner. WTC.ZI-zi/zi homozygous rats generally exhibit more conspicuous body tremor and much earlier occurrence of flaccid paresis than the original ZI strain. The average life span of the congenic strain is approximately nine months, which is also much shorter than that of the original ZI strain. Pathological analysis of the central nervous system of the congenic strain revealed more aggravated vacuolation and hypomyelination than in the original ZI strain. Establishment of the genetic profile with microsatellite markers showed that the congenic strain was genetically almost identical to the WTC strain except for a small chromosome segment bearing the zitter gene. Analysis of markers in this region implied that the length of the donor segment was approximately 13.4 centimorgans which corresponded to 0.65% of the total genome. Thus, these results suggested that expressional alterations of zitter gene were due to replacement of the genetic background from the original ZI strain to the WTC strain. Furthermore, the WTC.ZI-zi congenic strain could provide a refined tool for the analysis of zitter mutation, because the congenic strain has a strict control strain, WTC, and the length of the donor chromosome is genetically defined.

  6. Congener-specific egg contribution of polychlorinated biphenyls to nestlings in two passerine species

    International Nuclear Information System (INIS)

    Maul, Jonathan D.; Schuler, Lance J.; Halbrook, Richard S.; Lydy, Michael J.

    2010-01-01

    Quantifying polychlorinated biphenyl (PCB) residues in nestlings of avian species is a common method for assessing trophic transfer and risk at PCB-contaminated sites. The proportion of nestling PCB mass due to maternal transfer is often accounted for by subtracting total PCB mass in eggs from nestlings. However, variation in physicochemical properties and metabolism among congeners may lead to differences between egg contribution based on total PCBs and dioxin-like congeners. We examined congener-specific variation in contribution of PCBs from eggs to nestlings in tree swallows and European starlings. Egg contribution of total PCB mass was 14.3 and 16.2%, respectively, whereas contribution based on dioxin-like congeners was 14.8 and 13.6%, respectively. These data suggest that using total PCB mass in eggs to adjust estimates of PCB accumulation in nestlings may not reflect patterns for dioxin-like congeners, potentially over or under-estimating the risk of toxicity of PCBs. - Congener-specific contribution of PCBs from egg to nestlings was examined.

  7. Towards a Novel Patch Material for Cardiac Applications: Tissue-Specific Extracellular Matrix Introduces Essential Key Features to Decellularized Amniotic Membrane

    Directory of Open Access Journals (Sweden)

    Matthias Becker

    2018-03-01

    Full Text Available There is a growing need for scaffold material with tissue-specific bioactivity for use in regenerative medicine, tissue engineering, and for surgical repair of structural defects. We developed a novel composite biomaterial by processing human cardiac extracellular matrix (ECM into a hydrogel and combining it with cell-free amniotic membrane via a dry-coating procedure. Cardiac biocompatibility and immunogenicity were tested in vitro using human cardiac fibroblasts, epicardial progenitor cells, murine HL-1 cells, and human immune cells derived from buffy coat. Processing of the ECM preserved important matrix proteins as demonstrated by mass spectrometry. ECM coating did not alter the mechanical characteristics of decellularized amniotic membrane but did cause a clear increase in adhesion capacity, cell proliferation and viability. Activated monocytes secreted less pro-inflammatory cytokines, and both macrophage polarization towards the pro-inflammatory M1 type and T cell proliferation were prevented. We conclude that the incorporation of human cardiac ECM hydrogel shifts and enhances the bioactivity of decellularized amniotic membrane, facilitating its use in future cardiac applications.

  8. Methylsulfonyl polychlorinated biphenyls in fish from an electronic waste-recycling site in South China: levels, congener profiles, and chiral signatures.

    Science.gov (United States)

    Zhang, Ying; Wu, Jiang-Ping; Luo, Xiao-Jun; She, Ya-Zhe; Mo, Ling; Mai, Bi-Xian

    2012-11-01

    Great concerns have been raised about the fate and effects of polychlorinated biphenyls (PCBs) and other organic contaminants contained in electronic waste (e-waste) exported from industrialized countries at midlatitudes to subtropical and tropical regions. Information on the metabolites of these chemicals, for example, methylsulfonyl-PCBs (MeSO(2)-PCBs) in wildlife from the later regions is scarce. In the present study, 17 MeSO(2)-PCBs, including five chiral congeners, were detected in the muscle, liver, and brain tissues of two benthic fish species--northern snakehead and mud carp--from a small pond near an electronic waste recycling site in South China. The mean concentrations of the sum of the MeSO(2)-PCBs ranged from 80 to 340 ng/g lipid weight in the tissues, with relative higher levels in the liver than the muscle and brain tissues. These levels were one order of magnitude greater than the highest levels of MeSO(2)-PCBs previously reported in fish. The 3'-MeSO(2)-CB 87, 3'- and 4'-MeSO(2)-CB 101, 4-MeSO(2)-CB 110, and 4-MeSO(2)-CB 149 were dominant, collectively comprising more than 55% of the total MeSO(2)-PCBs. Except for 4-MeSO(2)-CB149, all of the investigated chiral MeSO(2)-PCBs displayed a clear, congener-specific enantiomeric enrichment in the tissues. No tissue-specific enantioselective retention of the enantiomers was observed in the investigated fish. This is the first report on chiral signatures of MeSO(2)-PCBs in fish tissues. Copyright © 2012 SETAC.

  9. Application of tritium-labeled complex technical mixture of PCB congeners as radiotracer in ecological investigations

    International Nuclear Information System (INIS)

    Kim, A.A.

    2005-01-01

    The quantitative analysis of PCBs (polychlorinated biphenyls) is enough difficult analytical task. According to IUPAC nomenclature it is described more than 200 possible PCB congeners from which about 150 congeners are present at an environment. At the same time in environment PCBs are present as complex technical mixes of congeners (trade names include Apirolio, Aroclor, Clophen, Fenchlor, Kanechlor, Phenoclor, Pyralene, Pyranol, Pyroclor, Santotherm FR, and Sovol). In routine practice of gas chromatography analysis the quantitative measurement of PCB marker congeners is applied. In the most samples containing PCBs, there are often several dozens of different congeners. For practical reasons, all of them are not always measured, but the most important congeners are used as indicators. In Belgian chicken incident, only seven abundant congeners were usually measured: congeners with IUPAC numbers 28, 52, 101, 118, 138, 153, and 180 (2,4,4 '-TriCB, 2,2 ', 5,5 '-TCB, 2,2 ', 4,5,5 '-PeCB, 2,3 ', 4,4 ', 5-PeCB, 2,2 ', 3,4,4 ', 5 '-HxCB, 2,2 ', 4,4 ', 5,5 '-HxCB, 2,2 ', 3,4,4 ', 5,5 '-HpCB, respectively). The seven congeners are estimated to constitute about one third of all PCBs in the contaminated feed. Such measurement can give the big error in a quantitative estimation of PCBs contents in a sample. As alternative method of quantitative measurement PCBs the radiochemical method with use radioactive labeled PCBs as radiotracer can be used. We had been developed a method of synthesis of labeled by thermally activated tritium a complex technical mixture of PCBs congeners - Sovol. We had been showed a basic opportunity of receiving of uniformly tritium labeled mixture of PCBs congeners without structural failure of mixture. The tritium labeled preparation of complex technical mixture of PCBs congeners (Sovol) has been received. On the basis of received tritium labeled preparation of PCBs (Sovol) we had been developed the following quantitative and qualitative radiochemical

  10. Gambogic Acid Is a Tissue-Specific Proteasome Inhibitor In Vitro and In Vivo

    Directory of Open Access Journals (Sweden)

    Xiaofen Li

    2013-01-01

    Full Text Available Gambogic acid (GA is a natural compound derived from Chinese herbs that has been approved by the Chinese Food and Drug Administration for clinical trials in cancer patients; however, its molecular targets have not been thoroughly studied. Here, we report that GA inhibits tumor proteasome activity, with potency comparable to bortezomib but much less toxicity. First, GA acts as a prodrug and only gains proteasome-inhibitory function after being metabolized by intracellular CYP2E1. Second, GA-induced proteasome inhibition is a prerequisite for its cytotoxicity and anticancer effect without off-targets. Finally, because expression of the CYP2E1 gene is very high in tumor tissues but low in many normal tissues, GA could therefore produce tissue-specific proteasome inhibition and tumor-specific toxicity, with clinical significance for designing novel strategies for cancer treatment.

  11. Involvement of an ent-copalyl diphosphate synthase in tissue-specific accumulation of specialized diterpenes in Andrographis paniculata.

    Science.gov (United States)

    Misra, Rajesh Chandra; Garg, Anchal; Roy, Sudeep; Chanotiya, Chandan Singh; Vasudev, Prema G; Ghosh, Sumit

    2015-11-01

    Ent-labdane-related diterpene (ent-LRD) specialized (i.e. secondary) metabolites of the medicinal plant kalmegh (Andrographis paniculata) have long been known for several pharmacological activities. However, our understanding of the ent-LRD biosynthetic pathway has remained largely incomplete. Since ent-LRDs accumulate in leaves, we carried out a comparative transcriptional analysis using leaf and root tissues, and identified 389 differentially expressed transcripts, including 223 transcripts that were preferentially expressed in leaf tissue. Analysis of the transcripts revealed various specialized metabolic pathways, including transcripts of the ent-LRD biosynthetic pathway. Two class II diterpene synthases (ApCPS1 and ApCPS2) along with one (ApCPS1') and two (ApCPS2' and ApCPS2″) transcriptional variants that were the outcomes of alternative splicing of the precursor mRNA and alternative transcriptional termination, respectively, were identified. ApCPS1 and ApCPS2 encode for 832- and 817-amino acids proteins, respectively, and are phylogenetically related to the dicotyledons ent-copalyl diphosphate synthases (ent-CPSs). The spatio-temporal patterns of ent-LRD metabolites accumulation and gene expression suggested a likely role for ApCPS1 in general (i.e. primary) metabolism, perhaps by providing precursor for the biosynthesis of phytohormone gibberellin (GA). However, ApCPS2 is potentially involved in tissue-specific accumulation of ent-LRD specialized metabolites. Bacterially expressed recombinant ApCPS2 catalyzed the conversion of (E,E,E)-geranylgeranyl diphosphate (GGPP), the general precursor of diterpenes to ent-copalyl diphosphate (ent-CPP), the precursor of ent-LRDs. Taken together, these results advance our understanding of the tissue-specific accumulation of specialized ent-LRDs of medicinal importance. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Tissue specific diurnal rhythms of metabolites and their regulation during herbivore attack in a native tobacco, Nicotiana attenuata.

    Directory of Open Access Journals (Sweden)

    Sang-Gyu Kim

    Full Text Available Ecological performance is all about timing and the endogenous clock that allows the entrainment of rhythms and anticipation of fitness-determining events is being rapidly characterized. How plants anticipate daily abiotic stresses, such as cold in early mornings and drought at noon, as well as biotic stresses, such as the timing of pathogen infections, is being explored, but little is known about the clock's role in regulating responses to insect herbivores and mutualists, whose behaviors are known to be strongly diurnally regulated and whose attack is known to reconfigure plant metabolomes. We developed a liquid chromatography-mass spectrometry procedure and analyzed its output with model-based peak picking algorithms to identify metabolites with diurnal accumulation patterns in sink/source leaves and roots in an unbiased manner. The response of metabolites with strong diurnal patterns to simulated attack from the specialist herbivore, Manduca sexta larvae was analyzed and annotated with in-house and public databases. Roots and leaves had largely different rhythms and only 10 ions of 182 oscillating ions in leaves and 179 oscillating ions in roots were rhythmic in both tissues: root metabolites mainly peaked at dusk or night, while leaf metabolites peaked during the day. Many oscillating metabolites showed tissue-specific regulation by simulated herbivory of which systemic responses in unattacked tissues were particularly pronounced. Diurnal and herbivory-elicited accumulation patterns of disaccharide, phenylalanine, tyrosine, lyciumoside I, coumaroyl tyramine, 12-oxophytodienoic acid and jasmonic acid and those of their related biosynthetic transcripts were examined in detail. We conclude that oscillating metabolites of N. attenuata accumulate in a highly tissue-specific manner and the patterns reveal pronounced diurnal rhythms in the generalized and specialized metabolism that mediates the plant's responses to herbivores and mutualists. We

  13. Diffuse reflectance spectroscopy for optical soft tissue differentiation as remote feedback control for tissue-specific laser surgery.

    Science.gov (United States)

    Stelzle, Florian; Tangermann-Gerk, Katja; Adler, Werner; Zam, Azhar; Schmidt, Michael; Douplik, Alexandre; Nkenke, Emeka

    2010-04-01

    Laser surgery does not provide haptic feedback for operating layer-by-layer and thereby preserving vulnerable anatomical structures like nerve tissue or blood vessels. Diffuse reflectance spectra can facilitate remote optical tissue differentiation. It is the aim of the study to use this technique on soft tissue samples, to set a technological basis for a remote optical feedback system for tissue-specific laser surgery. Diffuse reflectance spectra (wavelength range: 350-650 nm) of ex vivo types of soft tissue (a total of 10,800 spectra) of the midfacial region of domestic pigs were remotely measured under reduced environmental light conditions and analyzed in order to differentiate between skin, mucosa, muscle, subcutaneous fat, and nerve tissue. We performed a principal components (PC) analysis (PCA) to reduce the number of variables. Linear discriminant analysis (LDA) was utilized for classification. For the tissue differentiation, we calculated the specificity and sensitivity by receiver operating characteristic (ROC) analysis and the area under curve (AUC). Six PCs were found to be adequate for tissue differentiation with diffuse reflectance spectra using LDA. All of the types of soft tissue could be differentiated with high specificity and sensitivity. Only the tissue pairs nervous tissue/fatty tissue and nervous tissue/mucosa showed a decline of differentiation due to bio-structural similarity. However, both of these tissue pairs could still be differentiated with a specificity and sensitivity of more than 90%. Analyzing diffuse reflectance spectroscopy with PCA and LDA allows for remote differentiation of biological tissue. Considering the limitations of the ex vivo conditions, the obtained results are promising and set a basis for the further development of a feedback system for tissue-specific laser surgery. (c) 2010 Wiley-Liss, Inc.

  14. The absorption and translocation of polychlorinated biphenyl congeners by Cucurbita pepo ssp pepo.

    Science.gov (United States)

    Greenwood, Scott J; Rutter, Allison; Zeeb, Barbara A

    2011-08-01

    The mobility of polychlorinated biphenyl (PCB) congeners within Cucurbita pepo ssp pepo cv. Howden (pumpkin), a PCB phytoextracting plant, was investigated through a comparison of field-weathered soil, root, shoot, and xylem sap congener profiles. This is the first study to show the presence of PCBs in xylem sap (range: 0.03-0.18 μg·mL(-1)), confirming that PCB translocation throughout the plant occurs via this medium. A comparison of soil (5.2 ± 2.5 μg·g(-1)), root (27.1 ± 2.1 μg·g(-1)), shoot (range: 1.9 ± 0.5 μg·g(-1) - 8.2 ± 1.4 μg·g(-1)), and xylem sap (0.09 ± 0.04 μg·g(-1)) samples showed significant differences in congener profiles, with lower chlorinated congeners (predominately trichlorinated ones) found within xylem sap in higher amounts than higher chlorinated congeners. The total PCB concentrations of xylem sap samples collected at various lengths along the primary plant shoot were not significantly different from each other, while those of primary shoot tissue samples significantly decreased (two-sample t test, p = 0.01) as the distance from the plant base increased. PCA analysis of individual congeners in the roots, shoots and xylem sap indicated that movement of the PCB congeners in the plant was affected by the number of chlorines in the molecule, and hence possibly log K(ow) and molecular weight, but not by planarity.

  15. Will climate change increase hybridization risk between potential plant invaders and their congeners in Europe?

    Science.gov (United States)

    Klonner, Günther; Dullinger, Iwona; Wessely, Johannes; Bossdorf, Oliver; Carboni, Marta; Dawson, Wayne; Essl, Franz; Gattringer, Andreas; Haeuser, Emily; van Kleunen, Mark; Kreft, Holger; Moser, Dietmar; Pergl, Jan; Pyšek, Petr; Thuiller, Wilfried; Weigelt, Patrick; Winter, Marten; Dullinger, Stefan

    2017-08-01

    Interspecific hybridization can promote invasiveness of alien species. In many regions of the world, public and domestic gardens contain a huge pool of non-native plants. Climate change may relax constraints on their naturalization and hence facilitate hybridization with related species in the resident flora. Here, we evaluate this possible increase in hybridization risk by predicting changes in the overlap of climatically suitable ranges between a set of garden plants and their congeners in the resident flora. Europe. From the pool of alien garden plants, we selected those which (1) are not naturalized in Europe, but established outside their native range elsewhere in the world; (2) belong to a genus where interspecific hybridization has been previously reported; and (3) have congeners in the native and naturalized flora of Europe. For the resulting set of 34 alien ornamentals as well as for 173 of their European congeners, we fitted species distribution models and projected suitable ranges under the current climate and three future climate scenarios. Changes in range overlap between garden plants and congeners were then assessed by means of the true skill statistic. Projections suggest that under a warming climate, suitable ranges of garden plants will increase, on average, while those of their congeners will remain constant or shrink, at least under the more severe climate scenarios. The mean overlap in ranges among congeners of the two groups will decrease. Variation among genera is pronounced; however, and for some congeners, range overlap is predicted to increase significantly. Averaged across all modelled species, our results do not indicate that hybrids between potential future invaders and resident species will emerge more frequently in Europe when climate warms. These average trends do not preclude, however, that hybridization risk may considerably increase in particular genera.

  16. Metabolic features of newly established congenic diabetes-prone BB.SHR rat strains.

    Science.gov (United States)

    Klöting, I; Voigt, B; Kovács, P

    1998-01-01

    The well-known association of hypertension and diabetes mellitus and the lack of suitable animal models to study diabetic hypertension prompted us to transfer 4 chromosomal regions with quantitative trait loci (QTLs) for blood pressure of the spontaneously hypertensive SHR rat onto the genetic background of the diabetes-prone and normotensive BB/OK rat. Four congenic strains developed are named as BB. Sa (Chr.1), BB.Bp2 (Chr.18), BB.1K (Chr.20) and BB.Xs (Chr.X). Because the systolic blood pressure is significantly elevated in all congenics, renal related traits were investigated in serum and urine. Comparing BB/OK and their congenic derivatives, significant differences were found in all serum and in 7 out of 8 urine constituents studied. Most significant differences were found between BB/OK and BB.Bp2 rats. Significant differences were also found between the different congenic strains indicating that each congenic strain has its own phenotype and that each chromosomal region contains most probably further QTLs for some of the traits studied.

  17. Structural evolution and tissue-specific expression of tetrapod-specific second isoform of secretory pathway Ca2+-ATPase

    International Nuclear Information System (INIS)

    Pestov, Nikolay B.; Dmitriev, Ruslan I.; Kostina, Maria B.; Korneenko, Tatyana V.; Shakhparonov, Mikhail I.; Modyanov, Nikolai N.

    2012-01-01

    Highlights: ► Full-length secretory pathway Ca-ATPase (SPCA2) cloned from rat duodenum. ► ATP2C2 gene (encoding SPCA2) exists only in genomes of Tetrapoda. ► Rat and pig SPCA2 are expressed in intestines, lung and some secretory glands. ► Subcellular localization of SPCA2 may depend on tissue type. ► In rat duodenum, SPCA2 is localized in plasma membrane-associated compartments. -- Abstract: Secretory pathway Ca-ATPases are less characterized mammalian calcium pumps than plasma membrane Ca-ATPases and sarco-endoplasmic reticulum Ca-ATPases. Here we report analysis of molecular evolution, alternative splicing, tissue-specific expression and subcellular localization of the second isoform of the secretory pathway Ca-ATPase (SPCA2), the product of the ATP2C2 gene. The primary structure of SPCA2 from rat duodenum deduced from full-length transcript contains 944 amino acid residues, and exhibits 65% sequence identity with known SPCA1. The rat SPCA2 sequence is also highly homologous to putative human protein KIAA0703, however, the latter seems to have an aberrant N-terminus originating from intron 2. The tissue-specificity of SPCA2 expression is different from ubiquitous SPCA1. Rat SPCA2 transcripts were detected predominantly in gastrointestinal tract, lung, trachea, lactating mammary gland, skin and preputial gland. In the newborn pig, the expression profile is very similar with one remarkable exception: porcine bulbourethral gland gave the strongest signal. Upon overexpression in cultured cells, SPCA2 shows an intracellular distribution with remarkable enrichment in Golgi. However, in vivo SPCA2 may be localized in compartments that differ among various tissues: it is intracellular in epidermis, but enriched in plasma membranes of the intestinal epithelium. Analysis of SPCA2 sequences from various vertebrate species argue that ATP2C2 gene radiated from ATP2C1 (encoding SPCA1) during adaptation of tetrapod ancestors to terrestrial habitats.

  18. Ecological niche partitioning of the invasive dinoflagellate Prorocentrum minimum and its native congeners in the Baltic Sea.

    Science.gov (United States)

    Telesh, Irena V; Schubert, Hendrik; Skarlato, Sergei O

    2016-11-01

    This study analyses three decades of the peculiar bloom-formation history of the potentially toxic invasive planktonic dinoflagellates Prorocentrum minimum (Pavillard) Schiller in the SW Baltic Sea. We tested a research hypothesis that the unexpectedly long delay (nearly two decades) in population development of P. minimum prior to its first bloom was caused by competition with one or several closely related native dinoflagellate species due to ecological niche partitioning which hampered the spread and bloom-forming potential of the invader. We applied the ecological niche concept to a large, long-term phytoplankton database and analysed the invasion history and population dynamics of P. minimum in the SW Baltic Sea coastal waters using the data on phytoplankton composition, abundance and biomass. The ecological niche dimensions of P. minimum and its congener P. balticum were identified as the optimum environmental conditions for the species during the bloom events based on water temperature, salinity, pH, concentration of nutrients (PO 4 3- ; total phosphorus, TP; total nitrogen, TN; SiO 4 4- ), TN/TP-ratio and habitat type. The data on spatial distribution and ecological niche dimensions of P. minimum have contributed to the development of the "protistan species maximum concept". High microplankton diversity at critical salinities in the Baltic Sea may be considered as a possible reason for the significant niche overlap and strong competitive interactions among congeners leading to prolonged delay in population growth of P. minimum preceding its first bloom in the highly variable brackishwater environment. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Variation in Metabolic Rate among Individuals Is Related to Tissue-Specific Differences in Mitochondrial Leak Respiration.

    Science.gov (United States)

    Salin, Karine; Auer, Sonya K; Rudolf, Agata M; Anderson, Graeme J; Selman, Colin; Metcalfe, Neil B

    Standard metabolic rate (SMR) and maximum metabolic rate (MMR) typically vary two- or threefold among conspecifics, with both traits assumed to significantly impact fitness. However, the underlying mechanisms that determine such intraspecific variation are not well understood. We examined the influence of mitochondrial properties on intraspecific variation in SMR and MMR and hypothesized that if SMR supports the cost of maintaining the metabolic machinery required for MMR, then the mitochondrial properties underlying these traits should be shared. Mitochondrial respiratory capacity (leak and phosphorylating respiration) and mitochondrial content (cytochrome c oxidase activity) were determined in the liver and white muscle of brown trout Salmo trutta of similar age and maintenance conditions. SMR and MMR were uncorrelated across individuals and were not associated with the same mitochondrial properties, suggesting that they are under the control of separate physiological processes. Moreover, tissue-specific relationships between mitochondrial properties and whole-organism metabolic traits were observed. Specifically, SMR was positively associated with leak respiration in liver mitochondria, while MMR was positively associated with muscle mitochondrial leak respiration and mitochondrial content. These results suggest that a high SMR or MMR, rather than signaling a higher ability for respiration-driven ATP synthesis, may actually reflect greater dissipation of energy, driven by proton leak across the mitochondrial inner membrane. Knowledge of these links should aid interpretation of the potential fitness consequences of such variation in metabolism, given the importance of mitochondria in the utilization of resources and their allocation to performance.

  20. Tissue-specific expression of transfected human insulin genes in pluripotent clonal rat insulinoma lines induced during passage in vivo

    International Nuclear Information System (INIS)

    Madsen, O.D.; Andersen, L.C.; Michelsen, B.; Owerbach, D.; Larsson, L.I.; Lernmark, A.; Steiner, D.F.

    1988-01-01

    The pluripotent rat islet tumor cell line MSL-G2 expresses primarily glucagon or cholecystokinin and not insulin in vitro but changes phenotype completely after prolonged in vivo cultivation to yield small-sized hypoglycemic tumors composed almost entirely of insulin-producing beta cells. When a genomic DNA fragment containing the coding and upstream regulatory regions of the human insulin gene was stably transfected into MSL-G2 cells no measurable amounts of insulin or insulin mRNA were detected in vitro. However, successive transplantation of two transfected clones resulted in hypoglycemic tumors that efficiently coexpressed human and rat insulin as determined by human C-peptide-specific immunoreagents. These results demonstrate that cis-acting tissue-specific insulin gene enhancer elements are conserved between rat and human insulin genes. The authors propose that the in vivo differentiation of MSL-G2 cells and transfected subclones into insulin-producing cells reflects processes of natural beta-cell ontogeny leading to insulin gene expression

  1. Tissue-specific expression of insulin-like growth factor II mRNAs with distinct 5' untranslated regions

    International Nuclear Information System (INIS)

    Irminger, J.C.; Rosen, K.M.; Humble, R.E.; Villa-Komaroff, L.

    1987-01-01

    The authors have used RNA from human hypothalamus as template for the production of cDNAs encoding insulin-like growth factor II (IGF-II). The prohormone coding sequence of brain IGF-II RNA is identical to that found in liver; however, the 5' untranslated sequence of the brain cDNA has no homology to the 5' untranslated sequence of the previously reported liver cDNAs. By using hybridization to specific probes as well as a method based on the properties of RNase H, they found that the human IGF-II gene has at least three exons that encode alternative 5' untranslated regions and that are expressed in a tissue-specific manner. A probe specific to the brain cDNA 5' untranslated region hybridizes to a 6.0-kilobase transcript present in placenta, hypothalamus, adrenal gland, kidney, Wilms tumor, and a pheochromocytoma. The 5' untranslated sequence of the brain cDNA does not hybridize to a 5.3-kilobase transcript found in liver or to a 5.0-kb transcript found in pheochromocytoma. By using RNase H to specifically fragment the IGF-II transcripts into 3' and 5' fragments, they found that the RNAs vary in size due to differences in the 5' end but not the 3' end

  2. Development of a tissue-specific ribosome profiling approach in Drosophila enables genome-wide evaluation of translational adaptations.

    Science.gov (United States)

    Chen, Xun; Dickman, Dion

    2017-12-01

    Recent advances in next-generation sequencing approaches have revolutionized our understanding of transcriptional expression in diverse systems. However, measurements of transcription do not necessarily reflect gene translation, the process of ultimate importance in understanding cellular function. To circumvent this limitation, biochemical tagging of ribosome subunits to isolate ribosome-associated mRNA has been developed. However, this approach, called TRAP, lacks quantitative resolution compared to a superior technology, ribosome profiling. Here, we report the development of an optimized ribosome profiling approach in Drosophila. We first demonstrate successful ribosome profiling from a specific tissue, larval muscle, with enhanced resolution compared to conventional TRAP approaches. We next validate the ability of this technology to define genome-wide translational regulation. This technology is leveraged to test the relative contributions of transcriptional and translational mechanisms in the postsynaptic muscle that orchestrate the retrograde control of presynaptic function at the neuromuscular junction. Surprisingly, we find no evidence that significant changes in the transcription or translation of specific genes are necessary to enable retrograde homeostatic signaling, implying that post-translational mechanisms ultimately gate instructive retrograde communication. Finally, we show that a global increase in translation induces adaptive responses in both transcription and translation of protein chaperones and degradation factors to promote cellular proteostasis. Together, this development and validation of tissue-specific ribosome profiling enables sensitive and specific analysis of translation in Drosophila.

  3. Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

    Science.gov (United States)

    Ballester, Benoit; Medina-Rivera, Alejandra; Schmidt, Dominic; Gonzàlez-Porta, Mar; Carlucci, Matthew; Chen, Xiaoting; Chessman, Kyle; Faure, Andre J; Funnell, Alister PW; Goncalves, Angela; Kutter, Claudia; Lukk, Margus; Menon, Suraj; McLaren, William M; Stefflova, Klara; Watt, Stephen; Weirauch, Matthew T; Crossley, Merlin; Marioni, John C; Odom, Duncan T; Flicek, Paul; Wilson, Michael D

    2014-01-01

    As exome sequencing gives way to genome sequencing, the need to interpret the function of regulatory DNA becomes increasingly important. To test whether evolutionary conservation of cis-regulatory modules (CRMs) gives insight into human gene regulation, we determined transcription factor (TF) binding locations of four liver-essential TFs in liver tissue from human, macaque, mouse, rat, and dog. Approximately, two thirds of the TF-bound regions fell into CRMs. Less than half of the human CRMs were found as a CRM in the orthologous region of a second species. Shared CRMs were associated with liver pathways and disease loci identified by genome-wide association studies. Recurrent rare human disease causing mutations at the promoters of several blood coagulation and lipid metabolism genes were also identified within CRMs shared in multiple species. This suggests that multi-species analyses of experimentally determined combinatorial TF binding will help identify genomic regions critical for tissue-specific gene control. DOI: http://dx.doi.org/10.7554/eLife.02626.001 PMID:25279814

  4. Molecular Characterization and Tissue-specific Expression of a Novel FKBP38 Gene in the Cashmere Goat (Capra hircus).

    Science.gov (United States)

    Zheng, X; Hao, X Y; Chen, Y H; Zhang, X; Yang, J F; Wang, Z G; Liu, D J

    2012-06-01

    As a member of a subclass of immunophilins, it is controversial that FKBP38 acts an upstream regulator of mTOR signaling pathway, which control the process of cell-growth, proliferation and differentiation. In order to explore the relationship between FKBP38 and mTOR in the Cashmere goat (Capra hircus) cells, a full-length cDNA was cloned (GenBank accession number JF714970) and expression pattern was analyzed. The cloned FKBP38 gene is 1,248 bp in length, containing an open reading frame (ORF) from nucleotide 13 to 1,248 which encodes 411 amino acids, and 12 nucleotides in front of the initiation codon. The full cDNA sequence shares 98% identity with cattle, 94% with horse and 90% with human. The putative amino acid sequence shows the higher homology which is 98%, 97% and 94%, correspondingly. The bioinformatics analysis showed that FKBP38 contained a FKBP_C domain, two TPR domains and a TM domain. Psite analysis suggested that the ORF encoding protein contained a leucine-zipper pattern and a Prenyl group binding site (CAAX box). Tissue-specific expression analysis was performed by semi-quantitative RT-PCR and showed that the FKBP38 expression was detected in all the tested tissues and the highest level of mRNA accumulation was detected in testis, suggesting that FKBP38 plays an important role in goat cells.

  5. Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).

    Science.gov (United States)

    Spriggs, Andrew; Henderson, Steven T; Hand, Melanie L; Johnson, Susan D; Taylor, Jennifer M; Koltunow, Anna

    2018-02-09

    Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads.

  6. Variable expression of Cre recombinase transgenes precludes reliable prediction of tissue-specific gene disruption by tail-biopsy genotyping.

    Directory of Open Access Journals (Sweden)

    Tim J Schulz

    Full Text Available The Cre/loxP-system has become the system of choice for the generation of conditional so-called knockout mouse strains, i.e. the tissue-specific disruption of expression of a certain target gene. We here report the loss of expression of Cre recombinase in a transgenic mouse strain with increasing number of generations. This eventually led to the complete abrogation of gene expression of the inserted Cre cDNA while still being detectable at the genomic level. Conversely, loss of Cre expression caused an incomplete or even complete lack of disruption for the protein under investigation. As Cre expression in the tissue of interest in most cases cannot be addressed in vivo during the course of a study, our findings implicate the possibility that individual tail-biopsy genotypes may not necessarily indicate the presence or absence of gene disruption. This indicates that sustained post hoc analyses in regards to efficacy of disruption for every single study group member may be required.

  7. Life-long Maternal Cafeteria Diet Promotes Tissue-Specific Morphological Changes in Male Offspring Adult Rats

    Directory of Open Access Journals (Sweden)

    CAROLYNE D.S. SANTOS

    Full Text Available ABSTRACT Here, we evaluated whether the exposure of rats to a cafeteria diet pre- and/or post-weaning, alters histological characteristics in the White Adipose Tissue (WAT, Brown Adipose Tissue (BAT, and liver of adult male offspring. Female Wistar rats were divided into Control (CTL; fed on standard rodent chow and Cafeteria (CAF; fed with the cafeteria diet throughout life, including pregnancy and lactation. After birth, only male offspring (F1 were maintained and received the CTL or CAF diets; originating four experimental groups: CTL-CTLF1; CTL-CAFF1; CAF-CTLF1; CAF-CAFF1. Data of biometrics, metabolic parameters, liver, BAT and WAT histology were assessed and integrated using the Principal Component Analysis (PCA. According to PCA analysis worse metabolic and biometric characteristics in adulthood are associated with the post-weaning CAF diet compared to pre and post weaning CAF diet. Thus, the CTL-CAFF1 group showed obesity, higher deposition of fat in the liver and BAT and high fasting plasma levels of glucose, triglycerides and cholesterol. Interestingly, the association between pre and post-weaning CAF diet attenuated the obesity and improved the plasma levels of glucose and triglycerides compared to CTL-CAFF1 without avoiding the higher lipid accumulation in BAT and in liver, suggesting that the impact of maternal CAF diet is tissue-specific.

  8. Salt-Induced Tissue-Specific Cytosine Methylation Downregulates Expression of HKT Genes in Contrasting Wheat (Triticum aestivum L.) Genotypes.

    Science.gov (United States)

    Kumar, Suresh; Beena, Ananda Sankara; Awana, Monika; Singh, Archana

    2017-04-01

    Plants have evolved several strategies, including regulation of genes through epigenetic modifications, to cope with environmental stresses. DNA methylation is dynamically regulated through the methylation and demethylation of cytosine in response to environmental perturbations. High-affinity potassium transporters (HKTs) have accounted for the homeostasis of sodium and potassium ions in plants under salt stress. Wheat (Triticum aestivum L.) is sensitive to soil salinity, which impedes its growth and development, resulting in decreased productivity. The differential expression of HKTs has been reported to confer tolerance to salt stress in plants. In this study, we investigated variations in cytosine methylation and their effects on the expression of HKT genes in contrasting wheat genotypes under salt stress. We observed a genotype- and tissue-specific increase in cytosine methylation induced by NaCl stress that downregulated the expression of TaHKT2;1 and TaHKT2;3 in the shoot and root tissues of Kharchia-65, thereby contributing to its improved salt-tolerance ability. Although TaHKT1;4 was expressed only in roots and was downregulated under the stress in salt-tolerant genotypes, it was not regulated through variations in cytosine methylation. Thus, understanding epigenetic regulation and the function of HKTs would enable an improvement in salt tolerance and the development of salt-tolerant crops.

  9. A High-Dimensional Atlas of Human T Cell Diversity Reveals Tissue-Specific Trafficking and Cytokine Signatures.

    Science.gov (United States)

    Wong, Michael Thomas; Ong, David Eng Hui; Lim, Frances Sheau Huei; Teng, Karen Wei Weng; McGovern, Naomi; Narayanan, Sriram; Ho, Wen Qi; Cerny, Daniela; Tan, Henry Kun Kiaang; Anicete, Rosslyn; Tan, Bien Keem; Lim, Tony Kiat Hon; Chan, Chung Yip; Cheow, Peng Chung; Lee, Ser Yee; Takano, Angela; Tan, Eng-Huat; Tam, John Kit Chung; Tan, Ern Yu; Chan, Jerry Kok Yen; Fink, Katja; Bertoletti, Antonio; Ginhoux, Florent; Curotto de Lafaille, Maria Alicia; Newell, Evan William

    2016-08-16

    Depending on the tissue microenvironment, T cells can differentiate into highly diverse subsets expressing unique trafficking receptors and cytokines. Studies of human lymphocytes have primarily focused on a limited number of parameters in blood, representing an incomplete view of the human immune system. Here, we have utilized mass cytometry to simultaneously analyze T cell trafficking and functional markers across eight different human tissues, including blood, lymphoid, and non-lymphoid tissues. These data have revealed that combinatorial expression of trafficking receptors and cytokines better defines tissue specificity. Notably, we identified numerous T helper cell subsets with overlapping cytokine expression, but only specific cytokine combinations are secreted regardless of tissue type. This indicates that T cell lineages defined in mouse models cannot be clearly distinguished in humans. Overall, our data uncover a plethora of tissue immune signatures and provide a systemic map of how T cell phenotypes are altered throughout the human body. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Tissue specificity of 8-prenylnaringenin: protection from ovariectomy induced bone loss with minimal trophic effects on the uterus.

    Science.gov (United States)

    Hümpel, Michael; Isaksson, Päivi; Schaefer, Olaf; Kaufmann, Ulrike; Ciana, Paolo; Maggi, Adriana; Schleuning, Wolf-Dieter

    2005-11-01

    Plant secondary metabolites with estrogenic activity (phyto-estrogens) have been studied in the past as a potential alternative to classical hormone-replacement therapy (HRT) in menopausal women. No final verdict on the efficacy of soy or red clover based pharmaceutical preparations has been reached despite numerous clinical studies. We have studied the novel and most potent phyto-estrogen 8-prenylnaringenin (8-PN) in adult ovariectomized rats, an established animal model to mimic hormone dependent osteoporosis in menopausal women. Our results demonstrate that 8-PN can completely protect from ovariectomy induced bone-loss while exhibiting minimal, (dose independent) trophic effects on uterus and endometrium. It is estimated that at equivalent bone protective doses of 17beta-estradiol and 8-PN, the phyto-estrogen has a 10-fold lower stimulatory effect on uterus and endometrium. The bone tissue specific effect of 8-PN was confirmed in a transgenic reporter mouse model (ERE-Luc mice). Here we also found pronounced estrogenic activity in prostate. Present results add important aspects to the pharmacological profile of 8-PN and position this compound as an interesting alternative new candidate for treatment of peri- and postmenopausal symptoms.

  11. Molecular Characterization and Tissue-specific Expression of a Novel FKBP38 Gene in the Cashmere Goat (

    Directory of Open Access Journals (Sweden)

    X. Zheng

    2012-06-01

    Full Text Available As a member of a subclass of immunophilins, it is controversial that FKBP38 acts an upstream regulator of mTOR signaling pathway, which control the process of cell-growth, proliferation and differentiation. In order to explore the relationship between FKBP38 and mTOR in the Cashmere goat (Capra hircus cells, a full-length cDNA was cloned (GenBank accession number JF714970 and expression pattern was analyzed. The cloned FKBP38 gene is 1,248 bp in length, containing an open reading frame (ORF from nucleotide 13 to 1,248 which encodes 411 amino acids, and 12 nucleotides in front of the initiation codon. The full cDNA sequence shares 98% identity with cattle, 94% with horse and 90% with human. The putative amino acid sequence shows the higher homology which is 98%, 97% and 94%, correspondingly. The bioinformatics analysis showed that FKBP38 contained a FKBP_C domain, two TPR domains and a TM domain. Psite analysis suggested that the ORF encoding protein contained a leucine-zipper pattern and a Prenyl group binding site (CAAX box. Tissue-specific expression analysis was performed by semi-quantitative RT-PCR and showed that the FKBP38 expression was detected in all the tested tissues and the highest level of mRNA accumulation was detected in testis, suggesting that FKBP38 plays an important role in goat cells.

  12. Composites

    OpenAIRE

    Zhao, Hanqing; Guo, Yuanzheng

    2014-01-01

    This thesis was a literature study concerning composites. With composites becoming increasingly popular in various areas such as aerospace industry and construction, the research about composites has a significant meaning accordingly. This thesis was aim at introducing some basic information of polymer matrix composites including raw mate-rial, processing, testing, applications and recycling to make a rough understanding of this kind of material for readers. Polymeric matrices, fillers,...

  13. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2011-01-01

    Strategies are open compositions to be realised by improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound files will in some cases only provide a few minutes' sample. Please DOWNLOAD them to hear them in full...

  14. Composition

    DEFF Research Database (Denmark)

    2014-01-01

    Memory Pieces are open compositions to be realised solo by an improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound files will in some cases only provide a few minutes' sample. Please DOWNLOAD them to hear them...

  15. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2010-01-01

    New Year is an open composition to be realised by improvising musicians. It is included in "From the Danish Seasons" (see under this title). See more about my composition practise in the entry "Composition - General Introduction". This work is licensed under a Creative Commons "by-nc" License. You...

  16. Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression.

    Directory of Open Access Journals (Sweden)

    Matthew S Hestand

    Full Text Available Cellular mechanisms that achieve protein diversity in eukaryotes are multifaceted, including transcriptional components such as RNA splicing. Through alternative splicing, a single protein-coding gene can generate multiple mRNA transcripts and protein isoforms, some of which are tissue-specific. We have conducted qualitative and quantitative analyses of the Bodymap 2.0 messenger RNA-sequencing data from 16 human tissue samples and identified 209,363 splice junctions. Of these, 22,231 (10.6% were not previously annotated and 21,650 (10.3% were expressed in a tissue-restricted pattern. Tissue-restricted alternative splicing was found to be widespread, with approximately 65% of expressed multi-exon genes containing at least one tissue-specific splice junction. Interestingly, we observed many tissue-specific splice junctions not only in genes expressed in one or a few tissues, but also from gene loci with a broad pattern of expression.

  17. Predicting sediment sorption coefficients for linear alkylbenzenesulfonate congeners from polyacrylate-water partition coefficients at different salinities.

    NARCIS (Netherlands)

    Rico Rico, A.; Droge, S.T.J.; Hermens, J.L.M.

    2010-01-01

    The effect of the molecular structure and the salinity on the sorption of the anionic surfactant linear alkylbenzenesulfonate (LAS) to marine sediment has been studied. The analysis of several individual LAS congeners in seawater and of one specific LAS congener at different dilutions of seawater

  18. Process-diagnostic patterns of chlorobiphenyl congeners in two radiochronologically characterized sediment cores from the northern Baffin Bay

    DEFF Research Database (Denmark)

    Gustafsson, O.; Axelman, J.; Broman, D.

    2001-01-01

    , but distinctly different, sink processes acting on the PCB pool. The relative abundance of light-to-heavy congeners, in mid-shelf marine sediments of similar ages, between 40 degreesN and 76 degreesN latitude suggests a northward dilution of PCBs which is stronger attenuated for heavier congeners, consistent...

  19. Micelles versus Ribbons: How Congeners Drive the Self-Assembly of Acidic Sophorolipid Biosurfactants.

    Science.gov (United States)

    Dhasaiyan, Prabhu; Le Griel, Patrick; Roelants, Sophie; Redant, Emile; Van Bogaert, Inge N A; Prevost, Sylvain; Prasad, B L V; Baccile, Niki

    2017-03-17

    Sophorolipids (SLs), a class of microbially derived biosurfactants, are reported by different research groups to have different self-assembled structures (either micelles or giant ribbons) under the same conditions. Here we explore the reasons behind these contradictory results and attribute these differences to the role of specific congeners that are present in minute quantities. We show that a sample composed of a majority of oleic acid (C18:1) sophorolipid in the presence of only 0.5 % (or more) of congeners with stearic acid (C18:0) or linoleic acid (C18:2) results in the formation of micelles that are stable over long periods of time. Conversely, the presence of only 10 to 15 % of congeners with a stearic acid chain gives fibrillar structures instead of micelles. To study the mechanisms responsible, oleic acid SLs devoid of any other congeners were prepared. Very interestingly, this sample can self-assemble into either micelles or fibers depending on minute modifications to the self-assembly conditions. The findings are supported by light scattering, small-angle X-ray scattering, transmission electron microscopy under cryogenic conditions, high-pressure liquid chromatography, and NMR spectroscopy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Effect of highly bioaccumulated polychlorinated biphenyl congeners on estrogen and androgen receptor activity

    DEFF Research Database (Denmark)

    Bonefeld-Jørgensen, E.C.; Andersen, H. R.; Rasmussen, T.H.

    2001-01-01

    -tk-CAT) analysis the three congeners exhibited a significantly estrogen receptor-ligand mediated decrease of the chloramphenicol transferase activity in both control and 10 nM 17 beta -estradiol induced MCF-7 cells. In addition, PCB # 138 elicited a dose-dependent antagonistic effect on androgen receptor activity...

  1. Elevated PCDD/F levels and distinctive PCDD/F congener profiles in free range eggs.

    Science.gov (United States)

    Hsu, Jing-Fang; Chen, Chun; Liao, Pao-Chi

    2010-07-14

    Chicken eggs are one of the most important foods in the human diet all over the world, and the demand for eggs from free range hens has steadily increased. Congener-specific analyses of 17 polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were performed on 6 free range and 12 caged chicken egg samples collected in Taiwan. The mean level of PCDD/Fs in the free range egg samples was 5.7 (1.79/0.314) times higher than those in the caged egg samples. Principle component analysis revealed that at least three characteristic patterns of PCDD/F congener were observed among the 18 egg samples. The different PCDD/F congener patterns between free range and caged egg samples may reflect distinctive exposure scenarios among the free range and caged hens. We suggest that the differences of PCDD/F levels and congener patterns between free range and caged egg samples give rise to the issues related to the safety of eating free range chicken eggs. The present data may provide useful information for further investigation of the possible PCDD/F sources in the contaminated free range eggs.

  2. Adsorption of Ten Microcystin Congeners to Common Laboratory-Ware Is Solvent and Surface Dependent

    Directory of Open Access Journals (Sweden)

    Stefan Altaner

    2017-04-01

    Full Text Available Cyanobacteria can produce heptapetides called microcystins (MC which are harmful to humans due to their ability to inhibit cellular protein phosphatases. Quantitation of these toxins can be hampered by their adsorption to common laboratory-ware during sample processing and analysis. Because of their structural diversity (>100 congeners and different physico-chemical properties, they vary in their adsorption to surfaces. In this study, the adsorption of ten different MC congeners (encompassing non-arginated to doubly-arginated congeners to common laboratory-ware was assessed using different solvent combinations. Sample handling steps were mimicked with glass and polypropylene pipettes and vials with increasing methanol concentrations at two pH levels, before analysis by liquid chromatography-tandem mass spectrometry. We demonstrated that MC adsorb to polypropylene surfaces irrespective of pH. After eight successive pipet actions using polypropylene tips ca. 20% of the MC were lost to the surface material, which increased to 25%–40% when solutions were acidified. The observed loss was alleviated by changing the methanol (MeOH concentration in the final solvent. The required MeOH concentration varied depending on which congener was present. Microcystins only adsorbed to glass pipettes (loss up to 30% after eight pipet actions when in acidified aqueous solutions. The latter appeared largely dependent on the presence of ionizable groups, such as arginine residues.

  3. LMNA E82K mutation activates FAS and mitochondrial pathways of apoptosis in heart tissue specific transgenic mice.

    Directory of Open Access Journals (Sweden)

    Dan Lu

    Full Text Available The lamin A/C (LMNA, nuclear intermediate filament proteins, is a basic component of the nuclear lamina. Mutations in LMNA are associated with a broad range of laminopathies, congenital diseases affecting tissue regeneration and homeostasis. Heart tissue specific transgenic mice of human LMNA E82K, a mutation causing dilated cardiomyopathy, were generated. Lmna(E82K transgenic mouse lines exhibited thin-walled, dilated left and right ventricles, a progressive decrease of contractile function assessed by echocardiography. Abnormalities of the conduction system, myocytes disarray, collagen accumulation and increased levels of B-type natriuretic peptide (BNP, procollagen type III α1 (Col3α1 and skeletal muscle actin α1 (Actα1 were detected in the hearts of Lmna(E82K transgenic mice. The LMNA E82K mutation caused mislocation of LMNA in the nucleus and swollen mitochondria with loss of critae, together with the loss of nuclear envelope integrity. Most interestingly, we found that the level of apoptosis was 8.5-fold higher in the Lmna(E82K transgenic mice than that of non-transgenic (NTG mice. In the presence of the LMNA E82K, both of FAS and mitochondrial pathways of apoptosis were activated consistent with the increase of FAS expression, the release of cytochrome c from mitochondria to cytosol and activation of caspase-8, -9 and -3. Our results suggested that the apoptosis, at least for the LMNA E82K or the mutations in the rod region of Lamin A/C, might be an important mechanism causing continuous loss of myocytes and lead to myocardial dysfunction. It could be a potential therapeutic means to suppress and/or prevent inappropriate cardiac cell death in patients carrying LMNA mutation.

  4. Methylation of the promoter region may be involved in tissue-specific expression of the mouse terminal deoxynucleotidyl transferase gene.

    Science.gov (United States)

    Nourrit, F; Coquilleau, I; D'Andon, M F; Rougeon, F; Doyen, N

    1999-09-17

    The terminal deoxynucleotidyl transferase gene (TdT) is expressed in mice only in early B and T lymphoid precursors a few days after birth. Transactivating factors have been shown to contribute to the lymphoid specific expression of TdT, but they do not account entirely for the restriction of its expression to early precursors. Since tissue-specific expression can be modulated by other mechanisms such as DNA methylation and DNA accessibility, we evaluated the methylation pattern of the TdT gene in various expressing and non-expressing tissues and cell lines. Lymphoid and non-lymphoid organs differed significantly in their methylation profiles. In the thymus nearly complete demethylation of a Hha I site in the promoter was associated with high levels of TdT transcription. There was similar, but weaker demethylation of the TdT promoter in bone marrow, possibly due to the presence of a few TdT expressing B cell precursors. The same methylation status was also associated with TdT expression in different B and T cell lines. Kinetic studies of TdT gene demethylation and TdT transcription during thymus development showed that changes in methylation status were also involved in the differential expression of TdT in fetal and adult life. Footprinting experiments revealed the existence of three regions specifically protected by nuclear extracts from TdT -expressing cells. Together, these results suggest that promoter demethylation is involved in the control of TdT expression and implicate new promoter regions in this regulation. Copyright 1999 Academic Press.

  5. Plasma 25-Hydroxyvitamin D Is Related to Protein Signaling Involved in Glucose Homeostasis in a Tissue-Specific Manner

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    Lewan Parker

    2016-10-01

    Full Text Available Vitamin D has been suggested to play a role in glucose metabolism. However, previous findings are contradictory and mechanistic pathways remain unclear. We examined the relationship between plasma 25-hydroxyvitamin D (25(OHD, insulin sensitivity, and insulin signaling in skeletal muscle and adipose tissue. Seventeen healthy adults (Body mass index: 26 ± 4; Age: 30 ± 12 years underwent a hyperinsulinemic-euglycemic clamp, and resting skeletal muscle and adipose tissue biopsies. In this cohort, the plasma 25(OHD concentration was not associated with insulin sensitivity (r = 0.19, p = 0.56. However, higher plasma 25(OHD concentrations correlated with lower phosphorylation of glycogen synthase kinase-3 (GSK-3 αSer21 and βSer9 in skeletal muscle (r = −0.66, p = 0.015 and r = −0.53, p = 0.06, respectively and higher GSK-3 αSer21 and βSer9 phosphorylation in adipose tissue (r = 0.82, p < 0.01 and r = 0.62, p = 0.042, respectively. Furthermore, higher plasma 25(OHD concentrations were associated with greater phosphorylation of both protein kinase-B (AktSer473 (r = 0.78, p < 0.001 and insulin receptor substrate-1 (IRS-1Ser312 (r = 0.71, p = 0.01 in adipose tissue. No associations were found between plasma 25(OHD concentration and IRS-1Tyr612 phosphorylation in skeletal muscle and adipose tissue. The divergent findings between muscle and adipose tissue with regard to the association between 25(OHD and insulin signaling proteins may suggest a tissue-specific interaction with varying effects on glucose homeostasis. Further research is required to elucidate the physiological relevance of 25(OHD in each tissue.

  6. Timing of Tissue-specific Cell Division Requires a Differential Onset of Zygotic Transcription during Metazoan Embryogenesis*

    Science.gov (United States)

    Wong, Ming-Kin; Guan, Daogang; Ng, Kaoru Hon Chun; Ho, Vincy Wing Sze; An, Xiaomeng; Li, Runsheng; Ren, Xiaoliang

    2016-01-01

    Metazoan development demands not only precise cell fate differentiation but also accurate timing of cell division to ensure proper development. How cell divisions are temporally coordinated during development is poorly understood. Caenorhabditis elegans embryogenesis provides an excellent opportunity to study this coordination due to its invariant development and widespread division asynchronies. One of the most pronounced asynchronies is a significant delay of cell division in two endoderm progenitor cells, Ea and Ep, hereafter referred to as E2, relative to its cousins that mainly develop into mesoderm organs and tissues. To unravel the genetic control over the endoderm-specific E2 division timing, a total of 822 essential and conserved genes were knocked down using RNAi followed by quantification of cell cycle lengths using in toto imaging of C. elegans embryogenesis and automated lineage. Intriguingly, knockdown of numerous genes encoding the components of general transcription pathway or its regulatory factors leads to a significant reduction in the E2 cell cycle length but an increase in cell cycle length of the remaining cells, indicating a differential requirement of transcription for division timing between the two. Analysis of lineage-specific RNA-seq data demonstrates an earlier onset of transcription in endoderm than in other germ layers, the timing of which coincides with the birth of E2, supporting the notion that the endoderm-specific delay in E2 division timing demands robust zygotic transcription. The reduction in E2 cell cycle length is frequently associated with cell migration defect and gastrulation failure. The results suggest that a tissue-specific transcriptional activation is required to coordinate fate differentiation, division timing, and cell migration to ensure proper development. PMID:27056332

  7. A new method to determine tissue specific tissue factor thrombomodulin activities: endotoxin and particulate air pollution induced disbalance

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    Gerlofs-Nijland Miriam E

    2008-10-01

    Full Text Available Abstract Background Increase in tissue factor (TF and loss in thrombomodulin (TM antigen levels has been described in various inflammatory disorders. The functional consequences of such changes in antigen concentrations in the coagulation balance are, however, not known. This study was designed to assess the consequences of inflammation-driven organ specific functional properties of the procoagulant response. Methods Tissue specific procoagulant activity was assessed by adding tissue homogenate to normal human pool plasma and recording of the thrombin generation curve. The new technique was subsequently applied on two inflammation driven animal models: 1 mouse lipopolysaccharide (LPS induced endotoxemia and 2 spontaneously hypertensive rats exposed to environmental air pollution (particulate matter (PM. Results Addition of lung tissue from untreated animals to human plasma suppressed the endogenous thrombin potential (ETP (175 ± 61 vs. 1437 ± 112 nM.min for control. This inhibitory effect was due to TM, because a it was absent in protein C deficient plasma and b lungs from TMpro/pro mice allowed full thrombin generation (ETP: 1686 ± 209 nM.min. The inhibitory effect of TM was lost after LPS administration to mice, which induced TF activity in lungs of C57Bl/6 mice as well as increased the ETP (941 ± 523 vs. 194 ± 159 nM.min for control. Another pro-inflammatory stimulus, PM dose-dependently increased TF in the lungs of spontaneously hypertensive rats at 4 and 48 hours after PM exposure. The ETP increased up to 48 hours at the highest concentration of PM (1441 ± 289 nM.min vs. saline: 164 ± 64 nM.min, p Conclusion Inflammation associated procoagulant effects in tissues are dependent on variations in activity of the TF-TM balance. The application of these novel organ specific functional assays is a useful tool to monitor inflammation-driven shifts in the coagulation balance within animal or human tissues.

  8. Tissue-Specific Transcript Profiling for ABC Transporters in the Sequestering Larvae of the Phytophagous Leaf Beetle Chrysomela populi

    Science.gov (United States)

    Gretscher, René R.; Groth, Marco; Boland, Wilhelm; Burse, Antje

    2014-01-01

    Background Insects evolved ingenious adaptations to use extraordinary food sources. Particularly, the diet of herbivores enriched with noxious plant secondary metabolites requires detoxification mechanisms. Sequestration, which involves the uptake, transfer, and concentration of occasionally modified phytochemicals into specialized tissues or hemolymph, is one of the most successful detoxification strategies found in most insect orders. Due to the ability of ATP-binding cassette (ABC) carriers to transport a wide range of molecules including phytochemicals and xenobiotics, it is highly likely that they play a role in this sequestration process. To shed light on the role of ABC proteins in sequestration, we describe an inventory of putative ABC transporters in various tissues in the sequestering juvenile poplar leaf beetle, Chrysomela populi. Results In the transcriptome of C. populi, we predicted 65 ABC transporters. To link the proteins with a possible function, we performed comparative phylogenetic analyses with ABC transporters of other insects and of humans. While tissue-specific profiling of each ABC transporter subfamily suggests that ABCB, C and G influence the plant metabolite absorption in the gut, ABCC with 14 members is the preferred subfamily responsible for the excretion of these metabolites via Malpighian tubules. Moreover, salicin, which is sequestered from poplar plants, is translocated into the defensive glands for further deterrent production. In these glands and among all identified ABC transporters, an exceptionally high transcript level was observed only for Cpabc35 (Cpmrp). RNAi revealed the deficiency of other ABC pumps to compensate the function of CpABC35, demonstrating its key role during sequestration. Conclusion We provide the first comprehensive phylogenetic study of the ABC family in a phytophagous beetle species. RNA-seq data from different larval tissues propose the importance of ABC pumps to achieve a homeostasis of plant

  9. Tissue-specific transcript profiling for ABC transporters in the sequestering larvae of the phytophagous leaf beetle Chrysomela populi.

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    Anja S Strauss

    Full Text Available Insects evolved ingenious adaptations to use extraordinary food sources. Particularly, the diet of herbivores enriched with noxious plant secondary metabolites requires detoxification mechanisms. Sequestration, which involves the uptake, transfer, and concentration of occasionally modified phytochemicals into specialized tissues or hemolymph, is one of the most successful detoxification strategies found in most insect orders. Due to the ability of ATP-binding cassette (ABC carriers to transport a wide range of molecules including phytochemicals and xenobiotics, it is highly likely that they play a role in this sequestration process. To shed light on the role of ABC proteins in sequestration, we describe an inventory of putative ABC transporters in various tissues in the sequestering juvenile poplar leaf beetle, Chrysomela populi.In the transcriptome of C. populi, we predicted 65 ABC transporters. To link the proteins with a possible function, we performed comparative phylogenetic analyses with ABC transporters of other insects and of humans. While tissue-specific profiling of each ABC transporter subfamily suggests that ABCB, C and G influence the plant metabolite absorption in the gut, ABCC with 14 members is the preferred subfamily responsible for the excretion of these metabolites via Malpighian tubules. Moreover, salicin, which is sequestered from poplar plants, is translocated into the defensive glands for further deterrent production. In these glands and among all identified ABC transporters, an exceptionally high transcript level was observed only for Cpabc35 (Cpmrp. RNAi revealed the deficiency of other ABC pumps to compensate the function of CpABC35, demonstrating its key role during sequestration.We provide the first comprehensive phylogenetic study of the ABC family in a phytophagous beetle species. RNA-seq data from different larval tissues propose the importance of ABC pumps to achieve a homeostasis of plant-derived compounds and

  10. Tissue-specific transcript profiling for ABC transporters in the sequestering larvae of the phytophagous leaf beetle Chrysomela populi.

    Science.gov (United States)

    Strauss, Anja S; Wang, Ding; Stock, Magdalena; Gretscher, René R; Groth, Marco; Boland, Wilhelm; Burse, Antje

    2014-01-01

    Insects evolved ingenious adaptations to use extraordinary food sources. Particularly, the diet of herbivores enriched with noxious plant secondary metabolites requires detoxification mechanisms. Sequestration, which involves the uptake, transfer, and concentration of occasionally modified phytochemicals into specialized tissues or hemolymph, is one of the most successful detoxification strategies found in most insect orders. Due to the ability of ATP-binding cassette (ABC) carriers to transport a wide range of molecules including phytochemicals and xenobiotics, it is highly likely that they play a role in this sequestration process. To shed light on the role of ABC proteins in sequestration, we describe an inventory of putative ABC transporters in various tissues in the sequestering juvenile poplar leaf beetle, Chrysomela populi. In the transcriptome of C. populi, we predicted 65 ABC transporters. To link the proteins with a possible function, we performed comparative phylogenetic analyses with ABC transporters of other insects and of humans. While tissue-specific profiling of each ABC transporter subfamily suggests that ABCB, C and G influence the plant metabolite absorption in the gut, ABCC with 14 members is the preferred subfamily responsible for the excretion of these metabolites via Malpighian tubules. Moreover, salicin, which is sequestered from poplar plants, is translocated into the defensive glands for further deterrent production. In these glands and among all identified ABC transporters, an exceptionally high transcript level was observed only for Cpabc35 (Cpmrp). RNAi revealed the deficiency of other ABC pumps to compensate the function of CpABC35, demonstrating its key role during sequestration. We provide the first comprehensive phylogenetic study of the ABC family in a phytophagous beetle species. RNA-seq data from different larval tissues propose the importance of ABC pumps to achieve a homeostasis of plant-derived compounds and offer a basis for

  11. Tissue-specific and neural activity-regulated expression of human BDNF gene in BAC transgenic mice

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    Palm Kaia

    2009-06-01

    Full Text Available Abstract Background Brain-derived neurotrophic factor (BDNF is a small secreted protein that has important roles in the developing and adult nervous system. Altered expression or changes in the regulation of the BDNF gene have been implicated in a variety of human nervous system disorders. Although regulation of the rodent BDNF gene has been extensively investigated, in vivo studies regarding the human BDNF gene are largely limited to postmortem analysis. Bacterial artificial chromosome (BAC transgenic mice harboring the human BDNF gene and its regulatory flanking sequences constitute a useful tool for studying human BDNF gene regulation and for identification of therapeutic compounds modulating BDNF expression. Results In this study we have generated and analyzed BAC transgenic mice carrying 168 kb of the human BDNF locus modified such that BDNF coding sequence was replaced with the sequence of a fusion protein consisting of N-terminal BDNF and the enhanced green fluorescent protein (EGFP. The human BDNF-BAC construct containing all BDNF 5' exons preceded by different promoters recapitulated the expression of endogenous BDNF mRNA in the brain and several non-neural tissues of transgenic mice. All different 5' exon-specific BDNF-EGFP alternative transcripts were expressed from the transgenic human BDNF-BAC construct, resembling the expression of endogenous BDNF. Furthermore, BDNF-EGFP mRNA was induced upon treatment with kainic acid in a promotor-specific manner, similarly to that of the endogenous mouse BDNF mRNA. Conclusion Genomic region covering 67 kb of human BDNF gene, 84 kb of upstream and 17 kb of downstream sequences is sufficient to drive tissue-specific and kainic acid-induced expression of the reporter gene in transgenic mice. The pattern of expression of the transgene is highly similar to BDNF gene expression in mouse and human. This is the first study to show that human BDNF gene is regulated by neural activity.

  12. Effects of adeno-associated virus serotype and tissue-specific expression on circulating biomarkers of propionic acidemia.

    Science.gov (United States)

    Guenzel, Adam J; Hillestad, Matthew L; Matern, Dietrich; Barry, Michael A

    2014-09-01

    Propionic acidemia (PA) is an autosomal recessive inborn error of metabolism caused by deficiency of propionyl-CoA carboxylase (PCC). This enzyme is composed of six PCCA and six PCCB subunits and mediates a critical step in catabolism of odd chain fatty acids and certain amino acids. Current treatment options for PA are limited to stringent dietary restriction of protein consumption and some patients undergo elective liver transplantation. We previously generated a hypomorphic model of PA, designated Pcca(-/-)(A138T), with 2% of wild-type enzyme activity that mimics many aspects of the human disease. In this study, we used the differing tissue tropisms of adeno-associated virus (AAV) to probe the ability of liver or muscle-directed gene therapy to treat systemic aspects of this disease that affects many cell types. Systemic therapy with muscle-biased AAV1, liver-biased AAV8, and broadly tropic AAVrh10 mediated significant biochemical corrections in circulating propionylcarnitine (C3) and methyl citrate by all vectors. The innate tissue bias of AAV1 and AAV8 gene expression was made more specific by the use of muscle-specific muscle creatine kinase (specifically MCK6) and hepatocyte-specific transthyretin (TTR) promoters, respectively. Under these targeted conditions, both vectors mediated significant long-term correction of circulating metabolites, demonstrating that correction of muscle and likely other tissue types in addition to liver is necessary to fully correct pathology caused by PA. Liver-specific AAV8-TTR-PCCA mediated better correction than AAV1-MCK-PCCA. These data suggest that targeted gene therapy may be a viable alternative to liver transplantation for PA. They also demonstrate the effects of tissue-specific and broad gene therapy on a cell autonomous systemic genetic disease.

  13. Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn.

    Science.gov (United States)

    Herzog, Emilie M; Eggink, Alex J; Willemsen, Sten P; Slieker, Roderick C; Wijnands, Kim P J; Felix, Janine F; Chen, Jun; Stubbs, Andrew; van der Spek, Peter J; van Meurs, Joyce B; Steegers-Theunissen, Régine P M

    2017-10-01

    Preeclampsia (PE) carries increased risks of cardiovascular- and metabolic diseases in mothers and offspring during the life course. While the severe early-onset PE (EOPE) phenotype originates from impaired placentation in early pregnancy, late-onset PE (LOPE) is in particular associated with pre-existing maternal cardiovascular- and metabolic risk factors. We hypothesize that PE is associated with altered epigenetic programming of placental and fetal tissues and that these epigenetic changes might elucidate the increased cardiovascular- and metabolic disease susceptibility in PE offspring. A nested case-control study was conducted in The Rotterdam Periconceptional Cohort comprising 13 EOPE, 16 LOPE, and three control groups of 36 uncomplicated pregnancies, 27 normotensive fetal growth restricted and 20 normotensive preterm birth (PTB) complicated pregnancies. Placental tissue, newborn umbilical cord white blood cells (UC-WBC) and umbilical vein endothelial cells were collected and DNA methylation of cytosine-guanine dinucleotides was measured by the Illumina HumanMethylation450K BeadChip. An epigenome-wide analysis was performed by using multiple linear regression models. Epigenome-wide tissue-specific analysis between EOPE and PTB controls revealed 5001 mostly hypermethylated differentially methylated positions (DMPs) in UC-WBC and 869 mostly hypomethylated DMPs in placental tissue, situated in or close to genes associated with cardiovascular-metabolic developmental pathways. This study shows differential methylation in UC-WBC and placental tissue in EOPE as compared to PTB, identifying DMPs that are associated with cardiovascular system pathways. Future studies should examine these loci and pathways in more detail to elucidate the associations between prenatal PE exposure and the cardiovascular disease risk in offspring. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity.

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    Paulo M F Cunha

    2010-07-01

    Full Text Available Understanding how complex patterns of temporal and spatial expression are regulated is central to deciphering genetic programs that drive development. Gene expression is initiated through the action of transcription factors and their cofactors converging on enhancer elements leading to a defined activity. Specific constellations of combinatorial occupancy are therefore often conceptualized as rigid binding codes that give rise to a common output of spatio-temporal expression. Here, we assessed this assumption using the regulatory input of two essential transcription factors within the Drosophila myogenic network. Mutations in either Myocyte enhancing factor 2 (Mef2 or the zinc-finger transcription factor lame duck (lmd lead to very similar defects in myoblast fusion, yet the underlying molecular mechanism for this shared phenotype is not understood. Using a combination of ChIP-on-chip analysis and expression profiling of loss-of-function mutants, we obtained a global view of the regulatory input of both factors during development. The majority of Lmd-bound enhancers are co-bound by Mef2, representing a subset of Mef2's transcriptional input during these stages of development. Systematic analyses of the regulatory contribution of both factors demonstrate diverse regulatory roles, despite their co-occupancy of shared enhancer elements. These results indicate that Lmd is a tissue-specific modulator of Mef2 activity, acting as both a transcriptional activator and repressor, which has important implications for myogenesis. More generally, this study demonstrates considerable flexibility in the regulatory output of two factors, leading to additive, cooperative, and repressive modes of co-regulation.

  15. Sex- and Tissue-Specific Expression Profiles of Odorant Binding Protein and Chemosensory Protein Genes in Bradysia odoriphaga (Diptera: Sciaridae

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    Yunhe Zhao

    2018-04-01

    Full Text Available Bradysia odoriphaga is an agricultural pest insect affecting the production of Chinese chive and other liliaceous vegetables in China, and it is significantly attracted by sex pheromones and the volatiles derived from host plants. Despite verification of this chemosensory behavior, however, it is still unknown how B. odoriphaga recognizes these volatile compounds on the molecular level. Many of odorant binding proteins (OBPs and chemosensory proteins (CSPs play crucial roles in olfactory perception. Here, we identified 49 OBP and 5 CSP genes from the antennae and body transcriptomes of female and male adults of B. odoriphaga, respectively. Sequence alignment and phylogenetic analysis among Dipteran OBPs and CSPs were analyzed. The sex- and tissue-specific expression profiles of 54 putative chemosensory genes among different tissues were investigated by quantitative real-time PCR (qRT-PCR. qRT-PCR analysis results suggested that 22 OBP and 3 CSP genes were enriched in the antennae, indicating they might be essential for detection of general odorants and pheromones. Among these antennae-enriched genes, nine OBPs (BodoOBP2/4/6/8/12/13/20/28/33 were enriched in the male antennae and may play crucial roles in the detection of sex pheromones. Moreover, some OBP and CSP genes were enriched in non-antennae tissues, such as in the legs (BodoOBP3/9/19/21/34/35/38/39/45 and BodoCSP1, wings (BodoOBP17/30/32/37/44, abdomens and thoraxes (BodoOBP29/36, and heads (BodoOBP14/23/31 and BodoCSP2, suggesting that these genes might be involved in olfactory, gustatory, or other physiological processes. Our findings provide a starting point to facilitate functional research of these chemosensory genes in B. odoriphaga at the molecular level.

  16. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster.

    Science.gov (United States)

    Liu, Xiaochuan; Freitas, Jaime; Zheng, Dinghai; Oliveira, Marta S; Hoque, Mainul; Martins, Torcato; Henriques, Telmo; Tian, Bin; Moreira, Alexandra

    2017-12-01

    Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster , expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis -element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate. © 2017 Liu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  17. Tissue-specific regulation of CXCL9/10/11 chemokines in keratinocytes: Implications for oral inflammatory disease.

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    Alison Marshall

    Full Text Available The IFN-γ-inducible chemokines CXCL9, CXCL10, and CXCL11 play a key role in many inflammatory conditions, particularly those mediated by T cells. Therefore, the production of these chemokines in peripheral tissues could be instrumental in the pathophysiology of tissue-specific immunological diseases such as oral lichen planus (OLP. In the present study, we assessed the production of keratinocyte-derived CXCL9/10/11 under basal and inflammatory conditions and investigated whether these chemokines were involved in the pathogenesis of OLP. We used semi-quantitative PCR, ELISA, chemotaxis assays, and fluorescence-activated cell sorting (FACS to assess the expression and functional role of CXCL9/10/11 in oral keratinocytes (three strains of normal human oral keratinocytes (NHOK, and the H357 oral cancer cell line in the presence or absence of IFN-γ. CXCL9/10/11 were also assessed in tissues from normal patients and those with oral lichen planus (OLP. The time course study in oral keratinocytes treated with IFN-γ showed that expression of CXCL9/10/11 chemokines was significantly enhanced by IFN-γ in a time-dependent manner. In particular, CXCL10, a prominent chemokine that was overexpressed by IFN-γ-stimulated NHOK, was able to effectively recruit CD4 lymphocytes, mainly CD4+CD45RA- cells. Significantly higher levels of CXCL9/10/11 were found in tissues from patients with OLP compared to normal oral mucosa. Taken together, the results demonstrate that normal oral keratinocytes produce chemotactic molecules that mediate T cell recruitment. This study furthers understanding of chemokine production in oral keratinocytes and their role in the pathophysiology of oral mucosa, with particular relevance to OLP.

  18. New Therapeutic and Diagnostic Opportunities for Injured Tissue-Specific Targeting of Complement Inhibitors and Imaging Modalities

    Science.gov (United States)

    Holers, V. Michael; Tomlinson, Stephen; Kulik, Liudmila; Atkinson, Carl; Rohrer, Bärbel; Banda, Nirmal; Thurman, Joshua M.

    2016-01-01

    Despite substantial opportunity and commercial interest in developing drugs that modulate the complement system in a broad range of non-orphan indications, several obstacles remain to be overcome. Among these issues is the biophysical nature of complement proteins, whose circulating levels are typically very high and whose turnover rates are relatively rapid, especially in the setting of chronic inflammatory conditions. This situation necessitates the use of very high levels of therapeutic compounds in order to achieve both multi-pathway and multiple effector mechanism inhibition. In addition, one must avoid infectious complications or the systemic impairment of the other important physiological functions of complement. Herein we focus on the development of a novel therapeutic strategy based on injured tissue-specific targeting of complement inhibitors using the antigen-combining domains of a small subset of natural IgM antibodies, which as endogenous antibodies specifically recognize sites of local damage across a broad range of tissues and locally activate complement C3, resulting in C3 fragment covalent fixation. Because the use of such recombinant tissue-targeting inhibitors precludes the utility of measuring systemic levels of complement biomarkers or function, since a goal of this targeting strategy is to leave those processes intact and unimpeded, we also briefly describe a new method designed to quantitatively measure using imaging modalities the inhibition of generation of fixed C3 fragments at sites of inflammation/injury. In addition to the ability to determine whether complement activation is locally constrained with the use of inhibitors, there is also a broader application of this imaging approach to inflammatory and autoimmune diseases characterized by local complement activation. PMID:27282113

  19. Endogenous collagen peptide activation of CD1d-restricted NKT cells ameliorates tissue-specific inflammation in mice.

    Science.gov (United States)

    Liu, Yawei; Teige, Anna; Mondoc, Emma; Ibrahim, Saleh; Holmdahl, Rikard; Issazadeh-Navikas, Shohreh

    2011-01-01

    NKT cells in the mouse recognize antigen in the context of the MHC class I-like molecule CD1d and play an important role in peripheral tolerance and protection against autoimmune and other diseases. NKT cells are usually activated by CD1d-presented lipid antigens. However, peptide recognition in the context of CD1 has also been documented, although no self-peptide ligands have been reported to date. Here, we have identified an endogenous peptide that is presented by CD1d to activate mouse NKT cells. This peptide, the immunodominant epitope from mouse collagen type II (mCII707-721), was not associated with either MHC class I or II. Activation of CD1d-restricted mCII707-721-specific NKT cells was induced via TCR signaling and classical costimulation. In addition, mCII707-721-specific NKT cells induced T cell death through Fas/FasL, in an IL-17A-independent fashion. Moreover, mCII707-721-specific NKT cells suppressed a range of in vivo inflammatory conditions, including delayed-type hypersensitivity, antigen-induced airway inflammation, collagen-induced arthritis, and EAE, which were all ameliorated by mCII707-721 vaccination. The findings presented here offer new insight into the intrinsic roles of NKT cells in health and disease. Given the results, endogenous collagen peptide activators of NKT cells may offer promise as novel therapeutics in tissue-specific autoimmune and inflammatory diseases.

  20. Congener specificity in the accumulation of dioxins and dioxin-like compounds in zucchini plants grown hydroponically.

    Science.gov (United States)

    Inui, Hideyuki; Wakai, Taketo; Gion, Keiko; Yamazaki, Kiyoshi; Kim, Yun-Seok; Eun, Heesoo

    2011-01-01

    Zucchini cultivars Cucurbita pepo subsp. ovifera cv. Patty Green and subsp. pepo cv. Gold Rush were cultivated hydroponically in a nutrient solution supplemented with a mixture of dioxins and dioxin-like compounds. Patty Green and Gold Rush showed low and high accumulation of these compounds in the aerial parts respectively. In both cultivars, the accumulation of each congener negatively depended on its hydrophobicity. This suggests that desorption and solubilization were partly responsible for congener specificity of accumulation, since this was not found in soil experiments. In contrast, no clear difference in accumulation in the roots was observed between the cultivars, whereas the translocation factors, which are indicators of efficient translocation from the roots to the aerial parts, differed among the congeners hydrophobicity-dependently. There were positive correlations between accumulation in the roots and the hydrophobicity of the polychlorinated biphenyl congeners in both cultivars. These results indicate that translocation was also partly responsible for the congener specificity and accumulation concentrations.

  1. Bioaccumulation of PCBs in Arctic seabirds: influence of dietary exposure and congener biotransformation

    International Nuclear Information System (INIS)

    Borga, Katrine; Wolkers, Hans; Skaare, Janneche U.; Hop, Haakon; Muir, Derek C.G.; Gabrielsen, Geir W.

    2005-01-01

    Four seabird species and their prey (zooplankton or fish) were collected in the Barents Sea to determine how dietary exposure, cytochrome P450 (CYP) enzyme activities and sex influenced their hepatic PCB concentrations and accumulation patterns. Five males and five females from each seabird species (little auk (Alle alle), Bruennich's guillemot (Uria lomvia), black guillemot (Cepphus grylle) and black-legged kittiwake (Rissa tridactyla)) were analysed. PCB concentrations could not be explained directly by carbon source (δ 13 C) or trophic position (δ 15 N), but by a combination of dietary parameters (δ 13 C, δ 15 N, migratory pattern, age) and contaminant metabolism. Contrary to previous studies, the PCB pattern differed among seabirds, with a higher proportion of persistent congeners (% of PCB-153, R PCB-153 ) in black-legged kittiwake than in auks. The PCB pattern also differed among auks, with little auk as the most efficient biotransformer (highest R PCB-153 values of persistent congeners). Based on high R PCB-153 values, Bruennich's guillemot poorly metabolised ortho-meta-unsubstituted congeners, whereas black guillemot poorly metabolised meta-para unsubstituted congeners. Species-specific differences in PCB biotransformation were confirmed by metabolic indices, where PCB patterns in seabirds were adjusted for PCB pattern in prey. The relative contribution of ortho-meta-unsubstituted congeners to ΣPCBsdecreased with increasing EROD activity. There were no differences in PCB concentrations, PCB patterns or cytochrome P450 enzyme activities between males and females. CYP P450 activities (CYP1A- and CYP2B/3A-like: EROD and testosterone 6β-hydroxylation, respectively) were low and did not correlate with concentrations of non- or mono-ortho Cl-substituted PCBs (NO- and MO-PCBs), or with total toxic equivalent concentrations (TEQs) for dioxin-like effects of NO- and MO-PCBs. - Contaminant patterns is linked to phylogeny and species-specific differences in

  2. Tissue-specific analysis of glycogen synthase kinase-3α (GSK-3α in glucose metabolism: effect of strain variation.

    Directory of Open Access Journals (Sweden)

    Satish Patel

    Full Text Available BACKGROUND: Over-activity and elevated expression of glycogen synthase kinase-3 (GSK-3 has been implicated in the etiology of insulin resistance and Type 2 diabetes. Administration of specific GSK-3 inhibitors to diabetic or obese rodent models improves glycaemic control and insulin sensitivity. However, due to the indiscriminatory nature of these inhibitors, the relative contribution of the two isoforms of GSK-3 (GSK-3α and GSK-3β is not known. Recently, we demonstrated that an out-bred strain of mice (ICR lacking expression of GSK-3α in all tissues displayed improved insulin sensitivity and enhanced hepatic glucose metabolism. We also found that muscle (but not liver inactivation of GSK-3β conferred insulin and glucose sensitization in an in-bred strain of mice (C57BL/6. METHODOLOGY/PRINCIPAL FINDINGS: Here, we have employed tissue-specific deletion of GSK-3α, to examine the relative contribution of two insulin-sensitive tissues, muscle and liver, towards the insulin sensitization phenotype originally observed in the global GSK-3α KO animals. We found that mice in which GSK-3α has been inactivated in either skeletal-muscle or liver displayed no differences in glucose tolerance or insulin sensitivity compared to wild type littermates. Given the strain differences in our original analyses, we examined the insulin and glucose sensitivity of global GSK-3α KO animals bred onto a C57BL/6 background. These animals also revealed no significant differences in glucose metabolism/insulin sensitivity compared to their wild type littermates. Furthermore, deletion of hepatic GSK-3α on the out-bred, ICR background failed to reproduce the insulin sensitivity manifested by the global deletion of this isoform. CONCLUSIONS/SIGNIFICANCE: From these data we conclude that the improved insulin sensitivity and hepatic glucose homeostasis phenotype observed upon global inactivation of GSK-3α is strain-specific. We surmise that the insulin

  3. MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention

    Science.gov (United States)

    Tischner, Christin; Hofer, Annette; Wulff, Veronika; Stepek, Joanna; Dumitru, Iulia; Becker, Lore; Haack, Tobias; Kremer, Laura; Datta, Alexandre N.; Sperl, Wolfgang; Floss, Thomas; Wurst, Wolfgang; Chrzanowska-Lightowlers, Zofia; De Angelis, Martin Hrabe; Klopstock, Thomas; Prokisch, Holger; Wenz, Tina

    2015-01-01

    Mitochondrial diseases often exhibit tissue-specific pathologies, but this phenomenon is poorly understood. Here we present regulation of mitochondrial translation by the Mitochondrial Translation Optimization Factor 1, MTO1, as a novel player in this scenario. We demonstrate that MTO1 mediates tRNA modification and controls mitochondrial translation rate in a highly tissue-specific manner associated with tissue-specific OXPHOS defects. Activation of mitochondrial proteases, aberrant translation products, as well as defects in OXPHOS complex assembly observed in MTO1 deficient mice further imply that MTO1 impacts translation fidelity. In our mouse model, MTO1-related OXPHOS deficiency can be bypassed by feeding a ketogenic diet. This therapeutic intervention is independent of the MTO1-mediated tRNA modification and involves balancing of mitochondrial and cellular secondary stress responses. Our results thereby establish mammalian MTO1 as a novel factor in the tissue-specific regulation of OXPHOS and fine tuning of mitochondrial translation accuracy. PMID:25552653

  4. Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes

    Directory of Open Access Journals (Sweden)

    Reverter Antonio

    2008-09-01

    Full Text Available Abstract Background The tissue specificity of gene expression has been linked to a number of significant outcomes including level of expression, and differential rates of polymorphism, evolution and disease association. Recent studies have also shown the importance of exploring differential gene connectivity and sequence conservation in the identification of disease-associated genes. However, no study relates gene interactions with tissue specificity and disease association. Methods We adopted an a priori approach making as few assumptions as possible to analyse the interplay among gene-gene interactions with tissue specificity and its subsequent likelihood of association with disease. We mined three large datasets comprising expression data drawn from massively parallel signature sequencing across 32 tissues, describing a set of 55,606 true positive interactions for 7,197 genes, and microarray expression results generated during the profiling of systemic inflammation, from which 126,543 interactions among 7,090 genes were reported. Results Amongst the myriad of complex relationships identified between expression, disease, connectivity and tissue specificity, some interesting patterns emerged. These include elevated rates of expression and network connectivity in housekeeping and disease-associated tissue-specific genes. We found that disease-associated genes are more likely to show tissue specific expression and most frequently interact with other disease genes. Using the thresholds defined in these observations, we develop a guilt-by-association algorithm and discover a group of 112 non-disease annotated genes that predominantly interact with disease-associated genes, impacting on disease outcomes. Conclusion We conclude that parameters such as tissue specificity and network connectivity can be used in combination to identify a group of genes, not previously confirmed as disease causing, that are involved in interactions with disease causing

  5. Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum.

    Science.gov (United States)

    Rosa, Bruce A; Jasmer, Douglas P; Mitreva, Makedonka

    2014-02-01

    Caenorhabditis elegans has traditionally been used as a model for studying nematode biology, but its small size limits the ability for researchers to perform some experiments such as high-throughput tissue-specific gene expression studies. However, the dissection of individual tissues is possible in the parasitic nematode Ascaris suum due to its relatively large size. Here, we take advantage of the recent genome sequencing of Ascaris suum and the ability to physically dissect its separate tissues to produce a wide-scale tissue-specific nematode RNA-seq datasets, including data on three non-reproductive tissues (head, pharynx, and intestine) in both male and female worms, as well as four reproductive tissues (testis, seminal vesicle, ovary, and uterus). We obtained fundamental information about the biology of diverse cell types and potential interactions among tissues within this multicellular organism. Overexpression and functional enrichment analyses identified many putative biological functions enriched in each tissue studied, including functions which have not been previously studied in detail in nematodes. Putative tissue-specific transcriptional factors and corresponding binding motifs that regulate expression in each tissue were identified, including the intestine-enriched ELT-2 motif/transcription factor previously described in nematode intestines. Constitutively expressed and novel genes were also characterized, with the largest number of novel genes found to be overexpressed in the testis. Finally, a putative acetylcholine-mediated transcriptional network connecting biological activity in the head to the male reproductive system is described using co-expression networks, along with a similar ecdysone-mediated system in the female. The expression profiles, co-expression networks and co-expression regulation of the 10 tissues studied and the tissue-specific analysis presented here are a valuable resource for studying tissue-specific biological functions in

  6. Correlation between human maternal-fetal placental transfer and molecular weight of PCB and dioxin congeners/isomers.

    Science.gov (United States)

    Mori, Chisato; Nakamura, Noriko; Todaka, Emiko; Fujisaki, Takeyoshi; Matsuno, Yoshiharu; Nakaoka, Hiroko; Hanazato, Masamichi

    2014-11-01

    Establishing methods for the assessment of fetal exposure to chemicals is important for the prevention or prediction of the child's future disease risk. In the present study, we aimed to determine the influence of molecular weight on the likelihood of chemical transfer from mother to fetus via the placenta. The correlation between molecular weight and placental transfer rates of congeners/isomers of polychlorinated biphenyls (PCBs) and dioxins was examined. Twenty-nine sample sets of maternal blood, umbilical cord, and umbilical cord blood were used to measure PCB concentration, and 41 sample sets were used to analyze dioxins. Placental transfer rates were calculated using the concentrations of PCBs, dioxins, and their congeners/isomers within these sample sets. Transfer rate correlated negatively with molecular weight for PCB congeners, normalized using wet and lipid weights. The transfer rates of PCB or dioxin congeners differed from those of total PCBs or dioxins. The transfer rate for dioxin congeners did not always correlate significantly with molecular weight, perhaps because of the small sample size or other factors. Further improvement of the analytical methods for dioxin congeners is required. The findings of the present study suggested that PCBs, dioxins, or their congeners with lower molecular weights are more likely to be transferred from mother to fetus via the placenta. Consideration of chemical molecular weight and transfer rate could therefore contribute to the assessment of fetal exposure. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2014-01-01

    Cue Rondo is an open composition to be realised by improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound/video files will in some cases only provide a few minutes' sample, or the visuals will not appear at all....... Please DOWNLOAD them to see/hear them in full length! This work is licensed under a Creative Commons "by-nc" License. You may for non-commercial purposes use and distribute it, performance instructions as well as specially designated recordings, as long as the author is mentioned. Please see http...

  8. SW.B6-Soa(b) nontaster congenic strains completed and a sucrose octaacetate congenic quartet tested with other bitters.

    Science.gov (United States)

    Harder, D B; Gannon, K S; Whitney, G

    1996-10-01

    Ten SW.B6 SOA nontaster strains congenic with the SWR/J SOA taster inbred strain were bred via repeated backcross-intercross cycles, with selection for nontasting in each cycle. Preference ratio distributions and phenotypic proportions across cycles at 0.1 mM SOA were consistent with monogenic predictions. The SW.B6 mice completed a congenic quartet with the SWR/J, B6.SW SOA taster and C57BL/6J SOA nontaster strains. The Soa locus controlled avoidance differences within the quartet for SOA, raffinose undecaacetate, glucose pentaacetate and brucine. Background genes not linked to Soa controlled avoidance differences for L-phenylalanine and ethanol. Avoidance of bitter picric acid was influenced by the Soa locus, but avoidance of acetic acid was not. The quartet pattern for quinine HCl was unclear, with indications of both Soa and background effects. Two forms of ribose tetraacetate yielded different patterns. Avoidance differences controlled by the Soa locus were found for the pyranose form; however, all four strains avoided the furanose form. The pleiotropic effects of Soa allele substitution within the quartet were limited to a subset of bitter compounds.

  9. The role of congeners in the effects of different alcoholic beverages.

    Science.gov (United States)

    York, J L

    1984-01-01

    Five different alcoholic beverages were tested in rats to determine if congener content contributed to the hypothermia or motor impairment produced by the beverages. Solutions of cognac, scotch, tequila, vodka, and commercially supplied ethanol were diluted with physiological saline to form solutions containing 16% w/v ethanol, as verified by gas chromatographic analysis. All beverages were administered in doses containing 0 (saline), 1.6, 3.2, 4.8, or 6.4 g/kg ethanol (gastric intubation) in test sessions separated by 7 days (repeated measures design, N = 8 rats per group). Measurements of rectal temperature and motor impairment (rotarod performance) made at 0, 60, and 120 minutes postinjection revealed no noteworthy differences in either measure at 60 or 120 minutes postinjection at any of the 4 doses tested. Thus, no evidence for a contribution of congeners to beverage effects was observed.

  10. Comprehensive overview of the vertebrate p24 family: identification of a novel tissue-specifically expressed member

    NARCIS (Netherlands)

    Strating, J.; Bakel, van N.H.M.; Leunissen, J.A.M.; Martens, G.J.M.

    2009-01-01

    The members of the p24 protein family have an important but unclear role in transport processes in the early secretory pathway. The p24 family consists of four subfamilies (alpha, beta, gamma, and delta), whereby the exact composition of the family varies among species. Despite more than 15 years of

  11. A new sarasinoside congener, sarasinoside M2, from a marine sponge collected in the Solomon Islands.

    Science.gov (United States)

    Puilingi, Clyde Gorapava; Kudo, Yuta; Cho, Yuko; Konoki, Keiichi; Yotsu-Yamashita, Mari

    2017-02-01

    A new sarasinoside congener (sarasinoside M 2 ) and known sarasinoside B 1 were obtained from a marine sponge. Sarasinoside M 2 was suggested to have the same aglycon as sarasinoside M although the internal glucose in its sugar moiety is replaced by xylose. Sarasinosides B 1 and M 2 showed moderate cytotoxicity (approximate IC 50 5-18 μM) toward Neuro-2a and HepG2 cell lines.

  12. Effects of two PBDE congeners on the moulting enzymes of the freshwater amphipod Gammarus pulex

    International Nuclear Information System (INIS)

    Gismondi, Eric; Thomé, Jean-Pierre

    2014-01-01

    Polybrominated diphenyl ethers (PBDEs) are abundant in aquatic environment. However, only few studies have investigated their impacts on freshwater invertebrates. This work aimed to study the effects of BDE-47 and BDE-99 congeners on the chitobiase and chitinolytic enzymes activities of the freshwater amphipod Gammarus pulex, according to gender, PBDE concentration and time of exposure. In addition, the bioaccumulation of BDE-47 and BDE-99 were measured. Results revealed that females have bioaccumulated more PBDE than males, and BDE-99 was more accumulated than BDE-47. PBDE exposures for 96 h have caused chitobiase and chitinolytic enzymes inhibition. This study not only indicate the importance of taking into account various confounding factors (gender, congeners, concentration) to understand PBDE effects, but underline also disruptions of molting enzymes activities. These disturbances suggest effects on the gammarid development and reproduction, and consequently effects on the gammarid population, and on a larger scale, a dysfunction of the ecosystem. - Highlights: • G. pulex females bioaccumulate more PBDE than males. • PBDE exposure increases enzyme activities involved in moult process. • Gammarid gender, PBDE congener and concentration are confounding factors. - BDE-47 and BDE-99 are accumulated in Gammarus pulex males and females and have impacted the moulting process, since they influenced the moult enzymes activities

  13. Dechlorination of the dietary nona-chlorinated toxaphene congeners 62 and 50 into the octa-chlorinated toxaphene congeners 44 and 40 in zebrafish (Danio rerio) and Atlantic salmon (Salmo salar)

    Energy Technology Data Exchange (ETDEWEB)

    Berntssen, M.H.G., E-mail: marc.berntssen@nifes.no [National Institute of Nutrition and Seafood Research (NIFES), Postbox 2029 Nordnes, 5817 Bergen (Norway); Lundebye, A.-K.; Hop-Johannessen, L.; Lock, E.-J. [National Institute of Nutrition and Seafood Research (NIFES), Postbox 2029 Nordnes, 5817 Bergen (Norway)

    2012-05-15

    Graphical abstract: - Abstract: The relative feed-to-fish accumulation and possible biotransformation of the nona-chlorinated toxaphene congeners currently included in EU-legislation (CHB-50 and -62) and the octa-chlorinated congeners recommended by the European Food Safety Authority to be included in future surveillance of fish samples (CHB-40, 41, and 44) were investigated in the present study. Model fish Danio rerio were fed either (a) diets spiked with a combination as well as the pure individual toxaphene congeners CHB-50 or 62 or (b) diets spiked with the combination of CHB N-Ary-Summation 50 + 62 and/or CHB N-Ary-Summation 40 + 41 + 44. In addition, seawater adapted Atlantic salmon smolts were fed technical toxaphene enriched feeds for 62 days. Zebrafish fed a diet containing CHB-50 and CHB-62 accumulated newly formed CHB-40 and 41 and CHB-44, respectively. The biomagnifications factors (BMF) of the toxaphene congeners in Atlantic salmon muscle from the feeds spiked with technical toxaphene were significantly correlated with their relative lipophilicity (expressed as log K{sub ow}). An exception was CHB-44 which had a higher BMF than could be expected from its specific log K{sub ow}, reflecting that CHB-44 is a metabolite formed under dietary exposure to CHB-62. This paper reports the in vivo dechlorination of nona-chlorinated toxaphene congeners into octa-chlorinated congeners in feeding trials with a model fish (zebrafish) and an oily food fish (Atlantic salmon).

  14. Distinguishing PCB Isomeric Congeners with their Gas Chromatographic and Mass Spectrometric Ortho Effect using Comprehensive Gas Chromatography

    Science.gov (United States)

    The 209 polychlorinated biphenyl (PCB) congeners and associated nine isomeric groups (nine groups of PCBs with the same degree of chlorination) have been long recorded as high endocrine disrupting chemicals in the environment. Difficult analytical problems exist, in those frequen...

  15. Polychlorinated biphenyl residues in food and human milk: determination of co-planar and mono-ortho substituted congeners

    International Nuclear Information System (INIS)

    Boehm, V.; Schulte, E.; Thier, H.P.

    1993-01-01

    An analytical method is described for determining the residues of coplanar as well as mono-ortho substituted PCB congeners both exhibiting toxicological relevance, in foods of animal origin and in human milk. The unsophisticated procedure, convenient for routine analyses, includes the extraction of lipids, clean-up steps using liquid/liquid partition and column chromatography, fractionation of the congeners using HPLC on a special carbon column with an optimal gradient elution, and capillary column gas chromatography with electron capture or mass spectrometric detection. As preliminary results indicate, the low-chlorinated PCB technical products contribute more to the actual contamination of environment and foods than has been estimated so far. Obviously the co-planar congeners are accumulated during the food chain in a portion different from that found for the other congeners. (orig.)

  16. Bioaccumulation of PCBs in Arctic seabirds: influence of dietary exposure and congener biotransformation

    Energy Technology Data Exchange (ETDEWEB)

    Borga, Katrine [Norwegian Polar Institute, N-9296 Tromsoe (Norway)]. E-mail: katrine.borga@npolar.no; Wolkers, Hans [Norwegian Polar Institute, N-9296 Tromsoe (Norway); Skaare, Janneche U. [National Veterinary Institute, P.O. Box 8156 Dep., N-0033 Oslo (Norway); Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo (Norway); Hop, Haakon [Norwegian Polar Institute, N-9296 Tromsoe (Norway); Muir, Derek C.G. [National Water Research Institute, Environment Canada, Burlington, ON, L7R 4A6 (Canada); Gabrielsen, Geir W. [Norwegian Polar Institute, N-9296 Tromsoe (Norway)

    2005-04-01

    Four seabird species and their prey (zooplankton or fish) were collected in the Barents Sea to determine how dietary exposure, cytochrome P450 (CYP) enzyme activities and sex influenced their hepatic PCB concentrations and accumulation patterns. Five males and five females from each seabird species (little auk (Alle alle), Bruennich's guillemot (Uria lomvia), black guillemot (Cepphus grylle) and black-legged kittiwake (Rissa tridactyla)) were analysed. PCB concentrations could not be explained directly by carbon source ({delta}{sup 13}C) or trophic position ({delta}{sup 15}N), but by a combination of dietary parameters ({delta}{sup 13}C, {delta}{sup 15}N, migratory pattern, age) and contaminant metabolism. Contrary to previous studies, the PCB pattern differed among seabirds, with a higher proportion of persistent congeners (% of PCB-153, R{sub PCB-153}) in black-legged kittiwake than in auks. The PCB pattern also differed among auks, with little auk as the most efficient biotransformer (highest R{sub PCB-153} values of persistent congeners). Based on high R{sub PCB-153} values, Bruennich's guillemot poorly metabolised ortho-meta-unsubstituted congeners, whereas black guillemot poorly metabolised meta-para unsubstituted congeners. Species-specific differences in PCB biotransformation were confirmed by metabolic indices, where PCB patterns in seabirds were adjusted for PCB pattern in prey. The relative contribution of ortho-meta-unsubstituted congeners to {sigma}PCBsdecreased with increasing EROD activity. There were no differences in PCB concentrations, PCB patterns or cytochrome P450 enzyme activities between males and females. CYP P450 activities (CYP1A- and CYP2B/3A-like: EROD and testosterone 6{beta}-hydroxylation, respectively) were low and did not correlate with concentrations of non- or mono-ortho Cl-substituted PCBs (NO- and MO-PCBs), or with total toxic equivalent concentrations (TEQs) for dioxin-like effects of NO- and MO-PCBs. - Contaminant

  17. Release of Tissue-specific Proteins into Coronary Perfusate as a Model for Biomarker Discovery in Myocardial Ischemia/Reperfusion Injury

    DEFF Research Database (Denmark)

    Cordwell, Stuart; Edwards, Alistair; Liddy, Kiersten

    2012-01-01

    of 60 min reperfusion following brief, reversible ischemia (15 min; 15I/60R) for comparison with irreversible I/R (60I/60R). Perfusate proteins were separated using two-dimensional gel electrophoresis (2-DE) and identified by mass spectrometry (MS), revealing 26 tissue-specific proteins released during...... reperfusion post-15I. Proteins released during irreversible I/R (60I/60R) were profiled using gel-based (2-DE and one-dimensional gel electrophoresis coupled to liquid chromatography and tandem mass spectrometry; geLC–MS) and gel-free (LC–MS/MS) methods. A total of 192 tissue-specific proteins were identified......Diagnosis of acute coronary syndromes is based on protein biomarkers, such as the cardiac troponins (cTnI/cTnT) and creatine kinase (CK-MB) that are released into the circulation. Biomarker discovery is focused on identifying very low abundance tissue-derived analytes from within albumin...

  18. Multiple POU-binding motifs, recognized by tissue-specific nuclear factors, are important for Dll1 gene expression in neural stem cells

    International Nuclear Information System (INIS)

    Nakayama, Kohzo; Nagase, Kazuko; Tokutake, Yuriko; Koh, Chang-Sung; Hiratochi, Masahiro; Ohkawara, Takeshi; Nakayama, Noriko

    2004-01-01

    We cloned the 5'-flanking region of the mouse homolog of the Delta gene (Dll1) and demonstrated that the sequence between nucleotide position -514 and -484 in the 5'-flanking region of Dll1 played a critical role in the regulation of its tissue-specific expression in neural stem cells (NSCs). Further, we showed that multiple POU-binding motifs, located within this short sequence of 30 bp, were essential for transcriptional activation of Dll1 and also that multiple tissue-specific nuclear factors recognized these POU-binding motifs in various combinations through differentiation of NSCs. Thus, POU-binding factors may play an important role in Dll1 expression in developing NSCs

  19. Composition.

    Science.gov (United States)

    Communication: Journalism Education Today, 2002

    2002-01-01

    Considers how photography is more than just pointing a camera in the right direction. Explains that good pictures use elements of composition such as the Rule of Thirds, leading lines, framing and repetition of shapes. Presents 16 photographs from college and secondary school publications, and describes the techniques that makes them effective.…

  20. Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice.

    Science.gov (United States)

    Movahedi, Sara; Van de Peer, Yves; Vandepoele, Klaas

    2011-07-01

    Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.

  1. Lack of effects of a "sobering" product, "Eezup!", on the blood ethanol and congener alcohol concentration.

    Science.gov (United States)

    Wunder, Cora; Hain, Sarah; Koelzer, Sarah C; Paulke, Alexander; Verhoff, Marcel A; Toennes, Stefan W

    2017-09-01

    The lifestyle product 'Eezup!' appeared on the German market and promised to normalize energy metabolism. Among vitamins (B 1 , B 2 , B 6 , C, E and zinc), rice protein and fructose the addition of alcohol dehydrogenase and catalase enzymes is a novel approach. The product was advertised as capable of boosting the rate of alcohol elimination. Seventeen subjects (11 men, 6 women, 19-58 years old), participated in a two-way crossover drinking study. Unfiltered wheat beer (4.4g% alcohol content) was drank within one hour to reach blood alcohol concentrations of 1‰ (1g/kg whole blood). On one day "Eezup!" was taken according to the manufacturer's instructions before and after drinking which was substituted for a placebo on the second test day. Blood samples were taken during 9h and ethanol and congener alcohols were determined. A comparison of C max , t max , area under the curve (AUC) for ethanol and congener alcohols, and the hourly elimination rate of ethanol (β 60 ) was performed to investigate an effect of Eezup!. Ethanol concentrations (Cmax) were in the range of 0,63-1,00‰ (median 0,85‰) and 0.62-1.22‰ (median 0.84‰) in the placebo and "Eezup!" condition, respectively, and not statistically different. Also t max (1-2.5h) and AUCs did not differ. The ethanol elimination rates were 0.16‰/h (0.14-0.19‰/h) and 0.17‰/h (0.14-0.22 ‰/h) in the placebo and "Eezup!" condition without significant difference. The pharmacokinetic parameters of the congener alcohols (1-propanol, isobutanol, 3-methyl-1-butanol, 2-methyl-1-butanol) as well as of methanol did also not differ. The results of the present study failed to show any effect of the sobering product "Eezup!" on the amount of ethanol and congener alcohols absorbed (C max , t max, AUC) and on the ethanol elimination rate (β 60 ). Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Tissue-specific production of limonene in Camelina sativa with the Arabidopsis promoters of genes BANYULS and FRUITFULL.

    Science.gov (United States)

    Borghi, Monica; Xie, De-Yu

    2016-02-01

    Arabidopsis promoters of genes BANYULS and FRUITFULL are transcribed in Camelina. They triggered the transcription of limonene synthase and induced higher limonene production in seeds and fruits than CaMV 35S promoter. Camelina sativa (Camelina) is an oilseed crop of relevance for the production of biofuels and the plant has been target of a recent and intense program of genetic manipulation aimed to increase performance, seed yield and to modify the fatty acid composition of the oil. Here, we have explored the performance of two Arabidopsis thaliana (Arabidopsis) promoters in triggering transgene expression in Camelina. The promoters of two genes BANYULS (AtBAN pro ) and FRUITFULL (AtFUL pro ), which are expressed in seed coat and valves of Arabidopsis, respectively, have been chosen to induce the expression of limonene synthase (LS) from Citrus limon. In addition, the constitutive CaMV 35S promoter was utilized to overexpress LS in Camelina . The results of experiments revealed that AtBAN pro and AtFUL pro are actively transcribed in Camelina where they also retain specificity of expression in seeds and valves as previously observed in Arabidopsis. LS induced by AtBAN pro and AtFUL pro leads to higher limonene production in seeds and fruits than when the CaMV 35S was used to trigger the expression. In conclusion, the results of experiments indicate that AtBAN pro and AtFUL pro can be successfully utilized to induce the expression of the transgenes of interest in seeds and fruits of Camelina.

  3. CXCR6, a newly defined biomarker of tissue-specific stem cell asymmetric self-renewal, identifies more aggressive human melanoma cancer stem cells.

    Directory of Open Access Journals (Sweden)

    Rouzbeh Taghizadeh

    2010-12-01

    Full Text Available A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells. Recent investigations of a variety of tumor types have shown that phenotypically identifiable and isolable subfractions of cells possess the tumor-forming ability. In the present paper, using two lineage-related human melanoma cell lines, primary melanoma line IGR39 and its metastatic derivative line IGR37, two main observations are reported. The first one is the first phenotypic evidence to support the origin of melanoma cancer stem cells (CSCs from mutated tissue-specific stem cells; and the second one is the identification of a more aggressive subpopulation of CSCs in melanoma that are CXCR6+.We defined CXCR6 as a new biomarker for tissue-specific stem cell asymmetric self-renewal. Thus, the relationship between melanoma formation and ABCG2 and CXCR6 expression was investigated. Consistent with their non-metastatic character, unsorted IGR39 cells formed significantly smaller tumors than unsorted IGR37 cells. In addition, ABCG2+ cells produced tumors that had a 2-fold greater mass than tumors produced by unsorted cells or ABCG2- cells. CXCR6+ cells produced more aggressive tumors. CXCR6 identifies a more discrete subpopulation of cultured human melanoma cells with a more aggressive MCSC phenotype than cells selected on the basis of the ABCG2+ phenotype alone.The association of a more aggressive tumor phenotype with asymmetric self-renewal phenotype reveals a previously unrecognized aspect of tumor cell physiology. Namely, the retention of some tissue-specific stem cell attributes, like the ability to asymmetrically self-renew, impacts the natural history of human tumor development. Knowledge of this new aspect of tumor development and progression may provide new targets for cancer prevention and treatment.

  4. hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

    Directory of Open Access Journals (Sweden)

    Cheng-Hong Yang

    Full Text Available BACKGROUND: SAGE (serial analysis of gene expression is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers. METHODOLOGY/PRINCIPAL FINDINGS: To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are not in "inclusion", the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries. CONCLUSIONS/SIGNIFICANCE: The hSAGEing tool provides a combination of friendly cross-tissue analysis and an interface for comparing SAGE libraries for the first time. Some up- or down-regulated genes with tissue-specific or common tumor markers and suppressors are identified computationally. The tool is useful and convenient for in silico cancer transcriptomic studies and is freely available at http://bio.kuas.edu.tw/hSAGEing.

  5. hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

    Science.gov (United States)

    Yang, Cheng-Hong; Chuang, Li-Yeh; Shih, Tsung-Mu; Chang, Hsueh-Wei

    2010-12-17

    SAGE (serial analysis of gene expression) is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers. To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are not in "inclusion", the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM) and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries. The hSAGEing tool provides a combination of friendly cross-tissue analysis and an interface for comparing SAGE libraries for the first time. Some up- or down-regulated genes with tissue-specific or common tumor markers and suppressors are identified computationally. The tool is useful and convenient for in silico cancer transcriptomic studies and is freely available at http://bio.kuas.edu.tw/hSAGEing.

  6. Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks.

    Science.gov (United States)

    Wu, Mengmeng; Lin, Zhixiang; Ma, Shining; Chen, Ting; Jiang, Rui; Wong, Wing Hung

    2017-12-01

    Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been appealing for effective computational methods to facilitate the advanced analysis of the vast volume of existing and anticipated genetic data. Towards this goal, gene-level integrative GWAS analysis with the assumption that genes associated with a phenotype tend to be enriched in biological gene sets or gene networks has recently attracted much attention, due to such advantages as straightforward interpretation, less multiple testing burdens, and robustness across studies. However, existing methods in this category usually exploit non-tissue-specific gene networks and thus lack the ability to utilize informative tissue-specific characteristics. To overcome this limitation, we proposed a Bayesian approach called SIGNET (Simultaneously Inference of GeNEs and Tissues) to integrate GWAS data and multiple tissue-specific gene networks for the simultaneous inference of phenotype-associated genes and relevant tissues. Through extensive simulation studies, we showed the effectiveness of our method in finding both associated genes and relevant tissues for a phenotype. In applications to real GWAS data of 14 complex phenotypes, we demonstrated the power of our method in both deciphering genetic basis and discovering biological insights of a phenotype. With this understanding, we expect to see SIGNET as a valuable tool for integrative GWAS analysis, thereby boosting the prevention, diagnosis, and treatment of human inherited diseases and eventually facilitating precision medicine.

  7. E2a-Pbx1 induces aberrant expression of tissue-specific and developmentally regulated genes when expressed in NIH 3T3 fibroblasts.

    OpenAIRE

    Fu, X; Kamps, M P

    1997-01-01

    The E2a-Pbx1 oncoprotein contains the transactivation domain of E2a joined to the DNA-binding homeodomain (HD) of Pbx1. In mice, E2a-Pbx1 transforms T lymphoblasts and fibroblasts and blocks myeloblast differentiation. Pbx1 and E2a-Pbx1 bind DNA as heterodimers with other HD proteins whose expression is tissue specific. While the transactivation domain of E2a is required for all forms of transformation, DNA binding by the Pbx1 HD is essential for blocking myeloblast differentiation but dispen...

  8. Supplementary Material for: Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

    KAUST Repository

    Horiuchi, Youko

    2015-01-01

    Abstract Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis

  9. Geographic variation of PCB congeners in polar bears (Ursus maritimus) from Svalbard east to the Chukchi Sea

    Science.gov (United States)

    Andersen, M.; Lie, E.; Derocher, A.E.; Belikov, S.E.; Bernhoft, A.; Boltunov, Andrei N.; Garner, G.W.; Skaare, J.U.; Wiig, Øystein

    2001-01-01

    We present data on geographic variation in polychlorinated biphenyl (PCB) congeners in adult female polar bears (Ursus maritimus) from Svalbard eastward to the Chukchi Sea. Blood samples from 90 free-living polar bears were collected in 1987–1995. Six PCB congeners, penta to octa chlorinated (PCB-99, -118, -153, -156, -180, -194), were selected for this study. Differences between areas were found in PCB levels and congener patterns. Bears from Franz Josef Land (11,194 ng/g lipid weight) and the Kara Sea (9,412 ng/g lw) had similar ΣPCB levels and were higher than all other populations (Svalbard 5,043 ng/g lw, East Siberian Sea 3,564 ng/g lw, Chukchi Sea 2,465 ng/g lw). Svalbard PCB levels were higher than those from the Chukchi Sea. Our results, combined with earlier findings, indicate that polar bears from Franz Josef Land and the Kara Sea have the highest PCB levels in the Arctic. Decreasing trends were seen eastwards and westwards from this region. Of the congeners investigated in the present study, the lower chlorinated PCBs are increasing and the high chlorinated PCBs are decreasing from Svalbard eastward to the Chukchi Sea. Different pollution sources, compound transport patterns and regional prey differences could explain the variation in PCB congener levels and patterns between regions.

  10. Release and attenuation of PCB (polychlorinated biphenyl) congeners: Measurement of desorption kinetics and equilibrium sorption partition coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Girvin, D.C.; Sklarew, D.S.; Scott, A.J.; Zipperer, J.P. (Pacific Northwest Lab., Richland, WA (USA))

    1990-06-01

    Polychlorinated biphenyls (PCBs) have been used widely in electrical equipment such as capacitors and transformers because of their coolant-insulation properties. However, their use has been discontinued because of their perceived toxicity to humans and other organisms in conjunction with their environmental persistence. This report provides information on the desorption or release rates of individual PCB congeners from four utility substation soils contaminated with Aroclor mixtures when these soils are in contact with water and the distribution of these congeners between the rapidly and the slowly released fractions of the total congeners bound to the soils. In addition to this kinetic information, experimental equilibrium sorption (partition) coefficients for individual PCB congeners have been measured for a series of eight soils differing in their organic carbon and clay mineral contents, from various locations throughout the United States. From these coefficients, a predictive relationship was derived for estimating partitioning coefficients for soils and congeners for which no sorption data are available. 49 refs., 9 figs., 13 tabs.

  11. Effects of two PBDE congeners on the moulting enzymes of the freshwater amphipod Gammarus pulex.

    Science.gov (United States)

    Gismondi, Eric; Thomé, Jean-Pierre

    2014-08-01

    Polybrominated diphenyl ethers (PBDEs) are abundant in aquatic environment. However, only few studies have investigated their impacts on freshwater invertebrates. This work aimed to study the effects of BDE-47 and BDE-99 congeners on the chitobiase and chitinolytic enzymes activities of the freshwater amphipod Gammarus pulex, according to gender, PBDE concentration and time of exposure. In addition, the bioaccumulation of BDE-47 and BDE-99 were measured. Results revealed that females have bioaccumulated more PBDE than males, and BDE-99 was more accumulated than BDE-47. PBDE exposures for 96 h have caused chitobiase and chitinolytic enzymes inhibition. This study not only indicate the importance of taking into account various confounding factors (gender, congeners, concentration) to understand PBDE effects, but underline also disruptions of molting enzymes activities. These disturbances suggest effects on the gammarid development and reproduction, and consequently effects on the gammarid population, and on a larger scale, a dysfunction of the ecosystem. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Concentration of polychlorinated biphenyl (PCB) congeners in the muscle of Clarias gariepinus and sediment from inland rivers of southwestern Nigeria and estimated potential human health consequences.

    Science.gov (United States)

    Adeogun, Aina O; Chukwuka, Azubuike V; Okoli, Chukwunonso P; Arukwe, Augustine

    2016-01-01

    The distributions of polychlorinated biphenyl (PCB) congeners were determined in sediment and muscle of the African sharptooth catfish (Clarias gariepinus) from the Ogun and Ona rivers, southwest Nigeria. In addition, the effect of PCB congeners on condition factor (CF) and associated human health risk was assessed using muscle levels for a noncarcinogenic hazard quotient (HQ) calculation. Elevated concentrations of high-molecular-weight (HMW) PCB congeners were detected in sediment and fish downstream of discharge points of both rivers. A significant reduction in fish body weight and CF was observed to correlate with high PCB congener concentrations in the Ona River. A principal component (PC) biplot revealed significant site-related PCB congener distribution patterns for HMW PCB in samples from the Ogun River (71.3%), while the Ona River (42.6%) showed significant PCB congener patterns for low-molecular-weight (LMW) congeners. Biota-sediment accumulation factor (BSAF) was higher downstream for both rivers, presenting PCB congener-specific accumulation patterns in the Ona River. Significant decreases in fish body weight, length and CF were observed downstream compared to upstream in the Ona River. The non-carcinogenic HQ of dioxin-like congener 189 downstream in both rivers exceeded the HQ = 1 threshold for children and adults for both the Ogun and Ona rivers. Overall, our results suggest that industrial discharges contribute significantly to PCB inputs into these rivers, with potential for significant health implications for neighboring communities that utilize these rivers for fishing and other domestic purposes.

  13. Direct Lymph Node Vaccination of Lentivector/Prostate-Specific Antigen is Safe and Generates Tissue-Specific Responses in Rhesus Macaques

    Directory of Open Access Journals (Sweden)

    Bryan C. Au

    2016-02-01

    Full Text Available Anti-cancer immunotherapy is emerging from a nadir and demonstrating tangible benefits to patients. A variety of approaches are now employed. We are invoking antigen (Ag-specific responses through direct injections of recombinant lentivectors (LVs that encode sequences for tumor-associated antigens into multiple lymph nodes to optimize immune presentation/stimulation. Here we first demonstrate the effectiveness and antigen-specificity of this approach in mice challenged with prostate-specific antigen (PSA-expressing tumor cells. Next we tested the safety and efficacy of this approach in two cohorts of rhesus macaques as a prelude to a clinical trial application. Our vector encodes the cDNA for rhesus macaque PSA and a rhesus macaque cell surface marker to facilitate vector titering and tracking. We utilized two independent injection schemas demarcated by the timing of LV administration. In both cohorts we observed marked tissue-specific responses as measured by clinical evaluations and magnetic resonance imaging of the prostate gland. Tissue-specific responses were sustained for up to six months—the end-point of the study. Control animals immunized against an irrelevant Ag were unaffected. We did not observe vector spread in test or control animals or perturbations of systemic immune parameters. This approach thus offers an “off-the-shelf” anti-cancer vaccine that could be made at large scale and injected into patients—even on an out-patient basis.

  14. Differential domain evolution and complex RNA processing in a family of paralogous EPB41 (protein 4.1) genes facilitates expression of diverse tissue-specific isoforms

    Energy Technology Data Exchange (ETDEWEB)

    Parra, Marilyn; Gee, Sherry; Chan, Nadine; Ryaboy, Dmitriy; Dubchak, Inna; Narla, Mohandas; Gascard, Philippe D.; Conboy, John G.

    2004-07-15

    The EPB41 (protein 4.1) genes epitomize the resourcefulness of the mammalian genome to encode a complex proteome from a small number of genes. By utilizing alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing, EPB41, EPB41L2, EPB41L3, and EPB41L1 encode a diverse array of structural adapter proteins. Comparative genomic and transcript analysis of these 140kb-240kb genes indicates several unusual features: differential evolution of highly conserved exons encoding known functional domains, interspersed with unique exons whose size and sequence variations contribute substantially to intergenic diversity: alternative first exons, most of which map far upstream of the coding regions; and complex tissue-specific alternative pre-mRNA splicing that facilitates synthesis of functionally different complements of 4.1 proteins in various cells. Understanding the splicing regulatory networks that control protein 4.1 expression will be critical to a full appreciation of the many roles of 4.1 proteins in normal cell biology and their proposed roles in human cancer.

  15. Molecular cloning of tissue-specific transcripts of a transketolase-related gene: Implications for the evolution of new vertebrate genes

    Energy Technology Data Exchange (ETDEWEB)

    Coy, J.F.; Duebel, S.; Kioschis, P.; Delius, H.; Poustka, A. [Deutsches Krebsforschungszentrum, Heidelberg (Germany)] [and others

    1996-03-05

    As part of a systematic search for differentially expressed genes, we have isolated a novel transketolase-related gene (TKR) (HGMW-approved symbol TKT), located between the green color vision pigment gene (GCP) and the ABP-280 filamin gene (FLN1) in Xq28. Transcripts encoding tissue-specific protein isoforms could be isolated. Comparison with known transketolases (TK) demonstrated a TKR-specific deletion mutating one thiamine binding site. Genomic sequencing of the TKR gene revealed the presence of a pseudoexon as well as the acquisition of a tissue-specific spliced exon compared to TK. Since it has been postulated that the vertebrate genome arose by two cycles of tetraploidization from a cephalochordate genome, this could represent an example of the modulation of the function of a preexisting transketolase gene by gene duplication. Thiamine defiency is closely involved with two neurological disorders, Beriberi and Wernicke-Korsakoff syndromes, and in both of these conditions TK with altered activity are found. We discuss the possible involvement of TKR in explaining the observed variant transketolase forms. 34 refs., 4 figs., 1 tab.

  16. Tissue-Specific Methylation of Long Interspersed Nucleotide Element-1 of Homo Sapiens (L1Hs) During Human Embryogenesis and Roles in Neural Tube Defects.

    Science.gov (United States)

    Wang, L; Chang, S; Guan, J; Shangguan, S; Lu, X; Wang, Z; Wu, L; Zou, J; Zhao, H; Bao, Y; Qiu, Z; Niu, B; Zhang, T

    2015-01-01

    Epigenetic regulation of long interspersed nucleotide element-1 (LINE-1) retrotransposition events plays crucial roles during early development. Previously we showed that LINE-1 hypomethylation in neuronal tissues is associated with pathogenesis of neural tube defect (NTD). Herein, we further evaluated LINE-1 Homo sapiens (L1Hs) methylation in tissues derived from three germ layers of stillborn NTD fetuses, to define patterns of tissue specific methylation and site-specific hypomethylation at CpG sites within an L1Hs promoter region. Stable, tissue-specific L1Hs methylation patterns throughout three germ layer lineages of the fetus, placenta, and maternal peripheral blood were observed. Samples from maternal peripheral blood exhibited the highest level of L1Hs methylation (64.95%) and that from placenta showed the lowest (26.82%). Between samples from NTDs and controls, decrease in L1Hs methylation was only significant in NTD-affected brain tissue at 7.35%, especially in females (8.98%). L1Hs hypomethylation in NTDs was also associated with a significant increase in expression level of an L1Hs-encoded transcript in females (r = -0.846, p = 0.004). This could be due to genomic DNA instability and alternation in chromatins accessibility resulted from abnormal L1Hs hypomethylation, as showed in this study with HCT-15 cells treated with methylation inhibitor 5-Aza.

  17. Increased susceptibility to collagen-induced arthritis in female mice carrying congenic Cia40/Pregq2 fragments

    DEFF Research Database (Denmark)

    Liljander, Maria; Andersson, Åsa Inga Maria; Holmdahl, Rikard

    2008-01-01

    ABSTRACT: INTRODUCTION: Collagen-induced arthritis (CIA) in mice is a commonly used experimental model for rheumatoid arthritis (RA). We have previously identified a significant quantitative trait locus denoted Cia40 on chromosome 11 that affects CIA in older female mice. This locus colocalizes...... with another locus, denoted Pregq2, known to affect reproductive success. The present study was performed to evaluate the role of the Cia40 locus in congenic B10.Q mice and to identify possible polymorphic candidate genes, which may also be relevant in the context of RA. METHODS: Congenic B10.Q mice carrying...... an NFR/N fragment surrounding the Cia40/Pregq2 loci were created by 10 generations of backcrossing (N10). The congenic mice were investigated in the CIA model, and the incidence and severity of arthritis as well as the serum levels of anti-collagen II (CII) antibodies were recorded. RESULTS: Significant...

  18. Time-Trends and Congener Profiles of PBDEs and PCBs in California Peregrine Falcons (Falco peregrinus)

    Science.gov (United States)

    Park, June-Soo; Holden, Arthur; Chu, Vivian; Kim, Michele; Rhee, Alexandra; Patel, Puja; Shi, Yating; Linthicum, Janet; Walton, Brian J.; Mckeown, Karen; Jewell, Nicholas P.; Hooper, Kim

    2010-01-01

    High levels (µg/g lw) of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) were measured in peregrine falcon eggs from California (n = 90 eggs from 52 birds, 38 nest sites, collected 1986–2007, ΣPBDEs median = 4.53, range = 0.08–53.1). Over the past 22 years, PBDE levels more than tripled each decade in the eggs, whereas PCB levels had no significant changes. PBDE levels were highest in eggs from major California cities (“Big Cities”), whereas PCBs showed no difference across the regions. For PBDEs, Big City eggs had markedly different patterns from Coastal eggs:BDE-209 and the higher brominated PBDEs (hexa–nona) were dominant congeners in Big City eggs, while BDE-47 and -99 were dominant in Coastal eggs. In many of the birds that gave multiple eggs over time (“time series”), PBDE patterns changed over time: the high proportions of BDE-209 and higher brominated PBDEs (short half-lives) in young birds contrasted with increasingly higher proportions of BDE-153 (long half-life) and other lower brominated PBDEs as the birds aged. These data are consistent with metabolic debromination of BDE-209 (t1/2 = 1–2 weeks) to the lower brominated PBDEs, with accumulation over time of BDE-153 (t1/2 = 3–4 years). In contrast, PCB patterns showed no differences by locations, and did not change over time. Diet (prey birds) may explain the urban PBDE pattern, as the patterns in urban pigeons and peregrines were similar, with high proportions of BDE-209 and the higher-brominated PBDEs. Also, our prey data (feathers from peregrine nests) showed urban peregrines having a higher proportion (>2 fold) of granivorous/opportunistic birds (e.g., “introduced feral” pigeons, mourning doves, starlings) in their diet than coastal peregrines. In summary, these data indicate that BDE-209 exits consumer products as an environmental contaminant to be taken up by wildlife (particularly in urban locations), and undergoes metabolic debromination to the

  19. α-Fetoprotein promoter-driven Cre/LoxP-switched RNA interference for hepatocellular carcinoma tissue-specific target therapy.

    Directory of Open Access Journals (Sweden)

    Yuan-Fei Peng

    Full Text Available RNA interference (RNAi has recently emerged as a potential treatment modality for hepatocellular carcinoma (HCC therapy, but the lack of cellular targets and sustained efficacy limits its application. The purpose of this study is to develop an HCC tissue-specific RNAi system and investigate its possibility for HCC treatment.Two different HCC-specific RNAi systems in which therapeutic miRNA or shRNA against target gene (Beclin 1 was directly or indirectly driven by alpha-fetoprotein promoter (AFP-miRNA and AFP-Cre/LoxP-shRNA were constructed. Human HCC cell lines (HepG2, Hep3B and HCCLM3 and non-HCC cell lines (L-02, Hela and SW1116 were infected with the systems. The effectiveness and tissue-specificity of the systems were examined by Q-PCR and western blot analysis. The efficacy of the systems was further tested in mouse model of HCC by intravenous or intratumoral administration. The feasibility of the system for HCC treatment was evaluated by applying the system as adjuvant therapy to enhance sorafenib treatment. An AFP-Cre/LoxP-shRNA system targeting Atg5 gene (AFP-Cre/LoxP-shRNA-Atg5 was constructed and its efficacy in sensitizing HCC cells (MHCC97L/PLC to sorafenib treatment was examined by apoptosis assay in vitro and tumorigenesis assay in vivo.The AFP-miRNA system could silence target gene (Beclin 1 but required a high titer which was lethal to target cells. The AFP-Cre/LoxP-shRNA system could efficiently knockdown target gene while maintain high HCC specificity. Intratumoral injection of the AFP-Cre/LoxP-shRNA system could efficiently silence target gene (Beclin 1 in vivo while intravenous administration could not. The AFP-Cre/LoxP-shRNA system target Atg5 gene could significantly sensitize MHCC97L/PLC cells to sorafenib-induced apoptosis in vitro and tumor growth suppression in vivo.An efficient HCC tissue-specific RNAi system (AFP-Cre/LoxP-shRNA was successfully established. The system provides a usable tool for HCC-specific RNAi

  20. E2a-Pbx1 induces aberrant expression of tissue-specific and developmentally regulated genes when expressed in NIH 3T3 fibroblasts.

    Science.gov (United States)

    Fu, X; Kamps, M P

    1997-03-01

    The E2a-Pbx1 oncoprotein contains the transactivation domain of E2a joined to the DNA-binding homeodomain (HD) of Pbx1. In mice, E2a-Pbx1 transforms T lymphoblasts and fibroblasts and blocks myeloblast differentiation. Pbx1 and E2a-Pbx1 bind DNA as heterodimers with other HD proteins whose expression is tissue specific. While the transactivation domain of E2a is required for all forms of transformation, DNA binding by the Pbx1 HD is essential for blocking myeloblast differentiation but dispensable for fibroblast or T-lymphoblast transformation. These properties suggest (i) that E2a-Pbx1 causes cellular transformation by activating gene transcription, (ii) that transcription of E2a-Pbx1 target genes is normally regulated by ubiquitous Pbx proteins and tissue-specific partners, and (iii) that DNA-binding mutants of E2a-Pbx1 activate a subset of all gene targets. To test these predictions, genes induced in NIH 3T3 fibroblasts by E2a-Pbx1 were identified and examined for tissue- and stage-specific expression and their differential abilities to be upregulated by E2a-Pbx1 in NIH 3T3 fibroblasts and myeloblasts and by a DNA-binding mutant of E2a-Pbx1 in NIH 3T3 cells. Of 12 RNAs induced by E2a-Pbx1, 4 encoded known proteins (a J-C region of the immunoglobulin kappa light chain, natriuretic peptide receptor C, mitochondrial fumarase, and the 3',5'-cyclic nucleotide phosphodiesterase, PDE1A) and 5 encoded new proteins related to angiogenin, ion channels, villin, epidermal growth factor repeat proteins, and the human 2.19 gene product. Expression of many of these genes was tissue specific or developmentally regulated, and most were not expressed in fibroblasts, indicating that E2a-Pbx1 can induce ectopic expression of genes associated with lineage-specific differentiation.

  1. A four step model for the IL-6 amplifier, a regulator of chromic inflammations in tissue specific MHC class II-associated autoimmune diseases

    Directory of Open Access Journals (Sweden)

    Masaaki eMurakami

    2011-06-01

    Full Text Available It is thought autoimmune diseases are caused by the breakdown of self-tolerance, which suggests the recognition of specific antigens by autoreactive CD4+ T cells contribute to the specificity of autoimmune diseases. In several cases, however, even for diseases associated with class II MHC alleles, the causative tissue-specific antigens recognized by memory/activated CD4+ T cells have not been established. Rheumatoid arthritis (RA and arthritis in F759 knock-in mouse line (F759 mice are such examples, even though evidences support a pathogenic role for CD4+ T cells in both diseases. We have recently shown local events such as microbleeding together with an accumulation of activated CD4+ T cells in a manner independent of tissue antigen-recognitions induces arthritis in the joints of F759 mice. For example, local microbleeding-mediated CCL20 expression induced such an accumulation, causing arthritis development via chronic activation of an IL-17A-dependent IL-6 signaling amplification loop in type 1 collagen+ cells that is triggered by CD4+ T cell-derived cytokine(s such as IL-17A, which leads to the synergistic activation of STAT3 and NFκB in non hematopoietic cells in the joint. We named this loop the IL-6-mediated inflammation amplifier, or IL-6 amplifier. Thus, certain class II MHC–associated, tissue-specific autoimmune diseases may be induced by local events that cause an antigen-independent accumulation of effector CD4+ T cells followed by the induction of the IL-6 amplifier in the affected tissue. To explain this hypothesis, we have proposed a Four Step Model for MHC class II associated autoimmune diseases. The interaction of four local events results in chronic activation of the IL-6 amplifier, leading to the manifestation of autoimmune diseases. Thus, we have concluded the IL-6 amplifier is a critical regulator of chromic inflammations in tissue specific MHC class II-associated autoimmune diseases.

  2. A minimal peach type II chlorophyll a/b-binding protein promoter retains tissue-specificity and light regulation in tomato

    Directory of Open Access Journals (Sweden)

    Scorza Ralph

    2007-08-01

    Full Text Available Abstract Background Promoters with tissue-specificity are desirable to drive expression of transgenes in crops to avoid accumulation of foreign proteins in edible tissues/organs. Several photosynthetic promoters have been shown to be strong regulators of expression of transgenes in light-responsive tissues and would be good candidates for leaf and immature fruit tissue-specificity, if expression in the mature fruit were minimized. Results A minimal peach chlorophyll a/b-binding protein gene (Lhcb2*Pp1 promoter (Cab19 was isolated and fused to an uidA (β-glucuronidase [GUS] gene containing the PIV2 intron. A control vector carrying an enhanced mas35S CaMV promoter fused to uidA was also constructed. Two different orientations of the Cab19::GUS fusion relative to the left T-DNA border of the binary vector were transformed into tomato. Ten independent regenerants of each construct and an untransformed control line were assessed both qualitatively and quantitatively for GUS expression in leaves, fruit and flowers, and quantitatively in roots. Conclusion The minimal CAB19 promoter conferred GUS activity primarily in leaves and green fruit, as well as in response to light. GUS activity in the leaves of both Cab19 constructs averaged about 2/3 that observed with mas35S::GUS controls. Surprisingly, GUS activity in transgenic green fruit was considerably higher than leaves for all promoter constructs; however, in red, ripe fruit activities were much lower for the Cab19 promoter constructs than the mas35S::GUS. Although GUS activity was readily detectable in flowers and roots of mas35S::GUStransgenic plants, little activity was observed in plants carrying the Cab19 promoter constructs. In addition, the light-inducibility of the Cab19::GUS constructs indicated that all the requisite cis-elements for light responsiveness were contained on the Cab19 fragment. The minimal Cab19 promoter retains both tissue-specificity and light regulation and can be used to

  3. Antifungal activity of cinnamaldehyde and eugenol congeners against wood-rot fungi.

    Science.gov (United States)

    Cheng, Sen-Sung; Liu, Ju-Yun; Chang, Ed-Haun; Chang, Shang-Tzen

    2008-07-01

    In this study, the antifungal activities of cinnamaldehyde and eugenol congeners against white-rot fungus Lenzites betulina and brown-rot fungus Laetiporus sulphureus were evaluated and the relationships between the antifungal activity and the chemical structures were also examined. Results from antifungal tests revealed that cinnamaldehyde, alpha-methyl cinnamaldehyde, (E)-2-methylcinnamic acid, eugenol and isoeugenol exhibited strong antifungal activity against all fungi tested. Results derived from the chemical structure-antifungal activity relationship study suggested that compounds with an aldehyde group or an acid group, a conjugated double bond and a length of CH chain outside the ring affect their antifungal properties. Furthermore, the presence of the methyl moiety in the ortho position may have a considerable influence on the inhibitory action against L. betulina and L. sulphureus. In addition, the lipophilicity may play, in part, a crucial role in determining the toxicity of phenylpropenes.

  4. Spatial distribution of chlordanes and PCB congeners in soil in Cedar Rapids, Iowa, USA

    International Nuclear Information System (INIS)

    Martinez, Andres; Erdman, Nicholas R.; Rodenburg, Zachary L.; Eastling, Paul M.; Hornbuckle, Keri C.

    2012-01-01

    Residential soils from Cedar Rapids, Iowa, USA were collected and analyzed for chlordanes and polychlorinated biphenyls (PCBs). This study is one of the very few urban soil investigations in the USA. The chlordanes concentrations ranged from 0 to 7500 ng g −1 dry weight (d.w.), with a mean and standard deviation of 130 ± 920 ng g −1 d.w., which is about 1000 times larger than background levels. ΣPCB concentrations ranged from 3 to 1200 ng g −1 d.w., with a mean and standard deviation of 56 ± 160 ng g −1 d.w. and are about 10 times higher than world-wide background levels. Both groups exhibit considerable variability in chemical patterns and site-to-site concentrations. Although no measurements of dioxins were carried out, the potential toxicity due to the 12 dioxin-like PCBs found in the soil is in the same order of magnitude of the provisional threshold recommended by USEPA to perform soil remediation. - Graphical Abstract: Spatial location and measured concentrations of ΣPCB (left, 64 sites) and chlordanes (right, 66 sites) (ng g −1 d.w.) in soil from Cedar Rapids, Iowa. Samples were collected in August 2008. Estimated flood area was obtained from the Linn County Auditor's Office. Highlights: ► Chlordanes and PCBs congeners were measured in surficial soil from Cedar Rapids, Iowa. ► Measured values for both chemical groups are similar to other urban/industrial site around the world. ► This is one of the few urban soil studies in the USA. ► TEQs values are in the same order of magnitude of the provisional threshold recommended by USEPA to perform soil remediation. - Chlordane compounds (trans-, cis- and trans-nonachlor) and PCBs (164 peaks for 209 congeners) were measured in the soils of a small medium-sized American city.

  5. A four-step model for the IL-6 amplifier, a regulator of chronic inflammations in tissue-specific MHC class II-associated autoimmune diseases.

    Science.gov (United States)

    Murakami, Masaaki; Hirano, Toshio

    2011-01-01

    It is commonly thought that autoimmune diseases are caused by the breakdown of self-tolerance, which suggests the recognition of specific antigens by autoreactive CD4+ T cells contribute to the specificity of autoimmune diseases (Marrack et al., 2001; Mathis and Benoist, 2004). In several cases, however, even for diseases associated with class II major histocompatibility complex (MHC) alleles, the causative tissue-specific antigens recognized by memory/activated CD4+ T cells have not been established (Mocci et al., 2000; Skapenko et al., 2005). Rheumatoid arthritis (RA) and arthritis in F759 knock-in mice (F759 mice) are such examples (Atsumi et al., 2002; Brennan et al., 2002; Falgarone et al., 2009). These include associations with class II MHC and CD4 molecules; increased numbers of memory/activated CD4+ T cells; and improved outcomes in response to suppressions and/or deficiencies in class II MHC molecules, CD4+ T cells, and the T cell survival cytokine IL-7. Regarding the development of arthritis in F759 mice, it is not only the immune system, but also non-immune tissue that are involved, indicating that the importance of their interactions (Sawa et al., 2006, 2009; Ogura et al., 2008; Hirano, 2010; Murakami et al., 2011). Furthermore, we have shown that local events such as microbleeding together with an accumulation of activated CD4+ T cells in a manner independent of tissue antigen-recognitions induces arthritis in the joints of F759 mice (Murakami et al., 2011). For example, local microbleeding-mediated CCL20 expression induce such an accumulation, causing arthritis development via chronic activation of an IL-17A-dependent IL-6 signaling amplification loop in type 1 collagen+ cells that is triggered by CD4+ T cell-derived cytokine(s) such as IL-17A, which leads to the synergistic activation of STAT3 and NFκB in non-hematopoietic cells in the joint (Murakami et al., 2011). We named this loop the IL-6-mediated inflammation amplifier, or IL-6 amplifier for

  6. Novel insights into structure-function mechanism and tissue-specific expression profiling of full-length dxr gene from Cymbopogon winterianus.

    Science.gov (United States)

    Devi, Kamalakshi; Dehury, Budheswar; Phukon, Munmi; Modi, Mahendra Kumar; Sen, Priyabrata

    2015-01-01

    The 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR; EC1.1.1.267), an NADPH-dependent reductase, plays a pivotal role in the methylerythritol 4-phosphate pathway (MEP), in the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) into MEP. The sheath and leaf of citronella (Cymbopogon winterianus) accumulates large amount of terpenes and sesquiterpenes with proven medicinal value and economic uses. Thus, sequencing of full length dxr gene and its characterization seems to be a valuable resource in metabolic engineering to alter the flux of isoprenoid active ingredients in plants. In this study, full length DXR from citronella was characterized through in silico and tissue-specific expression studies to explain its structure-function mechanism, mode of cofactor recognition and differential expression. The modelled DXR has a three-domain architecture and its active site comprised of a cofactor (NADPH) binding pocket and the substrate-binding pocket. Molecular dynamics simulation studies indicated that DXR model retained most of its secondary structure during 10 ns simulation in aqueous solution. The modelled DXR superimposes well with its closest structural homolog but subtle variations in the charge distribution over the cofactor recognition site were noticed. Molecular docking study revealed critical residues aiding tight anchoring NADPH within the active pocket of DXR. Tissue-specific differential expression analysis using semi-quantitative RT-PCR and qRT-PCR in various tissues of citronella plant revealed distinct differential expression of DXR. To our knowledge, this is the first ever report on DXR from the important medicinal plant citronella and further characterization of this gene will open up better avenues for metabolic engineering of secondary metabolite pathway genes from medicinal plants in the near future.

  7. Novel insights into structure–function mechanism and tissue-specific expression profiling of full-length dxr gene from Cymbopogon winterianus

    Science.gov (United States)

    Devi, Kamalakshi; Dehury, Budheswar; Phukon, Munmi; Modi, Mahendra Kumar; Sen, Priyabrata

    2015-01-01

    The 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR; EC1.1.1.267), an NADPH-dependent reductase, plays a pivotal role in the methylerythritol 4-phosphate pathway (MEP), in the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) into MEP. The sheath and leaf of citronella (Cymbopogon winterianus) accumulates large amount of terpenes and sesquiterpenes with proven medicinal value and economic uses. Thus, sequencing of full length dxr gene and its characterization seems to be a valuable resource in metabolic engineering to alter the flux of isoprenoid active ingredients in plants. In this study, full length DXR from citronella was characterized through in silico and tissue-specific expression studies to explain its structure–function mechanism, mode of cofactor recognition and differential expression. The modelled DXR has a three-domain architecture and its active site comprised of a cofactor (NADPH) binding pocket and the substrate-binding pocket. Molecular dynamics simulation studies indicated that DXR model retained most of its secondary structure during 10 ns simulation in aqueous solution. The modelled DXR superimposes well with its closest structural homolog but subtle variations in the charge distribution over the cofactor recognition site were noticed. Molecular docking study revealed critical residues aiding tight anchoring NADPH within the active pocket of DXR. Tissue-specific differential expression analysis using semi-quantitative RT-PCR and qRT-PCR in various tissues of citronella plant revealed distinct differential expression of DXR. To our knowledge, this is the first ever report on DXR from the important medicinal plant citronella and further characterization of this gene will open up better avenues for metabolic engineering of secondary metabolite pathway genes from medicinal plants in the near future. PMID:25941629

  8. Effects of chronic exposure to waterborne copper and nickel in binary mixture on tissue-specific metal accumulation and reproduction in fathead minnow (Pimephales promelas).

    Science.gov (United States)

    Driessnack, Melissa K; Jamwal, Ankur; Niyogi, Som

    2017-10-01

    The current study evaluated the interactive effects of chronic waterborne copper (Cu) and nickel (Ni) exposure on tissue-specific metal accumulation and reproductive performance in fathead minnow (Pimephales promelas). Fish trios (1 male: 2 female; n = 5-6) were exposed for 21 days to: (i) control (no added Cu or Ni), (ii) waterborne Cu (45 μg/L), (iii) waterborne Ni (270 μg/L), and (iv) binary mixture of waterborne Cu and Ni (45 and 270 μg/L, respectively). Fish fecundity (cumulative egg production) was found to be the most sensitive reproductive endpoint, and the interaction of Cu and Ni elicited an additive effect on egg production. Tissue-specific accumulation of both metals was not influenced by the interaction of Cu and Ni, except an increased Cu and Ni burden in the carcass and ovary, respectively, were recorded. The expressions of hepatic estrogen receptor genes (ER-α and ER-β) and the circulating estradiol level in females were also not affected by the metal-mixture treatment. However, co-exposure to waterborne Cu and Ni resulted in a significant downregulation of the hepatic vitellogenin gene in females, which was associated with the maximum upregulation of the hepatic metallothionein gene. In addition, a significant alteration of ovarian histopathology (decreased abundance of post-vitellogenic follicles, and increased follicular atresia) was also observed only in females exposed to Cu and Ni in mixture. Collectively, these observations suggest that chronic waterborne exposure to Cu and Ni in binary mixture may impair fish reproductive capacity by inducing histopathological damage in ovarian tissue, and disrupting of energy homeostasis in fish. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Identification of CTLA2A, DEFB29, WFDC15B, SERPINA1F and MUP19 as Novel Tissue-Specific Secretory Factors in Mouse.

    Directory of Open Access Journals (Sweden)

    Jibin Zhang

    Full Text Available Secretory factors in animals play an important role in communication between different cells, tissues and organs. Especially, the secretory factors with specific expression in one tissue may reflect important functions and unique status of that tissue in an organism. In this study, we identified potential tissue-specific secretory factors in the fat, muscle, heart, lung, kidney and liver in the mouse by analyzing microarray data from NCBI's Gene Expression Omnibus (GEO public repository and searching and predicting their subcellular location in GeneCards and WoLF PSORT, and then confirmed tissue-specific expression of the genes using semi-quantitative PCR reactions. With this approach, we confirmed 11 lung, 7 liver, 2 heart, 1 heart and muscle, 7 kidney and 2 adipose and liver-specific secretory factors. Among these genes, 1 lung-specific gene--CTLA2A (cytotoxic T lymphocyte-associated protein 2 alpha, 3 kidney-specific genes--SERPINA1F (serpin peptidase inhibitor, Clade A, member 1F, WFDC15B (WAP four-disulfide core domain 15B and DEFB29 (defensin beta 29 and 1 liver-specific gene--MUP19 (major urinary protein 19 have not been reported as secretory factors. These genes were tagged with hemagglutinin at the 3'end and then transiently transfected to HEK293 cells. Through protein detection in cell lysate and media using Western blotting, we verified secretion of the 5 genes and predicted the potential pathways in which they may participate in the specific tissue through data analysis of GEO profiles. In addition, alternative splicing was detected in transcripts of CTLA2A and SERPINA1F and the corresponding proteins were found not to be secreted in cell culture media. Identification of novel secretory factors through the current study provides a new platform to explore novel secretory factors and a general direction for further study of these genes in the future.

  10. Epigenetic events determine tissue-specific toxicity of inhalational exposure to the genotoxic chemical 1,3-butadiene in male C57BL/6J mice.

    Science.gov (United States)

    Chappell, Grace; Kobets, Tetyana; O'Brien, Bridget; Tretyakova, Natalia; Sangaraju, Dewakar; Kosyk, Oksana; Sexton, Kenneth G; Bodnar, Wanda; Pogribny, Igor P; Rusyn, Ivan

    2014-12-01

    1,3-Butadiene (BD), a widely used industrial chemical and a ubiquitous environmental pollutant, is a known human carcinogen. Although genotoxicity is an established mechanism of the tumorigenicity of BD, epigenetic effects have also been observed in livers of mice exposed to the chemical. To better characterize the diverse molecular mechanisms of BD tumorigenicity, we evaluated genotoxic and epigenotoxic effects of BD exposure in mouse tissues that are target (lung and liver) and non-target (kidney) for BD-induced tumors. We hypothesized that epigenetic alterations may explain, at least in part, the tissue-specific differences in BD tumorigenicity in mice. We evaluated the level of N-7-(2,3,4-trihydroxybut-1-yl)guanine adducts and 1,4-bis-(guan-7-yl)-2,3-butanediol crosslinks, DNA methylation, and histone modifications in male C57BL/6 mice exposed to filtered air or 425 ppm of BD by inhalation (6 h/day, 5 days/week) for 2 weeks. Although DNA damage was observed in all three tissues of BD-exposed mice, variation in epigenetic effects clearly existed between the kidneys, liver, and lungs. Epigenetic alterations indicative of genomic instability, including demethylation of repetitive DNA sequences and alterations in histone-lysine acetylation, were evident in the liver and lung tissues of BD-exposed mice. Changes in DNA methylation were insignificant in the kidneys of treated mice, whereas marks of condensed heterochromatin and transcriptional silencing (histone-lysine trimethylation) were increased. These modifications may represent a potential mechanistic explanation for the lack of tumorigenesis in the kidney. Our results indicate that differential tissue susceptibility to chemical-induced tumorigenesis may be attributed to tissue-specific epigenetic alterations. Published by Oxford University Press on behalf of the Society of Toxicology 2014. This work is written by US Government employees and is in the public domain in the US.

  11. Gene Electrotransfer of Plasmid with Tissue Specific Promoter Encoding shRNA against Endoglin Exerts Antitumor Efficacy against Murine TS/A Tumors by Vascular Targeted Effects.

    Directory of Open Access Journals (Sweden)

    Monika Stimac

    Full Text Available Vascular targeted therapies, targeting specific endothelial cell markers, are promising approaches for the treatment of cancer. One of the targets is endoglin, transforming growth factor-β (TGF-β co-receptor, which mediates proliferation, differentiation and migration of endothelial cells forming neovasculature. However, its specific, safe and long-lasting targeting remains the challenge. Therefore, in our study we evaluated the transfection efficacy, vascular targeted effects and therapeutic potential of the plasmid silencing endoglin with the tissue specific promoter, specific for endothelial cells marker endothelin-1 (ET (TS plasmid, in comparison to the plasmid with constitutive promoter (CON plasmid, in vitro and in vivo. Tissue specificity of TS plasmid was demonstrated in vitro on several cell lines, and its antiangiogenic efficacy was demonstrated by reducing tube formation of 2H11 endothelial cells. In vivo, on a murine mammary TS/A tumor model, we demonstrated good antitumor effect of gene electrotransfer (GET of either of both plasmids in treatment of smaller tumors still in avascular phase of growth, as well as on bigger tumors, already well vascularized. In support to the observations on predominantly vascular targeted effects of endoglin, histological analysis has demonstrated an increase in necrosis and a decrease in the number of blood vessels in therapeutic groups. A significant antitumor effect was observed in tumors in avascular and vascular phase of growth, possibly due to both, the antiangiogenic and the vascular disrupting effect. Furthermore, the study indicates on the potential use of TS plasmid in cancer gene therapy since the same efficacy as of CON plasmid was determined.

  12. An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality

    Directory of Open Access Journals (Sweden)

    Marc Galland

    2017-11-01

    Full Text Available Although rice is a key crop species, few studies have addressed both rice seed physiological and nutritional quality, especially at the tissue level. In this study, an exhaustive “multi-omics” dataset on the mature rice seed was obtained by combining transcriptomics, label-free shotgun proteomics and metabolomics from embryo and endosperm, independently. These high-throughput analyses provide a new insight on the tissue-specificity related to rice seed quality. Foremost, we pinpointed that extensive post-transcriptional regulations occur at the end of rice seed development such that the embryo proteome becomes much more diversified than the endosperm proteome. Secondly, we observed that survival in the dry state in each seed compartment depends on contrasted metabolic and enzymatic apparatus in the embryo and the endosperm, respectively. Thirdly, it was remarkable to identify two different sets of starch biosynthesis enzymes as well as seed storage proteins (glutelins in both embryo and endosperm consistently with the supernumerary embryo hypothesis origin of the endosperm. The presence of a putative new glutelin with a possible embryonic favored abundance is described here for the first time. Finally, we quantified the rate of mRNA translation into proteins. Consistently, the embryonic panel of protein translation initiation factors is much more diverse than that of the endosperm. This work emphasizes the value of tissue-specificity-centered “multi-omics” study in the seed to highlight new features even from well-characterized pathways. It paves the way for future studies of critical genetic determinants of rice seed physiological and nutritional quality.

  13. An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality

    Science.gov (United States)

    Galland, Marc; He, Dongli; Lounifi, Imen; Arc, Erwann; Clément, Gilles; Balzergue, Sandrine; Huguet, Stéphanie; Cueff, Gwendal; Godin, Béatrice; Collet, Boris; Granier, Fabienne; Morin, Halima; Tran, Joseph; Valot, Benoit; Rajjou, Loïc

    2017-01-01

    Although rice is a key crop species, few studies have addressed both rice seed physiological and nutritional quality, especially at the tissue level. In this study, an exhaustive “multi-omics” dataset on the mature rice seed was obtained by combining transcriptomics, label-free shotgun proteomics and metabolomics from embryo and endosperm, independently. These high-throughput analyses provide a new insight on the tissue-specificity related to rice seed quality. Foremost, we pinpointed that extensive post-transcriptional regulations occur at the end of rice seed development such that the embryo proteome becomes much more diversified than the endosperm proteome. Secondly, we observed that survival in the dry state in each seed compartment depends on contrasted metabolic and enzymatic apparatus in the embryo and the endosperm, respectively. Thirdly, it was remarkable to identify two different sets of starch biosynthesis enzymes as well as seed storage proteins (glutelins) in both embryo and endosperm consistently with the supernumerary embryo hypothesis origin of the endosperm. The presence of a putative new glutelin with a possible embryonic favored abundance is described here for the first time. Finally, we quantified the rate of mRNA translation into proteins. Consistently, the embryonic panel of protein translation initiation factors is much more diverse than that of the endosperm. This work emphasizes the value of tissue-specificity-centered “multi-omics” study in the seed to highlight new features even from well-characterized pathways. It paves the way for future studies of critical genetic determinants of rice seed physiological and nutritional quality. PMID:29213276

  14. The impact of laser ablation on optical soft tissue differentiation for tissue specific laser surgery-an experimental ex vivo study

    Directory of Open Access Journals (Sweden)

    Stelzle Florian

    2012-06-01

    Full Text Available Abstract Background Optical diffuse reflectance can remotely differentiate various bio tissues. To implement this technique in an optical feedback system to guide laser surgery in a tissue-specific way, the alteration of optical tissue properties by laser ablation has to be taken into account. It was the aim of this study to evaluate the general feasibility of optical soft tissue differentiation by diffuse reflectance spectroscopy under the influence of laser ablation, comparing the tissue differentiation results before and after laser intervention. Methods A total of 70 ex vivo tissue samples (5 tissue types were taken from 14 bisected pig heads. Diffuse reflectance spectra were recorded before and after Er:YAG-laser ablation. The spectra were analyzed and differentiated using principal component analysis (PCA, followed by linear discriminant analysis (LDA. To assess the potential of tissue differentiation, area under the curve (AUC, sensitivity and specificity was computed for each pair of tissue types before and after laser ablation, and compared to each other. Results Optical tissue differentiation showed good results before laser exposure (total classification error 13.51%. However, the tissue pair nerve and fat yielded lower AUC results of only 0.75. After laser ablation slightly reduced differentiation results were found with a total classification error of 16.83%. The tissue pair nerve and fat showed enhanced differentiation (AUC: 0.85. Laser ablation reduced the sensitivity in 50% and specificity in 80% of the cases of tissue pair comparison. The sensitivity of nerve–fat differentiation was enhanced by 35%. Conclusions The observed results show the general feasibility of tissue differentiation by diffuse reflectance spectroscopy even under conditions of tissue alteration by laser ablation. The contrast enhancement for the differentiation between nerve and fat tissue after ablation is assumed to be due to laser removal of the

  15. Pure non-dioxin-like PCB congeners suppress induction of the AhR-dependent endpoints in rat liver cells

    NARCIS (Netherlands)

    Brenerová, J.; Hamers, T.; Kamstra, J.H.; Vondráček, J.; Strapáčová, S.; Andersson, P.L.; Machala, M.

    2016-01-01

    The relative potencies of non-ortho-substituted coplanar polychlorinated biphenyl (PCB) congeners to activate the aryl hydrocarbon receptor (AhR) and to cause the AhR-dependent toxic events are essential for their risk assessment. Since some studies suggested that abundant non-dioxin-like PCB

  16. Response to Ecological Risk Assessment Forum Request for Information on the Benefits of PCB Congener-Specific Analyses

    Science.gov (United States)

    In August, 2001, the Ecological Risk Assessment Forum (ERAF) submitted a formal question to the Ecological Risk Assessment Support Center (ERASC) on the benefits of evaluating PCB congeners in environmental samples. This question was developed by ERAF members Bruce Duncan and Cla...

  17. Long-term trends in mercury and PCB congener concentrations in gannet (Morus bassanus) eggs in Britain

    International Nuclear Information System (INIS)

    Pereira, M. Gloria; Walker, Lee A.; Best, Jennifer; Shore, Richard F.

    2009-01-01

    Gannet (Morus bassanus) eggs from Bass Rock (North Sea) and Ailsa Craig (eastern Atlantic) were monitored for PCB congeners (1990-2004) and total mercury (1974-2004). Congener profiles for both colonies were dominated by PCBs 153, 138, 180, 118 and 170. All declined in concentration at Ailsa Craig but some (153, 170, 180) remained stable or increased slightly at Bass Rock. Egg congener concentrations at Bass Rock were typically 10-fold higher than at Ailsa Craig by 2002, and Principal Component Analysis indicated that colony differences were driven by the dominant congeners. Egg mercury concentrations were significantly lower at Bass Rock than at Ailsa Craig and temporal trends differed, there being a significant decline at Ailsa Craig but a marginal increase at Bass Rock. Our results suggest there may be differences in contamination between the eastern Atlantic and North Sea and/or there are colony differences in prey selection and associated contaminant loads. - Monitoring of PCBs and Hg in gannet eggs reveals contrasting temporal patterns between colonies on the eastern Atlantic and North Sea coasts of Britain

  18. TISSUE DISTRIBUTION OF PCBS AND ORGANOCHLORINE PESTICIDES IN ALASKAN NORTHERN FUR SEALS: COMPARISON OF VARIOUS CONGENER CLASSIFICATION SCHEMES

    Science.gov (United States)

    Polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) are believed to adversely affect reproduction and cause health problems in Pinnipeds 1-4. In this study, 145 PCB congeners and OCPs were analyzed in 10 juvenile male northern fur seals, Callorhinus ursinus, collected from Alaskan...

  19. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.

    Science.gov (United States)

    Londin, Eric; Loher, Phillipe; Telonis, Aristeidis G; Quann, Kevin; Clark, Peter; Jing, Yi; Hatzimichael, Eleftheria; Kirino, Yohei; Honda, Shozo; Lally, Michelle; Ramratnam, Bharat; Comstock, Clay E S; Knudsen, Karen E; Gomella, Leonard; Spaeth, George L; Hark, Lisa; Katz, L Jay; Witkiewicz, Agnieszka; Rostami, Abdolmohamad; Jimenez, Sergio A; Hollingsworth, Michael A; Yeh, Jen Jen; Shaw, Chad A; McKenzie, Steven E; Bray, Paul; Nelson, Peter T; Zupo, Simona; Van Roosbroeck, Katrien; Keating, Michael J; Calin, George A; Yeo, Charles; Jimbo, Masaya; Cozzitorto, Joseph; Brody, Jonathan R; Delgrosso, Kathleen; Mattick, John S; Fortina, Paolo; Rigoutsos, Isidore

    2015-03-10

    Two decades after the discovery of the first animal microRNA (miRNA), the number of miRNAs in animal genomes remains a vexing question. Here, we report findings from analyzing 1,323 short RNA sequencing samples (RNA-seq) from 13 different human tissue types. Using stringent thresholding criteria, we identified 3,707 statistically significant novel mature miRNAs at a false discovery rate of ≤ 0.05 arising from 3,494 novel precursors; 91.5% of these novel miRNAs were identified independently in 10 or more of the processed samples. Analysis of these novel miRNAs revealed tissue-specific dependencies and a commensurate low Jaccard similarity index in intertissue comparisons. Of these novel miRNAs, 1,657 (45%) were identified in 43 datasets that were generated by cross-linking followed by Argonaute immunoprecipitation and sequencing (Ago CLIP-seq) and represented 3 of the 13 tissues, indicating that these miRNAs are active in the RNA interference pathway. Moreover, experimental investigation through stem-loop PCR of a random collection of newly discovered miRNAs in 12 cell lines representing 5 tissues confirmed their presence and tissue dependence. Among the newly identified miRNAs are many novel miRNA clusters, new members of known miRNA clusters, previously unreported products from uncharacterized arms of miRNA precursors, and previously unrecognized paralogues of functionally important miRNA families (e.g., miR-15/107). Examination of the sequence conservation across vertebrate and invertebrate organisms showed 56.7% of the newly discovered miRNAs to be human-specific whereas the majority (94.4%) are primate lineage-specific. Our findings suggest that the repertoire of human miRNAs is far more extensive than currently represented by public repositories and that there is a significant number of lineage- and/or tissue-specific miRNAs that are uncharacterized.

  20. Structural evolution and tissue-specific expression of tetrapod-specific second isoform of secretory pathway Ca{sup 2+}-ATPase

    Energy Technology Data Exchange (ETDEWEB)

    Pestov, Nikolay B., E-mail: korn@mail.ibch.ru [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Dmitriev, Ruslan I.; Kostina, Maria B. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Korneenko, Tatyana V. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Department of Physiology and Pharmacology, University of Toledo College of Medicine, 3000 Arlington Ave., Toledo, OH 43614 (United States); Shakhparonov, Mikhail I. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Modyanov, Nikolai N., E-mail: nikolai.modyanov@utoledo.edu [Department of Physiology and Pharmacology, University of Toledo College of Medicine, 3000 Arlington Ave., Toledo, OH 43614 (United States)

    2012-01-27

    Highlights: Black-Right-Pointing-Pointer Full-length secretory pathway Ca-ATPase (SPCA2) cloned from rat duodenum. Black-Right-Pointing-Pointer ATP2C2 gene (encoding SPCA2) exists only in genomes of Tetrapoda. Black-Right-Pointing-Pointer Rat and pig SPCA2 are expressed in intestines, lung and some secretory glands. Black-Right-Pointing-Pointer Subcellular localization of SPCA2 may depend on tissue type. Black-Right-Pointing-Pointer In rat duodenum, SPCA2 is localized in plasma membrane-associated compartments. -- Abstract: Secretory pathway Ca-ATPases are less characterized mammalian calcium pumps than plasma membrane Ca-ATPases and sarco-endoplasmic reticulum Ca-ATPases. Here we report analysis of molecular evolution, alternative splicing, tissue-specific expression and subcellular localization of the second isoform of the secretory pathway Ca-ATPase (SPCA2), the product of the ATP2C2 gene. The primary structure of SPCA2 from rat duodenum deduced from full-length transcript contains 944 amino acid residues, and exhibits 65% sequence identity with known SPCA1. The rat SPCA2 sequence is also highly homologous to putative human protein KIAA0703, however, the latter seems to have an aberrant N-terminus originating from intron 2. The tissue-specificity of SPCA2 expression is different from ubiquitous SPCA1. Rat SPCA2 transcripts were detected predominantly in gastrointestinal tract, lung, trachea, lactating mammary gland, skin and preputial gland. In the newborn pig, the expression profile is very similar with one remarkable exception: porcine bulbourethral gland gave the strongest signal. Upon overexpression in cultured cells, SPCA2 shows an intracellular distribution with remarkable enrichment in Golgi. However, in vivo SPCA2 may be localized in compartments that differ among various tissues: it is intracellular in epidermis, but enriched in plasma membranes of the intestinal epithelium. Analysis of SPCA2 sequences from various vertebrate species argue that ATP2C2

  1. Pharmacokinetic Properties of Adenosine Amine Congener in Cochlear Perilymph after Systemic Administration

    Directory of Open Access Journals (Sweden)

    Hao Chang

    2017-01-01

    Full Text Available Noise-induced hearing loss (NIHL is a global health problem affecting over 5% of the population worldwide. We have shown previously that acute noise-induced cochlear injury can be ameliorated by administration of drugs acting on adenosine receptors in the inner ear, and a selective A1 adenosine receptor agonist adenosine amine congener (ADAC has emerged as a potentially effective treatment for cochlear injury and resulting hearing loss. This study investigated pharmacokinetic properties of ADAC in rat perilymph after systemic (intravenous administration using a newly developed liquid chromatography-tandem mass spectrometry detection method. The method was developed and validated in accordance with the USA FDA guidelines including accuracy, precision, specificity, and linearity. Perilymph was sampled from the apical turn of the cochlea to prevent contamination with the cerebrospinal fluid. ADAC was detected in cochlear perilymph within two minutes following intravenous administration and remained in perilymph above its minimal effective concentration for at least two hours. The pharmacokinetic pattern of ADAC was significantly altered by exposure to noise, suggesting transient changes in permeability of the blood-labyrinth barrier and/or cochlear blood flow. This study supports ADAC development as a potential clinical otological treatment for acute sensorineural hearing loss caused by exposure to traumatic noise.

  2. Hydroxylated PBDE metabolites in rat blood after exposure to a mixture of PBDE congeners

    Energy Technology Data Exchange (ETDEWEB)

    Malmberg, T.; Athanasiadou, M.; Marsh, G.; Bergman, Aa. [Department of Environmental Chemistry, Stockholm (Sweden); Brandt, I. [Uppsala Univ. (Sweden). Dept. of Environmental Toxicology

    2004-09-15

    Halogenated aromatic compounds are in general both hydrophobic and slowly reacting chemicals, often referred to as persistent organic pollutants (POPs). These chemicals are however by no means inert. They are instead undergoing metabolism in wildlife and humans leading to the formation of halogenated phenolic compounds (HPCs) and when certain structural criteria are fulfilled methyl sulfone metabolites may be formed. Interestingly, a large number of HPCs are retained in blood and up to almost 50 of those have been structurally identified in human plasma. The majority of all HPCs identified until now are OH-PCBs. The OH-PCBs retained in plasma or serum are substituted with the hydroxyl group in preferentially the para position, or as in a limited number of cases the meta position, holding chlorine atoms on both sides of the hydroxyl group. The OHPCBs are retained due to strong competitive thyroxine binding to transthyretin (TTR). Until now, no studies have been performed to determine if also PBDE metabolites, OH-PBDEs, are retained in the blood of e.g. rats. The aim of of this study was to determine the potential OH-PBDE profile in blood after dosing equimolar amounts of seven PBDE congeners to rats.

  3. Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans.

    Science.gov (United States)

    Ahmad, Aijaz; Wani, Mohmmad Younus; Khan, Amber; Manzoor, Nikhat; Molepo, Julitha

    2015-01-01

    We previously reported the antifungal properties of a monoterpene phenol "Eugenol" against different Candida strains and have observed that the addition of methyl group to eugenol drastically increased its antimicrobial potency. Based on the results and the importance of medicinal synthetic chemistry, we synthesized eugenol-tosylate and its congeners (E1-E6) and tested their antifungal activity against different clinical fluconazole (FLC)- susceptible and FLC- resistant C. albicans isolates alone and in combination with FLC by determining fractional inhibitory concentration indices (FICIs) and isobolograms calculated from microdilution assays. Minimum inhibitory concentration (MIC) results confirmed that all the tested C. albicans strains were variably susceptible to the semi-synthetic derivatives E1-E6, with MIC values ranging from 1-62 μg/ml. The test compounds in combination with FLC exhibited either synergy (36%), additive (41%) or indifferent (23%) interactions, however, no antagonistic interactions were observed. The MICs of FLC decreased 2-9 fold when used in combination with the test compounds. Like their precursor eugenol, all the derivatives showed significant impairment of ergosterol biosynthesis in all C. albicans strains coupled with down regulation of the important ergosterol biosynthesis pathway gene-ERG11. The results were further validated by docking studies, which revealed that the inhibitors snugly fitting the active site of the target enzyme, mimicking fluconazole, may well explain their excellent inhibitory activity. Our results suggest that these compounds have a great potential as antifungals, which can be used as chemosensitizing agents with the known antifungal drugs.

  4. Congenic strain confirms putative quantitative trait locus for body weight in the rat.

    Science.gov (United States)

    Kovács, P; Voigt, B; Klöting, I

    1998-04-01

    Quantitative trait loci (QTLs) affecting body weight were investigated in the backcross population derived from non-diabetic BB/OK and spontaneously hypertensive rat (SHR) strains. The F1 hybrids were backcrossed onto SHR rats, and QTL analysis was performed separately with the resulting backcross populations for each sex on Chromosomes (Chrs) 1, 3, 4, 10, 13, and 18. The body weight was determined at the age of 14 weeks, and the statistical analysis was performed with MAPMAKER/QTL 1.1b computer program. According to the stringent threshold for a lod score of 3.0, markers on Chr 1 were found to be linked with body weight. The QTL with a peak lod score (5.1) on Chr 1 for a male population was located within markers Igf2 and D1Mgh12. In contrast, in the female population the body weight affecting QTL (lod = 5.7) on Chr 1 was located between the D1Mit3 and Lsn markers. The existence of QTLs on Chr 1 affecting body weight in the male population was confirmed by congenic BB.Sa rats, carrying chromosomal region of SHR (Sa-Igf2) on the genetic background of BB rat.

  5. Hydrocortisone-induced embryotoxicity and embryonic drug disposition in H-2 congenic mice

    International Nuclear Information System (INIS)

    Roberts, L.S.G.

    1986-01-01

    Congenic mouse strains C57BL/10Sn (B10) and B10.A/SgSn(B10A), genetically different only at the H-2 complex, were compared for sensitivity to glucocorticoid-induced embryotoxicity and embryonic drug disposition. B10A mice dosed intramuscularly with 0, 100, 150 and 200 mg hydrocortisone/kg body weight on gestational day twelve, and B10 mice injected with 0, 200, 400, 600, and 800 mg/kg, were evaluated at dissection on gestational day eighteen for signs of toxicity. In both strains, probit analysis of cleft palate production demonstrated a linear dose response. The ED50 for cleft palate production demonstrates a linear dose response. The ED50 for cleft palate production in B10A mice was 143.6 mg/kg and 512.0 mg/kg for the B10 strain. Embryonic exposure was evaluated by administration of 3 H-hydrocortisone (5 uCi/mouse) to pregnant mice on day twelve of gestation, at the ED50 for cleft palate production in B10A strain. The purposes of the experiment were to quantify the difference in susceptibility to steroid-induced cleft palate, determine if a milder manifestation of embryotoxicity, fetal growth retardation, occurred at sub-clefting dosages, and determine if the difference in sensitivity to hydrocortisone-induced embryotoxicity was the result of an underlying difference in embryonic exposure to the teratogen

  6. Tri(pyridylmethyl)phosphine: the elusive congener of TPA shows surprisingly different coordination behavior.

    Science.gov (United States)

    Whiteoak, Christopher J; Nobbs, James D; Kiryushchenkov, Evgeny; Pagano, Sandro; White, Andrew J P; Britovsek, George J P

    2013-06-17

    Tri(pyridylmethyl)phosphine (TPPh), the remarkably elusive congener of tri(pyridylmethyl)amine (TPA), has been prepared, as well as the relative tri(N-methyl-pyridylamino)phosphine (TPAMP). The coordination properties of these new ligands have been evaluated for chromium(III), iron(II), and ruthenium(II) complexes and compared with the related TPA complexes. In all cases, a different coordination behavior has been observed whereby TPPh and TPAMP always act as tridentate ligands. A chromium(III) complex [Cr(TPPh)Cl3] has been prepared, which has shown low ethylene oligomerization activity. Octahedral low spin iron(II) complexes [Fe(TPPh)2](2+) and [Fe(TPAMP)2](2+) were obtained with two ligands bound to the metal center. Ruthenium(II) chloro complexes of TPA and TPPh undergo ligand exchange reactions in acetonitrile, and the ruthenium(II) complex [Ru(MeCN)2(TPA)](2+) can be oxidized by m-CPBA in acetonitrile to give a transient ruthenium(IV) oxo complex [Ru(O)(MeCN)(TPA)](2+). Attempts to generate high valent ruthenium(IV) oxo TPPh or TPAMP complexes could not be achieved, probably due to insufficient stabilization by these strong field ligands.

  7. The tissue-specific Rep8/UBXD6 tethers p97 to the endoplasmic reticulum membrane for degradation of misfolded proteins.

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    Louise Madsen

    Full Text Available The protein known as p97 or VCP in mammals and Cdc48 in yeast is a versatile ATPase complex involved in several biological functions including membrane fusion, protein folding, and activation of membrane-bound transcription factors. In addition, p97 plays a central role in degradation of misfolded secretory proteins via the ER-associated degradation pathway. This functional diversity of p97 depends on its association with various cofactors, and to further our understanding of p97 function it is important that these cofactors are identified and analyzed. Here, we isolate and characterize the human protein named Rep8 or Ubxd6 as a new cofactor of p97. Mouse Rep8 is highly tissue-specific and abundant in gonads. In testes, Rep8 is expressed in post-meiotic round spermatids, whereas in ovaries Rep8 is expressed in granulosa cells. Rep8 associates directly with p97 via its UBX domain. We show that Rep8 is a transmembrane protein that localizes to the ER membrane with its UBX domain facing the cytoplasm. Knock-down of Rep8 expression in human cells leads to a decreased association of p97 with the ER membrane and concomitantly a retarded degradation of misfolded ER-derived proteasome substrates. Thus, Rep8 tethers p97 to the ER membrane for efficient ER-associated degradation.

  8. Alternative splicing and tissue-specific elastin misassembly act as biological modifiers of human elastin gene frameshift mutations associated with dominant cutis laxa.

    Science.gov (United States)

    Sugitani, Hideki; Hirano, Eiichi; Knutsen, Russell H; Shifren, Adrian; Wagenseil, Jessica E; Ciliberto, Christopher; Kozel, Beth A; Urban, Zsolt; Davis, Elaine C; Broekelmann, Thomas J; Mecham, Robert P

    2012-06-22

    Elastin is the extracellular matrix protein in vertebrates that provides elastic recoil to blood vessels, the lung, and skin. Because the elastin gene has undergone significant changes in the primate lineage, modeling elastin diseases in non-human animals can be problematic. To investigate the pathophysiology underlying a class of elastin gene mutations leading to autosomal dominant cutis laxa, we engineered a cutis laxa mutation (single base deletion) into the human elastin gene contained in a bacterial artificial chromosome. When expressed as a transgene in mice, mutant elastin was incorporated into elastic fibers in the skin and lung with adverse effects on tissue function. In contrast, only low levels of mutant protein incorporated into aortic elastin, which explains why the vasculature is relatively unaffected in this disease. RNA stability studies found that alternative exon splicing acts as a modifier of disease severity by influencing the spectrum of mutant transcripts that survive nonsense-mediated decay. Our results confirm the critical role of the C-terminal region of tropoelastin in elastic fiber assembly and suggest tissue-specific differences in the elastin assembly pathway.

  9. Alternative Splicing and Tissue-specific Elastin Misassembly Act as Biological Modifiers of Human Elastin Gene Frameshift Mutations Associated with Dominant Cutis Laxa*

    Science.gov (United States)

    Sugitani, Hideki; Hirano, Eiichi; Knutsen, Russell H.; Shifren, Adrian; Wagenseil, Jessica E.; Ciliberto, Christopher; Kozel, Beth A.; Urban, Zsolt; Davis, Elaine C.; Broekelmann, Thomas J.; Mecham, Robert P.

    2012-01-01

    Elastin is the extracellular matrix protein in vertebrates that provides elastic recoil to blood vessels, the lung, and skin. Because the elastin gene has undergone significant changes in the primate lineage, modeling elastin diseases in non-human animals can be problematic. To investigate the pathophysiology underlying a class of elastin gene mutations leading to autosomal dominant cutis laxa, we engineered a cutis laxa mutation (single base deletion) into the human elastin gene contained in a bacterial artificial chromosome. When expressed as a transgene in mice, mutant elastin was incorporated into elastic fibers in the skin and lung with adverse effects on tissue function. In contrast, only low levels of mutant protein incorporated into aortic elastin, which explains why the vasculature is relatively unaffected in this disease. RNA stability studies found that alternative exon splicing acts as a modifier of disease severity by influencing the spectrum of mutant transcripts that survive nonsense-mediated decay. Our results confirm the critical role of the C-terminal region of tropoelastin in elastic fiber assembly and suggest tissue-specific differences in the elastin assembly pathway. PMID:22573328

  10. Evolutionary rate heterogeneity between multi- and single-interface hubs across human housekeeping and tissue-specific protein interaction network: Insights from proteins' and its partners' properties.

    Science.gov (United States)

    Biswas, Kakali; Acharya, Debarun; Podder, Soumita; Ghosh, Tapash Chandra

    2017-12-02

    Integrating gene expression into protein-protein interaction network (PPIN) leads to the construction of tissue-specific (TS) and housekeeping (HK) sub-networks, with distinctive TS- and HK-hubs. All such hub proteins are divided into multi-interface (MI) hubs and single-interface (SI) hubs, where MI hubs evolve slower than SI hubs. Here we explored the evolutionary rate difference between MI and SI proteins within TS- and HK-PPIN and observed that this difference is present only in TS, but not in HK-class. Next, we explored whether proteins' own properties or its partners' properties are more influential in such evolutionary discrepancy. Statistical analyses revealed that this evolutionary rate correlates negatively with protein's own properties like expression level, miRNA count, conformational diversity and functional properties and with its partners' properties like protein disorder and tissue expression similarity. Moreover, partial correlation and regression analysis revealed that both proteins' and its partners' properties have independent effects on protein evolutionary rate. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. A comprehensive genome-wide study on tissue-specific and abiotic stress-specific miRNAs in Triticum aestivum.

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    Ritu Pandey

    Full Text Available Productivity of wheat crop is largely dependent on its growth and development that, in turn, is mainly regulated by environmental conditions, including abiotic stress factors. miRNAs are key regulators of gene expression networks involved in diverse aspects of development and stress responses in plants. Using high-throughput sequencing of eight small RNA libraries prepared from diverse abiotic stresses and tissues, we identified 47 known miRNAs belonging to 20 families, 49 true novel and 1030 candidate novel miRNAs. Digital gene expression analysis revealed that 257 miRNAs exhibited tissue-specific expression and 74 were associated with abiotic stresses. Putative target genes were predicted for miRNAs identified in this study and their grouping into functional categories indicated that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three known miRNAs (miR156, miR160 and miR164 confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by the corresponding miRNAs. Mapping of the sequenced data onto the wheat progenitors and closely related monocots revealed a large number of evolutionary conserved miRNAs. Additional expression profiling of some of these miRNAs in other abiotic stresses underline their involvement in multiple stresses. Our findings provide valuable resource for an improved understanding of the role of miRNAs in stress tolerance as well as plant development.

  12. Persistent Foot-and-Mouth Disease Virus Infection in the Nasopharynx of Cattle; Tissue-Specific Distribution and Local Cytokine Expression.

    Directory of Open Access Journals (Sweden)

    Juan M Pacheco

    Full Text Available Tissues obtained post-mortem from cattle persistently infected with foot-and-mouth disease virus (FMDV were analyzed to characterize the tissue-specific localization of FMDV and partial transcriptome profiles for selected immunoregulatory cytokines. Analysis of 28 distinct anatomic sites from 21 steers infected with FMDV serotype A, O or SAT2, had the highest prevalence of overall viral detection in the dorsal nasopharynx (80.95% and dorsal soft palate (71.43%. FMDV was less frequently detected in laryngeal mucosal tissues, oropharyngeal mucosal sites, and lymph nodes draining the pharynx. Immunomicroscopy indicated that within persistently infected mucosal tissues, FMDV antigens were rarely detectable within few epithelial cells in regions of mucosa-associated lymphoid tissue (MALT. Transcriptome analysis of persistently infected pharyngeal tissues by qRT-PCR for 14 cytokine genes indicated a general trend of decreased mRNA levels compared to uninfected control animals. Although, statistically significant differences were not observed, greatest suppression of relative expression (RE was identified for IP-10 (RE = 0.198, IFN-β (RE = 0.269, IL-12 (RE = 0.275, and IL-2 (RE = 0.312. Increased relative expression was detected for IL-6 (RE = 2.065. Overall, this data demonstrates that during the FMDV carrier state in cattle, viral persistence is associated with epithelial cells of the nasopharynx in the upper respiratory tract and decreased levels of mRNA for several immunoregulatory cytokines in the infected tissues.

  13. Characterization of the tissue-specific expression of phenylalanine ammonia-lyase gene promoter from loblolly pine (Pinus taeda) in Nicotiana tabacum.

    Science.gov (United States)

    Osakabe, Yuriko; Osakabe, Keishi; Chiang, Vincent L

    2009-09-01

    We isolated the 5' flanking region of a gene for phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) from Pinus taeda, PtaPAL. To investigate the tissue-specific expression of the PtaPAL promoter, histochemical assay of GUS activity was performed using the transgenic tobacco expressing the PtaPAL promoter-GUS. The region of -897 to -420 in PtaPAL promoter showed high activities in the secondary xylem and response to bending stress. To characterize the cis-regulatory functions of the promoters for enzymes in phenylpropanoid biosynthesis, we examined the activity of chimeric promoters of PtaPAL and a 4-coumarate CoA ligase, Pta4CL alpha. The chimeric promoter showed similar activity as the Pta4CL alpha promoter. Electrophoretic mobility shift assays implicated -897 to -674 of PtaPAL promoter containing cis-elements of the expression in xylem of Pinus taeda. The results suggested that AC elements of PtaPAL have multiple functions in the expression under the various developmental stages and stress conditions in the transgenic tobacco.

  14. Differential accumulation of β-carotene and tissue specific expression of phytoene synthase (MaPsy) gene in banana (Musa sp) cultivars.

    Science.gov (United States)

    Dhandapani, R; Singh, V P; Arora, A; Bhattacharya, R C; Rajendran, Ambika

    2017-12-01

    An experiment was conducted with twelve major Indian banana cultivars to investigate the molecular relationship between the differential accumulation of β-carotene in peel and pulp of the banana fruit and carotenoid biosynthetic pathway genes. The high performance liquid chromatography showed that all banana cultivars accumulated two-three fold more β-carotene in non-edible portion of the banana fruit. However, Nendran , a famous orange fleshed cultivar of South India, had high β-carotene content (1362 µg/100 g) in edible pulp. The gene encoding Musa accuminata phytoene synthase ( MaPsy ) was successfully amplified using a pair of degenerate primers designed from Oncidium orchid. The deduced amino acid sequences shared a high level of identity to phytoene synthase gene from other plants. Gene expression analysis confirmed the presence of two isoforms ( MaPsy1 and MaPsy2 ) of MaPsy gene in banana fruits. Presence of two isoforms of MaPsy gene in peel and one in pulp confirmed the differential accumulation of β-carotene in banana fruits. However, Nendran accumulated more β-carotene in edible pulp due to presence of both the isoforms of MaPsy gene. Thus, carotenoid accumulation is a tissue specific process strongly dependent on differential expression pattern of two isoforms of MaPsy gene in banana.

  15. Characterization of intravitreally delivered capsid mutant AAV2-Cre vector to induce tissue-specific mutations in murine retinal ganglion cells.

    Science.gov (United States)

    Langouet-Astrie, Christophe J; Yang, Zhiyong; Polisetti, Sraavya M; Welsbie, Derek S; Hauswirth, William W; Zack, Donald J; Merbs, Shannath L; Enke, Raymond A

    2016-10-01

    Targeted expression of Cre recombinase in murine retinal ganglion cells (RGCs) by viral vector is an effective strategy for creating tissue-specific gene knockouts for investigation of genetic contribution to RGC degeneration associated with optic neuropathies. Here we characterize dosage, efficacy and toxicity for sufficient intravitreal delivery of a capsid mutant Adeno-associated virus 2 (AAV2) vector encoding Cre recombinase. Wild type and Rosa26 (R26) LacZ mice were intravitreally injected with capsid mutant AAV2 viral vectors. Murine eyes were harvested at intervals ranging from 2 weeks to 15 weeks post-injection and were assayed for viral transduction, transgene expression and RGC survival. 10(9) vector genomes (vg) were sufficient for effective in vivo targeting of murine ganglion cell layer (GCL) retinal neurons. Transgene expression was observed as early as 2 weeks post-injection of viral vectors and persisted to 11 weeks. Early expression of Cre had no significant effect on RGC survival, while significant RGC loss was detected beginning 5 weeks post-injection. Early expression of viral Cre recombinase was robust, well-tolerated and predominantly found in GCL neurons suggesting this strategy can be effective in short-term RGC-specific mutation studies in experimental glaucoma models such as optic nerve crush and transection experiments. RGC degeneration with Cre expression for more than 4 weeks suggests that Cre toxicity is a limiting factor for targeted mutation strategies in RGCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea).

    Science.gov (United States)

    Sharma, Ranu; Rawat, Vimal; Suresh, C G

    2017-12-01

    The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species. Around 50% NBS-LRRs reside in macro-syntenic blocks underlining positional conservation along with sequence conservation of NBS-LRR genes in chickpea. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. Four cis -regulatory elements namely WBOX, DRE, CBF, and GCC boxes, that commonly occur in resistance genes, were present in the promoter regions of these genes. Further, the findings will provide a strong background to use candidate disease resistance NBS-encoding genes and identify their specific roles in chickpea.

  17. Temporal and tissue specific regulation of RP-associated splicing factor genes PRPF3, PRPF31 and PRPC8--implications in the pathogenesis of RP.

    Directory of Open Access Journals (Sweden)

    Huibi Cao

    2011-01-01

    Full Text Available Genetic mutations in several ubiquitously expressed RNA splicing genes such as PRPF3, PRP31 and PRPC8, have been found to cause retina-specific diseases in humans. To understand this intriguing phenomenon, most studies have been focused on testing two major hypotheses. One hypothesis assumes that these mutations interrupt retina-specific interactions that are important for RNA splicing, implying that there are specific components in the retina interacting with these splicing factors. The second hypothesis suggests that these mutations have only a mild effect on the protein function and thus affect only the metabolically highly active cells such as retinal photoreceptors.We examined the second hypothesis using the PRPF3 gene as an example. We analyzed the spatial and temporal expression of the PRPF3 gene in mice and found that it is highly expressed in retinal cells relative to other tissues and its expression is developmentally regulated. In addition, we also found that PRP31 and PRPC8 as well as snRNAs are highly expressed in retinal cells.Our data suggest that the retina requires a relatively high level of RNA splicing activity for optimal tissue-specific physiological function. Because the RP18 mutation has neither a debilitating nor acute effect on protein function, we suggest that retinal degeneration is the accumulative effect of decades of suboptimal RNA splicing due to the mildly impaired protein.

  18. MsJ1, an alfalfa DnaJ-like gene, is tissue-specific and transcriptionally regulated during cell cycle.

    Science.gov (United States)

    Frugis, G; Mele, G; Giannino, D; Mariotti, D

    1999-06-01

    DnaJ-like proteins are molecular chaperones that regulate Hsp70 ATPase activity both in protein folding, assembly and disassembly of protein complexes. Here we report the isolation of MsJ1, an alfalfa gene encoding a protein homologous to cytosolic DnaJ-like proteins. MsJ1 was induced under heat-shock treatment in both leaves and stems of adult plants. In the absence of heat shock MsJ1 expression was tissue-specific with the highest levels of mRNA in roots and in embryonal structures. High levels of transcript were also detected in cotyledons where active degradation of storage protein occurs. In synchronized alfalfa suspension-cultured cells the MsJ1 transcript was actively expressed and showed a phase-specific modulation during cell cycle with a 2-fold induction in G2/M. These findings suggest that DnaJ-like proteins play an active role in regulating normal cellular events like protein degradation, morphogenesis and cell cycle progression.

  19. Genome-Wide Comprehensive Analysis the Molecular Phylogenetic Evaluation and Tissue-Specific Expression of SABATH Gene Family in Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2017-12-01

    Full Text Available The plant SABATH gene family is a group of O-methyltransferases (O-MTs, which belongs to the S-adenosyl-l-methionine-dependent methyltransferases (SAM-MTs. The resulting reaction products of SABATH genes play an important role in various processes of plant development. In this study, a total of 30 SABATH genes were detected in Salvia miltiorrhiza, which is an important medicinal plant, widely used to treat cardiovascular disease. Multiple sequence alignment and phylogenetic analyses showed that SmSABATH genes could be classified into three groups. The ratios of non-synonymous (Ka and synonymous (Ks substitution rates of 11 pairs paralogous of SmSABATH genes revealed that the SmSABATH genes had gone through purifying selection. Positive selection analyses using site models and branch-site models indicated that SmSABATH genes had undergone selective pressure for adaptive evolution. Functional divergence analyses suggested that the SmSABATH subgroup genes were divergent in terms of functions and positive selection sites that contributed to a functional divergence among the subgroups that were detected. Tissue-specific expression showed that the SABATH gene family in S. miltiorrhiza was primarily expressed in stems and leaves.

  20. Mouse thymic epithelial cell lines expressing "Aire" and peripheral tissue-specific antigens reproduce in vitro negative selection of T cells.

    Science.gov (United States)

    Yamaguchi, Yoshitaka; Takayanagi, Atsushi; Chen, Jiabing; Sakai, Kosuke; Kudoh, Jun; Shimizu, Nobuyoshi

    2011-08-15

    In the human thymus, AIRE (autoimmune regulator) gene is expressed in a very limited type of medullary thymic epithelial cells (mTECs) and no cognate cell lines are available, hence the molecular analysis of AIRE gene function has been difficult. To improve this situation, we attempted to isolate Aire-expressing cells and established three cell lines (Aire⁺TEC1, Aire⁺TEC2, Aire⁺DC) from the abnormally enlarged thymus, which was developed in the transgenic mice expressing SV40 T-antigen driven by the mouse Aire gene promoter. When these Aire⁺ cell lines were co-cultured with fresh thymocytes, they adhered to the majority of thymocytes and induced apoptosis as if negative selection of T-cells in the thymus is occurring in vitro. Further analysis revealed that these Aire⁺ cell lines are derived from mTECs and exhibit characteristic natures of "antigen presenting cells" including several distinct abilities: to express a variety of peripheral tissue-specific antigens, to produce immunoproteasome and immunological synapse, and to express some of TNFSFs (tumor necrosis factor super families). Thus, the newly established Aire⁺ cell lines will be invaluable for the further detailed analysis of AIRE gene function in the central tolerance of immunity and autoimmune disease. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Comparative analysis of purified Pacific and Caribbean ciguatoxin congeners and related marine toxins using a modified ELISA technique.

    Science.gov (United States)

    Campora, Cara E; Hokama, Y; Ebesu, Joanne S M

    2006-01-01

    The monoclonal antibody to ciguatoxin (CTX) produced from a hybridoma cell line was assayed for the detection of four congeners of CTX: Pacific ciguatoxin-1 (P-CTX-1), Pacific ciguatoxin-2 (P-CTX-2), Pacific ciguatoxin-3 (P-CTX-3), and Caribbean ciguatoxin-1 (C-CTX-1) and related marine toxins, including domoic acid, palytoxin, and okadaic acid, using a modified enzyme-linked immunosorbent assay (ELISA). Lower detection limits were assessed and linearity was statistically established (P<0.05) for P-CTX-1, P-CTX-2, and P-CTX-3 and C-CTX-1 at concentrations ranging from 0 to 5.00 ng, while the other marine toxins showed statistically insignificant cross-reactivities at similar concentrations. Thus, the monoclonal antibody to CTX is able to specifically detect various CTX congeners at levels comparable to those naturally occurring in ciguatoxic fish. (c) 2006 Wiley-Liss, Inc.

  2. Polychlorinated Biphenyl (PCB congener concentrations in aquatic birds. Case study: Ilha Grande Bay, Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    ALDO PACHECO FERREIRA

    2013-01-01

    Full Text Available Livers from 108 birds found prostrate or dead in Ilha Grande Bay between 2005 and 2010 were analyzed for 16 PCB congeners (IUPAC numbers 8, 18, 28, 31, 52, 77, 101, 118, 126, 128, 138, 149, 153, 169, 170, and 180. The species analyzed were Egretta caerulea (Linnaeus 1758, Nycticorax nycticorax (Linnaeus 1758, Egretta thula (Molina 1782, and Ardea cocoi (Linnaeus 1766. The analysis were performed using Origin software (7.5, 2004 with a significant level of p<0.05. Data were checked for adherence to the standard assumptions of parametric tests using the Kolmogorov-Smirnov test for normality and the Levene's test for homogeneity of variances. This has revealed differences in concentration for some congeners. Results indicate relatively low PCBs contamination in aquatic birds, but it is implied the close relationship of environmental contamination, showing potential power of widespread biological and mutagenic adverse effects in trophic levels, and therefore, signalling risk to human health.

  3. Levels and congener profiles of polybrominated diphenyl ethers (PBDEs) in Zebra mussels (D. polymorpha) from Lake Maggiore (Italy)

    Energy Technology Data Exchange (ETDEWEB)

    Binelli, A. [Department of Biology, Via Celoria 26, University of Milan, 20133 Milan (Italy)], E-mail: andrea.binelli@unimi.it; Guzzella, L.; Roscioli, C. [IRSA-CNR, 20047 Brugherio (Milan) (Italy)

    2008-06-15

    Several congeners of polybrominated diphenyl ethers (PBDEs) were monitored in 14 different sampling stations of Lake Maggiore, the second largest Italian lake in regard to surface, volume and average depth, using the sentinel-organism Zebra mussel (Dreissena polymorpha). Results revealed a moderate contamination with {sigma}PBDE levels (BDE-17, -28, -47, -66, -71, -85, -99, -100, -138, -153, -154, -183, -190 and -209) ranging from 40 to 447 ng g{sup -1} lipid weight which are similar to those found in environments polluted by deposition or atmospheric transport. The general order of decreasing congener contribution to the total load was BDE-47 > -99 > -100 > -209, which closely reflected patterns observed in mussels collected in freshwater ecosystems worldwide. - This study shows the first data of PBDE contamination in freshwater invertebrates from Mediterranean basin.

  4. Levels and congener profiles of polybrominated diphenyl ethers (PBDEs) in Zebra mussels (D. polymorpha) from Lake Maggiore (Italy)

    International Nuclear Information System (INIS)

    Binelli, A.; Guzzella, L.; Roscioli, C.

    2008-01-01

    Several congeners of polybrominated diphenyl ethers (PBDEs) were monitored in 14 different sampling stations of Lake Maggiore, the second largest Italian lake in regard to surface, volume and average depth, using the sentinel-organism Zebra mussel (Dreissena polymorpha). Results revealed a moderate contamination with ΣPBDE levels (BDE-17, -28, -47, -66, -71, -85, -99, -100, -138, -153, -154, -183, -190 and -209) ranging from 40 to 447 ng g -1 lipid weight which are similar to those found in environments polluted by deposition or atmospheric transport. The general order of decreasing congener contribution to the total load was BDE-47 > -99 > -100 > -209, which closely reflected patterns observed in mussels collected in freshwater ecosystems worldwide. - This study shows the first data of PBDE contamination in freshwater invertebrates from Mediterranean basin

  5. Levels and congener profiles of polybrominated diphenyl ethers (PBDEs) in Zebra mussels (D. polymorpha) from Lake Maggiore (Italy).

    Science.gov (United States)

    Binelli, A; Guzzella, L; Roscioli, C

    2008-06-01

    Several congeners of polybrominated diphenyl ethers (PBDEs) were monitored in 14 different sampling stations of Lake Maggiore, the second largest Italian lake in regard to surface, volume and average depth, using the sentinel-organism Zebra mussel (Dreissena polymorpha). Results revealed a moderate contamination with summation operatorPBDE levels (BDE-17, -28, -47, -66, -71, -85, -99, -100, -138, -153, -154, -183, -190 and -209) ranging from 40 to 447ngg(-1) lipid weight which are similar to those found in environments polluted by deposition or atmospheric transport. The general order of decreasing congener contribution to the total load was BDE-47>-99>-100>-209, which closely reflected patterns observed in mussels collected in freshwater ecosystems worldwide.

  6. A divergent approach to the synthesis of simplexides and congeners via a late-stage olefin cross-metathesis reaction.

    Science.gov (United States)

    Li, Jiakun; Li, Wei; Yu, Biao

    2013-08-14

    Simplexides constitute a unique group of immunosuppressive glycolipids that demonstrate antiproliferative activities against activated T-cell lymphocytes via a unique non-cytotoxic inhibition. To investigate the structure-activity relationship of the varied long-chain secondary alcohols on simplexides, we developed an efficient and divergent route to the synthesis of simplexides and congeners, taking advantage of a late-stage olefin cross-metathesis reaction.

  7. Polychlorinated biphenyls (PCBs) in industrial and municipal effluents: Concentrations, congener profiles, and partitioning onto particulates and organic carbon

    Energy Technology Data Exchange (ETDEWEB)

    Balasubramani, Aparna, E-mail: aparna.27889@gmail.com; Howell, Nathan L., E-mail: nlhowell@central.uh.edu; Rifai, Hanadi S., E-mail: rifai@uh.edu

    2014-03-01

    Wastewater effluent samples were collected in the summer of 2009 from 16 different locations which included municipal and industrial wastewater treatment plants and petrochemical industrial outfalls in the Houston area. The effluent samples were analyzed for all 209 polychlorinated biphenyls (PCBs) congeners using high resolution gas chromatography/high resolution mass spectrometry (HRGC/HRMS) using the USEPA method 1668A. The total PCBs (∑ 209) concentration in the dissolved medium ranged from 1.01 to 8.12 ng/L and ranged from 2.03 to 31.2 ng/L in the suspended medium. Lighter PCB congeners exhibited highest concentrations in the dissolved phase whereas, in the suspended phase, heavier PCBs exhibited the highest concentrations. The PCB homolog concentrations were dominated by monochlorobiphenyls through hexachlorobiphenyls, with dichlorobiphenyls exhibiting the highest concentration amongst them at most of the effluent outfalls, in the suspended phase. Both total suspended solids (TSS) and various organic carbon fractions played an important role in the distribution of the suspended fractions of PCBs in the effluents. The log K{sub oc} values determined in the effluents suggest that effluent PCB loads might have more risk and impact than what standard partitioning models predict. - Highlights: • 209 PCB congeners were measured in 16 different municipal and industrial effluents. • PCB congener differences were elucidated for the various effluent types. • In addition to log K{sub ow}, organic carbon and TSS affect partitioning of PCBs. • High concentrations of homolog 2 maybe due to biotransformation of PCBs.

  8. Occurrence and specific congener profile of 40 polybrominated diphenyl ethers in river and coastal sediments from Portugal.

    Science.gov (United States)

    Lacorte, Sílvia; Guillamón, Míriam; Martínez, Elena; Viana, Paula; Barceló, Damià

    2003-03-01

    Forty polybrominated diphenyl ethers (PBDEs), from mono- through hepta-brominated, were analyzed in river and coastal sediment samples of the eight main river basins of Portugal to investigate the occurrence, geographical distribution, and detailed congener profiles. Thirty-two sediment samples taken along the different rivers from inland to the open sea revealed an increase toward the river mouth with a total PBDE concentration of 20 ng/g-dw, and levels decreased to 0.5 ng/g-dw in coastal sediments. PBDEs were detected in all samples analyzed, indicating a diffuse source of pollution in the aquatic environments. Maximum levels were encountered in sediments collected close to urban and industrial areas. Of 40 congeners included in the analytical work, 17 congeners were detected in river sediments. BDE 47 was found in all samples analyzed whereas BDEs 100 and 99 were found in more than 26 out of 32 samples analyzed at concentrations from 0.03 to 10 ng/g-dw. This study is unique in showing the presence of previously nondescribed lower brominated PBDEs in riverine and marine sediments. BDEs 7, 11, 12+13, 15, 30, 32, 17, 25, 28+33, 49, 75, and 71 were identified in two to five samples with a median of 0.03-0.55 ng/g-dw. The analytical method developed consisted of the use of Soxhlet extraction with a novel cleanup method employing alumina cartridges and analysis by gas chromatography-mass spectrometry operated in negative chemical ionization mode.

  9. Validation of Simple Sequence Length Polymorphism Regions of Commonly Used Mouse Strains for Marker Assisted Speed Congenics Screening

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    Channabasavaiah B. Gurumurthy

    2015-01-01

    Full Text Available Marker assisted speed congenics technique is commonly used to facilitate backcrossing of mouse strains in nearly half the time it normally takes otherwise. Traditionally, the technique is performed by analyzing PCR amplified regions of simple sequence length polymorphism (SSLP markers between the recipient and donor strains: offspring with the highest number of markers showing the recipient genome across all chromosomes is chosen for the next generation. Although there are well-defined panels of SSLP makers established between certain pairs of mice strains, they are incomplete for most strains. The availability of well-established marker sets for speed congenic screens would enable the scientific community to transfer mutations across strain backgrounds. In this study, we tested the suitability of over 400 SSLP marker sets among 10 mouse strains commonly used for generating genetically engineered models. The panel of markers presented here can readily identify the specified strains and will be quite useful in marker assisted speed congenic screens. Moreover, unlike newer single nucleotide polymorphism (SNP array methods which require sophisticated equipment, the SSLP markers panel described here only uses PCR and agarose gel electrophoresis of amplified products; therefore it can be performed in most research laboratories.

  10. Validation of simple sequence length polymorphism regions of commonly used mouse strains for marker assisted speed congenics screening.

    Science.gov (United States)

    Gurumurthy, Channabasavaiah B; Joshi, Poonam S; Kurz, Scott G; Ohtsuka, Masato; Quadros, Rolen M; Harms, Donald W; Lloyd, K C Kent

    2015-01-01

    Marker assisted speed congenics technique is commonly used to facilitate backcrossing of mouse strains in nearly half the time it normally takes otherwise. Traditionally, the technique is performed by analyzing PCR amplified regions of simple sequence length polymorphism (SSLP) markers between the recipient and donor strains: offspring with the highest number of markers showing the recipient genome across all chromosomes is chosen for the next generation. Although there are well-defined panels of SSLP makers established between certain pairs of mice strains, they are incomplete for most strains. The availability of well-established marker sets for speed congenic screens would enable the scientific community to transfer mutations across strain backgrounds. In this study, we tested the suitability of over 400 SSLP marker sets among 10 mouse strains commonly used for generating genetically engineered models. The panel of markers presented here can readily identify the specified strains and will be quite useful in marker assisted speed congenic screens. Moreover, unlike newer single nucleotide polymorphism (SNP) array methods which require sophisticated equipment, the SSLP markers panel described here only uses PCR and agarose gel electrophoresis of amplified products; therefore it can be performed in most research laboratories.

  11. Seasonal variability of polychlorinated biphenyls (PCBs) and polychlorinated diphenyl ethers (PBDEs) congener profiles in butter in Poland: dietary risk evaluation.

    Science.gov (United States)

    Roszko, Marek; Szymczyk, Krystyna; Rzepkowska, Małgorzata; Jędrzejczak, Renata

    2014-01-01

    Various statistical methods have been employed to analyse in details seasonal diversification of polychlorinated biphenyl (PCB)/polybrominated diphenyl ether (PBDE) congener profiles found in butter fat. The variability of the PCB/PBDE congener profiles indicates the presence of various sources of the milk fat contamination. The obtained results suggest that the environmental chemical background has the highest share in the contamination sources pattern. Ion trap mass spectrometry coupled to high-resolution gas chromatography with semi-permeable membrane dialysis sample cleanup was used for determination of PCBs and PBDEs in milk fat. Determined butter fat PCB profiles were similar to the profiles characteristic for Aroclor 1254 technical mixture. Our data indicate that dietary intake of PCB/PBDE with milk and milk products may be estimated to be about 717.5 pg kg b.w.(-1) day(-1) for six-indicator PCBs, 0.329 (equivalent toxicity, TEQ) pg kg b.w.(-1) day(-1) for 12 DL PCBs and 50 pg kg b.w.(-1) day(-1) for PBDEs (sum of 14 congeners).

  12. Genome-wide identification and expression profiling reveal tissue-specific expression and differentially-regulated genes involved in gibberellin metabolism between Williams banana and its dwarf mutant.

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    Chen, Jingjing; Xie, Jianghui; Duan, Yajie; Hu, Huigang; Hu, Yulin; Li, Weiming

    2016-05-27

    Dwarfism is one of the most valuable traits in banana breeding because semi-dwarf cultivars show good resistance to damage by wind and rain. Moreover, these cultivars present advantages of convenient cultivation, management, and so on. We obtained a dwarf mutant '8818-1' through EMS (ethyl methane sulphonate) mutagenesis of Williams banana 8818 (Musa spp. AAA group). Our research have shown that gibberellins (GAs) content in 8818-1 false stems was significantly lower than that in its parent 8818 and the dwarf type of 8818-1 could be restored by application of exogenous GA3. Although GA exerts important impacts on the 8818-1 dwarf type, our understanding of the regulation of GA metabolism during banana dwarf mutant development remains limited. Genome-wide screening revealed 36 candidate GA metabolism genes were systematically identified for the first time; these genes included 3 MaCPS, 2 MaKS, 1 MaKO, 2 MaKAO, 10 MaGA20ox, 4 MaGA3ox, and 14 MaGA2ox genes. Phylogenetic tree and conserved protein domain analyses showed sequence conservation and divergence. GA metabolism genes exhibited tissue-specific expression patterns. Early GA biosynthesis genes were constitutively expressed but presented differential regulation in different tissues in Williams banana. GA oxidase family genes were mainly transcribed in young fruits, thus suggesting that young fruits were the most active tissue involved in GA metabolism, followed by leaves, bracts, and finally approximately mature fruits. Expression patterns between 8818 and 8818-1 revealed that MaGA20ox4, MaGA20ox5, and MaGA20ox7 of the MaGA20ox gene family and MaGA2ox7, MaGA2ox12, and MaGA2ox14 of the MaGA2ox gene family exhibited significant differential expression and high-expression levels in false stems. These genes are likely to be responsible for the regulation of GAs content in 8818-1 false stems. Overall, phylogenetic evolution, tissue specificity and differential expression analyses of GA metabolism genes can provide a

  13. The neuropeptides and protein hormones of the agricultural pest fruit fly Bactrocera dorsalis: What do we learn from the genome sequencing and tissue-specific transcriptomes?

    Science.gov (United States)

    Gui, Shun-Hua; Jiang, Hong-Bo; Smagghe, Guy; Wang, Jin-Jun

    2017-12-01

    Neuropeptides and protein hormones are very important signaling molecules, and are involved in the regulation and coordination of various physiological processes in invertebrates and vertebrates. Using a bioinformatics approach, we screened the recently sequenced genome and six tissue-specific transcriptome databases (central nervous system, fat body, ovary, testes, male accessory glands, antennae) of the oriental fruit fly (Bactrocera dorsalis) that is economically one of the most important pest insects of tropical and subtropical fruit. Thirty-nine candidate genes were found to encode neuropeptides or protein hormones. These include most of the known insect neuropeptides and protein hormones, with the exception of adipokinetic hormone-corazonin-related peptide, allatropin, diuretic hormone 34, diuretic hormone 45, IMFamide, inotocin, and sex peptide. Our results showed the neuropeptides and protein hormones of Diptera insects appear to have a reduced repertoire compared to some other insects. Moreover, there are also differences between B. dorsalis and the super-model of Drosophila melanogaster. Interesting features of the oriental fruit fly are the absence of genes coding for sex peptide and the presence of neuroparsin and two genes coding neuropeptide F. The majority of the identified neuropeptides and protein hormones is present in the central nervous system, with only a limited number of these in the other tissues. Moreover, we predicted their physiological functions via comparing with data of FlyBase and FlyAtlas. Taken together, owing to the large number of identified peptides, this study can be used as a reference about structure, tissue distribution and physiological functions for comparative studies in other model and important pest insects. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Identifier (ID) elements are not preferentially located to brain-specific genes: high ID element representation in other tissue-specific- and housekeeping genes of the rat.

    Science.gov (United States)

    Goldman, Andrés; Capoano, Carlos A; González-López, Evangelina; Geisinger, Adriana

    2014-01-01

    BC1 is a short non-coding RNA from rodents, which is transcribed by RNA pol III. Its RNA is highly abundant in the brain, where it exerts a post-transcriptional regulatory role in dendrites. Upon transcription, retroposition and insertion, BC1 gives rise to a subclass of short interspersed repetitive sequences (SINEs) named identifier (ID) elements. IDs can become integrated inside non-coding regions of RNA pol II transcription units, and - although challenged by a couple of reports - their preferential location to brain-specific genes has been long proposed. Furthermore, an additional, cis-regulatory role in the control of brain-specific pol II-directed transcripts has been suggested for these sequences. In this work we used Northern blot and in silico analyses to examine IDs' location among pol II transcription units in different tissues, and in housekeeping genes. ID sequences appeared distributed in a similar fashion within tissue-specific hnRNA populations of the brain, testis and liver, and within housekeeping primary transcripts as well. Moreover, when the lengths of the unprocessed transcripts were considered, ID representation was higher in housekeeping ones. On the other hand, ID elements appeared similarly distributed among the different gene regions, with the obvious exclusion of those sequences where strict constraints for proper gene expression exist. Altogether, the widespread distribution of ID elements in all the analyzed genes - including housekeeping - and in all gene regions, suggests a random location, raising questions about the specific cis-regulatory role of those sequences. © 2013 Elsevier B.V. All rights reserved.

  15. Age-related methylation patterning of housekeeping genes and tissue-specific genes is distinct between the stomach antrum and body.

    Science.gov (United States)

    Hong, Seung-Jin; Lee, Hwa-Jeong; Oh, Jung-Hwan; Jung, Sung-Hoon; Min, Ki-Ouk; Choi, Sang-Wook; Rhyu, Mun-Gan

    2013-06-01

    The methylation-variable sites around CpG islands are frequently overmethylated in Helicobacter pylori-infected stomachs. Age-related patterns of the overmethylation changes were compared between the fast-growing antrum cells and the slow-growing body cells. A total of 316 H. pylori-positive tissues and 380 H. pylori-negative tissues were obtained by endoscopic biopsy. The methylation-variable sites of ten housekeeping genes and nine tissue-specific genes were semiquantitatively analyzed, based on the ten-level classification of methylation-specific PCR intensity. The overmethylated genes were scored when their methylation levels were higher than an intermediate level of each gene common in the H. pylori-negative mucosa. The age-dependent methylation level of the inactive APC gene observed similarly in the antrum and the body was used as an age standard of methylation variation in a biopsy tissue. The overmethylation of housekeeping genes and stomach-specific genes rapidly increased to a high plateau frequency in the young-aged APC methylation cases (mean age: 43 years) in the H. pylori-positive antrum. In the H. pylori-positive body, most of the overmethylated housekeeping genes slowly increased to a peak frequency in the middle-aged APC methylation cases (mean age: 53 years). The housekeeping gene pairs showed high correlations (Spearman's correlation coefficient > 0.4) in both the antrum and the body. The overmethylation of housekeeping genes rapidly and slowly increased to a high frequency in concordance with a rapid and slow growth of epithelial cells in the H. pylori-infected stomach.

  16. Single nucleotide polymorphisms and domain/splice variants modulate assembly and elastomeric properties of human elastin. Implications for tissue specificity and durability of elastic tissue.

    Science.gov (United States)

    Miao, Ming; Reichheld, Sean E; Muiznieks, Lisa D; Sitarz, Eva E; Sharpe, Simon; Keeley, Fred W

    2017-05-01

    Polymeric elastin provides the physiologically essential properties of extensibility and elastic recoil to large arteries, heart valves, lungs, skin and other tissues. Although the detailed relationship between sequence, structure and mechanical properties of elastin remains a matter of investigation, data from both the full-length monomer, tropoelastin, and smaller elastin-like polypeptides have demonstrated that variations in protein sequence can affect both polymeric assembly and tensile mechanical properties. Here we model known splice variants of human tropoelastin (hTE), assessing effects on shape, polymeric assembly and mechanical properties. Additionally we investigate effects of known single nucleotide polymorphisms in hTE, some of which have been associated with later-onset loss of structural integrity of elastic tissues and others predicted to affect material properties of elastin matrices on the basis of their location in evolutionarily conserved sites in amniote tropoelastins. Results of these studies show that such sequence variations can significantly alter both the assembly of tropoelastin monomers into a polymeric network and the tensile mechanical properties of that network. Such variations could provide a temporal- or tissue-specific means to customize material properties of elastic tissues to different functional requirements. Conversely, aberrant splicing inappropriate for a tissue or developmental stage or polymorphisms affecting polymeric assembly could compromise the functionality and durability of elastic tissues. To our knowledge, this is the first example of a study that assesses the consequences of known polymorphisms and domain/splice variants in tropoelastin on assembly and detailed elastomeric properties of polymeric elastin. © 2016 Wiley Periodicals, Inc.

  17. Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease.

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    Qiongshi Lu

    2017-07-01

    Full Text Available Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer's disease (LOAD. Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson's disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available at http://genocanyon.med.yale.edu/GenoSkyline.

  18. Effect of tissue-specific acetylcholinesterase inhibitor C-547 on α3β4 and αβεδ acetylcholine receptors in COS cells.

    Science.gov (United States)

    Lindovský, Jiří; Petrov, Konstantin; Krůšek, Jan; Reznik, Vladimir S; Nikolsky, Eugeny E; Vyskočil, František

    2012-08-05

    The C-547 is the most effective muscle and tissue-specific anticholinesterase among alkylammonium derivatives of 6-methyluracil (ADEMS) acting in nanomolar concentrations on locomotor muscles but not on respiratory muscles, smooth muscles and heart and brain acetylcholine esterases (AChE). When applied systematically it could influence peripheral acetylcholine receptors. The aim of the present study was to investigate the effect of C-547 on rat α3β4 (ganglionic type) and αβεδ (muscle type) nicotinic receptors expressed in COS cells. Currents evoked by rapid application of acetylcholine or nicotine were recorded in whole-cell mode by electrophysiological patch-clamp technique 2-4 days after cell transfection by plasmids coding the α3β4 or αβεδ combination of receptor subunits. In cells sensitive to acetylcholine, the application of C-547 evoked no responses. When acetylcholine was applied during an already running application of C-547, acetylcholine responses were only inhibited at concentrations higher than 10(-7)M. This inhibition is not voltage-dependent, but is accompanied by an increased rate of desensitization. Thus in both types of receptors, effective doses are approximately 100 times higher than those inhibiting AChE in leg muscles and similar to those inhibiting respiratory diaphragm muscles and external intercostal muscles. These observations show that C-547 can be considered for symptomatic treatment of myasthenia gravis and other congenital myasthenic syndromes as an inhibitor of AChE in leg muscles at concentrations much lower than those inhibiting muscle and ganglion types of acetylcholine receptors. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Bipartite recognition of DNA by TCF/Pangolin is remarkably flexible and contributes to transcriptional responsiveness and tissue specificity of wingless signaling.

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    Hilary C Archbold

    2014-09-01

    Full Text Available The T-cell factor (TCF family of transcription factors are major mediators of Wnt/β-catenin signaling in metazoans. All TCFs contain a High Mobility Group (HMG domain that possesses specific DNA binding activity. In addition, many TCFs contain a second DNA binding domain, the C-clamp, which binds to DNA motifs referred to as Helper sites. While HMG and Helper sites are both important for the activation of several Wnt dependent cis-regulatory modules (W-CRMs, the rules of what constitutes a functional HMG-Helper site pair are unknown. In this report, we employed a combination of in vitro binding, reporter gene analysis and bioinformatics to address this question, using the Drosophila family member TCF/Pangolin (TCF/Pan as a model. We found that while there were constraints for the orientation and spacing of HMG-Helper pairs, the presence of a Helper site near a HMG site in any orientation increased binding and transcriptional response, with some orientations displaying tissue-specific patterns. We found that altering an HMG-Helper site pair from a sub-optimal to optimal orientation/spacing dramatically increased the responsiveness of a W-CRM in several fly tissues. In addition, we used the knowledge gained to bioinformatically identify two novel W-CRMs, one that was activated by Wnt/β-catenin signaling in the prothoracic gland, a tissue not previously connected to this pathway. In sum, this work extends the importance of Helper sites in fly W-CRMs and suggests that the type of HMG-Helper pair is a major factor in setting the threshold for Wnt activation and tissue-responsiveness.

  20. Sex-related and tissue-specific effects of tobacco smoking on brain atrophy: assessment in a large longitudinal cohort of healthy elderly

    Directory of Open Access Journals (Sweden)

    Quentin eDuriez

    2014-11-01

    Full Text Available We investigated the cross-sectional and longitudinal effects of tobacco smoking on brain atrophy in a large cohort of healthy elderly participants (65 to 80 years. MRI was used for measuring whole brain (WB, gray matter (GM, white matter (WM, and hippocampus (HIP volumes at study entry time (baseline, N=1,451, and the annualized rates of variation of these volumes using a 4-year follow-up MRI in a subpart of the cohort (N=1,111. Effects of smoking status (never, former, or current smoker at study entry and of lifetime tobacco consumption on these brain phenotypes were studied using sex-stratified AN(COVAs, including other health parameters as covariates. At baseline, male current smokers had lower GM, while female current smokers had lower WM. In addition, female former smokers exhibited reduced baseline HIP, the reduction being correlated with lifetime tobacco consumption. Longitudinal analyses demonstrated that current smokers, whether men or women, had larger annualized rates of HIP atrophy, as compared to either current or former smokers, independent of their lifetime consumption of tobacco. There was no effect of smoking on the annualized rate of WM loss. In all cases, measured sizes of these tobacco-smoking effects were of the same order of magnitude than those of age, and larger than effect sizes of any other covariate. These results demonstrate gender- and tissue specific effects of tobacco smoking on brain atrophy. They indicate that tobacco smoking is a major factor of brain aging, with notable effects on the hippocampus annualized-rate of atrophy after the age of 65.

  1. Tissue-specific root ion profiling reveals essential roles of the CAX and ACA calcium transport systems in response to hypoxia in Arabidopsis.

    Science.gov (United States)

    Wang, Feifei; Chen, Zhong-Hua; Liu, Xiaohui; Colmer, Timothy David; Zhou, Meixue; Shabala, Sergey

    2016-06-01

    Waterlogging is a major abiotic stress that limits the growth of plants. The crucial role of Ca(2+) as a second messenger in response to abiotic and biotic stimuli has been widely recognized in plants. However, the physiological and molecular mechanisms of Ca(2+) distribution within specific cell types in different root zones under hypoxia is poorly understood. In this work, whole-plant physiological and tissue-specific Ca(2+) changes were studied using several ACA (Ca(2+)-ATPase) and CAX (Ca(2+)/proton exchanger) knock-out Arabidopsis mutants subjected to waterlogging treatment. In the wild-type (WT) plants, several days of hypoxia decreased the expression of ACA8, CAX4, and CAX11 by 33% and 50% compared with the control. The hypoxic treatment also resulted in an up to 11-fold tissue-dependent increase in Ca(2+) accumulation in root tissues as revealed by confocal microscopy. The increase was much higher in stelar cells in the mature zone of Arabidopsis mutants with loss of function for ACA8, ACA11, CAX4, and CAX11 In addition, a significantly increased Ca(2+) concentration was found in the cytosol of stelar cells in the mature zone after hypoxic treatment. Three weeks of waterlogging resulted in dramatic loss of shoot biomass in cax11 plants (67% loss in shoot dry weight), while in the WT and other transport mutants this decline was only 14-22%. These results were also consistent with a decline in leaf chlorophyll fluorescence (F v/F m). It is suggested that CAX11 plays a key role in maintaining cytosolic Ca(2+) homeostasis and/or signalling in root cells under hypoxic conditions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  2. Post-mortem stability of RNA in skeletal muscle and adipose tissue and the tissue-specific expression of myostatin, perilipin and associated factors in the horse.

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    Philippa K Morrison

    Full Text Available Obesity, a major concern for equine welfare, is highly prevalent in the leisure horse population. Skeletal-muscle and adipose tissues are important determinants of maintenance energy requirements. The myostatin and perilipin pathways play key roles in the regulation of muscle mass and lipolysis respectively and have both been associated with obesity predisposition in other mammalian species. High quality samples, suitable for molecular biology, are an essential prerequisite for detailed investigations of gene and protein expression. Hence, this study has evaluated a the post-mortem stability of RNA extracted from skeletal-muscle and adipose-tissues collected under commercial conditions and b the tissue-specific presence of myostatin, the moystatin receptor (activin receptor IIB, ActRIIB, follistatin and perilipin, genes and proteins across a range of equine tissues. Objectives were addressed using tissues from 7 Thoroughbred horses presented for slaughter at a commercial abattoir; a samples were collected at 7 time-points from Masseter muscle and perirenal adipose from 5 minutes to 6 hours post-mortem. Extracted RN was appraised by Optical Density analysis and agarose-gel electrophoresis. b Quantitative real time PCR and Western Blotting were used to evaluate gene and protein expression in anatomically-defined samples collected from 17 tissues (6 organs, 4 skeletal muscles and 7 discrete adipose depots. The results indicate that, under the present collection conditions, intact, good quality RNA could be extracted from skeletal-muscle for up to 2 hours post-mortem. However, RNA from adipose tissue may be more susceptible to degradation/contamination and samples should be collected no later than 30 minutes post-mortem. The data also show that myostatin and ActRIIB genes and proteins were almost exclusively expressed in skeletal muscle. The follistatin gene showed a more diverse gene expression profile, with expression evident in several organs

  3. Tissue specific expression of potent insecticidal, Allium sativum leaf agglutinin (ASAL) in important pulse crop, chickpea (Cicer arietinum L.) to resist the phloem feeding Aphis craccivora.

    Science.gov (United States)

    Chakraborti, Dipankar; Sarkar, Anindya; Mondal, Hossain Ali; Das, Sampa

    2009-08-01

    The phloem sap-sucking hemipteran insect, Aphis craccivora, commonly known as cowpea aphid, cause major yield loss of important food legume crop chickpea. Among different plant lectins Allium sativum leaf agglutinin (ASAL), a mannose binding lectin was found to be potent antifeedant for sap sucking insect A. craccivora. Present study describes expression of ASAL in chickpea through Agrobacterium-mediated transformation of "single cotyledon with half embryo" explant. ASAL was expressed under the control of CaMV35S promoter for constitutive expression and phloem specific rolC promoter for specifically targeting the toxin at feeding site, using pCAMBIA2301 vector containing plant selection marker nptII. Southern blot analysis demonstrated the integration and copy number of chimeric ASAL gene in chickpea and its inheritance in T(1) and T(2) progeny plants. Expression of ASAL in T(0) and T(1) plants was confirmed through northern and western blot analysis. The segregation pattern of ASAL transgene was observed in T(1) progenies, which followed the 3:1 Mendelian ratio. Enzyme linked immunosorbant assay (ELISA) determined the level of ASAL expression in different transgenic lines in the range of 0.08-0.38% of total soluble protein. The phloem tissue specific expression of ASAL gene driven by rolC promoter has been monitored by immunolocalization analysis of mature stem sections. Survival and fecundity of A. craccivora decreased to 11-26% and 22-42%, respectively when in planta bioassay conducted on T(1) plants compared to untransformed control plant which showed 85% survival. Thus, through unique approach of phloem specific expression of novel insecticidal lectin (ASAL), aphid resistance has been successfully achieved in chickpea.

  4. Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Pradhan, Seema; Kant, Chandra; Verma, Subodh; Bhatia, Sabhyata

    2017-01-01

    The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.

  5. Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence.

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    Yang Liu

    Full Text Available This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1 approach for normal brain tissues (estimated T1 700-2000 ms at 3.0T. The relative mean estimation error (MSE for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms. The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

  6. Tissue-specific expression and post-translational modifications of plant- and bacterial-type phosphoenolpyruvate carboxylase isozymes of the castor oil plant, Ricinus communis L.

    Science.gov (United States)

    O’Leary, Brendan; Fedosejevs, Eric T.; Hill, Allyson T.; Bettridge, James; Park, Joonho; Rao, Srinath K.; Leach, Craig A.; Plaxton, William C.

    2011-01-01

    This study employs transcript profiling together with immunoblotting and co-immunopurification to assess the tissue-specific expression, protein:protein interactions, and post-translational modifications (PTMs) of plant- and bacterial-type phosphoenolpyruvate carboxylase (PEPC) isozymes (PTPC and BTPC, respectively) in the castor plant, Ricinus communis. Previous studies established that the Class-1 PEPC (PTPC homotetramer) of castor oil seeds (COS) is activated by phosphorylation at Ser-11 and inhibited by monoubiquitination at Lys-628 during endosperm development and germination, respectively. Elimination of photosynthate supply to developing COS by depodding caused the PTPC of the endosperm and cotyledon to be dephosphorylated, and then subsequently monoubiquitinated in vivo. PTPC monoubiquitination rather than phosphorylation is widespread throughout the castor plant and appears to be the predominant PTM of Class-1 PEPC that occurs in planta. The distinctive developmental patterns of PTPC phosphorylation versus monoubiquitination indicates that these two PTMs are mutually exclusive. By contrast, the BTPC: (i) is abundant in the inner integument, cotyledon, and endosperm of developing COS, but occurs at low levels in roots and cotyledons of germinated COS, (ii) shows a unique developmental pattern in leaves such that it is present in leaf buds and young expanding leaves, but undetectable in fully expanded leaves, and (iii) tightly interacts with co-expressed PTPC to form the novel and allosterically-desensitized Class-2 PEPC heteromeric complex. BTPC and thus Class-2 PEPC up-regulation appears to be a distinctive feature of rapidly growing and/or biosynthetically active tissues that require a large anaplerotic flux from phosphoenolpyruvate to replenish tricarboxylic acid cycle C-skeletons being withdrawn for anabolism. PMID:21841182

  7. Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease.

    Science.gov (United States)

    Lu, Qiongshi; Powles, Ryan L; Abdallah, Sarah; Ou, Derek; Wang, Qian; Hu, Yiming; Lu, Yisi; Liu, Wei; Li, Boyang; Mukherjee, Shubhabrata; Crane, Paul K; Zhao, Hongyu

    2017-07-01

    Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system) increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells) provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer's disease (LOAD). Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson's disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available at http://genocanyon.med.yale.edu/GenoSkyline.

  8. Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease

    Science.gov (United States)

    Abdallah, Sarah; Ou, Derek; Wang, Qian; Hu, Yiming; Lu, Yisi; Liu, Wei; Li, Boyang; Mukherjee, Shubhabrata; Crane, Paul K.; Zhao, Hongyu

    2017-01-01

    Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system) increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells) provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer’s disease (LOAD). Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson’s disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available at http://genocanyon.med.yale.edu/GenoSkyline. PMID:28742084

  9. Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus.

    Science.gov (United States)

    Bai, Yun; Zhang, Zhuangzhi; Jin, Lei; Kang, Hui; Zhu, Yongqiang; Zhang, Lu; Li, Xia; Ma, Fengshou; Zhao, Li; Shi, Baoxin; Li, Jun; McManus, Donald P; Zhang, Wenbao; Wang, Shengyue

    2014-08-29

    MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown. Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with different patterns in the three life stages examined. Furthermore, considering both the previously reported and newly predicted miRNAs, 25 conserved miRNAs families were identified in the E. granulosus genome. Comparing the presence or absence of these miRNA families with the free-living Schmidtea mediterranea, we found 13 conserved miRNAs are lost in E. granulosus, most of which are tissue-specific and involved in the development of ciliated cells, the gut and sensory organs. Finally, GO enrichment analysis of the differentially expressed miRNAs and their potential targets indicated that they may be involved in bi-directional development, nutrient metabolism and nervous system development in E. granulosus. This study has, for the first time, provided a comprehensive description of the different expression patterns of miRNAs in three distinct life cycle stages of E. granulosus. The analysis supports earlier suggestions that the loss of miRNAs in the Platyhelminths might be related to morphological simplification. These results may help in the exploration of the mechanism of interaction between this parasitic worm and its definitive and intermediate hosts, providing information that can be used to develop new interventions and therapeutics for the control of cystic

  10. Tissue-specific direct microtransfer of nanomaterials into Drosophila embryos as a versatile in vivo test bed for nanomaterial toxicity assessment

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    Vega-Alvarez S

    2014-04-01

    Full Text Available Sasha Vega-Alvarez,1 Adriana Herrera,2 Carlos Rinaldi,2–4 Franklin A Carrero-Martínez1,5 1Department of Biology, 2Department of Chemical Engineering, University of Puerto Rico-Mayagüez, Mayagüez, Puerto Rico; 3J Crayton Pruitt Family Department of Biomedical Engineering, 4Department of Chemical Engineering, University of Florida, Gainesville, FL, USA; 5Department of Anatomy and Neuroscience, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico Abstract: Nanomaterials are the subject of intense research, focused on their synthesis, modification, and biomedical applications. Increased nanomaterial production and their wide range of applications imply a higher risk of human and environmental exposure. Unfortunately, neither environmental effects nor toxicity of nanomaterials to organisms are fully understood. Cost-effective, rapid toxicity assays requiring minimal amounts of materials are needed to establish both their biomedical potential and environmental safety standards. Drosophila exemplifies an efficient and cost-effective model organism with a vast repertoire of in vivo tools and techniques, all with high-throughput scalability and screening feasibility throughout its life cycle. Here we report tissue specific nanomaterial assessment through direct microtransfer into target tissues. We tested several nanomaterials with potential biomedical applications such as single-wall carbon nanotubes, multiwall carbon nanotubes, silver, gold, titanium dioxide, and iron oxide nanoparticles. Assessment of nanomaterial toxicity was conducted by evaluating progression through developmental morphological milestones in Drosophila. This cost-effective assessment method is amenable to high-throughput screening. Keywords: nanotoxicity, Drosophila, microtransfer, nanoparticle, iron oxide, silver, gold, titanium dioxide, carbon nanotube

  11. Analysis of transcriptional regulation and tissue-specific expression of Avicennia marina Plasma Membrane Protein 3 suggests it contributes to Na(+) transport and homoeostasis in A. marina.

    Science.gov (United States)

    Chidambaram, Rajalakshmi; Venkataraman, Gayatri; Parida, Ajay

    2015-07-01

    Plasma membrane proteins (PMP3) play a role in cation homoeostasis. The 5' flanking sequence of stress inducible, Avicennia marina PMP3 (AmPMP3prom) was transcriptionally fused to (a) GUS or (b) GFP-AmPMP3 and analyzed in transgenic tobacco. Tissue-histochemical GUS and GFP:AmPMP3 localization are co-incident under basal and stress conditions. AmPMP3prom directed GUS activity is highest in roots. Basal transcription is conferred by a 388bp segment upstream of the translation start site. A 463bp distal enhancer in the AmPMP3prom confers enhanced expression under salinity in all tissues and also responds to increases in salinity. The effect of a central, stem-specific negative regulatory region is suppressed by the distal enhancer. The A. marina rhizosphere encounters dynamic changes in salinity at the inter-tidal interface. The complex, tissue-specific transcriptional responsiveness of AmPMP3 to salinity appears to have evolved in response to these changes. Under salinity, guard cell and phloem-specific expression of GFP:AmPMP3 is highly enhanced. Mesophyll, trichomes, bundle sheath, parenchymatous cortex and xylem parenchyma also show GFP:AmPMP3 expression. Cis-elements conferring stress, root and vascular-specific expression are enriched in the AmPMP3 promoter. Pronounced vascular-specific AmPMP3 expression suggests a role in salinity induced Na(+) transport, storage, and secretion in A. marina. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Retinal projections to the subcortical visual system in congenic albino and pigmented rats

    Science.gov (United States)

    Fleming, Mark D.; Benca, Ruth M.; Behan, Mary

    2007-01-01

    The primary visual pathway in albino mammals is characterized by an increased decussation of retinal ganglion cell axons at the optic chiasm and an enhanced contralateral projection to the dorsal lateral geniculate nucleus. In contrast to the primary visual pathway, little is known about the organization of retinal input to most nuclei of the subcortical visual system in albino mammals. The subcortical visual system is a large group of retinorecipient nuclei in the diencephalon and mesencephalon. These areas mediate a range of behaviors that include both circadian and acute responses to light. We used a congenic strain of albino and pigmented rats with a mutation at the c locus for albinism (Fischer 344-c/+; La Vail and Lawson, 1986) to quantitatively assess the effects of albinism on retinal projections to a number of subcortical visual nuclei including the ventral lateral hypothalamus (VLH), ventral lateral preoptic area (VLPO), olivary pretectal nucleus (OPN), posterior limitans (PLi), commissural pretectal area (CPA), intergeniculate leaflet (IGL), ventral lateral geniculate nucleus (vLGN) and superior colliculus (SC). Following eye injections of the neuroanatomical tracer cholera toxin-β, the distribution of anterogradely transported label was measured. The retinal projection to the contralateral VLH, PLi, CPA and IGL was enhanced in albino rats. No significant differences were found between albino and pigmented rats in retinal input to the VLPO, OPN and vLGN. These findings raise the possibility that enhanced retinofugal projections to subcortical visual nuclei in albinos may underlie some light-mediated behaviors that differ between albino and pigmented mammals. PMID:16996223

  13. Mapping and Congenic Dissection of Genetic Loci Contributing to Hyperglycemia and Dyslipidemia in Mice.

    Directory of Open Access Journals (Sweden)

    Weibin Shi

    Full Text Available Patients with dyslipidemia have an increased risk of developing type 2 diabetes, and diabetic patients often have dyslipidemia. Potential genetic connections of fasting plasma glucose with plasma lipid profile were evaluated using hyperlipidemic mice.225 male F2 mice were generated from BALB/cJ (BALB and SM/J(SM Apoe-deficient (Apoe-/- mice and fed a Western diet for 5 weeks. Fasting plasma glucose and lipid levels of F2 mice were measured before and after 5 weeks of Western diet and quantitative trait locus (QTL analysis was performed using data collected from these two time points. 144 SNP(single nucleotide polymorphism markers across the entire genome were typed.One major QTL (logarithm of odds ratio (LOD: 6.46 peaked at 12.7 cM on chromosome 9,Bglu16, and 3 suggestive QTLs on chromosomes 15, 18 and X were identified for fasting glucose, and over 10 loci identified for lipid traits. Bglu16 was adjacent to a major QTL, Hdlq17, for high-density lipoprotein (HDL cholesterol (LOD: 6.31, peak: 19.1 cM. A congenic strain with a donor chromosomal region harboring Bglu16 and Hdlq17 on the Apoe-/- background showed elevations in plasma glucose and HDL levels. Fasting glucose levels were significantly correlated with non-HDL cholesterol and triglyceride levels, especially on the Western diet, but only marginally correlated with HDL levels in F2 mice.We have demonstrated a correlative relationship between fasting glucose and plasma lipids in a segregating F2 population under hyperlipidemic conditions, and this correlation is partially due to genetic linkage between the two disorders.

  14. Organochlorines in egg samples from Norwegian birds of prey: congener-, isomer- and enantiomer specific considerations.

    Science.gov (United States)

    Herzke, D; Kallenborn, R; Nygård, T

    2002-05-27

    The content of chlorinated persistent organic pollutants was determined in a total of 44 egg samples from 8 different raptor species collected throughout Norway in the period 1991-1997. The content of 8 chlorinated bornanes, 9 chlorinated pesticides, and 15 polychlorinated biphenyl congeners (PCB) were determined. The highest average concentrations for PCB were found for eggs from White-tailed Sea Eagle and Peregrine Falcon (average sum PCB concentration: 8.9 and 9.1 microg/g wet weight (w.w.), respectively). Merlin and Sparrowhawk eggs were the highest contaminated with chlorinated pesticides (average sum pesticide concentration: 3.0 and 4.3 microg/g w.w.). For the first time, the content of chlorobornanes was determined in Norwegian birds of prey eggs. However, only minor contamination compared to PCBs and conventional chlorinated pesticides was found. The highest sum concentration was determined for White-tailed Sea Eagle eggs (0.09 microg/g w.w.). No chlorobornane contamination was found in Osprey and Merlin eggs. No spatial and regional specific trends or pattern distribution were found for organochlorine contamination in the egg samples analysed. In order to gain information about enantiomer specific bioaccumulation and biotransformation capacity of the organism, enantioselective analyses was performed for the chiral contaminants trans-chlordane, oxy-chlordane and the chlorobornane B9-1679 (Parlar #50). Indications for species-dependent deviation from the racemic distribution (enantiomeric ratio = 1) were found. Peregrine Falcon and Merlin eggs were characterised with an extremely high enantiomeric excess of the (-)-trans-chlordane (enantiomeric ratio (ER) birds of prey eggs analysed.

  15. Comparative developmental toxicity of planar polychlorinated biphenyl congeners in chickens, American kestrels, and common terns

    Science.gov (United States)

    Hoffman, D.J.; Melancon, M.J.; Klein, P.N.; Eisemann, J.D.; Spann, J.W.

    1998-01-01

    The effects of PCB congeners, PCB 126 (3,3',4,4',5-pentaCB) and PCB 77 (3,3'4,4'-tetraCB), were examined in chicken (Gallus gallus), American kestrel (Falco sparverius), and common tern (Sterna hirundo) embryos through hatching, following air cell injections on day 4. PCB 126 caused malformations and edema in chickens starting at 0.3 ppb, in kestrels at 2.3 ppb, but in terns only at levels affecting hatching success (44 ppb). Extent of edema was most severe in chickens and least in terns. Defects of the beak were common in all species, but with crossed beak most prevalent in terns. Effects on embryo growth were most apparent for PCB 126 in chickens and kestrels. The approximate LD50 for PCB 126 in chickens was 0.4 ppb, in kestrels was 65 ppb, and in terns was 104 ppb. The approximate LD50 for PCB 77 in chickens was 2.6 ppb and in kestrels was 316 ppb. Induction of cytochrome P450 associated monooxygenase activity (EROD activity) by PCB 126 in chick embryo liver was about 800 times more responsive than in tern and at least 1000 times more responsive than in kestrel. High concentrations of PCB 126 found in bald eagle eggs are nearly 20-fold higher than the lowest toxic concentration tested in kestrels. Concentrations of PCB 126 causing low level toxic effects in common tern eggs are comparable to highest levels in common terns and Forster's terns in the field, suggesting additional involvement of other compounds in the Great Lakes.

  16. A cautionary note on ignoring polygenic background when mapping quantitative trait loci via recombinant congenic strains.

    Science.gov (United States)

    Loredo-Osti, J Concepción

    2014-01-01

    In gene mapping, it is common to test for association between the phenotype and the genotype at a large number of loci, i.e., the same response variable is used repeatedly to test a large number of non-independent and non-nested hypotheses. In many of these genetic problems, the underlying model is a mixed model consistent of one or very few major genes concurrently with a genetic background effect, usually thought as of polygenic nature and, consequently, modeled through a random effects term with a well-defined covariance structure dependent upon the kinship between individuals. Either because the interest lies only on the major genes or to simplify the analysis, it is habitual to drop the random effects term and use a simple linear regression model, sometimes complemented with testing via resampling as an attempt to minimize the consequences of this practice. Here, it is shown that dropping the random effects term has not only extreme negative effects on the control of the type I error rate, but it is also unlikely to be fixed by resampling because, whenever the mixed model is correct, this practice does not allow to meet some basic requirements of resampling in a gene mapping context. Furthermore, simulations show that the type I error rates when the random term is ignored can be unacceptably high. As an alternative, this paper introduces a new bootstrap procedure to handle the specific case of mapping by using recombinant congenic strains under a linear mixed model. A simulation study showed that the type I error rates of the proposed procedure are very close to the nominal ones, although they tend to be slightly inflated for larger values of the random effects variance. Overall, this paper illustrates the extent of the adverse consequences of ignoring random effects term due to polygenic factors while testing for genetic linkage and warns us of potential modeling issues whenever simple linear regression for a major gene yields multiple significant linkage

  17. Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans.

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    Aijaz Ahmad

    Full Text Available We previously reported the antifungal properties of a monoterpene phenol "Eugenol" against different Candida strains and have observed that the addition of methyl group to eugenol drastically increased its antimicrobial potency. Based on the results and the importance of medicinal synthetic chemistry, we synthesized eugenol-tosylate and its congeners (E1-E6 and tested their antifungal activity against different clinical fluconazole (FLC- susceptible and FLC- resistant C. albicans isolates alone and in combination with FLC by determining fractional inhibitory concentration indices (FICIs and isobolograms calculated from microdilution assays. Minimum inhibitory concentration (MIC results confirmed that all the tested C. albicans strains were variably susceptible to the semi-synthetic derivatives E1-E6, with MIC values ranging from 1-62 μg/ml. The test compounds in combination with FLC exhibited either synergy (36%, additive (41% or indifferent (23% interactions, however, no antagonistic interactions were observed. The MICs of FLC decreased 2-9 fold when used in combination with the test compounds. Like their precursor eugenol, all the derivatives showed significant impairment of ergosterol biosynthesis in all C. albicans strains coupled with down regulation of the important ergosterol biosynthesis pathway gene-ERG11. The results were further validated by docking studies, which revealed that the inhibitors snugly fitting the active site of the target enzyme, mimicking fluconazole, may well explain their excellent inhibitory activity. Our results suggest that these compounds have a great potential as antifungals, which can be used as chemosensitizing agents with the known antifungal drugs.

  18. Phthalate esters and childhood asthma: A systematic review and congener-specific meta-analysis.

    Science.gov (United States)

    Li, Ming-Chieh; Chen, Chi-Hsien; Guo, Yue Leon

    2017-10-01

    Exposure to phthalate esters (PAEs) has been associated with childhood asthma, but the congener-specific effects of PAEs on childhood asthma were unclear. We aimed to systematically review and meta-analyze observational studies on the associations between specific effects of PAEs and the risk of childhood asthma. Relevant studies were identified by searching three databases up to October 20, 2016. The reference lists of the retrieved articles were also reviewed. We included observational studies that reported risk estimates with 95% confidence intervals (CIs) for the associations between phthalate exposure and the risk of childhood asthma. Fixed-effects models were generally applied to calculate pooled risk estimates. When heterogeneity was present, random-effects models were applied. A total of nine studies featuring 43 data points were included in our final meta-analyses. Results indicated that the benzyl butyl phthalate (BBzP) exposure had a significant association with the risk of childhood asthma. The Odd Ratios (ORs) were from 1.39 to 1.41 for different combination strategies. Subgroup analyses by different exposure period or samples used showed that prenatal exposure to BBzP had a stronger association with the risk of childhood asthma (OR = 1.38, 95% CI = 1.09-1.75), compared to those with postnatal exposure. Besides, the association was evident when the phthalate exposure was measured from dust samples. The OR for the associations between di-2-ethylhexyl phthalate (DEHP) in dust and childhood asthma was 2.71 (95% CI = 1.39-5.28), and 2.08 (95% CI = 1.10-3.92) for BBzP. Our study suggested a positive association between DEHP and BBzP exposure and childhood asthma. Future studies are warranted to identify the underlying mechanisms of the association. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Identification of ten KB425796-A congeners from Paenibacillus sp. 530603 using an antifungal assay against Aspergillus fumigatus in combination with micafungin.

    Science.gov (United States)

    Kai, Hirohito; Yamashita, Midori; Takase, Shigehiro; Hashimoto, Michizane; Muramatsu, Hideyuki; Nakamura, Ikuko; Yoshikawa, Koji; Kanasaki, Ryuichi; Ezaki, Masami; Nitta, Kumiko; Watanabe, Masato; Inamura, Noriaki; Fujie, Akihiko

    2013-08-01

    The discovery and characterization of natural congeners is one approach for understanding the relationship between chemical structure and biological function. We recently isolated the novel antifungal metabolite KB425796-A produced by the recently isolated bacterium Paenibacillus sp. 530603. On the basis of morphological changes of Aspergillus fumigatus induced by KB425796-A in combination with micafungin, we developed a highly sensitive screening method for the specific detection of KB425796-A congeners. Using this method, we isolated ten congeners of KB425796-A, named KB425796-B, -C, -D, -E, -F, -G, -H, -I, -J and -K, which exhibited diverse antifungal potencies against A. fumigatus. One of the most potent congeners, KB425796-C, had antifungal activities against several micafungin-resistant infectious fungi. KB425796-C can be a potential drug candidate for treating micafungin-resistant fungal infections.

  20. Quantitative structure-activity relationship (QSAR) studies for predicting activation of the ryanodine receptor type 1 channel complex (RyR1) by polychlorinated biphenyl (PCB) congeners.

    Science.gov (United States)

    Rayne, Sierra; Forest, Kaya

    2010-01-01

    A quantitative structure-activity relationship (QSAR) was developed to predict the congener specific ryanodine receptor type RyR1 activity of all 209 polychlorinated biphenyl (PCB) congeners. A three-variable QSAR equation was obtained via stepwise forward linear regression on an unsupervised forward selection reduced data set from an initial database. Application of the QSAR towards predicting EC(2x) values for all 209 PCB congeners indicated good agreement in substitution pattern trends between the experimental and estimated data sets. The QSAR model predicts a less than two-fold increase in maximal potency among all congeners outside the experimental database, and it appears that no high-potency PCB congeners with EC(2x) values much less than 0.2 microM exist. Increasing RyR1-neuro toxicity equivalents with increasing homologue number and Aroclor chlorination likely reflect indirect molecular controls on toxicity, since congeners with multiple ortho substituents-the primary structural feature controlling a lack of coplanarity and resulting neurotoxicity-are more likely to be found in higher homologues.

  1. Nitrogen forms influence microcystin concentration and composition via changes in cyanobacterial community structure.

    Directory of Open Access Journals (Sweden)

    Marie-Eve Monchamp

    Full Text Available The eutrophication of freshwaters is a global health concern as lakes with excess nutrients are often subject to toxic cyanobacterial blooms. Although phosphorus is considered the main element regulating cyanobacterial biomass, nitrogen (N concentration and more specifically the availability of different N forms may influence the overall toxicity of blooms. In this study of three eutrophic lakes prone to cyanobacterial blooms, we examined the effects of nitrogen species and concentrations and other environmental factors in influencing cyanobacterial community structure, microcystin (MC concentrations and MC congener composition. The identification of specific MC congeners was of particular interest as they vary widely in toxicity. Different nitrogen forms appeared to influence cyanobacterial community structure leading to corresponding effects on MC concentrations and composition. Total MC concentrations across the lakes were largely explained by a combination of abiotic factors: dissolved organic nitrogen, water temperature and ammonium, but Microcystis spp. biomass was overall the best predictor of MC concentrations. Environmental factors did not appear to affect MC congener composition directly but there were significant associations between specific MC congeners and particular species. Based on redundancy analyses (RDA, the relative biomass of Microcystis aeruginosa was associated with MC-RR, M. wesenbergii with MC-LA and Aphanizomenon flos-aquae with MC-YR. The latter two species are not generally considered capable of MC production. Total nitrogen, water temperature, ammonium and dissolved organic nitrogen influenced the cyanobacterial community structure, which in turn resulted in differences in the dominant MC congener and the overall toxicity.

  2. Prolactin receptor, growth hormone receptor, and putative somatolactin receptor in Mozambique tilapia: tissue specific expression and differential regulation by salinity and fasting.

    Science.gov (United States)

    Pierce, A L; Fox, B K; Davis, L K; Visitacion, N; Kitahashi, T; Hirano, T; Grau, E G

    2007-01-01

    , liver levels of GHR1 and GHR2 transcripts, and liver and muscle levels of IGF-I transcripts were unaffected by fasting. These results clearly indicate tissue specific expression and differential physiological regulation of GH family receptors in the tilapia.

  3. Comparison of congener profiles of polychlorinated biphenyls between Yu-cheng children and a potential food source

    Energy Technology Data Exchange (ETDEWEB)

    Lung Shih-Chun Candice [Research Center for Environmental Changes, Academia Sinica, Taipei (Taiwan); Guo Yu-Liang Leon; Chang Ho-Yuan [Dept. of Environmental and Occupational Health, Coll. of Medicine, National Cheng Kung Univ., Tainan (Taiwan)

    2004-09-15

    In 1979, about two thousand people in central Taiwan were intoxicated by consumption of the rice oil that was contaminated with polychlorinated biphenyls (PCBs). This ''Yu-cheng'' incident was one of the two human tragedies which people ingested substantial amounts of PCBs within a short period of time. Some of the follow-up epidemiological studies focused on the children born to the exposed mothers, the Yu-cheng children, since they could be exposed to PCBs via breast-feeding or transplacental transfer. This report presents the results of the serum PCB levels of the 21 Yu-cheng children with a congener-specific analysis. On the other hand, fish consumption is thought to be the single most important exposure route to PCBs to the general public; thus, it is crucial to understand PCB exposure from fish consumption. In a separated study to assess PCB contamination in fish, PCB congener concentrations in tilapia (Oreochromis hybrids), the most popular fish in Taiwan, were evaluated. The consumption quantity of tilapia is the highest throughout the Island. It is mostly farmed in fresh water but can also be bred in saltwater. This report presents the concentrations and profiles in the serums of the Yu-cheng children. The congener profile is compared with PCB profile in the serum of Yu-cheng women reported previously and that in one of the potentially significant exposure source, tilapia, conducted in a separated work. Remarkable similarity between the profile of Yu-cheng children and that of the tilapia is revealed and discussed.

  4. Bioaccumulation and biotransformation of 61 polychlorinated biphenyl and four polybrominated diphenyl ether congeners in juvenile American kestrels (Falco sparverius).

    Science.gov (United States)

    Drouillard, Ken G; Fernie, Kimberly J; Letcher, Robert J; Shutt, Laird J; Whitehead, Megan; Gebink, Wouter; Bird, David M

    2007-02-01

    This study examined the bioaccumulation and dietary retention of 61 polychlorinated biphenyl (PCB) and four polybrominated diphenyl ether (PBDE) congeners in juvenile American kestrels (Falco sparverius). American kestrels were exposed to contaminants via egg injection and daily gavage dosing over the posthatch-to-fledgling period. Retention factors for PCBs were dependent on chemical hydrophobicity and chlorine substitution patterns and ranged from less than 1 to 16.4% for PCBs having vicinal hydrogen substitutions at meta-, para- carbons on at least one of the phenyl rings and between 13.2 and 81.5% for congeners containing chlorine substitutions at 4,4'-, 3',4,5'-, 3,4',5-, or 3,3',5,5'-positions. These results indicate that juveniles are capable of biotransforming PCBs according to the same structure-activity rules as adults. A toxicokinetic model, initially parameterized using adult toxicokinetic parameters, was used to describe concentration trends in juveniles over time. The adult model overestimated PCB concentrations but provided an adequate fit when elimination rate constants were increased by a factor of 12.7. Retention factors for the PBDE congeners 2,2',4,4'-tetrabromodiphenyl ether (BDE 47), 2,2',4,4',6-pentabromodiphenyl ether (BDE 100), 2,2',4,4',5-pentabromodiphenyl ether (BDE 99), and 2,2',4,4',5,5'-hexabromodiphenyl ether (BDE 153) were from 7.8 to 45.3% of the total dose. The retention of BDE 47 was similar that observed for readily cleared PCBs, whereas the remaining PBDEs exhibited retention factors consistent with those of persistent PCBs. Half-lives for PBDEs in juveniles were estimated to range from 5.6 to 44.7 d. Assuming differences in PBDE toxicokinetics between juveniles and adults similar to those measured for PCBs, adult American kestrel PBDE half-lives are expected to range from 72 to 572 d.

  5. Isolation of rhamnolipids-producing cultures from faeces: Influence of interspecies communication on the yield of rhamnolipid congeners.

    Science.gov (United States)

    Woźniak-Karczewska, Marta; Myszka, Kamila; Sznajdrowska, Agata; Szulc, Alicja; Zgoła-Grześkowiak, Agnieszka; Ławniczak, Łukasz; Corvini, Philippe F-X; Chrzanowski, Łukasz

    2017-05-25

    The aim of this study was to evaluate the ability of bacterial cultures isolated from cattle, poultry or pig faeces and manure to produce rhamnolipids, as well as to investigate the influence of interspecies communication on possible quantitative differences in the production of rhamnolipid congeners. Initial screening methods (oil spreading, drop collapse, haemolytic activity and emulsification activity) showed that approximately 36% of the 51 isolated cultures exhibited the ability to produce biosurfactants. Subsequent studies using a selected culturable mixed culture (which included Enterococcus faecalis, Pseudomonas aeruginosa and Escherichia coli) revealed that only P. aeruginosa was able to produce this biosurfactant. HPLC-MS analysis showed that the surface active compounds were rhamnolipids. Further comparative studies confirmed that the total yield of rhamnolipids was notably higher in the bioreactor inoculated with the selected mixed culture (940.58±1.10mg/L) compared to the bioreactor inoculated with the axenic strain of P. aeruginosa (108.47±0.41mg/L). Twelve rhamnolipid congeners were identified during cultivation of the selected mixed culture, whereas six congeners were detected during cultivation of the sole axenic strain of P. aeruginosa. Furthermore, increased production of rhamnolipids was observed when the concentration of autoinducer molecules (AI-2) responsible for interspecies signaling increased, suggesting the influence of quorum-sensing communication on biosynthesis efficiency. This observation may be of importance for large-scale production of this biosurfactant, as it opens new possible solutions based on the use of mixed cultures or external addition of stimulating autoinducers. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Isolation of a Genomic Region Affecting Most Components of Metabolic Syndrome in a Chromosome-16 Congenic Rat Model.

    Directory of Open Access Journals (Sweden)

    Lucie Šedová

    Full Text Available Metabolic syndrome is a highly prevalent human disease with substantial genomic and environmental components. Previous studies indicate the presence of significant genetic determinants of several features of metabolic syndrome on rat chromosome 16 (RNO16 and the syntenic regions of human genome. We derived the SHR.BN16 congenic strain by introgression of a limited RNO16 region from the Brown Norway congenic strain (BN-Lx into the genomic background of the spontaneously hypertensive rat (SHR strain. We compared the morphometric, metabolic, and hemodynamic profiles of adult male SHR and SHR.BN16 rats. We also compared in silico the DNA sequences for the differential segment in the BN-Lx and SHR parental strains. SHR.BN16 congenic rats had significantly lower weight, decreased concentrations of total triglycerides and cholesterol, and improved glucose tolerance compared with SHR rats. The concentrations of insulin, free fatty acids, and adiponectin were comparable between the two strains. SHR.BN16 rats had significantly lower systolic (18-28 mmHg difference and diastolic (10-15 mmHg difference blood pressure throughout the experiment (repeated-measures ANOVA, P < 0.001. The differential segment spans approximately 22 Mb of the telomeric part of the short arm of RNO16. The in silico analyses revealed over 1200 DNA variants between the BN-Lx and SHR genomes in the SHR.BN16 differential segment, 44 of which lead to missense mutations, and only eight of which (in Asb14, Il17rd, Itih1, Syt15, Ercc6, RGD1564958, Tmem161a, and Gatad2a genes are predicted to be damaging to the protein product. Furthermore, a number of genes within the RNO16 differential segment associated with metabolic syndrome components in human studies showed polymorphisms between SHR and BN-Lx (including Lpl, Nrg3, Pbx4, Cilp2, and Stab1. Our novel congenic rat model demonstrates that a limited genomic region on RNO16 in the SHR significantly affects many of the features of metabolic

  7. OXIDATION OF POLYCHLORINATED BIPHENYLS BY LIVER TISSUE SLICES FROM PHENOBARBITAL-PRETREATED MICE IS CONGENER-SPECIFIC AND ATROPSELECTIVE

    OpenAIRE

    Wu, Xianai; Duffel, Michael; Lehmler, Hans-Joachim

    2013-01-01

    Mouse models are powerful tools to study the developmental neurotoxicity of polychlorinated biphenyls (PCBs); however, studies of the oxidation of chiral PCB congeners to potentially neurotoxic hydroxylated metabolites (OH-PCBs) in mice have not been reported. Here we investigate the atropselective oxidation of chiral PCB 91 (2,2',3,4',6-pentachlorobiphenyl), PCB 95 (2,2',3,5',6-pentachlorobiphenyl), PCB 132 (2,2',3,3',4,6'-hexachlorobiphenyl), PCB 136 (2,2',3,3',6,6'-hexachlorobiphenyl) and ...

  8. Alcohol congener analysis in a forensic context: detection of iso-α-acids to confirm beer consumption

    OpenAIRE

    Rodda, Luke Neil

    2017-01-01

    Alcohol abuse is a leading factor in many crimes and accidents with beer being the oldest and most widely consumed alcoholic beverage in the world. This research has focused on iso-α-acids (IAA) derived from the hop plant (Humulus lupulus L.) used in brewing and found in beer. Additionally, three structurally similar but chemically-altered IAA known as “reduced IAA” (rho-, tetrahydro- and hexahydro-IAA), are also beer-specific ingredient congeners found in beer, specifically used in green or ...

  9. Dietary exposure of juvenile common sole (Solea solea L.) to polybrominated diphenyl ethers (PBDEs): Part 1. Bioaccumulation and elimination kinetics of individual congeners and their debrominated metabolites

    Energy Technology Data Exchange (ETDEWEB)

    Munschy, C., E-mail: cmunschy@ifremer.f [Institut Francais de Recherche pour l' Exploitation de la Mer (IFREMER), Laboratory of Biogeochemistry of Organic Contaminants, Rue de l' Ile d' Yeu, BP 21105, 44311 Nantes Cedex 3 (France); Heas-Moisan, K.; Tixier, C.; Olivier, N. [Institut Francais de Recherche pour l' Exploitation de la Mer (IFREMER), Laboratory of Biogeochemistry of Organic Contaminants, Rue de l' Ile d' Yeu, BP 21105, 44311 Nantes Cedex 3 (France); Gastineau, O.; Le Bayon, N.; Buchet, V. [Institut Francais de Recherche pour l' Exploitation de la Mer (IFREMER), Laboratory of Adaptation, Reproduction and Nutrition of marine fish, BP 70, 29280 Plouzane (France)

    2011-01-15

    The uptake and elimination of six PBDE congeners (BDE-28, -47, -99, -100, -153, -209) were studied in juvenile common sole (Solea solea L.) exposed to spiked contaminated food over a three-month period, then depurated over a five-month period. The results show that all of the studied PBDEs accumulate in fish tissues, including the higher brominated congener BDE-209. Several additional PBDE congeners were identified in the tissues of exposed fish, revealing PBDE transformation, mainly via debromination. The identified congeners originating from PBDE debromination include BDE-49 and BDE-202 and a series of unidentified tetra-, penta-, and hepta- BDEs. Contaminant assimilation efficiencies (AEs) were related to their hydrophobicity (log K{sub ow}) and influenced by PBDE biotransformation. Metabolism via debromination appears to be a major degradation route of PBDEs in juvenile sole in comparison to biotransformation into hydroxylated metabolites. - Juvenile sole exposed to artificially-contaminated food accumulate PBDEs, including the higher brominated congeners, and have a debromination capacity.

  10. Congener-specific levels and patterns of polychlorinated biphenyls in edible fish tissue from the central Red Sea coast of Saudi Arabia

    KAUST Repository

    Batang, Zenon B.

    2016-08-01

    All 209 congeners of polychlorinated biphenyls (PCBs) in edible fish tissue from the central Red Sea coast (Jeddah region) of Saudi Arabia were analyzed by isotope dilution high-resolution gas chromatography–mass spectrometry. The upper-bound total PCB (ΣPCB) levels in nine commonly consumed fish species from three areas were 0.2–82.5 ng/g wet weight (17–8450 ng/g lipid weight), which were at the lower end of reported global range and far below international tolerance limits (500–3000 ng/g ww). Dioxin-like congeners contributed up to 12.8% (mean 6.5%) to ΣPCB in tissue samples, with the total PCB toxic equivalencies (TEQs) at a tolerable range (0.05–2.6 pg TEQ/g ww or 2–238 pg TEQ/g lw) for all species. PCB profiles were dominated by moderately chlorinated homologs, mainly hexachlorobiphenyls, but less chlorinated congeners were also consistently elevated, notably in Siganus rivulatus (Area III) and Mugil cephalus (Area I). It remains to be ascertained if the latter were breakdown products or due to fresh inputs. The top congeners based on dominance by both occurrence and abundance were identified as potential markers of ΣPCB in fish tissue, which can be used for future selective biomonitoring in case of reasonable constraints on full congener approach.

  11. Cucurbita spp. and Cucumis sativus enhance the dissipation of polychlorinated biphenyl congeners by stimulating soil microbial community development

    International Nuclear Information System (INIS)

    Qin, Hua; Brookes, Philip C.; Xu, Jianming

    2014-01-01

    A number of Cucurbita species have the potential to extract polychlorinated biphenyls (PCBs) from soil, but their impact on the soil microbial communities responsible for PCB degradation remains unclear. A greenhouse experiment was conducted to investigate the effect of three Cucurbita and one Cucumis species on PCB dissipation and soil microbial community structure. Compared to the unplanted control, enhanced losses of PCBs (19.5%–42.7%) were observed in all planted soils. Cucurbita pepo and Cucurbita moschata treatments were more efficient in PCB dissipation, and have similar patterns of soil phospholipid fatty acids (PLFAs) and PCB congener profiles. Cucurbita treatments tend to have higher soil microbial biomass than Cucumis. Gram-negative (G − ) bacteria were significantly correlated with PCB degradation rates (R 2 = 0.719, p − bacteria were correlated with dissipation of the penta homologue group (R 2 = 0.590, p − bacteria contributed significantly to soil PCB dissipation. • Fungi have a great potential in the dissipation of high chlorinated biphenyls. -- Cucurbita associated fungi and G − bacteria have important influence on soil PCB dissipation rate and congener profile

  12. A 25-Year Experience of Gastroenteropancreatic Neuroendocrine Tumors and Somatostatin (Congeners) Analogs: From Symptom Control to Antineoplastic Therapy.

    Science.gov (United States)

    O'Dorisio, Thomas M; Anthony, Lowell B

    2015-01-01

    Radioimmunoassay technology was utilized in the discovery of somatostatin and was quickly brought into therapeutics; however, it took the development of somatostatin congeners to solve its limitations of a short half-life. Therapeutic medical control of hyperhormonal states such as acromegaly, carcinoid syndrome and VIPoma significantly advanced from a nonspecific approach to one that specifically and effectively targeted the underlying pathophysiology. Clinical care was transformed from nonspecific symptom control to one of a significant improvement in not only quality of life, but also quantity of life. These data submitted to US and European regulatory authorities for approval included many investigative sites with no uniform protocol and multiple investigational new drugs, and have not been previously published. This review includes the original data demonstrating the transformational impact this class of agents had on specific disease subsets resulting in regulatory approval 25 years ago. Autoradiography techniques using somatostatin resulted in identifying, localizing and characterizing its receptor subtypes. Translating in vitro data to in vivo resulted in scintigraphic whole body and SPECT scans with (111)In-pentetreotide and was incorporated into standard clinical care 20 years ago. (68)Ga-octreotide congeners using PET scanning offers a major imaging advance. Peptide receptor radiotherapy has evolved over the last 2 decades and utilizes several therapeutic isotopes, including (90)Y and (177)Lu. © 2015 S. Karger AG, Basel.

  13. Tracking polychlorinated biphenyls (PCBs) congener patterns in Newark Bay surface sediment using principal component analysis (PCA) and positive matrix factorization (PMF).

    Science.gov (United States)

    Saba, Tarek; Su, Steave

    2013-09-15

    PCB congener data for Newark Bay surface sediments were analyzed using PCA and PMF, and relationships between the outcomes from these two techniques were explored. The PCA scores plot separated the Lower Passaic River Mouth samples from North Newark Bay, thus indicating dissimilarity. Although PCA was able to identify subareas in the Bay system with specific PCB congener patterns (e.g., higher chlorinated congeners in Elizabeth River), further conclusions reading potential PCB source profiles or potential upland source areas were not clear for the PCA scores plot. PMF identified five source factors, and explained the Bay sample congener profiles as a mix of these Factors. This PMF solution was equivalent to (1) defining an envelope that encompasses all samples on the PCA scores plot, (2) defining source factors that plot on that envelope, and (3) explaining the congener profile for each Bay sediment sample (inside the scores plot envelope) as a mix of factors. PMF analysis allowed identifying characteristic features in the source factor congener distributions that allowed tracking of source factors to shoreline areas where PCB inputs to the Bay may have originated. The combined analysis from PCA and PMF showed that direct discharges to the Bay are likely the dominant sources of PCBs to the sediment. Review of historical upland activities and regulatory files will be needed, in addition to the PCA and PMF analysis, to fully reconstruct the history of operations and PCB releases around the Newark Bay area that impacted the Bay sediment. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Polychlorinated Biphenyls and Polychlorinated Dioxins-Furans in Lake Trout and Whitefish Composite Samples from Commercial Fisheries in Lakes Erie, Huron, and Superior.

    Science.gov (United States)

    Rawn, Dorothea F K; Dowd, Michael; Scuby, Matthew J S; Pantazopoulos, Peter P; Feeley, Mark

    2017-08-01

    Polychlorinated biphenyls (PCBs; sum of 36 congeners) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs; sum of 17 2,3,7,8-substituted congeners) were measured in 93 composite samples prepared from individual lake trout (Salvelinus namaycush) and whitefish (Coregonus clupeaformis) samples collected from Lake Erie, Lake Huron, and Lake Superior. All samples had detectable concentrations of PCBs and PCDD/Fs; maximum PCB concentrations in both trout (750 ng g -1 whole weight [ww]) and whitefish (210 ng g -1 ww) were found in composites from fish collected from Lake Huron. The maximum toxic equivalent concentration was found in a lake trout composite sample from Lake Huron (53 pg g -1 ww). PCB and PCDD/F congener profiles were comparable to patterns observed in fishes collected from other regions of Canada, although concentrations were above those found in other regions. A positive correlation was found between PCB concentrations determined using the historical Aroclor equivalency method and those determined using the sum of the congeners measured (r 2 = 0.871; Spearman correlation r = 0.917) or using the six indicator PCB congeners (28, 52, 101, 138, 153, and 180; r 2 = 0.850; Spearman correlation r = 0.935). PCBs were the dominant contributor to the overall toxic equivalent concentrations in the fish composite samples tested. These findings provide insight into PCB and PCDD/F concentrations in two commercially important fish species over a discrete time period.

  15. Cucurbita spp. and Cucumis sativus enhance the dissipation of polychlorinated biphenyl congeners by stimulating soil microbial community development.

    Science.gov (United States)

    Qin, Hua; Brookes, Philip C; Xu, Jianming

    2014-01-01

    A number of Cucurbita species have the potential to extract polychlorinated biphenyls (PCBs) from soil, but their impact on the soil microbial communities responsible for PCB degradation remains unclear. A greenhouse experiment was conducted to investigate the effect of three Cucurbita and one Cucumis species on PCB dissipation and soil microbial community structure. Compared to the unplanted control, enhanced losses of PCBs (19.5%-42.7%) were observed in all planted soils. Cucurbita pepo and Cucurbita moschata treatments were more efficient in PCB dissipation, and have similar patterns of soil phospholipid fatty acids (PLFAs) and PCB congener profiles. Cucurbita treatments tend to have higher soil microbial biomass than Cucumis. Gram-negative (G(-)) bacteria were significantly correlated with PCB degradation rates (R(2) = 0.719, p Cucurbita related soil microorganisms could play an important role in remediation of PCB contaminated soils. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Development of transcriptome-derived SSR markers for Hoya ledongensis (Apocynaceae) and cross-amplification in a congener.

    Science.gov (United States)

    Chen, Zheng; Deng, Yuncheng; Zhou, Renchao; He, Shaoyun

    2016-09-01

    To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H. ledongensis. The number of alleles per microsatellite locus ranged from two to 11. The observed and expected heterozygosities for the 12 loci ranged from 0.133 to 0.867 and 0.128 to 0.894, respectively. Cross-species amplification was successful for these 12 loci in the congeneric species H. jianfenglingensis. These polymorphic transcriptome-derived simple sequence repeat markers have the potential to be used as multilocus molecular markers to study the population genetics and natural hybridization in species of Hoya.

  17. Different Responses of an Invasive Clonal Plant Wedelia trilobata and its Native Congener to Gibberellin: Implications for Biological Invasion.

    Science.gov (United States)

    Dai, Zhi-Cong; Fu, Wei; Qi, Shan-Shan; Zhai, De-Li; Chen, Si-Chong; Wan, Ling-Yun; Huang, Ping; Du, Dao-Lin

    2016-02-01

    The invasive clonal plant Wedelia trilobata contains higher levels of ent-kaurane diterpenes, which are precursors of gibberellins (GAs), and higher rates of clonal growth than its native congener W. chinensis in invaded habitats. We hypothesized that the higher levels of endogenous GAs facilitate greater ramet growth in W. trilobata compared with W. chinensis. We quantified endogenous levels of GA1+3 in the two species and compared their growth responses to the changes of endogenous and exogenous GA3 by using short-term and long-term hydroponics experiments. After a period of homogeneous cultivation, levels of endogenous GA1+3 were higher in W. trilobata than in W. chinensis. The reduction of endogenous GAs repressed the emergence of adventitious roots and the growth of W. trilobata in the initial cultivation stage, and inhibited its shoot elongation and biomass. Levels of endogenous GA1+3 were positively correlated with the length of shoots and adventitious roots of W. trilobata. Adventitious roots of W. trilobata also emerged earlier and grew faster when treated with exogenous GA3. In contrast, exogenous GA3 treatment inhibited the length of adventitious roots in W. chinensis, and levels of endogenous GA1+3 did not correlate with shoot or adventitious root length. Our study suggests that GAs accelerate the rapid clonal growth of W. trilobata, more than that of its native congener W. chinensis, illustrating the relationship between plant hormones and the clonal growth of invasive plants. These findings are important for understanding the mechanisms associated with the invasiveness of clonal plants and their potential management.

  18. Seasonal variations of PCDD/Fs congeners in air, soil and eggs from a Polish small-scale farm.

    Science.gov (United States)

    Węgiel, Malgorzata; Chrząszcz, Ryszard; Maślanka, Anna; Grochowalski, Adam

    2018-02-03

    The transfer of dioxin from the environment to the food is a problem in a consumers' health protection. The study aimed to determine the concentration of dioxins in free-range chicken eggs, air and soil samples, collected during 12 months on an individual small farm, located in Małopolska region, Poland. In the majority of analyzed eggs, the concentrations of dioxin exceeded several times the legal limit of 2.5 pg WHO-TEQ g-1fat. Seasonal changes in the PCDD/Fs congeners in egg, air and soil samples were studied. During the winter season, when the combustion processes of the solid fuel in domestic furnaces are intensive, the PM10 concentration in the Małopolska region exceeds the legal limit (50μg/m3) even eight times. In this period, eggs, air and soil samples showed a higher share of PCDFs with a specific contribution of 2,3,7,8-TCDF. During the summer months, in the egg, air and soil samples, the share of PCDDs is higher with dominant OCDD and 1,2,3,4,6,7,8-HpCDDs, showing the effect of other combustion processes such as grass utilization or burning plastic wastes in controlled fires. In August, the month of the highest average air temperature and lowest rainfall amount, the highest toxicity of PCDD/Fs in eggs (9.52pgWHO-TEQ g-1fat) was found. Due to the similarity of the shares of PCDD/Fs congeners in total WHO-TEQ value we can take into account the influence of toxicity of PCDD/Fs in the air and soil on the toxicity in the eggs. Copyright © 2018. Published by Elsevier Ltd.

  19. (+)Lysergic acid diethylamide, but not its nonhallucinogenic congeners, is a potent serotonin 5HT1C receptor agonist

    International Nuclear Information System (INIS)

    Burris, K.D.; Breeding, M.; Sanders-Bush, E.

    1991-01-01

    Activation of central serotonin 5HT2 receptors is believed to be the primary mechanism whereby lysergic acid diethylamide (LSD) and other hallucinogens induce psychoactive effects. This hypothesis is based on extensive radioligand binding and electrophysiological and behavioral studies in laboratory animals. However, the pharmacological profiles of 5HT2 and 5HT1C receptors are similar, making it difficult to distinguish between effects due to activation of one or the other receptor. For this reason, it was of interest to investigate the interaction of LSD with 5HT1C receptors. Agonist-stimulated phosphoinositide hydrolysis in rat choroid plexus was used as a direct measure of 5HT1C receptor activation. (+)LSD potently stimulated phosphoinositide hydrolysis in intact choroid plexus and in cultures of choroid plexus epithelial cells, with EC50 values of 9 and 26 nM, respectively. The effect of (+)LSD in both systems was blocked by 5HT receptor antagonists with an order of activity consistent with interaction at 5HT1C receptors. Neither (+)-2-bromo-LSD nor lisuride, two nonhallucinogenic congeners of LSD, were able to stimulate 5HT1C receptors in cultured cells or intact choroid plexus. In contrast, lisuride, like (+)LSD, is a partial agonist at 5HT2 receptors in cerebral cortex slices and in NIH 3T3 cells transfected with 5HT2 receptor cDNA. The present finding that (+)LSD, but not its nonhallucinogenic congeners, is a 5HT1C receptor agonist suggests a possible role for these receptors in mediating the psychoactive effects of LSD

  20. Coexposure of dioxin-like polychlorinated biphenyls and polychlorinated dibenzo-p-dioxins and dibenzofurans in free-range hens and implications derived from congener profile analysis.

    Science.gov (United States)

    Lin, Chingju; Hsu, Jing-Fang; Liao, Pao-Chi

    2012-02-29

    The consumption of free-range eggs is becoming more popular worldwide. We analyzed the levels of 12 dioxin-like polychlorinated biphenyls (dl-PCBs) and their congener profiles from 6 free-range and 12 caged egg samples. The mean levels of dl-PCBs in the free-range samples were 5.4 times higher than those in caged eggs. All egg samples exhibited at least two characteristic dl-PCB congener patterns, which reflected distinctive contamination sources. Additionally, for the first time, we demonstrated that the dl-PCB levels in the free-range eggs were highly correlated with elevated levels of 17 polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) (r = 0.986; p free-range hens. Cluster analysis of congener patterns implied that this coexposure scenario could be attributed to distinct dl-PCB and PCDD/F sources. This congener profile information provides insights from a different perspective for further identifying potential dl-PCB and PCDD/F sources in the polluted free-range eggs.

  1. Effects of hydroxy-polychlorinated biphenyl (OH-PCB) congeners on the xenobiotic biotransformation gene expression patterns in primary culture of Atlantic salmon (Salmo salar) hepatocytes.

    Science.gov (United States)

    Mortensen, Anne S; Braathen, Marte; Sandvik, Morten; Arukwe, Augustine

    2007-11-01

    Hydroxylated metabolites of PCBs [OH-PCBs] represent new health and environmental concern because they have been shown to have agonist or antagonist interactions with hormone receptors (HRs) or hormone-receptor mediated responses. The present study was designed to investigate the estrogenic potency based on anti-AhR signalling effect of three 4-OH substituted PCB congeners (#107, #146 and #187), one 3-OH substituted congener (#138), and the pharmaceutical synthetic estrogen, ethynylestradiol (EE2) in fish in vitro system using primary culture of Atlantic salmon hepatocytes. The effects were studied by quantifying changes in transcripts with gene-sequence primer pairs for a suite of gene responses (AhRalpha, ARNT, CYP1A1, CYP3A, UGT and GST) belonging to the xenobiotic biotransformation system. Our data show that OH-PCB congeners and EE2, decreased AhRalpha and ARNT transcript levels, and CYP1A1, UGT and GST gene expressions, together with CYP3A gene expression. The decreased expression of transcripts for xenobiotic biotransformation system is related to the concentration of individual OH-PCB congener and these responses are typical of reported estrogenic and estrogen-like effects on the CYP system. Modulation of biotransformation pathways by OH-PCBs may alter xenobiotic metabolism leading to the production of toxic reactive molecules, altering pharmacokinetics and diminishing the clearance rate of individual chemicals from the organism.

  2. Tissue Distribution of Polychlorinated Biphenyls and Organochlorine Pesticides and Potential Toxicity to Alaskan Northern Fur Seals Assessed Using PCBs Congener Specific Mode of Action Schemes

    Science.gov (United States)

    The concentrations of 145 polychlorinated biphenyl (PCB) congeners were measured using gas chromatography-ion trap mass spectrometry in 8 different tissues (blubber, brain, heart, kidney, liver, lung, muscle, and reproductive tissues) of 10 Alaskan northern fur seals. The mean concentrations of bot...

  3. Reproductive characteristics differed in a series of B-congenic lines of white leghorns evidently indicating significant influence of major histocompatibility complex in chickens

    Science.gov (United States)

    Reproductive characteristics were compared between a series of seven B-congenic lines of White Leghorns retrospectively using eight year’s reproduction records.The records encompass a total of 33,010 fertile eggs set to hatch under controlled conditions, which were collected accumulatively from 2,1...

  4. Effects of oral exposure to naturally-occurring and synthetic deoxynivalenol congeners on proinflammatory cytokine and chemokine mRNA expression in the mouse

    International Nuclear Information System (INIS)

    Wu, Wenda; He, Kaiyu; Zhou, Hui-Ren; Berthiller, Franz; Adam, Gerhard; Sugita-Konishi, Yoshiko; Watanabe, Maiko; Krantis, Anthony; Durst, Tony; Zhang, Haibin; Pestka, James J.

    2014-01-01

    The foodborne mycotoxin deoxynivalenol (DON) induces a ribotoxic stress response in mononuclear phagocytes that mediate aberrant multi-organ upregulation of TNF-α, interleukins and chemokines in experimental animals. While other DON congeners also exist as food contaminants or pharmacologically-active derivatives, it is not known how these compounds affect expression of these cytokine genes in vivo. To address this gap, we compared in mice the acute effects of oral DON exposure to that of seven relevant congeners on splenic expression of representative cytokine mRNAs after 2 and 6 h. Congeners included the 8-ketotrichothecenes 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), fusarenon X (FX), nivalenol (NIV), the plant metabolite DON-3-glucoside (D3G) and two synthetic DON derivatives with novel satiety-inducing properties (EN139528 and EN139544). DON markedly induced transient upregulation of TNF-α IL-1β, IL-6, CXCL-2, CCL-2 and CCL-7 mRNA expressions. The two ADONs also evoked mRNA expression of these genes but to a relatively lesser extent. FX induced more persistent responses than the other DON congeners and, compared to DON, was: 1) more potent in inducing IL-1β mRNA, 2) approximately equipotent in the induction of TNF-α and CCL-2 mRNAs, and 3) less potent at upregulating IL-6, CXCL-2, and CCL-2 mRNAs. EN139528's effects were similar to NIV, the least potent 8-ketotrichothecene, while D3G and EN139544 were largely incapable of eliciting cytokine or chemokine mRNA responses. Taken together, the results presented herein provide important new insights into the potential of naturally-occurring and synthetic DON congeners to elicit aberrant mRNA upregulation of cytokines associated with acute and chronic trichothecene toxicity. - Highlights: • We compared effects of DON congeners on biomarker proinflammatory genes in mice. • Oral DON induced splenic IL-1β, IL-6, TNF-α,CXCL-2, CCL-2 and CCL-7 mRNAs. • 8-Ketotrichothecene ranking

  5. Effects of oral exposure to naturally-occurring and synthetic deoxynivalenol congeners on proinflammatory cytokine and chemokine mRNA expression in the mouse

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenda [College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095 (China); Dept. of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824 (United States); He, Kaiyu [Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Dept. of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 (United States); Zhou, Hui-Ren [Dept. of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824 (United States); Berthiller, Franz [Christian Doppler Laboratory for Mycotoxin Metabolism and Center for Analytical Chemistry, University of Natural Resources and Life Sciences, Tulln (Austria); Adam, Gerhard [Dept. of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (Austria); Sugita-Konishi, Yoshiko [Food and Life Sciences, Azabu University, 1-17-71 Fuchinobe Chuo-ku, Sagamihara, Kanagawa Pref., 252-5201 (Japan); Watanabe, Maiko [Division of Microbiology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya, Tokyo 158-8501 (Japan); Krantis, Anthony [Dept. of Cellular and Molecular Medicine, University of Ottawa (Canada); Durst, Tony [Dept. of Chemistry, University of Ottawa (Canada); Zhang, Haibin [College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095 (China); Pestka, James J., E-mail: pestka@msu.edu [Dept. of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824 (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Dept. of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 (United States)

    2014-07-15

    The foodborne mycotoxin deoxynivalenol (DON) induces a ribotoxic stress response in mononuclear phagocytes that mediate aberrant multi-organ upregulation of TNF-α, interleukins and chemokines in experimental animals. While other DON congeners also exist as food contaminants or pharmacologically-active derivatives, it is not known how these compounds affect expression of these cytokine genes in vivo. To address this gap, we compared in mice the acute effects of oral DON exposure to that of seven relevant congeners on splenic expression of representative cytokine mRNAs after 2 and 6 h. Congeners included the 8-ketotrichothecenes 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), fusarenon X (FX), nivalenol (NIV), the plant metabolite DON-3-glucoside (D3G) and two synthetic DON derivatives with novel satiety-inducing properties (EN139528 and EN139544). DON markedly induced transient upregulation of TNF-α IL-1β, IL-6, CXCL-2, CCL-2 and CCL-7 mRNA expressions. The two ADONs also evoked mRNA expression of these genes but to a relatively lesser extent. FX induced more persistent responses than the other DON congeners and, compared to DON, was: 1) more potent in inducing IL-1β mRNA, 2) approximately equipotent in the induction of TNF-α and CCL-2 mRNAs, and 3) less potent at upregulating IL-6, CXCL-2, and CCL-2 mRNAs. EN139528's effects were similar to NIV, the least potent 8-ketotrichothecene, while D3G and EN139544 were largely incapable of eliciting cytokine or chemokine mRNA responses. Taken together, the results presented herein provide important new insights into the potential of naturally-occurring and synthetic DON congeners to elicit aberrant mRNA upregulation of cytokines associated with acute and chronic trichothecene toxicity. - Highlights: • We compared effects of DON congeners on biomarker proinflammatory genes in mice. • Oral DON induced splenic IL-1β, IL-6, TNF-α,CXCL-2, CCL-2 and CCL-7 mRNAs. • 8-Ketotrichothecene ranking

  6. An Intergenic Region Shared by At4g35985 and At4g35987 in Arabidopsis thaliana Is a Tissue Specific and Stress Inducible Bidirectional Promoter Analyzed in Transgenic Arabidopsis and Tobacco Plants

    Science.gov (United States)

    Banerjee, Joydeep; Sahoo, Dipak Kumar; Dey, Nrisingha; Houtz, Robert L.; Maiti, Indu Bhushan

    2013-01-01

    On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85) showed stronger expression (about 3.5 fold) compared to the At4g35987 promoter (P87). The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold) under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications. PMID:24260266

  7. Tissue-Specific Transcriptome and Hormonal Regulation of Pollinated and Parthenocarpic Fig (Ficus carica L. Fruit Suggest that Fruit Ripening is Coordinated by the Reproductive Part of the Syconium

    Directory of Open Access Journals (Sweden)

    Yogev Rosianski

    2016-11-01

    Full Text Available In the unconventional climacteric fig (Ficus carica fruit, pollinated and parthenocarpic fruit of the same genotype exhibit different ripening characteristics. Integrative comparative analyses of tissue-specific transcript and of hormone levels during fruit repining from pollinated vs. parthenocarpic fig fruit were employed to unravel the similarities and differences in their regulatory processes during fruit repining. Assembling tissue-specific transcripts into 147,000 transcripts with 53,000 annotated genes provided new insights into the spatial distribution of many classes of regulatory and structural genes, including those related to color, taste and aroma, storage, protein degradation, seeds and embryos, chlorophyll, and hormones. Comparison of the pollinated and parthenocarpic tissues during fruit ripening showed differential gene expression, especially in the fruit inflorescence. The distinct physiological green phase II and ripening phase III differed significantly in their gene-transcript patterns in both pulp and inflorescence tissues. Gas chromatographic analysis of whole fruits enabled the first determination of ripening-related hormone levels from pollinated and non-pollinated figs. Ethylene and auxin both increased during fruit ripening, irrespective of pollination, whereas no production of active gibberellins or cytokinins was found in parthenocarpic or pollinated ripening fruit. Tissue-specific transcriptome revealed apparent different metabolic gene patterns for ethylene, auxin and ABA in pollinated vs. parthenocarpic fruit, mostly in the fruit inflorescence. Our results demonstrate that the production of abscisic acid (ABA, non-active ABA–GE conjugate and non-active indoleacetic acid (IAA–Asp conjugate in pollinated fruits is much higher than in parthenocarpic fruits. We suggest that fruit ripening is coordinated by the reproductive part of the syconium and the differences in ABA production between pollinated and

  8. Tissue-Specific Transcriptome and Hormonal Regulation of Pollinated and Parthenocarpic Fig (Ficus caricaL.) Fruit Suggest that Fruit Ripening Is Coordinated by the Reproductive Part of the Syconium.

    Science.gov (United States)

    Rosianski, Yogev; Doron-Faigenboim, Adi; Freiman, Zohar E; Lama, Kumar; Milo-Cochavi, Shira; Dahan, Yardena; Kerem, Zohar; Flaishman, Moshe A

    2016-01-01

    In the unconventional climacteric fig ( Ficus carica ) fruit, pollinated and parthenocarpic fruit of the same genotype exhibit different ripening characteristics. Integrative comparative analyses of tissue-specific transcript and of hormone levels during fruit repining from pollinated vs. parthenocarpic fig fruit were employed to unravel the similarities and differences in their regulatory processes during fruit repining. Assembling tissue-specific transcripts into 147,000 transcripts with 53,000 annotated genes provided new insights into the spatial distribution of many classes of regulatory and structural genes, including those related to color, taste and aroma, storage, protein degradation, seeds and embryos, chlorophyll, and hormones. Comparison of the pollinated and parthenocarpic tissues during fruit ripening showed differential gene expression, especially in the fruit inflorescence. The distinct physiological green phase II and ripening phase III differed significantly in their gene-transcript patterns in both pulp and inflorescence tissues. Gas chromatographic analysis of whole fruits enabled the first determination of ripening-related hormone levels from pollinated and non-pollinated figs. Ethylene and auxin both increased during fruit ripening, irrespective of pollination, whereas no production of active gibberellins or cytokinins was found in parthenocarpic or pollinated ripening fruit. Tissue-specific transcriptome revealed apparent different metabolic gene patterns for ethylene, auxin and ABA in pollinated vs. parthenocarpic fruit, mostly in the fruit inflorescence. Our results demonstrate that the production of abscisic acid (ABA), non-active ABA-GE conjugate and non-active indoleacetic acid (IAA)-Asp conjugate in pollinated fruits is much higher than in parthenocarpic fruits. We suggest that fruit ripening is coordinated by the reproductive part of the syconium and the differences in ABA production between pollinated and parthenocarpic fig fruit

  9. Tissue-Specific Transcriptome and Hormonal Regulation of Pollinated and Parthenocarpic Fig (Ficus carica L.) Fruit Suggest that Fruit Ripening Is Coordinated by the Reproductive Part of the Syconium

    Science.gov (United States)

    Rosianski, Yogev; Doron-Faigenboim, Adi; Freiman, Zohar E.; Lama, Kumar; Milo-Cochavi, Shira; Dahan, Yardena; Kerem, Zohar; Flaishman, Moshe A.

    2016-01-01

    In the unconventional climacteric fig (Ficus carica) fruit, pollinated and parthenocarpic fruit of the same genotype exhibit different ripening characteristics. Integrative comparative analyses of tissue-specific transcript and of hormone levels during fruit repining from pollinated vs. parthenocarpic fig fruit were employed to unravel the similarities and differences in their regulatory processes during fruit repining. Assembling tissue-specific transcripts into 147,000 transcripts with 53,000 annotated genes provided new insights into the spatial distribution of many classes of regulatory and structural genes, including those related to color, taste and aroma, storage, protein degradation, seeds and embryos, chlorophyll, and hormones. Comparison of the pollinated and parthenocarpic tissues during fruit ripening showed differential gene expression, especially in the fruit inflorescence. The distinct physiological green phase II and ripening phase III differed significantly in their gene-transcript patterns in both pulp and inflorescence tissues. Gas chromatographic analysis of whole fruits enabled the first determination of ripening-related hormone levels from pollinated and non-pollinated figs. Ethylene and auxin both increased during fruit ripening, irrespective of pollination, whereas no production of active gibberellins or cytokinins was found in parthenocarpic or pollinated ripening fruit. Tissue-specific transcriptome revealed apparent different metabolic gene patterns for ethylene, auxin and ABA in pollinated vs. parthenocarpic fruit, mostly in the fruit inflorescence. Our results demonstrate that the production of abscisic acid (ABA), non-active ABA–GE conjugate and non-active indoleacetic acid (IAA)–Asp conjugate in pollinated fruits is much higher than in parthenocarpic fruits. We suggest that fruit ripening is coordinated by the reproductive part of the syconium and the differences in ABA production between pollinated and parthenocarpic fig fruit

  10. An intergenic region shared by At4g35985 and At4g35987 in Arabidopsis thaliana is a tissue specific and stress inducible bidirectional promoter analyzed in transgenic arabidopsis and tobacco plants.

    Directory of Open Access Journals (Sweden)

    Joydeep Banerjee

    Full Text Available On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985 are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85 showed stronger expression (about 3.5 fold compared to the At4g35987 promoter (P87. The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications.

  11. The sweet potato RbcS gene (IbRbcS1) promoter confers high-level and green tissue-specific expression of the GUS reporter gene in transgenic Arabidopsis.

    Science.gov (United States)

    Tanabe, Noriaki; Tamoi, Masahiro; Shigeoka, Shigeru

    2015-08-10

    Sweet potato is an important crop because of its high yield and biomass production. We herein investigated the potential of the promoter activity of a small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RbcS) from sweet potato (Ipomoea batatas) in order to develop the high expression system of exogenous DNA in Arabidopsis. We isolated two different cDNAs (IbRbcS1 and IbRbcS2) encoding RbcS from sweet potato. Their predicted amino acid sequences were well conserved with the mature RbcS protein of other plants. The tissue-specific expression patterns of these two genes revealed that expression of IbRbcS1 was specific to green tissue, whereas that of IbRbcS2 was non-photosynthetic tissues such as roots and tubers. These results suggested that IbRbcS1 was predominantly expressed in the green tissue-specific of sweet potato over IbRbcS2. Therefore, the IbRbcS1 promoter was transformed into Arabidopsis along with β-glucuronidase (GUS) as a reporter gene. GUS staining and semi-quantitative RT-PCR showed that the IbRbcS1 promoter conferred the expression of the GUS reporter gene in green tissue-specific and light-inducible manners. Furthermore, qPCR showed that the expression levels of GUS reporter gene in IbRbcS1 pro:GUS were same as those in CaMV 35S pro:GUS plants. These results suggest that the IbRbcS1 promoter is a potentially strong foreign gene expression system for genetic transformation in plants. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Editor's Highlight: Congener-Specific Disposition of Chiral Polychlorinated Biphenyls in Lactating Mice and Their Offspring: Implications for PCB Developmental Neurotoxicity.

    Science.gov (United States)

    Kania-Korwel, Izabela; Lukasiewicz, Tracy; Barnhart, Christopher D; Stamou, Marianna; Chung, Haeun; Kelly, Kevin M; Bandiera, Stelvio; Lein, Pamela J; Lehmler, Hans-Joachim

    2017-07-01

    Chiral polychlorinated biphenyl (PCB) congeners have been implicated by laboratory and epidemiological studies in PCB developmental neurotoxicity. These congeners are metabolized by cytochrome P450 (P450) enzymes to potentially neurotoxic hydroxylated metabolites (OH-PCBs). The present study explores the enantioselective disposition and toxicity of 2 environmentally relevant, neurotoxic PCB congeners and their OH-PCB metabolites in lactating mice and their offspring following dietary exposure of the dam. Female C57BL/6N mice (8-weeks old) were fed daily, beginning 2 weeks prior to conception and continuing throughout gestation and lactation, with 3.1 µmol/kg bw/d of racemic 2,2',3,5',6-pentachlorobiphenyl (PCB 95) or 2,2',3,3',6,6'-hexachlorobiphenyl (PCB 136) in peanut butter; controls received vehicle (peanut oil) in peanut butter. PCB 95 levels were higher than PCB 136 levels in both dams and pups, consistent with the more rapid metabolism of PCB 136 compared with PCB 95. In pups and dams, both congeners were enriched for the enantiomer eluting second on enantioselective gas chromatography columns. OH-PCB profiles in lactating mice and their offspring were complex and varied according to congener, tissue and age. Developmental exposure to PCB 95 versus PCB 136 differentially affected the expression of P450 enzymes as well as neural plasticity (arc and ppp1r9b) and thyroid hormone-responsive genes (nrgn and mbp). The results suggest that the enantioselective metabolism of PCBs to OH-PCBs may influence neurotoxic outcomes following developmental exposures, a hypothesis that warrants further investigation. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. Congener-specific metabolism and sequestration of dioxin-like compounds by cytochrome P450 1A induced in the liver of crows from Tokyo, Japan

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, M.; Iwata, H.; Tanabe, S. [Ehime Univ., Matsuyama (Japan); Yoneda, K.; Hashimoto, T. [Japan Wildlife Research Center, Tokyo (Japan)

    2004-09-15

    Jungle crow (JC; Corvus macrorhynchos) is a useful bioindicator for monitoring contaminants in urban areas, because this species is residential, occupies a same habitat as human, and feeds variety of foods including domestic waste and garbage. Therefore, JCs may accumulate environmental contaminants such as polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and coplanar polychlorinated biphenyls (Co-PCBs), which are released by human activities. Induction of cytochrome P450 (CYP) 1A is a responsive mechanism elicited by exposure to dioxinlike compounds including PCDDs/DFs and Co-PCBs. Toxicokinetic behavior of dioxin-like compounds in organisms is controlled by excretion, metabolism and absorption. These processes are, at least partly, dependent on CYP1A expression in addition to chemical structure and number of chlorine substitution of each congener. Low chlorinated congeners such as 2378-T{sub 4}CDD, 2378- T{sub 4}CDF, 12378-P{sub 5}CDD and 33'44'-PCB were easily metabolized by CYP1A1/2 in rat liver microsomes. PCDDs/DFs accumulate in hepatic tissue to a greater extent than adipose tissue in rats and mice. Recent study using transgenic CYP1A2 knockout mice demonstrated that CYP1A2 is responsible for the sequestration of 2378-T{sub 4}CDD and 23478-P{sub 5}CDF in hepatic tissue. Therefore, CYP1A is considered as a key factor responsible for toxicokinetics of dioxin-like compounds. However, there's no comprehensive data on the contribution of CYP1A to the toxicokinetics of dioxin-like congeners in wild populations. In this study, we investigated contamination levels of PCDDs/DFs and Co-PCBs in liver and breast muscle of JCs from Tokyo, Japan, and interactions of dioxin-like congeners with hepatic CYP to elucidate congener-specific toxicokinetics related to CYP expression in JC.

  14. Effects of oral exposure to naturally-occurring and synthetic deoxynivalenol congeners on proinflammatory cytokine and chemokine mRNA expression in the mouse.

    Science.gov (United States)

    Wu, Wenda; He, Kaiyu; Zhou, Hui-Ren; Berthiller, Franz; Adam, Gerhard; Sugita-Konishi, Yoshiko; Watanabe, Maiko; Krantis, Anthony; Durst, Tony; Zhang, Haibin; Pestka, James J

    2014-07-15

    The foodborne mycotoxin deoxynivalenol (DON) induces a ribotoxic stress response in mononuclear phagocytes that mediate aberrant multi-organ upregulation of TNF-α, interleukins and chemokines in experimental animals. While other DON congeners also exist as food contaminants or pharmacologically-active derivatives, it is not known how these compounds affect expression of these cytokine genes in vivo. To address this gap, we compared in mice the acute effects of oral DON exposure to that of seven relevant congeners on splenic expression of representative cytokine mRNAs after 2 and 6h. Congeners included the 8-ketotrichothecenes 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), fusarenon X (FX), nivalenol (NIV), the plant metabolite DON-3-glucoside (D3G) and two synthetic DON derivatives with novel satiety-inducing properties (EN139528 and EN139544). DON markedly induced transient upregulation of TNF-α IL-1β, IL-6, CXCL-2, CCL-2 and CCL-7 mRNA expressions. The two ADONs also evoked mRNA expression of these genes but to a relatively lesser extent. FX induced more persistent responses than the other DON congeners and, compared to DON, was: 1) more potent in inducing IL-1β mRNA, 2) approximately equipotent in the induction of TNF-α and CCL-2 mRNAs, and 3) less potent at upregulating IL-6, CXCL-2, and CCL-2 mRNAs. EN139528's effects were similar to NIV, the least potent 8-ketotrichothecene, while D3G and EN139544 were largely incapable of eliciting cytokine or chemokine mRNA responses. Taken together, the results presented herein provide important new insights into the potential of naturally-occurring and synthetic DON congeners to elicit aberrant mRNA upregulation of cytokines associated with acute and chronic trichothecene toxicity. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Biodegradation of complex naphthenic acid mixtures and a probable link between congener profiles and aquatic toxicity

    Energy Technology Data Exchange (ETDEWEB)

    Toor, N.; Franz, E.; Liber, K. [Saskatchewan Univ., Saskatoon, SK (Canada); Han, X.; Martin, J. [Alberta Univ., Edmonton, AB (Canada); MacKinnon, M. [Syncrude Canada Ltd., Edmonton, AB (Canada)

    2009-07-01

    This presentation reported on a study that evaluated the potential for the biodegradation and associated reduction in aquatic toxicity of oil sands process-affected waters (OSPWs) using flow-through laboratory wetland microcosms. Changes in the composition of naphthenic acids (NAs) over a period of 52 weeks were also identified. OSPWs from Syncrude and Suncor were used in the experiments. The 2 types of OSPWs were enriched with nitrogen and phosphorus and had short and long hydraulic retention times (HRTs) of 40 and 400 days. HPLC/QTOF analysis was used to track changes in NA mixture profiles in each treatment over time. The biodegradation of NAs in Suncor OSPW was considerably faster than that of Syncrude OSPW. The biodegradation of NAs in both sources of OSPW was enhanced under longer HRTs, but the influence of nutrient addition was minimal. NAs that had the lowest degrees of cyclization and lowest carbon number were found to degrade faster, which is consistent with previous trends observed for aerobic microbial degradation of NAs using laboratory incubations. The 3 most persistent fractions of NA homologues were also identified within the NA mixture fingerprint, which may explain the lack of correlation between the mostly unchanged toxicological response as measured by Microtox and the 78 per cent reduction in total NA concentration over the study period.

  16. Relationships between congener distribution patterns of PCDDs, PCDFs, PCNs, PCBs, PCBzs and PCPhs formed during flue gas cooling

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Stina, E-mail: stina.jansson@chem.umu.se [Department of Chemistry, Umea University, SE-901 87 Umea (Sweden); Swedish University of Agricultural Sciences, Unit of Biomass Technology and Chemistry, SE-901 83 Umea (Sweden); Andersson, Patrik L., E-mail: patrik.andersson@chem.umu.se [Department of Chemistry, Umea University, SE-901 87 Umea (Sweden)

    2012-02-01

    The congener patterns of mono- to octa-chlorinated dibenzo-p-dioxins (PC{sub 1-8}DD), dibenzofurans (PC{sub 1-8}DF), naphthalenes (PC{sub 1-8}N), mono- to deca-chlorinated biphenyls (PC{sub 1-10}B), di- to hexa-chlorinated benzenes (PC{sub 2-6}Bz) and mono- to penta-chlorinated phenols (PC{sub 1-5}Ph) in flue gas samples collected simultaneously at 450 Degree-Sign C, 300 Degree-Sign C and 200 Degree-Sign C in the post-combustion zone during waste incineration in a laboratory-scale reactor in a previous study, were in this study evaluated using principal component analysis (PCA). To our knowledge this is the most comprehensive chemical and multivariate analysis to date of the thermal formation of dioxins. The PCA indicated that different formation pathways occur in the temperature regions 450-300 Degree-Sign C and 300-200 Degree-Sign C, and reflected a chlorination effect of PCDF and PCDD between 450 Degree-Sign C and 200 Degree-Sign C which could not be discerned or was less pronounced for the other compound groups. Toxic equivalents (TEQs) of PCDDs, PCDFs and PCBs, as well as total TEQ values (TEQ{sub Total}) were also calculated, and correlations between changes in levels of specific congeners and the TEQs were explored in the PCA. Levels of four HxCDF congeners and 1,2,3,4,8-, 1,2,3,7,8-PeCDF and 2,3,4,7,8-PeCDF showed the strongest correlations with TEQ{sub Total} (R{sup 2} {>=} 0.9). In addition, levels of 1,2,4-TriCBz correlated strongly with TEQ{sub Total} (R{sup 2} > 0.7), supporting previous reports that it may be a potential indicator of the TEQ. - Highlights: Black-Right-Pointing-Pointer Different pathways dominating between 450-300 Degree-Sign C and 300-200 Degree-Sign C, respectively. Black-Right-Pointing-Pointer Chlorination of PCDD/Fs between 450 Degree-Sign C and 200 Degree-Sign C but not for the other chloroaromatics. Black-Right-Pointing-Pointer Best TEQ{sub Total} correlations for four HxCDFs, and 1,2,3,4,8-/1,2,3,7,8- and 2,3,4,7,8-PeCDF. Black

  17. Effects of cytochalasin congeners, microtubule-directed agents, and doxorubicin alone or in combination against human ovarian carcinoma cell lines in vitro

    International Nuclear Information System (INIS)

    Trendowski, Matthew; Christen, Timothy D.; Acquafondata, Christopher; Fondy, Thomas P.

    2015-01-01

    Although the actin cytoskeleton is vital for carcinogenesis and subsequent pathology, no microfilament-directed agent has been approved for cancer chemotherapy. One of the most studied classes of microfilament-directed agents has been the cytochalasins, mycotoxins known to disrupt the formation of actin polymers. In the present study, we sought to determine the effects of cytochalasin congeners toward human drug sensitive and multidrug resistant cell lines. SKOV3 human ovarian carcinoma and several multidrug resistant derivatives were tested for sensitivity against a panel of nine cytochalasin congeners, as well as three clinically approved chemotherapeutic agents (doxorubicin, paclitaxel, and vinblastine). In addition, verapamil, a calcium ion channel blocker known to reverse P-glycoprotein (P-gp) mediated drug resistance, was used in combination with multiple cytochalasin congeners to determine whether drug sensitivity could be increased. While multidrug resistant SKVLB1 had increased drug tolerance (was more resistant) to most cytochalasin congeners in comparison to drug sensitive SKOV3, the level of resistance was 10 to 1000-fold less for the cytochalasins than for any of the clinically approved agents. While cytochalasins did not appear to alter the expression of ATP binding cassette (ABC) transporters, several cytochalasins appeared to inhibit the activity of ABC transporter-mediated efflux of rhodamine 123 (Rh123), suggesting that these congeners do have affinity for drug efflux pumps. Cytochalasins also appeared to significantly decrease the F/G-actin ratio in both drug sensitive and drug resistant cells, indicative of marked microfilament inhibition. The cytotoxicity of most cytochalasin congeners could be increased with the addition of verapamil, and the drug sensitivity of resistant SKVLB1 to the clinically approved antineoplastic agents could be increased with the addition of cytochalasins. As assessed by isobolographic analysis and Chou

  18. Pollination Biology of Potentilla recta (Sulfur Cinquefoil and Its Cooccurring Native Congener Potentilla gracilis in Northeastern Oregon

    Directory of Open Access Journals (Sweden)

    James McIver

    2012-01-01

    Full Text Available Pollination biology of the invasive plant sulfur cinquefoil (Potentilla recta L. and it's native cooccurring congener slender cinquefoil (P. gracilis Dougl. ex. Hook. was studied from 2002–2004, at four sites in northeastern Oregon, USA The native cinquefoil flowered first for five weeks, followed by the invasive for five weeks, with two weeks overlap in mid-June. Invasive flowers attracted 74 species and 543 individuals; the native attracted 93 species and 619 individuals. The most important pollinators for the invasive, in order of importance, were: Apis mellifera, Ceratina nanula, Halictus tripartitus, Lasioglossum sisymbrii, and Bombus rufocinctus; for the native: C. nanula, Trichodes ornatus, H. ligatus, L. sisymbrii, and L. olympiae. The invasive produced higher numbers of seeds per plant, having greater mass per unit vegetation. Mean seed size was lower for the invasive when pollinators were allowed access to flowers, but seed size increased linearly with more complete exclusion of pollinators; the native showed no such response to pollinator exclusion. Compared to the native, nearly twice as many seeds germinated for sulfur cinquefoil (35.0% versus 19.5%, with seeds germinating over a longer period of time. Results are discussed as they relate to the invasiveness of sulfur cinquefoil relative to the native.

  19. Development of transcriptome-derived SSR markers for Hoya ledongensis (Apocynaceae) and cross-amplification in a congener1

    Science.gov (United States)

    Chen, Zheng; Deng, Yuncheng; Zhou, Renchao; He, Shaoyun

    2016-01-01

    Premise of the study: To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. Methods and Results: Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H. ledongensis. The number of alleles per microsatellite locus ranged from two to 11. The observed and expected heterozygosities for the 12 loci ranged from 0.133 to 0.867 and 0.128 to 0.894, respectively. Cross-species amplification was successful for these 12 loci in the congeneric species H. jianfenglingensis. Conclusions: These polymorphic transcriptome-derived simple sequence repeat markers have the potential to be used as multilocus molecular markers to study the population genetics and natural hybridization in species of Hoya. PMID:27672524

  20. Passive air monitoring of PCBs and PCNs across East Asia: a comprehensive congener evaluation for source characterization.

    Science.gov (United States)

    Hogarh, Jonathan Nartey; Seike, Nobuyasu; Kobara, Yuso; Habib, Ahsan; Nam, Jae-Jak; Lee, Jong-Sik; Li, Qilu; Liu, Xiang; Li, Jun; Zhang, Gan; Masunaga, Shigeki

    2012-02-01

    A comprehensive congener specific evaluation of polychlorinated biphenyls (PCBs) and polychlorinated naphthalenes (PCNs) in the atmosphere was conducted across East Asia in spring 2008, applying polyurethane foam (PUF) disk passive air sampler (PAS) as monitoring device. Mean concentrations derived for Japan, China and Korea were 184 ± 24, 1100 ± 118, and 156 ± 20 pg m(-3) for ∑(202) PCBs, and 9.5 ± 1.5, 61 ± 6, and 16 ± 2.4 pg m(-3) for ∑(63) PCNs, respectively. Relative to reported data from 2004, the present results suggest that air PCBs concentrations have not changed much in Japan and Korea, while it has increased by one order of magnitude in China. From principal component analysis, combustion emerged highly culpable in contemporary emissions of both PCBs and PCNs across the East Asian sub-region. Another factor derived as important to air PCBs was re-emissions/volatilization. Signals from PCBs formulations were also picked, but their general importance was virtually consigned to the re-emissions/volatilization tendencies. On the contrary, counterpart PCNs formulations did not appear to contribute much to air PCNs. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Carnitine congener mildronate protects against stress- and haloperidol-induced impairment in memory and brain protein expression in rats.

    Science.gov (United States)

    Beitnere, Ulrika; Dzirkale, Zane; Isajevs, Sergejs; Rumaks, Juris; Svirskis, Simons; Klusa, Vija

    2014-12-15

    The present study investigates the efficacy of mildronate, a carnitine congener, to protect stress and haloperidol-induced impairment of memory in rats and the expression of brain protein biomarkers involved in synaptic plasticity, such as brain-derived neurotrophic factor (BDNF), acetylcholine esterase and glutamate decarboxylase 67 (GAD67). Two amnesia models were used: 2h immobilization stress and 3-week haloperidol treatment. Stress caused memory impairment in the passive avoidance test and induced a significant 2-fold BDNF elevation in hippocampal and striatal tissues that was completely inhibited by mildronate. Mildronate decreased the level of GAD67 (but not acetylcholine esterase) expression by stress. Haloperidol decrease by a third hippocampal BDNF and acetylcholine esterase (but not GAD67) expression, which was normalized by mildronate; it also reversed the haloperidol-induced memory impairment in Barnes test. The results suggest the usefulness of mildronate as protector against neuronal disturbances caused by stress or haloperidol. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Synthesis, evaluation against Leishmania amazonensis and cytotoxicity assays in macrophages of sixteen new congeners Morita-Baylis-Hillman adducts.

    Science.gov (United States)

    Silva, Fábio P L; de Assis, Priscilla A C; Junior, Claudio G L; de Andrade, Natália G; da Cunha, Saraghina M D; Oliveira, Márcia R; Vasconcellos, Mário L A A

    2011-09-01

    We report the design, synthesis, in vitro evaluation against Leishmania amazonensis (IC(50)), cytotoxicity assays in macrophages (CC(50)), and selectivity index (SICC(50)/IC(50)) of sixteen new congeners aromatic Morita-Baylis-Hillman adducts 1-16. The 1-16 were prepared in good to excellent yields (58%-97%) from the "one pot" Morita-Baylis-Hillman Reaction between the aldehydes 29-36 and the acrylates 27 or 28 under DABCO as promoter. The MBHA 2-[Hydroxy(2-nitrophenyl)propyl] propanoate (1, IC(50) = 7.52 μg/mL or 28.38 μM; CC(50) = 35.77 μg/mL or 134.98 μM; SI = 4.75) and 2-[Hydroxy(2-nitrophenyl)hydroxyethyl] propanoate (9, IC(50) = 5.48 μg/mL or 20.52 μM; CC(50) = 29.81 μg/mL or 111.64c μM and, SI = 5.43) were the most effective and safe evaluated compounds. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  3. Congener-specific determination of ultratrace levels of chlorinated and brominated polycyclic aromatic hydrocarbons in atmosphere and industrial stack gas by isotopic dilution gas chromatography/high resolution mass spectrometry method.

    Science.gov (United States)

    Jin, Rong; Liu, Guorui; Zheng, Minghui; Fiedler, Heidelore; Jiang, Xiaoxu; Yang, Lili; Wu, Xiaolin; Xu, Yang

    2017-08-04

    Isotopic dilution gas chromatography combined with high resolution mass spectrometry (GC/HRMS) has overwhelming advantages with respect to the accuracy of congener-specific ultratrace analysis of complex persistent organic pollutants (POPs) in environmental matrices. However, an isotopic dilution GC/HRMS method for analysis of chlorinated and brominated polycyclic aromatic hydrocarbons (Cl-PAHs and Br-PAHs) using 13 C-labelled congeners as internal standards has not been established. In this study, a method for identification and quantification of 38 congeners of Cl-PAHs and Br-PAHs in atmosphere and stack gas samples from waste incinerators was developed using the isotopic dilution GC/HRMS technique. The instrumental detection limits of the GC/HRMS method ranged from 0.2pg to 1.8pg for Cl-PAH congeners, and 0.7pg to 2.7pg for Br-PAH congeners, which were about three orders of magnitude lower than those of the GC/quadrupole MS method. This new method developed was also the first to enable determination of Cl-PAH and Br-PAH homologs comprising congeners with the same molecular skeleton and chlorine or bromine substitution numbers. Among the detected congeners, seven Cl-PAH congeners and thirteen Br-PAH congeners that were abundant in the atmosphere and stack gases released from waste incinerators were firstly detected in real samples and reported using the established isotopic dilution GC/HRMS method. The developed isotopic dilution GC/HRMS is significant and needed for better studying the environmental behavior and health risk of Cl-PAHs and Br-PAHs. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Levels and congener pattern of polychlorinated biphenyl and organochlorine pesticide residues in bluefin tuna (Thunnus thynnus) from the Straits of Messina (Sicily, Italy).

    Science.gov (United States)

    Di Bella, G; Licata, P; Bruzzese, A; Naccari, C; Trombetta, D; Lo Turco, V; Dugo, G; Richetti, A; Naccari, F

    2006-08-01

    The aim of this study is to assess the accumulation of OCs and PCBs in Thunnus thynnus and to elucidate the suitability of this species as a bioindicator for monitoring contaminations of these compounds in the marine ecosystems of the Straits of Messina. This investigation was conducted on fat, liver and muscle samples of 14 T. thynnus collected during April 2004. Quantitative determination of OCs and PCBs in the various samples examined has been carried out using GC-ECD and GC-MS. The results obtained show the presence of low concentrations of p,p'-DDE and PCB congeners (138, 153 and 180) in all fat, liver and muscle samples caught in the Straits of Messina. Concentrations of p,p'-DDE and PCB congeners (138, 153 and 180) in all the samples examined were below MRLs (CE n. 97/41, 1999/65 and 1999/71).

  5. Candidate chromosome 1 disease susceptibility genes for Sjogren’s syndrome xerostomia are narrowed by novel NOD.B10 congenic mice

    Science.gov (United States)

    Mongini, Patricia K. A.; Kramer, Jill M.; Ishikawa, Tomo-o; Herschman, Harvey; Esposito, Donna

    2014-01-01

    Sjogren’s syndrome (SS) is characterized by salivary gland leukocytic infiltrates and impaired salivation (xerostomia). Cox-2 (Ptgs2) is located on chromosome 1 within the span of the Aec2 region. In an attempt to demonstrate that COX-2 drives antibody-dependent hyposalivation, NOD.B10 congenic mice bearing a Cox-2flox gene were generated. A congenic line with non-NOD alleles in Cox-2-flanking genes failed manifest xerostomia. Further backcrossing yielded disease-susceptible NOD.B10 Cox-2flox lines; fine genetic mapping determined that critical Aec2 genes lie within a 1.56 to 2.17 Mb span of DNA downstream of Cox-2. Bioinformatics analysis revealed that susceptible and non-susceptible lines exhibit non-synonymous coding SNPs in 8 protein-encoding genes of this region, thereby better delineating candidate Aec2 alleles needed for SS xerostomia. PMID:24685748

  6. Improved separation and quantification of dioxin and furan congeners using novel low-bleed capillary gas chromatography columns and mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Dorman, F. [Restek Corporation, Bellefonte, PA (United States); Reese, S. [Folsom Lake College, Folsom, CA (United States); Reiner, E.; MacPherson, K. [Ontario Ministry of the Environment, Ottawa, Ontario (Canada); Focant, J. [Liege Univ. (Belgium); Cochran, J. [LECO Corporation, St. Josephs, MI (United States)

    2004-09-15

    This presentation will address the development of two new stationary phase chemistries that allow for improved separation of the toxic dioxin and furan congeners. Using conventional high-resolution mass spectrometry, it is possible to separate all of the congeners of interest in a single analysis on one column. Quantitation values from standard reference materials, fly ash, and previously characterized samples will be shown as evidence of how this separation is faster and more accurate than has previously been available. Finally results from comprehensive two-dimensional GC coupled to time-of-flight MS will be shown to demonstrate how this technique can rival the high-resolution method in terms of quality of information.

  7. Tissue specificity of endothelin binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Bolger, G.T.; Liard, F.; Krogsrud, R.; Thibeault, D.; Jaramillo, J. (BioMega, Inc., Laval, Quebec (Canada))

    1990-09-01

    A measurement was made of the binding of 125I-labeled endothelin (125I-ET) to crude membrane fractions prepared from rat aorta, atrium, ventricle, portal vein, trachea, lung parenchyma, vas deferens, ileum, bladder, and guinea-pig taenia coli and lung parenchyma. Scatchard analysis of 125I-ET binding in all tissues indicated binding to a single class of saturable sites. The affinity and density of 125I-ET binding sites varied between tissues. The Kd of 125I-ET binding was approximately 0.5 nM for rat aorta, trachea, lung parenchyma, ventricle, bladder, and vas deferens, and guinea-pig taenia coli and lung parenchyma, 1.8 nM for rat portal vein and atrium, and 3.3 nM for ileum. The Bmax of 125I-ET binding had the following rank order of density in rat tissues: trachea greater than lung parenchyma = vas deferens much greater than aorta = portal vein = atrium greater than bladder greater than ventricle = ileum. The properties of 125I-ET endothelin binding were characterized in rat ventricular membranes. 125I-ET binding was time dependent, reaching a maximum within 45-60 min at 25 degrees C. The calculated microassociation constant was 9.67 x 10(5) s-1 M-1. Only 15-20% of 125I-ET dissociated from its binding site even when dissociation was studied as long as 3 h. Preincubation of ventricular membranes with ET prevented binding of 125I-ET. 125I-ET binding was destroyed by boiling of ventricular membranes and was temperature, pH, and cation (Ca2+, Mg2+, and Na+) dependent.

  8. Tissue-specific MR contrast agents

    Energy Technology Data Exchange (ETDEWEB)

    Weinmann, Hanns-Joachim E-mail: hannsjoachim.weinmann@schering.de; Ebert, Wolfgang; Misselwitz, Bernd; Schmitt-Willich, Heribert

    2003-04-01

    The purpose of this review is to outline recent trends in contrast agent development for magnetic resonance imaging. Up to now, small molecular weight gadolinium chelates are the workhorse in contrast enhanced MRI. These first generation MR contrast agents distribute into the intravascular and interstitial space, thus allowing the evaluation of physiological parameters, such as the status or existence of the blood-brain-barrier or the renal function. Shortly after the first clinical use of paramagnetic metallochelates in 1983, compounds were suggested for liver imaging and enhancing a cardiac infarct. Meanwhile, liver specific contrast agents based on gadolinium, manganese or iron become reality. Dedicated blood pool agents will be available within the next years. These gadolinium or iron agents will be beneficial for longer lasting MRA procedures, such as cardiac imaging. Contrast enhanced lymphography after interstitial or intravenous injection will be another major step forward in diagnostic imaging. Metastatic involvement will be seen either after the injection of ultrasmall superparamagnetic iron oxides or dedicated gadolinium chelates. The accumulation of both compound classes is triggered by an uptake into macrophages. It is likely that similar agents will augment MRI of atheriosclerotic plaques, a systemic inflammatory disease of the arterial wall. Thrombus-specific agents based on small gadolinium labeled peptides are on the horizon. It is very obvious that the future of cardiovascular MRI will benefit from the development of new paramagnetic and superparamagnetic substances. The expectations for new tumor-, pathology- or receptor-specific agents are high. However, is not likely that such a compound will be available for daily routine MRI within the next decade.

  9. Early Alterations in Operant Performance and Prominent Huntingtin Aggregation in a Congenic F344 Rat Line of the Classical CAGn51trunc Model of Huntington Disease

    OpenAIRE

    Anne-Christine Plank; Fabio Canneva; Kerstin A. Raber; Yvonne K. Urbach; Julia Dobner; Maja Puchades; Jan G. Bjaalie; Clarissa Gillmann; Tobias Bäuerle; Olaf Riess; Hoa H. P. Nguyen; Stephan von Hörsten

    2018-01-01

    The transgenic rat model of Huntington disease expressing a fragment of mutant HTT (tgHD rat) has been thoroughly characterized and reproduces hallmark symptoms of human adult-onset HD. Pursuing the optimization of this model for evaluation of translational therapeutic approaches, the F344 inbred rat strain was considered as advantageous genetic background for the expression of the HD transgenic construct. In the present study, a novel congenic line of the SPRDtgHD transgenic model of HD, car...

  10. Biomagnification of higher brominated PBDE congeners in an urban terrestrial food web in north China based on field observation of prey deliveries.

    Science.gov (United States)

    Yu, Le-Huan; Luo, Xiao-Jun; Wu, Jiang-Ping; Liu, Li-Yu; Song, Jie; Sun, Quan-Hui; Zhang, Xiu-Lan; Chen, Da; Mai, Bi-Xian

    2011-06-15

    As an important group of brominated flame retardants, polybrominated diphenyl ethers (PBDEs) persist in the wildlife food webs. However, the biomagnification of PBDEs has not been adequately studied in the terrestrial food webs. In this study, a terrestrial food web composed of common kestrels, sparrows, rats, grasshoppers, and dragonflies in the urban environment from northern China was obtained. A field prey delivery study, reinforced by δ¹³C and δ¹⁵N analyses, indicates that sparrows are the primary prey items of common kestrels. Concentrations of PBDEs were in the following order: common kestrel > sparrow > rat > grasshopper and dragonfly with BDE-209 as the dominant congener. Biomagnification factors (BMFs) were calculated as the ratio between the lipid normalized concentrations in the predator and prey. The highest BMF (6.9) was determined for BDE-153 in sparrow/common kestrel food chain. Other higher brominated congeners, such as BDE-202, -203, -154, -183, -197, and -209, were also biomagnified in this terrestrial food chain with BMF of 1.3-4.7. BDE-47, -99, and -100 were found to be biodiluted from sparrow to common kestrel (BMFs American kestrels from another study. Retention factors and metabolism of BDE congeners may be confounding factors influencing the measured BMFs in this current study.

  11. Single Targeted Exon Mutation Creates a True Congenic Mouse for Competitive Hematopoietic Stem Cell Transplantation: The C57BL/6-CD45.1STEM Mouse

    Directory of Open Access Journals (Sweden)

    Francois E. Mercier

    2016-06-01

    Full Text Available Defining the molecular regulators of hematopoietic stem and progenitor cells (HSPCs requires in vivo functional analyses. Competitive bone marrow transplants (BMTs compare control and test HSPCs to demonstrate the functional role of a genetic change or chemical perturbation. Competitive BMT is enabled by antibodies that specifically recognize hematopoietic cells from congenic mouse strains due to variants of the cell surface protein CD45, designated CD45.1 and CD45.2. The current congenic competitor strain, B6.SJL-Ptprca Pepcb/BoyJ (CD45.1, has a substantial inherent disadvantage in competition against the C57BL/6 (CD45.2 strain, confounding experimental interpretation. Despite backcrossing, the congenic interval over which the B6.SJL-Ptprca Pepcb/BoyJ strain differs is almost 40 Mb encoding ∼300 genes. Here, we demonstrate that a single amino acid change determines the CD45.1 epitope. Further, we report on the single targeted exon mutant (STEM mouse strain, CD45.1STEM, which is functionally equivalent to CD45.2 cells in competitive BMT. This strain will permit the precise definition of functional roles for candidate genes using in vivo HSPC assays.

  12. Analysis of biosurfactants from industrially viable Pseudomonas strain isolated from crude oil suggests how rhamnolipids congeners affect emulsification property and antimicrobial activity.

    Science.gov (United States)

    Das, Palashpriya; Yang, Xin-Ping; Ma, Luyan Z

    2014-01-01

    Rhamnolipid biosurfactants produced mainly by Pseudomonas sp. had been reported to possess a wide range of potential industrial application. These biosurfactants are produced as monorhamnolipid (MRL) and di-rhamnolipid (DRL) congeners. The present study deals with rhamnolipid biosurfactants produced by three bacterial isolates from crude oil. Biosurfactants produced by one of the strains (named as IMP67) was found to be very efficacious based on its critical micelle concentration value and hydrocarbon emulsification property. Strikingly, antimicrobial, and anti-biofilm potential of this biosurfactant were higher than biosurfactants produced by other two strains. Thin layer chromatography analysis and rhamnose quantification showed that the rhamnolipids of IMP67 had more MRL congeners than biosurfactants of the other two strains. Emulsification and antimicrobial actions were affected by manual change of MRL and DRL congener proportions. Increase of MRL proportion enhanced emulsification index and antimicrobial property to Gram negative bacteria. This result indicated that the ratio of MRL and DRL affected the emulsification potentials of rhamnolipids, and suggested that high emulsification potentials might enhance rhamnolipids to penetrate the cell wall of Gram negative bacteria. In line with this finding, rhamnolipids of IMP67 also reduced the MIC of some antibiotics against bacteria, suggesting their synergistic role with the antibiotics.

  13. Analysis of biosurfactants from industrially-viable Pseudomonas strain isolated from crude oil suggests how rhamnolipids congeners affect on emulsification property and antimicrobial activity

    Directory of Open Access Journals (Sweden)

    Palashpriya eDas

    2014-12-01

    Full Text Available Rhamnolipid biosurfactants produced mainly by Pseudomonas sp. had been reported to possess a wide range of potential industrial application. These biosurfactants are produced as monorhamnolipid (MRL and di-rhamnolipid (DRL congeners. The present study deals with rhamnolipid biosurfactants produced by three bacterial isolates from crude oil. Biosurfactants produced by one of the strains (named as IMP67 was found to be very efficacious based on its critical micelle concentration (CMC value and hydrocarbon emulsification property. Strikingly, antimicrobial and anti-biofilm potential of this biosurfactant were higher than biosurfactants produced by other two strains. Thin layer chromatography (TLC analysis and rhamnose quantification showed that the rhamnolipids of IMP67 had more MRL congeners than biosurfactants of the other two strains. Emulsification and antimicrobial actions were affected by manual change of MRL and DRL congener proportions. Increase of MRL proportion enhanced emulsification index and antimicrobial property to Gram negative bacteria. This result indicated that the ratio of MRL and DRL affect the emulsification potentials of rhamnolipids, and suggested that high emulsification potentials might enhance rhamnolipids to penetrate the cell wall of Gram negative bacteria. In consistent, rhamnolipids of IMP67 reduced the MIC of some antibiotics against bacteria, suggesting the potential of biosurfactant as antibiotics synergist.

  14. Prenatal exposure to a polychlorinated biphenyl (PCB congener influences fixation duration on biological motion at 4-months-old: a preliminary study.

    Directory of Open Access Journals (Sweden)

    Hirokazu Doi

    Full Text Available Adverse effects of prenatal exposure to polychlorinated biphenyl (PCB congeners on postnatal brain development have been reported in a number of previous studies. However, few studies have examined the effects of prenatal PCB exposure on early social development. The present study sought to increase understanding of the neurotoxicity of PCBs by examining the relationship between PCB congener concentrations in umbilical cord blood and fixation patterns when observing upright and inverted biological motion (BM at four-months after birth. The development of the ability to recognize BM stimuli is considered a hallmark of socio-cognitive development. The results revealed a link between dioxin-like PCB #118 concentration and fixation pattern. Specifically, four-month-olds with a low-level of prenatal exposure to PCB #118 exhibited a preference for the upright BM over inverted BM, whereas those with a relatively high-level of exposure did not. This finding supports the proposal that prenatal PCB exposure impairs the development of social functioning, and indicates the importance of congener-specific analysis in the risk analysis of the adverse effects of PCB exposure on the brain development.

  15. Bioenergetics-based modeling of individual PCB congeners in nestling tree swallows from two contaminated sites on the Upper Hudson River, New York

    Science.gov (United States)

    Nichols, John W.; Echols, Kathy R.; Tillitt, Donald E.; Secord, Anne L.; McCarty, John P.

    2004-01-01

    A bioenergetics-based model was used to simulate the accumulation of total PCBs and 20 PCB congeners by nestling tree swallows at two contaminated sites on the Upper Hudson River, New York. PCB concentrations in birds were calculated as the sum of inherited residues and those acquired through consumption of contaminated insects. Close agreement between simulations and measured residues in 5-, 10-, and 15-day-old nestlings was obtained when PCB concentrations in the diet were set equal to those in food boli taken from adult birds. These simulations were further optimized by fitting the value of a dietary assimilation efficiency constant. Fitted constants for both sites were similar and averaged about 0.7. An evaluation of model performance for individual congeners provided no evidence of metabolic biotransformation. The results of this study are consistent with a companion effort in which principal components analysis was used to compare PCB congener patterns in insects and in tree swallow eggs, nestlings, and adults. Together, these studies establish a quantitative linkage between nestling tree swallows and the insects that they consume and provide strong support for the use of nestling swallows as a biomonitoring species for exposure assessment.

  16. Cross-talk between the glucocorticoid receptor and MyoD family inhibitor domain-containing protein provides a new mechanism for generating tissue-specific responses to glucocorticoids.

    Science.gov (United States)

    Oakley, Robert H; Busillo, John M; Cidlowski, John A

    2017-04-07

    Glucocorticoids are primary stress hormones that regulate many physiological processes, and synthetic derivatives of these molecules are widely used in the clinic. The molecular factors that govern tissue specificity of glucocorticoids, however, are poorly understood. The actions of glucocorticoids are mediated by the glucocorticoid receptor (GR). To discover new proteins that interact with GR and modulate its function, we performed a yeast two-hybrid assay. The MyoD family inhibitor domain-containing protein (MDFIC) was identified as a binding partner for GR. MDFIC associated with GR in the cytoplasm of cells, and treatment with glucocorticoids resulted in the dissociation of the GR-MDFIC complex. To investigate the function of the GR-MDFIC interaction, we performed a genome-wide microarray in intact and MDFIC-deficient A549 cells that were treated with glucocorticoids. A large cohort of genes was differentially regulated by GR depending on the presence or absence of MDFIC. These gene changes were strongly associated with inflammation, and glucocorticoid regulation of the inflammatory response was altered in MDFIC-deficient cells. At a molecular level, the interaction of MDFIC with GR altered the phosphorylation status of the receptor. We demonstrate in COS-1 cells that changes in receptor phosphorylation underlie the ability of MDFIC to regulate the transcriptional activity of GR. Finally, we show that GR directly represses the MDFIC gene, revealing a negative feedback loop by which glucocorticoids limit MDFIC activity. These findings identify a new binding partner for cytoplasmic GR that modulates the receptor transcriptome and contributes to the tissue-specific actions of glucocorticoids. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Effects of dietary cadmium exposure on tissue-specific cadmium accumulation, iron status and expression of iron-handling and stress-inducible genes in rainbow trout: Influence of elevated dietary iron

    Energy Technology Data Exchange (ETDEWEB)

    Kwong, Raymond W.M. [Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3 (Canada); Andres, Jose A. [Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2 (Canada); Niyogi, Som, E-mail: som.niyogi@usask.ca [Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2 (Canada)

    2011-03-15

    Recent evidences suggest that dietary cadmium (Cd) uptake likely occurs via the dietary iron (Fe) uptake pathway in freshwater fish, at least in part. The present study investigated the interactive effects of dietary Cd and Fe in juvenile rainbow trout (Oncorhynchus mykiss). Fish were treated for four weeks with four different diets: normal Fe, high Fe, normal Fe plus Cd, and high Fe plus Cd. Physiological parameters, tissue-specific Fe and Cd level, plasma Fe status, and tissue-specific mRNA expression of transferrin, metallothioneins (MT-A and MT-B) and heat shock proteins 70 (HSP70a and HSP70b) were analyzed. Exposure to dietary Cd increased Cd burden in the following order: intestine > kidney > stomach > liver > gill > carcass. Interestingly, high dietary Fe reduced Cd accumulation in the stomach and intestine as well as in the wholebody of fish. Dietary Cd increased hepatic transferrin mRNA expression and total Fe binding capacity in the plasma, indicating the effect of Cd on Fe handling in fish. The mRNA expression of MTs and HSP70s was also increased in various tissues following dietary Cd exposure, however the response profile of different MT and HSP70 genes was not consistent among different tissues. In general, MT-A was more responsive to Cd exposure in the intestine and liver, whereas MT-B was more responsive in the kidney. Similarly, HSP70a expression was more sensitive to Cd exposure than HSP70b, particularly in the intestine. Interestingly, high Fe diet suppressed Cd-induced induction of transferrin, MT and HSP70 genes in various tissues. Overall, our study suggests that elevated dietary Fe can reduce Cd accumulation and ameliorate Cd-induced stress responses in freshwater fish.

  18. Effects of dietary cadmium exposure on tissue-specific cadmium accumulation, iron status and expression of iron-handling and stress-inducible genes in rainbow trout: Influence of elevated dietary iron

    International Nuclear Information System (INIS)

    Kwong, Raymond W.M.; Andres, Jose A.; Niyogi, Som

    2011-01-01

    Recent evidences suggest that dietary cadmium (Cd) uptake likely occurs via the dietary iron (Fe) uptake pathway in freshwater fish, at least in part. The present study investigated the interactive effects of dietary Cd and Fe in juvenile rainbow trout (Oncorhynchus mykiss). Fish were treated for four weeks with four different diets: normal Fe, high Fe, normal Fe plus Cd, and high Fe plus Cd. Physiological parameters, tissue-specific Fe and Cd level, plasma Fe status, and tissue-specific mRNA expression of transferrin, metallothioneins (MT-A and MT-B) and heat shock proteins 70 (HSP70a and HSP70b) were analyzed. Exposure to dietary Cd increased Cd burden in the following order: intestine > kidney > stomach > liver > gill > carcass. Interestingly, high dietary Fe reduced Cd accumulation in the stomach and intestine as well as in the wholebody of fish. Dietary Cd increased hepatic transferrin mRNA expression and total Fe binding capacity in the plasma, indicating the effect of Cd on Fe handling in fish. The mRNA expression of MTs and HSP70s was also increased in various tissues following dietary Cd exposure, however the response profile of different MT and HSP70 genes was not consistent among different tissues. In general, MT-A was more responsive to Cd exposure in the intestine and liver, whereas MT-B was more responsive in the kidney. Similarly, HSP70a expression was more sensitive to Cd exposure than HSP70b, particularly in the intestine. Interestingly, high Fe diet suppressed Cd-induced induction of transferrin, MT and HSP70 genes in various tissues. Overall, our study suggests that elevated dietary Fe can reduce Cd accumulation and ameliorate Cd-induced stress responses in freshwater fish.

  19. Contamination levels and congener distributions of PCDDs, PCDFs and Co-PCBs in several fast foods in Japan.

    Science.gov (United States)

    Amakura, Yoshiaki; Tsutsumi, Tomoaki; Sasaki, Kumiko; Maitani, Tamio

    2003-12-01

    We determined the concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and coplanar polychlorinated biphenyls (Co-PCBs) in three types of fast foods [(1) seventeen hamburgers and two hot dogs, (2) six portions of fried potatoes and (3) three chicken products] obtained from fast food shops or convenience stores in Japan. All samples tested showed low toxic equivalent quantity (TEQ) levels of dioxins in the range of 0.001-0.083 pg-TEQ/g wet weight (0.006-0.053 pg-TEQ/g for hamburgers and hot dogs, 0.001-0.083 pg-TEQ/g for fried potatoes and 0.053-0.065 pg-TEQ/g for chicken products). The congener profile in hamburgers and hot dogs suggested that the total TEQ was mainly determined by Co-PCBs, especially by 3,3',4,4',5-PeCB (#126), which accounted for 44% of the total TEQ value. Findings for animal foods such as beef and cheese were consistent with this result. For fried potatoes, PCDD/Fs accounted for 94% of the total TEQ value, and 2,3,4,7,8-PeCDF accounted for 32% of PCDD/Fs. Dioxins in the chicken products consisted of 3,3',4,4',5-PeCB (#126) and 1,2,3,7,8-PeCDD, which accounted for 23% and 21% of the total TEQ, respectively. If an adult (50 kg weight) eats 150 g of hamburger, 100 g of potatoes and 150 g of chicken, the daily intake is estimated to be 0.299 pg-TEQ/kg b.w./day using the average values (0.022, 0.028 and 0.059 pg-TEQ/g, respectively) obtained in this study. This value corresponds to 7.5% of the tolerable daily intake (TDI) for PCDD/Fs and Co-PCBs in Japan.

  20. Dioxin congener patterns in commercial catfish from the United States and the indication of mineral clays as the potential source.

    Science.gov (United States)

    Huwe, J K; Archer, J C

    2013-01-01

    Since 1991 the US Department of Agriculture (USDA) has conducted annual surveys of pesticide residues in foods under the Agricultural Marketing Service's Pesticide Data Program (PDP). To assess chemical residues in domestically marketed catfish products, 1479 catfish samples were collected during the 2008-2010 PDPs. A subset of 202 samples was analysed for 17 toxic polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The average pattern of the individual PCDD/F congener concentrations in the catfish was rather unique in that it had almost no measurable amounts of polychlorinated dibenzofurans (PCDFs), but all PCDDs were present. This pattern was more dominant in the domestically produced catfish products than in the imported products (China/Taiwan). Comparison of the pattern to known sources of PCDD/Fs showed strong similarities to the pattern of PCDD/Fs found in kaolin clays which have often been used as anti-caking agents in animal feeds. To investigate whether catfish feeds may be the source of the PCDD/Fs found in the catfish, archived catfish feed data from a US Food and Drug Administration (USFDA) database were examined. In 61 out of 112 feed samples, the PCDD concentrations were 50 times higher than the PCDF concentrations and resembled the pattern found in the catfish products and in clays mined in the south-eastern United States. Although the source of PCDD/Fs in domestically marketed catfish products cannot be definitively established, mined clay products used in feeds should be considered a likely source and, given the wide concentration range of PCDD/Fs that has been found in clays, a critical control point for PCDD/Fs entrance to the food supply.

  1. Long-range atmospheric transport of three toxaphene congeners across Europe. Modeling by chained single-box FATEMOD program.

    Science.gov (United States)

    Paasivirta, Jaakko; Sinkkonen, Seija; Nikiforov, Vladimir; Kryuchkov, Fedor; Kolehmainen, Erkki; Laihia, Katri; Valkonen, Arto; Lahtinen, Manu

    2009-03-01

    Since toxaphene (polychlorocamphene, polychloropinene, or strobane) mixtures were applied for massive insecticide use in the 1960s to replace the use of DDT, some of their congeners have been found at high latitudes far away from the usage areas. Especially polychlorinated bornanes have demonstrated dominating congeners transported by air up to the Arctic areas. Environmental fate modeling has been applied to monitor this phenomenon using parallel zones of atmosphere around the globe as interconnected environments. These zones, shown in many meteorological maps, however, may not be the best way to configure atmospheric transport in air trajectories. The latter could also be covered by connecting a chain of simple model boxes. We aim to study this alternative approach by modeling the trajectory chain using catchment boxes of our FATEMOD model. Polychlorobornanes analyzed in biota of the Barents Sea offered one case to study this modeling alternative, while toxaphene has been and partly still is used massively at southern East Europe and around rivers flowing to the Aral Sea. Pure model substances of three polychlorobornanes (toxaphene congeners P26, P50, and P62) were synthesized, their environmentally important thermal properties measured by differential scanning calorimetry, as evaluated from literature data, and their temperature dependences estimated by the QSPR programs VPLEST, WATSOLU, and TDLKOW. The evaluated property parameters were used to model their atmospheric long-range transport from toxaphene heavy usage areas in Ukraine and Aral/SyrDarja/AmuDarja region areas, through East Europe and Northern Norway (Finnmarken) to the Barents Sea. The time period used for the emission model was June 1997. Usual weather conditions in June were applied in the model, which was constructed by chaining FATEMOD model boxes of the catchment's areas along assumed maximal air flow trajectories. Analysis of the three chlorobornanes in toxaphene mixtures function as a basis

  2. Genetic Dissection of Quantitative Trait Loci for Hemostasis and Thrombosis on Mouse Chromosomes 11 and 5 Using Congenic and Subcongenic Strains

    Science.gov (United States)

    Hoover-Plow, Jane; Sa, Qila; Huang, Menggui; Grondolsky, Jessica

    2013-01-01

    Susceptibility to thrombosis varies in human populations as well as many inbred mouse strains. Only a small portion of this variation has been identified, suggesting that there are unknown modifier genes. The objective of this study was to narrow the quantitative trait locus (QTL) intervals previously identified for hemostasis and thrombosis on mouse distal chromosome 11 (Hmtb6) and on chromosome 5 (Hmtb4 and Hmtb5). In a tail bleeding/rebleeding assay, a reporter assay for hemostasis and thrombosis, subcongenic strain (6A-2) had longer clot stability time than did C57BL/6J (B6) mice but a similar time to the B6-Chr11A/J consomic mice, confirming the Hmtb6 phenotype. Six congenic and subcongenic strains were constructed for chromosome 5, and the congenic strain, 2A-1, containing the shortest A/J interval (16.6 cM, 26.6 Mbp) in the Hmtb4 region, had prolonged clot stability time compared to B6 mice. In the 3A-2 and CSS-5 mice bleeding time was shorter than for B6, mice confirming the Hmtb5 QTL. An increase in bleeding time was identified in another congenic strain (3A-1) with A/J interval (24.8 cM, 32.9 Mbp) in the proximal region of chromosome 5, confirming a QTL for bleeding previously mapped to that region and designated as Hmtb10. The subcongenic strain 4A-2 with the A/J fragment in the proximal region had a long occlusion time of the carotid artery after ferric chloride injury and reduced dilation after injury to the abdominal aorta compared to B6 mice, suggesting an additional locus in the proximal region, which was designated Hmtb11 (5 cM, 21.4 Mbp). CSS-17 mice crossed with congenic strains, 3A-1 and 3A-2, modified tail bleeding. Using congenic and subcongenic analysis, candidate genes previously identified and novel genes were identified as modifiers of hemostasis and thrombosis in each of the loci Hmtb6, Hmtb4, Hmtb10, and Hmtb11. PMID:24147020

  3. Polychlorinated biphenyls in settled dust from informal electronic waste recycling workshops and nearby highways in urban centers and suburban industrial roadsides of Chennai city, India: Levels, congener profiles and exposure assessment.

    Science.gov (United States)

    Chakraborty, Paromita; Prithiviraj, Balasubramanian; Selvaraj, Sakthivel; Kumar, Bhupander

    2016-12-15

    Polychlorinated biphenyls (PCBs) were quantified in settled dust collected from informal electronic waste (e-waste) recycling workshops and nearby highways in the urban centers and roadside dust from the suburban industrial belt of Chennai city in India. Further dust samples were subjected to a high resolution field emission scanning electron microscope equipped with an energy dispersive X-ray spectrometer (FESEM/EDX) to characterize the shape, size and elemental composition of the dust particles. Geomean of total PCB concentration followed the following order: informal e-waste metal recovery workshops (53ngg -1 )>e-waste dismantling sites (3.6ngg -1 )>nearby highways (1.7ngg -1 )>suburban industrial roadsides (1.6ngg -1 ). In e-waste workshops, tetra, penta and hexa-PCB homologs contributed two third of Σ 26 PCB concentration. Informal e-waste recycling workshops contributed more than 80% concentration of all the PCB congeners loaded in the first principal component. Predominance of dioxin like PCBs, PCB-l14, -118 and -126 in the e-waste metal recovery sites were presumably due to combustion and pyrolytic processes performed during recycling of electrical components. According to the morphology and elemental composition, settled dust from e-waste workshops were irregular particles heavily embedded with toxic metals and industrial roadside dust were distinct angular particles. FESEM revealed that average particle size (in Ferret diameter) increased in the following order: e-waste recycling workshops (0.5μm)waste recycling workshops engaged in metal recovery were found with maximum toxicity equivalents (TEQs) for dl-PCBs and potential cancer risk (10 -6 -10 -4 ) for both adult and children. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Tissue-Specific Floral Transcriptome Analysis of the Sexually Deceptive Orchid Chiloglottis trapeziformis Provides Insights into the Biosynthesis and Regulation of Its Unique UV-B Dependent Floral Volatile, Chiloglottone 1

    Directory of Open Access Journals (Sweden)

    Darren C. J. Wong

    2017-07-01

    Full Text Available The Australian sexually deceptive orchid, Chiloglottis trapeziformis, employs a unique UV-B-dependent floral volatile, chiloglottone 1, for specific male wasp pollinator attraction. Chiloglottone 1 and related variants (2,5-dialkylcyclohexane-1,3-diones, represent a unique class of specialized metabolites presumed to be the product of cyclization between two fatty acid (FA precursors. However, the genes involved in the biosynthesis of precursors, intermediates, and transcriptional regulation remains to be discovered. Chiloglottone 1 production occurs in the aggregation of calli (callus on the labellum under continuous UV-B light. Therefore, deep sequencing, transcriptome assembly, and differential expression (DE analysis were performed across different tissue types and UV-B treatments. Transcripts expressed in the callus and labellum (∼23,000 transcripts were highly specialized and enriched for a diversity of known and novel metabolic pathways. DE analysis between chiloglottone-emitting callus versus the remainder of the labellum showed strong coordinated induction of entire FA biosynthesis and β-oxidation pathways including genes encoding Ketoacyl-ACP Synthase, Acyl-CoA Oxidase, and Multifunctional Protein. Phylogenetic analysis revealed potential gene duplicates with tissue-specific differential regulation including two Acyl-ACP Thioesterase B and a Ketoacyl-ACP Synthase genes. UV-B treatment induced the activation of UVR8-mediated signaling and large-scale transcriptome changes in both tissues, however, neither FA biosynthesis/β-oxidation nor other lipid metabolic pathways showed clear indications of concerted DE. Gene co-expression network analysis identified three callus-specific modules enriched with various lipid metabolism categories. These networks also highlight promising candidates involved in the cyclization of chiloglottone 1 intermediates (e.g., Bet v I and dimeric α,β barrel proteins and orchestrating regulation of precursor

  5. Influence of elevated alkalinity and natural organic matter (NOM) on tissue-specific metal accumulation and reproductive performance in fathead minnows during chronic, multi-trophic exposures to a metal mine effluent.

    Science.gov (United States)

    Ouellet, Jacob D; Dubé, Monique G; Niyogi, Som

    2013-09-01

    Metal bioavailability in aquatic organisms is known to be influenced by various water chemistry parameters. The present study examined the influence of alkalinity and natural organic matter (NOM) on tissue-specific metal accumulation and reproductive performance of fathead minnows (Pimephales promelas) during environmentally relevant chronic exposures to a metal mine effluent (MME). Sodium bicarbonate (NaHCO3) or NOM (as commercial humic acid) were added to a Canadian MME [45 percent process water effluent (PWE)] in order to evaluate whether increases in alkalinity (3-4 fold) or NOM (~1.5-3mg/L dissolved organic carbon) would reduce metal accumulation and mitigate reproductive toxicity in fathead minnows during a 21-day multi-trophic exposure. Eleven metals (barium, boron, cobalt, copper, lithium, manganese, molybdenum, nickel, rubidium, selenium, and strontium) were elevated in the 45 percent PWE relative to the reference water. Exposure to the unmodified 45 percent PWE resulted in a decrease of fathead minnow egg production (~300 fewer eggs/pair) relative to the unmodified reference water, over the 21-day exposure period. Water chemistry modifications produced a modest decrease in free ion activity of some metals (as shown by MINTEQ, Version 3) in the 45 percent PWE exposure water, but did not alter the metal burden in the treatment-matched larval Chironomus dilutus (the food source of fish during exposure). The tissue-specific metal accumulation increased in fish exposed to the 45 percent PWE relative to the reference water, irrespective of water chemistry modifications, and the tissue metal concentrations were found to be similar between fish in the unmodified and modified 45 percent PWE (higher alkalinity or NOM) treatments. Interestingly however, increased alkalinity and NOM markedly improved fish egg production both in the reference water (~500 and ~590 additional eggs/pair, respectively) and 45 percent PWE treatments (~570 and ~260 additional eggs

  6. A comparative tissue-specific metabolite analysis and determination of protodioscin content in Asparagus species used in traditional Chinese medicine and Ayurveda by use of laser microdissection, UHPLC-QTOF/MS and LC-MS/MS.

    Science.gov (United States)

    Jaiswal, Yogini; Liang, Zhitao; Ho, Alan; Chen, Hubiao; Zhao, Zhongzhen

    2014-01-01

    Asparagus is esteemed in Traditional Chinese Medicine and Ayurveda, and it is commercially one of the most important drugs in the global herbal market. Comparative metabolite profiling of different species would help in determining the similarities and ascertain their validity for being used as substitutes for each other. Laser microdissection (LMD) facilitates identification of metabolites in specific tissues, and thus it can aid in exploration of metabolic pathways in target tissues. To compare tissue-specific metabolites and protodioscin content of Asparagus cochinchinensis (Lour.) Merr. and Asparagus racemosus Willd. used in China and India. Metabolite analysis of laser-dissected tissues was carried out using UHPLC-QTOF/MS and LC-MS/MS. The protodioscin contents were determined and the method was validated as per the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use guidelines. Metabolite analysis reveals that the velamen tissue, among other tissues such as cortex, vascular bundles and pith, contained maximum components, specifically those belonging to the steroidal saponin class. Although the metabolite profiles were similar, the content of protodioscin was found to be higher in Chinese than Indian species. The study provided a suitable methodology for metabolite profiling and protodioscin content determination of Asparagus by use of LMD, UHPLC-QTOF/MS and LC-MS/MS. The similarities in metabolite profiles indicate that Asparagus species from India and China can serve as substitute for each other in various therapeutic and pharmaceutical applications. Copyright © 2014 John Wiley & Sons, Ltd.

  7. CD8+ T cells are crucial for the ability of congenic normal mice to reject highly immunogenic sarcomas induced in nude mice with 3-methylcholanthrene

    DEFF Research Database (Denmark)

    Boesen, M; Svane, I M; Engel, A M

    2000-01-01

    An attempt was made to identify the selection pressures put upon a growing tumour by CD8+ T cells. To this end tumours induced with 3-methylcholanthrene in T cell-deficient nude mice and in congenic T cell-competent nu/+ mice were transplanted to nu/+ recipients. The rejection rate of the sarcomas...... from nude mice was almost twice that of the sarcomas from nu/+ mice. Depletion of CD8+ T cells from nu/+ recipients prior to transplantation made them accept nude tumours that were consistently rejected by untreated nu/+ recipients. These findings suggest that a methylcholanthrene sarcoma during its...

  8. Comparison of proposed frameworks for grouping polychlorinated biphenyl congener data applied to a case-control pilot study of prostate cancer

    International Nuclear Information System (INIS)

    Ritchie, Justine M.; Vial, Scott L.; Fuortes, Laurence J.; Robertson, Larry W.; Guo, Haijun; Reedy, Victoria E.; Smith, Elaine M.

    2005-01-01

    Although the commercial synthesis of polychlorinated biphenyls (PCBs) has been banned in the United States for several decades, they are persistent in the environment with exposure mainly being through diet. The biologic and toxic effects of PCBs and their metabolites are due in part to their ability to interact with several cellular and nuclear receptors, thereby altering signaling pathways and gene transcription. These effects include endocrine modulation and disruption. Therefore, the natural history of cancer in tissues expressing these receptors may be modulated by PCB congeners, which are known to have estrogenic, antiestrogenic, and other hormonal effects. Several frameworks for grouping PCB congeners based on these interactions have been proposed. We conducted a hospital-based, case-control pilot study of 58 prostate cancer cases and 99 controls to evaluate the association between the proposed PCB groupings and the risk of prostate cancer. Serum samples were analyzed for a total of 30 PCBs. In multivariate analyses, the odds of prostate cancer among men with the highest concentrations of moderately chlorinated PCBs or PCBs with phenobarbital-like activities (constitutively active receptor (CAR) agonists) was over two times that among men with the lowest concentrations. Increasing trends in risk across the concentration levels were also observed. These results suggest that a higher burden of PCBs that are CAR agonists may be positively associated with an increased risk of prostate cancer and they encourage further research in this area

  9. Early Alterations in Operant Performance and Prominent Huntingtin Aggregation in a Congenic F344 Rat Line of the Classical CAGn51trunc Model of Huntington Disease

    Directory of Open Access Journals (Sweden)

    Anne-Christine Plank

    2018-01-01

    Full Text Available The transgenic rat model of Huntington disease expressing a fragment of mutant HTT (tgHD rat has been thoroughly characterized and reproduces hallmark symptoms of human adult-onset HD. Pursuing the optimization of this model for evaluation of translational therapeutic approaches, the F344 inbred rat strain was considered as advantageous genetic background for the expression of the HD transgenic construct. In the present study, a novel congenic line of the SPRDtgHD transgenic model of HD, carrying 51 CAG repeats, was generated on the F344 rat genetic background. To assess the behavioral phenotype, classical assays investigating motor function, emotion, and sensorimotor gating were applied, along with automated screening of metabolic and activity parameters as well as operant conditioning tasks. The neuropathological phenotype was analyzed by immunohistochemistry and ex vivo magnetic resonance imaging. F344tgHD rats displayed markedly reduced anxiety-like behavior in the social interaction test and elevated impulsivity traits already at 3 months of age. Neuropathologically, reduced striatal volume and pronounced aggregation of mutant huntingtin in several brain regions were detected at later disease stage. In conclusion, the congenic F344tgHD model reproduces key aspects of the human HD phenotype, substantiating its value for translational therapeutic approaches.

  10. Early Alterations in Operant Performance and Prominent Huntingtin Aggregation in a Congenic F344 Rat Line of the Classical CAGn51trunc Model of Huntington Disease.

    Science.gov (United States)

    Plank, Anne-Christine; Canneva, Fabio; Raber, Kerstin A; Urbach, Yvonne K; Dobner, Julia; Puchades, Maja; Bjaalie, Jan G; Gillmann, Clarissa; Bäuerle, Tobias; Riess, Olaf; Nguyen, Hoa H P; von Hörsten, Stephan

    2018-01-01

    The transgenic rat model of Huntington disease expressing a fragment of mutant HTT (tgHD rat) has been thoroughly characterized and reproduces hallmark symptoms of human adult-onset HD. Pursuing the optimization of this model for evaluation of translational therapeutic approaches, the F344 inbred rat strain was considered as advantageous genetic background for the expression of the HD transgenic construct. In the present study, a novel congenic line of the SPRDtgHD transgenic model of HD, carrying 51 CAG repeats, was generated on the F344 rat genetic background. To assess the behavioral phenotype, classical assays investigating motor function, emotion, and sensorimotor gating were applied, along with automated screening of metabolic and activity parameters as well as operant conditioning tasks. The neuropathological phenotype was analyzed by immunohistochemistry and ex vivo magnetic resonance imaging. F344tgHD rats displayed markedly reduced anxiety-like behavior in the social interaction test and elevated impulsivity traits already at 3 months of age. Neuropathologically, reduced striatal volume and pronounced aggregation of mutant huntingtin in several brain regions were detected at later disease stage. In conclusion, the congenic F344tgHD model reproduces key aspects of the human HD phenotype, substantiating its value for translational therapeutic approaches.

  11. PCDD/F and PCB multi-media ambient concentrations, congener patterns and occurrence in a Mediterranean coastal lagoon (Etang de Thau, France)

    Energy Technology Data Exchange (ETDEWEB)

    Castro-Jimenez, J. [European Commission-DG Joint Research Centre, Institute for Environment and Sustainability(IES), TP 290, Via Enrico Fermi, 1. 21020 Ispra (Vatican City State, Holy See,) (Italy)], E-mail: javier.castro-jimenez@jrc.it; Deviller, G.; Ghiani, M.; Loos, R.; Mariani, G.; Skejo, H.; Umlauf, G.; Wollgast, J. [European Commission-DG Joint Research Centre, Institute for Environment and Sustainability(IES), TP 290, Via Enrico Fermi, 1. 21020 Ispra (Vatican City State, Holy See,) (Italy); Laugier, T. [Ifremer, Laboratory of Environmental Resources, Bd Jean Monnet, BP 171, 34203 Sete Cedex (France); Heas-Moisan, K.; Leaute, F.; Munschy, C.; Tixier, C.; Tronczynski, J. [Ifremer, Laboratory of Biogeochemistry of Organic Contaminants, BP 21105, 44311 Nantes Cedex 3 (France)

    2008-11-15

    Ambient concentrations, congener patterns and multi-media distribution of PCDD/Fs and PCBs were determined in air, water, sediment and mussels in a semi-enclosed marine ecosystem (Thau lagoon, France). {sigma}2,3,7,8-PCDD/F and {sigma}7ICES PCB air concentrations (0.2-1.4 and 31-57 pg m{sup -3}, respectively) were typical of rural areas. Concentrations in the water column were very low for PCDD/Fs (163-476 fg L{sup -1}) and low for PCBs (138-708 pg L{sup -1}). PCDD/F and PCB concentrations found in surface sediment (0.15-1.6 and 2.5-33 ng g{sup -1} d.w., respectively) and mussel (13-21 pg g{sup -1} d.w. and 10-39 ng g{sup -1} d.w., respectively) were medium levels. PCDD/F congener patterns observed in air, water particulate phase and sediments were similar suggesting direct coupling among these compartments and atmospheric inputs of PCDD/Fs into the lagoon. Conversely, for the same set of samples, similar patterns were not observed for PCBs in the mentioned compartments. - Multi-media ambient concentrations and distribution of PCDD/Fs and PCBs in Thau Lagoon provide insight into the POPs behavior in semi-enclosed marine ecosystems.

  12. IL-10 Production Is Critical for Sustaining the Expansion of CD5+ B and NKT Cells and Restraining Autoantibody Production in Congenic Lupus-Prone Mice.

    Directory of Open Access Journals (Sweden)

    Yuriy Baglaenko

    Full Text Available The development and progression of systemic lupus erythematosus is mediated by the complex interaction of genetic and environmental factors. To decipher the genetics that contribute to pathogenesis and the production of pathogenic autoantibodies, our lab has focused on the generation of congenic lupus-prone mice derived from the New Zealand Black (NZB strain. Previous work has shown that an NZB-derived chromosome 4 interval spanning 32 to 151 Mb led to expansion of CD5+ B and Natural Killer T (NKT cells, and could suppress autoimmunity when crossed with a lupus-prone mouse strain. Subsequently, it was shown that CD5+ B cells but not NKT cells derived from these mice could suppress the development of pro-inflammatory T cells. In this paper, we aimed to further resolve the genetics that leads to expansion of these two innate-like populations through the creation of additional sub-congenic mice and to characterize the role of IL-10 in the suppression of autoimmunity through the generation of IL-10 knockout mice. We show that expansion of CD5+ B cells and NKT cells localizes to a chromosome 4 interval spanning 91 to 123 Mb, which is distinct from the region that mediates the majority of the suppressive phenotype. We also demonstrate that IL-10 is critical to restraining autoantibody production and surprisingly plays a vital role in supporting the expansion of innate-like populations.

  13. IL-10 Production Is Critical for Sustaining the Expansion of CD5+ B and NKT Cells and Restraining Autoantibody Production in Congenic Lupus-Prone Mice.

    Science.gov (United States)

    Baglaenko, Yuriy; Manion, Kieran P; Chang, Nan-Hua; Gracey, Eric; Loh, Christina; Wither, Joan E

    2016-01-01

    The development and progression of systemic lupus erythematosus is mediated by the complex interaction of genetic and environmental factors. To decipher the genetics that contribute to pathogenesis and the production of pathogenic autoantibodies, our lab has focused on the generation of congenic lupus-prone mice derived from the New Zealand Black (NZB) strain. Previous work has shown that an NZB-derived chromosome 4 interval spanning 32 to 151 Mb led to expansion of CD5+ B and Natural Killer T (NKT) cells, and could suppress autoimmunity when crossed with a lupus-prone mouse strain. Subsequently, it was shown that CD5+ B cells but not NKT cells derived from these mice could suppress the development of pro-inflammatory T cells. In this paper, we aimed to further resolve the genetics that leads to expansion of these two innate-like populations through the creation of additional sub-congenic mice and to characterize the role of IL-10 in the suppression of autoimmunity through the generation of IL-10 knockout mice. We show that expansion of CD5+ B cells and NKT cells localizes to a chromosome 4 interval spanning 91 to 123 Mb, which is distinct from the region that mediates the majority of the suppressive phenotype. We also demonstrate that IL-10 is critical to restraining autoantibody production and surprisingly plays a vital role in supporting the expansion of innate-like populations.

  14. Tissue-specific transplantation antigen P35B (TSTA3) immune response-mediated metabolism coupling cell cycle to postreplication repair network in no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) by biocomputation.

    Science.gov (United States)

    Wang, Lin; Huang, Juxiang; Jiang, Minghu; Lin, Hong

    2012-06-01

    We constructed the low-expression tissue-specific transplantation antigen P35B (TSTA3) immune response-mediated metabolism coupling cell cycle to postreplication repair network in no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) compared with high-expression (fold change ≥ 2) human hepatocellular carcinoma in GEO data set, by using integration of gene regulatory network inference method with gene ontology analysis of TSTA3-activated up- and downstream networks. Our results showed TSTA3 upstream-activated CCNB2, CKS1B, ELAVL3, GAS7, NQO1, NTN1, OCRL, PLA2G1B, REG3A, SSTR5, etc. and TSTA3 downstream-activated BAP1, BRCA1, CCL20, MCM2, MS4A2, NTN1, REG1A, TP53I11, VCAN, SLC16A3, etc. in no-tumor hepatitis/cirrhotic tissues. TSTA3-activated network enhanced the regulation of apoptosis, cyclin-dependent protein kinase activity, cell migration, insulin secretion, transcription, cell division, cell proliferation, DNA replication, postreplication repair, cell differentiation, T-cell homeostasis, neutrophil-mediated immunity, neutrophil chemotaxis, interleukin-8 production, inflammatory response, immune response, B-cell activation, humoral immune response, actin filament organization, xenobiotic metabolism, lipid metabolism, phospholipid metabolism, leukotriene biosynthesis, organismal lipid catabolism, phosphatidylcholine metabolism, arachidonic acid secretion, activation of phospholipase A2, deoxyribonucleotide biosynthesis, heterophilic cell adhesion, activation of MAPK activity, signal transduction by p53 class mediator resulting in transcription of p21 class mediator, G-protein-coupled receptor protein signaling pathway, response to toxin, acute-phase response, DNA damage response, intercellular junction assembly, cell communication, and cell recognition, as a result of inducing immune response-mediated metabolism coupling cell cycle to postreplication repair in no-tumor hepatitis/cirrhotic tissues.

  15. Targeted Expression of Stromelysin-1 in Mammary Gland Provides Evidence for a Role of Proteinases in Branching Morphogenesis and the Requirement for an Intact Basement Membrane for Tissue-specific Gene Expression

    Energy Technology Data Exchange (ETDEWEB)

    Sympson, Carolyn J; Talhouk, Rabih S; Alexander, Caroline M; Chin, Jennie R; Cliff, Shirley M; Bissell, Mina J; Werb, Zena

    1994-05-01

    The extracellular matrix (ECM) is an important regulator of the differentiated phenotype of mammary epithelial cells in culture. Despite the fact that ECM-degrading enzymes have been implicated in morphogenesis and tissue remodeling, there is little evidence for a direct role for such regulation in vivo. We generated transgenic mice that express autoactivated isoforms of the matrix metalloproteinase stromelysin-1, under the control of the whey acidic protein gene promoter, to examine the effect of inappropriate expression of this enzyme. Stromelysin-1 is implicated as the primary player in the loss of basement membrane and loss of function in the mammary gland during involution. The transgene was expressed at low levels in mammary glands of virgin female mice, leading to an unexpected phenotype: The primary ducts had supernumerary branches and showed precocious development of alveoli that expressed beta-casein at levels similar to that of an early- to mid-pregnant gland. Lactating glands showed high levels of transgene expression, with accumulation at the basement membrane, and a decrease in laminin and collagen IV, resulting in a loss of basement membrane integrity; this was accompanied by a dramatic alteration of alveolar morphology, with decreased size and shrunken lumina containing little beta-casein. During pregnancy, expression of endogenous whey acidic protein and beta-casein was reduced in transgenic glands, confirming the observed dependence of milk protein transcription of ECM in mammary epithelial cells in culture. These data provide direct evidence that stromelysin-1 activity can be morphogenic for mammary epithelial cells, inducing hyperproliferation and differentiation in virgin animals, and that its lytic activity can, indeed, disrupt membrane integrity and reduce mammary-specific function. We conclude that the balance of ECM-degrading enzymes with their inhibitors, and the associated regulation of ECM structure, is crucial for tissue-specific gene

  16. Chow fed UC Davis strain female Lepr fatty Zucker rats exhibit mild glucose intolerance, hypertriglyceridemia, and increased urine volume, all reduced by a Brown Norway strain chromosome 1 congenic donor region.

    Directory of Open Access Journals (Sweden)

    Craig H Warden

    Full Text Available Our objective is to identify genes that influence the development of any phenotypes of type 2 diabetes (T2D or kidney disease in obese animals. We use the reproductively isolated UC Davis fatty Zucker strain rat model in which the defective chromosome 4 leptin receptor (LeprfaSte/faSte results in fatty obesity. We previously produced a congenic strain with the distal half of chromosome 1 from the Brown Norway strain (BN on a Zucker (ZUC background (BN.ZUC-D1Rat183-D1Rat90. Previously published studies in males showed that the BN congenic donor region protects from some phenotypes of renal dysfunction and T2D. We now expand our studies to include females and expand phenotyping to gene expression. We performed diabetes and kidney disease phenotyping in chow-fed females of the BN.ZUC-D1Rat183-D1Rat90 congenic strain to determine the specific characteristics of the UC Davis model. Fatty LeprfaSte/faSte animals of both BN and ZUC genotype in the congenic donor region had prediabetic levels of fasting blood glucose and blood glucose 2 hours after a glucose tolerance test. We observed significant congenic strain chromosome 1 genotype effects of the BN donor region in fatty females that resulted in decreased food intake, urine volume, glucose area under the curve during glucose tolerance test, plasma triglyceride levels, and urine glucose excretion per day. In fatty females, there were significant congenic strain BN genotype effects on non-fasted plasma urea nitrogen, triglyceride, and creatinine. Congenic region genotype effects were observed by quantitative PCR of mRNA from the kidney for six genes, all located in the chromosome 1 BN donor region, with potential effects on T2D or kidney function. The results are consistent with the hypothesis that the BN genotype chromosome 1 congenic region influences traits of both type 2 diabetes and kidney function in fatty UC Davis ZUC females and that there are many positional candidate genes.

  17. Non-coplanar polychlorinated biphenyls (PCBs) are direct agonists for the human pregnane-X receptor and constitutive androstane receptor, and activate target gene expression in a tissue-specific manner

    Energy Technology Data Exchange (ETDEWEB)

    Al-Salman, Fadheela; Plant, Nick, E-mail: N.Plant@Surrey.ac.uk

    2012-08-15

    The polychlorinated biphenyl group possesses high environmental persistence, leading to bioaccumulation and a number of adverse effects in mammals. Whilst coplanar PCBs elicit their toxic effects through agonism of the aryl hydrocarbon receptor; however, non-coplanar PCBs are not ligands for AhR, but may be ligands for members of the nuclear receptor family of proteins. To better understand the biological actions of non-coplanar PCBs, we have undertaken a systematic analysis of their ability to activate PXR and CAR-mediated effects. Cells were exposed to a range of non-coplanar PCBs (99, 138, 153, 180 and 194), or the coplanar PCB77: Direct activation of PXR and CAR was measured using a mammalian receptor activation assay in human liver cells, with rifampicin and CITCO used as positive controls ligands for PXR and CAR, respectively; activation of target gene expression was examined using reporter gene plasmids for CYP3A4 and MDR1 transfected into liver, intestine and lung cell lines. Several of the non-coplanar PCBs directly activated PXR and CAR, whilst the coplanar PCB77 did not. Non-coplanar PCBs were also able to activate PXR/CAR target gene expression in a substitution- and tissue-specific manner. Non-coplanar PCBs act as direct activators for the nuclear receptors PXR and CAR, and are able to elicit transcriptional activation of target genes in a substitution- and tissue-dependent manner. Chronic activation of PXR/CAR is linked to adverse effects and must be included in any risk assessment of PCBs. -- Highlights: ► Several Non-coplanar PCBs are able to directly activate both PXR and CAR in vitro. ► PCB153 is the most potent direct activator of PXR and CAR nuclear receptors. ► Non-coplanar PCB activation of CYP3A4/MDR1 reporter genes is structure-dependent. ► Non-coplanar PCB activate CYP3A4/MDR1 reporter genes in a tissue-dependent. ► PCB153 is the most potent activator of PXR/CAR target gene in all tissues.

  18. PCBs and PCDD/Fs in soil from informal e-waste recycling sites and open dumpsites in India: Levels, congener profiles and health risk assessment.

    Science.gov (United States)

    Chakraborty, Paromita; Selvaraj, Sakthivel; Nakamura, Masafumi; Prithiviraj, Balasubramanian; Cincinelli, Alessandra; Bang, John J

    2018-04-15

    Growth of informal electronic waste (e-waste) recycling sector is an emerging problem for India. The presence of halogenated compounds in e-wastes may result in the formation of persistent organic pollutants like polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) during recycling processes. We therefore investigated PCBs and PCDD/Fs in surface soils explicitly from the informal e-waste recycling sites and nearby open dumpsites of major metropolitan cities from four corners of India, viz., New Delhi (North), Kolkata (East), Mumbai (West) and Chennai (South). In the informal e-waste recycling sites, the range of Σ 26 PCBs (0.4-488ng/g) and ƩPCDD/Fs (1.0-10.6ng/g) were higher than Ʃ 26 PCBs (0.3-21ng/g) and ƩPCDD/Fs (0.15-7.3ng/g) from open dumpsites. In the e-waste sites, ƩPCDDs were found with increasing trend from ƩTetraCDD to OctaCDD, whereas ƩPCDFs showed a reverse trend. The dominance of PCDF congeners and maximum toxicity equivalents (TEQ) for both PCDDs (17pg TEQ/g) and PCDFs (82pg TEQ/g) at Mandoli in New Delhi has been related to intensive precious metal recovery process using acid bath. Among dumpsites, highest TEQ for PCDD/Fs was observed at Kodangaiyur dumpsite of Chennai (CN DS -02, 45pg TEQ/g). Positive Matrix Factorization (PMF) model identified distinct congener pattern based on the functional activities, such as e-waste dismantling, shredding, precious metal recovery and open burning in dumpsites. E-waste metal recovery factor was loaded with 86-91% of PCB-77, -105, -114, -118 and 30% of PCB-126, possibly associated with the burning of wires during the copper extraction process. Almost 70% of the Ʃ 26 PCB concentrations was comprised of the dioxin-like PCB congeners with a maximum concentration of 437ng/g at New Moore market in Chennai, followed by Wire Lane (102ng/g), in Mumbai. We speculate that PCB-126 might have resulted from combustion of plastic materials in e-waste stream and dumped waste

  19. Autoradiographic localization of adenosine A1 receptors in rat brain using [3H]XCC, a functionalized congener of 1,3-dipropylxanthine

    International Nuclear Information System (INIS)

    Jarvis, M.J.; Williams, M.; Jacobson, K.A.

    1987-01-01

    Quantitative autoradiography was used to visualize the anatomical distribution of adenosine receptors labeled by the carboxylic acid congener of 1,3-dipropylxanthine, [ 3 Hi](8-(p-carbonxymethyloxy) phenyl-1,3 dipropylxanthine)([ 3 H]XCC) in rat brain. [ 3 H]XCC was observed to specifically bind to rat brain sagittal sections in a heterogenous pattern. Saturation experiments revealed that [ 3 H]XCC binds with nanomolar affinity to 20μm frozen tissue sections with the highest binding densities occurring in the hippocampus and cerebellum. Both the binding characteristics and regional receptor distribution obtained with [ 3 H]XCC demonstrate the potential usefulness of this new ligand in the study of adenosine A 1 receptors. 13 refs. (Author)

  20. In vitro study on the agonistic and antagonistic activities of bisphenol-S and other bisphenol-A congeners and derivatives via nuclear receptors

    International Nuclear Information System (INIS)

    Molina-Molina, José-Manuel; Amaya, Esperanza; Grimaldi, Marina; Sáenz, José-María; Real, Macarena; Fernández, Mariana F.; Balaguer, Patrick; Olea, Nicolás

    2013-01-01

    Bisphenols are a group of chemicals structurally similar to bisphenol-A (BPA) in current use as the primary raw material in the production of polycarbonate and epoxy resins. Some bisphenols are intended to replace BPA in several industrial applications. This is the case of bisphenol-S (BPS), which has an excellent stability at high temperature and resistance to sunlight. Studies on the endocrine properties of BPS have focused on its interaction with human estrogen receptor alpha (hERα), but information on its interaction with other nuclear receptors is scarce. The aim of this study was to investigate interactions of BPS, BPF, BPA and its halogenated derivatives, tetrachlorobisphenol A (TCBPA), and tetrabromobisphenol A (TBBPA), with human estrogen receptors (hERα and hERβ), androgen receptor (hAR), and pregnane X receptor (hPXR), using a panel of in vitro bioassays based on competitive binding to nuclear receptors (NRs), reporter gene expression, and cell proliferation assessment. BPS, BPF, and BPA efficiently activated both ERs, while TCBPA behaved as weak hERα agonist. Unlike BPF and BPA, BPS was more active in the hERβ versus hERα assay. BPF and BPA were full hAR antagonists (BPA > BPF), whereas BPA and BPS were weak hAR agonists. Only BPA, TCBPA, and TBBPA, were hPXR agonists (TCBPA > TBBPA > BPA). These findings provide evidence that BPA congeners and derivatives disrupt multiple NRs and may therefore interfere with the endocrine system. Hence, further research is needed to evaluate the potential endocrine-disrupting activity of putative BPA substitutes. - Highlights: • We investigated the agonist/antagonist activities of BPS, BPF, BPA, TCBPA and TBBPA. • The direct interaction of these compounds with hERα, hERβ, hAR and hPXR was studied. • BPA congeners and derivatives were found to disrupt multiple NRs. • Further evaluation of their role as endocrine-disrupting chemicals is needed

  1. Effects of in ovo exposure to PCBs (coplanar congener, kanechlor mixture, hydroxylated metabolite) on the developing cell-mediated immunity in chickens

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, J.; Matsuda, M.; Kawano, M.; Wakimoto, T. [Faculty of Agriculture, Ehime Univ., Matsuyama, Ehime (Japan); Kashima, Y. [Dept. of Hygiene, Yokohama City Univ. School of Medicine, Yokohama (Japan)

    2004-09-15

    Polychlorinated biphenyls (PCBs) are wide spread environmental contaminants and known to cause various adverse effects on health of human and wildlife. Immune system is one of the several targets for toxic effects of PCBs and its normal balance is often disrupted by the exposure of the compounds. For example, PCBs may induce immune suppression and result in increased susceptibility to bacterial and viral infections, or conversely, excessive immune enhancement may cause adverse outcomes including as autoimmune disease and anergy. Therefore immune function is regarded as one of an important endpoint in toxicological risk assessment. There are a number of studies shown that neonatal organisms perinatally exposed to polyhalogenated aromatic hydrocarbons (PHAHs) such as PCBs have severer effects on their immune system than adult. Dioxins and coplanar PCB congeners, structurally planar PHAHs are known to have high affinity for aryl hydrocarbon receptor (AhR). 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (TCDD) have the strongest affinity among such compounds and these are considered to act on immune system through AhR. On the other hand, such as non-planar PCB congeners with low affinity for AhR, which are abundantly contained in commercial PCB preparations have non-additive (antagonistic) effects on immune function. Prenatal exposure of TCDD to rodent induced abnormal lymphoid development in the thymus and thymus-dependent immune functions were remarkably disturbed. Although several experimental studies in mammals have been carried out on the developmental immunotoxicity of PCBs, there are still limited information available on avian species. Thus in this study, prenatal exposure to low level of PCBs and the effects on the developing immune system were investigated with chicken as a model animal of avian species, especially it is focused on the cell-mediated immune function.

  2. Comparison of the toxicity using body residues of DDE and select PCB congeners to the midge, Chironomus riparius, in partial-life cycle tests.

    Science.gov (United States)

    Hwang, H; Fisher, S W; Kim, K; Landrum, P F

    2004-01-01

    Due to the long time course required to achieve steady state with highly lipophilic contaminants such as PCBs (polychlorinated biphenyls), data derived from short-term toxicity tests may lead to an erroneous interpretation of hazard. In addition, PCBs bioaccumulated over time can cause sublethal impairments in organisms at concentrations much lower than required for mortality. Here, the body residues of 1,1-dichloro-2,2-bis-p-chlorophenyl ethane (DDE) and select PCB congeners associated with a spectrum of chronic effects in the midge, Chironomus riparius, were evaluated. The route of exposure was ingestion of the PCB-contaminated alga, Chlorella vulgarus, and trout chow loaded with the selected test compound. Two separate exposures of midges were performed. In the first experiment, midges were exposed from the second instar to the pupal stage. In the second exposure, midges were exposed from the second instar to the adult stage. A variety of sublethal endpoints was monitored, including developmental time within a stadium, body weight, and fecundity for the female adult. The dose was assessed as the whole body residue concentration of the contaminant. Overall, the midge concentration increased with increasing exposure concentration in algae and trout chow. Body weight at the end of each stadium was the assessment parameter that was least significantly affected among the test endpoints monitored. In contrast, a significant increase in development time was the endpoint that was most frequently observed in response to contaminant exposure. Reduction in fecundity was found only for DDE-exposed midges. These data, in which chronic endpoints are related to body residues, suggest that body residues will be useful in defining sublethal hazards of DDE and some PCB congeners.

  3. Congener-specific analysis of polychlorinated naphthalenes (PCNs) in the major Chinese technical PCB formulation from a stored Chinese electrical capacitor.

    Science.gov (United States)

    Huang, Jun; Yu, Gang; Yamauchi, Makoto; Matsumura, Toru; Yamazaki, Norimasa; Weber, Roland

    2015-10-01

    Impurity of polychlorinated naphthalenes (PCNs) in commercial polychlorinated biphenyl (PCB) formulations has been recognized as a relevant source of PCNs in the environment. Congener-specific analysis of most main PCB formulations has been accomplished previously, excluding the Chinese product. The insulating oil in a stored Chinese electric capacitor containing the major Chinese technical formulation "PCB3" was sampled and tested by isotope dilution technology using high-resolution gas chromatography coupled to high-resolution mass spectrometry (HRGC/HRMS). The detected concentration of PCNs in the Chinese PCB oil sample was 1,307.5 μg/g and therefore significantly higher than that reported in PCB formulations from other countries, as well as that in the transformer oil (ASKAREL Nr 1740) additionally tested in the present study for comparison. Based on the measurement, the total amount of PCNs in Chinese PCB3 oil is estimated to be 7.8 t, which would mean only 0.005 % of global production of PCNs of 150,000 t. The homolog profile is similar to those of PCN in Aroclor 1262 and Clophen A40, where the contributions from hexa-CNs and hepta-CNs are predominant and accounted for similar proportions. The Toxic Equivalent Quantity (TEQ) concentration of dioxin-like PCN congeners is 0.47 μg TEQ/g, with the dominant contributors of CN-73 and CN-66/67. This TEQ content from PCN is higher than that in most other PCB formulations with the exemption of the Russian Sovol formulation. The total TEQ in the historic 6,000 t of the Chinese PCB3 formulation is estimated to be 2.8 kg TEQ.

  4. The invasive plant Alternanthera philoxeroides was suppressed more intensively than its native congener by a native generalist: implications for the biotic resistance hypothesis.

    Directory of Open Access Journals (Sweden)

    Shufeng Fan

    Full Text Available Prior studies on preferences of native herbivores for native or exotic plants have tested both the enemy release hypothesis and the biotic resistance hypothesis and have reported inconsistent results. The different levels of resistance of native and exotic plants to native herbivores could resolve this controversy, but little attention has been paid to this issue. In this study, we investigated population performance, photosynthesis, leaf nitrogen concentration, and the constitutive and induced resistances of the successful invasive plant, Alternanthera philoxeroides, and its native congener, Alternanthera sessilis, in the presence of three population densities of the grasshopper, Atractomorpha sinensis. When the grasshopper was absent, leaf biomass, total biomass, photosynthesis, and leaf nitrogen concentration of A. philoxeroides were higher than those of A. sessilis. However, the morphological and physiological performances of A. philoxeroides were all decreased more intensively than A. sessilis after herbivory by grasshoppers. Especially as the concentrations of constitutive lignin and cellulose in leaf of A. philoxeroides were higher than A. sessilis, A. philoxeroides exhibited increased leaf lignin concentration to reduce its palatability only at severe herbivore load, whereas, leaf lignin, cellulose, and polyphenolic concentrations of A. sessilis all increased with increasing herbivory pressure, and cellulose and polyphenolic concentrations were higher in A. sessilis than in A. philoxeroides after herbivory. Our study indicated that the capability of the invasive plant to respond to native insect damage was lower than the native plant, and the invasive plant was suppressed more intensively than its native congener by the nat