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Sample records for monitoring specific tissues

  1. Tissue specific electrochemical fingerprinting.

    Directory of Open Access Journals (Sweden)

    Pavlina Sobrova

    Full Text Available BACKGROUND: Proteomics and metalloproteomics are rapidly developing interdisciplinary fields providing enormous amounts of data to be classified, evaluated and interpreted. Approaches offered by bioinformatics and also by biostatistical data analysis and treatment are therefore of extreme interest. Numerous methods are now available as commercial or open source tools for data processing and modelling ready to support the analysis of various datasets. The analysis of scientific data remains a big challenge, because each new task sets its specific requirements and constraints that call for the design of a targeted data pre-processing approach. METHODOLOGY/PRINCIPAL FINDINGS: This study proposes a mathematical approach for evaluating and classifying datasets obtained by electrochemical analysis of metallothionein in rat 9 tissues (brain, heart, kidney, eye, spleen, gonad, blood, liver and femoral muscle. Tissue extracts were heated and then analysed using the differential pulse voltammetry Brdicka reaction. The voltammograms were subsequently processed. Classification models were designed making separate use of two groups of attributes, namely attributes describing local extremes, and derived attributes resulting from the level=5 wavelet transform. CONCLUSIONS/SIGNIFICANCE: On the basis of our results, we were able to construct a decision tree that makes it possible to distinguish among electrochemical analysis data resulting from measurements of all the considered tissues. In other words, we found a way to classify an unknown rat tissue based on electrochemical analysis of the metallothionein in this tissue.

  2. Tissue Specific Labeling in Proteomics

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    Evelyn Ramberger

    2017-07-01

    Full Text Available Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.

  3. Application of microdialysis in tissue engineering monitoring

    Institute of Scientific and Technical Information of China (English)

    Zhaohui Li; Zhanfeng Cui

    2008-01-01

    In this review article,the microdialysis for tissue engineering monitoring is discussed.Among various monitoring techniques,microdialysis is advantageous for its capacity of perfusion on-line,and off-line multiple parameter monitoring.Following a description on the general system and performance,the main challenges to apply this technique for reliable long term monitoring are outlined.Further opportunities are identified.

  4. Housekeeping and tissue-specific genes in mouse tissues

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    St-Amand Jonny

    2007-05-01

    Full Text Available Abstract Background This study aims to characterize the housekeeping and tissue-specific genes in 15 mouse tissues by using the serial analysis of gene expression (SAGE strategy which indicates the relative level of expression for each transcript matched to the tag. Results Here, we identified constantly expressed housekeeping genes, such as eukaryotic translation elongation factor 2, which is expressed in all tissues without significant difference in expression levels. Moreover, most of these genes were not regulated by experimental conditions such as steroid hormones, adrenalectomy and gonadectomy. In addition, we report previously postulated housekeeping genes such as peptidyl-prolyl cis-trans isomerase A, glyceraldehyde-3-phosphate dehydrogenase and beta-actin, which are expressed in all the tissues, but with significant difference in their expression levels. We have also identified genes uniquely detected in each of the 15 tissues and other tissues from public databases. Conclusion These identified housekeeping genes could represent appropriate controls for RT-PCR and northern blot when comparing the expression levels of genes in several tissues. The results reveal several tissue-specific genes highly expressed in testis and pituitary gland. Furthermore, the main function of tissue-specific genes expressed in liver, lung and bone is the cell defence, whereas several keratins involved in cell structure function are exclusively detected in skin and vagina. The results from this study can be used for example to target a tissue for agent delivering by using the promoter of tissue-specific genes. Moreover, this study could be used as basis for further researches on physiology and pathology of these tissues.

  5. Multisite Tissue Oxygenation Monitoring Indicates Organ-Specific Flow Distribution and Oxygen Delivery Related to Low Cardiac Output in Preterm Infants With Clinical Sepsis

    NARCIS (Netherlands)

    van der Laan, Michelle E.; Roofthooft, Marcus T. R.; Fries, Marian W. A.; Schat, Trijntje E.; Bos, Arend F.; Berger, Rolf M. F.; Kooi, Elisabeth M. W.

    Objectives: Cardiac output may be compromised in preterm infants with sepsis. Whether low cardiac output is associated with low tissue oxygen supply in these patients is unclear. The aim of the current study was to assess the association between cardiac output, assessed by echocardiography, and

  6. Multisite Tissue Oxygenation Monitoring Indicates Organ-Specific Flow Distribution and Oxygen Delivery Related to Low Cardiac Output in Preterm Infants With Clinical Sepsis

    NARCIS (Netherlands)

    van der Laan, Michelle E.; Roofthooft, Marcus T. R.; Fries, Marian W. A.; Schat, Trijntje E.; Bos, Arend F.; Berger, Rolf M. F.; Kooi, Elisabeth M. W.

    2016-01-01

    Objectives: Cardiac output may be compromised in preterm infants with sepsis. Whether low cardiac output is associated with low tissue oxygen supply in these patients is unclear. The aim of the current study was to assess the association between cardiac output, assessed by echocardiography, and tiss

  7. Tissue Specific Promoters in Colorectal Cancer

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    A. R. Rama

    2015-01-01

    Full Text Available Colorectal carcinoma is the third most prevalent cancer in the world. In the most advanced stages, the use of chemotherapy induces a poor response and is usually accompanied by other tissue damage. Significant progress based on suicide gene therapy has demonstrated that it may potentiate the classical cytotoxic effects in colorectal cancer. The inconvenience still rests with the targeting and the specificity efficiency. The main target of gene therapy is to achieve an effective vehicle to hand over therapeutic genes safely into specific cells. One possibility is the use of tumor-specific promoters overexpressed in cancers. They could induce a specific expression of therapeutic genes in a given tumor, increasing their localized activity. Several promoters have been assayed into direct suicide genes to cancer cells. This review discusses the current status of specific tumor-promoters and their great potential in colorectal carcinoma treatment.

  8. Tissue Specific Promoters in Colorectal Cancer

    Science.gov (United States)

    Rama, A. R.; Aguilera, A.; Melguizo, C.; Caba, O.; Prados, J.

    2015-01-01

    Colorectal carcinoma is the third most prevalent cancer in the world. In the most advanced stages, the use of chemotherapy induces a poor response and is usually accompanied by other tissue damage. Significant progress based on suicide gene therapy has demonstrated that it may potentiate the classical cytotoxic effects in colorectal cancer. The inconvenience still rests with the targeting and the specificity efficiency. The main target of gene therapy is to achieve an effective vehicle to hand over therapeutic genes safely into specific cells. One possibility is the use of tumor-specific promoters overexpressed in cancers. They could induce a specific expression of therapeutic genes in a given tumor, increasing their localized activity. Several promoters have been assayed into direct suicide genes to cancer cells. This review discusses the current status of specific tumor-promoters and their great potential in colorectal carcinoma treatment. PMID:26648599

  9. Cell-specific monitoring of protein synthesis in vivo.

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    Nikos Kourtis

    Full Text Available Analysis of general and specific protein synthesis provides important information, relevant to cellular physiology and function. However, existing methodologies, involving metabolic labelling by incorporation of radioactive amino acids into nascent polypeptides, cannot be applied to monitor protein synthesis in specific cells or tissues, in live specimens. We have developed a novel approach for monitoring protein synthesis in specific cells or tissues, in vivo. Fluorescent reporter proteins such as GFP are expressed in specific cells and tissues of interest or throughout animals using appropriate promoters. Protein synthesis rates are assessed by following fluorescence recovery after partial photobleaching of the fluorophore at targeted sites. We evaluate the method by examining protein synthesis rates in diverse cell types of live, wild type or mRNA translation-defective Caenorhabditis elegans animals. Because it is non-invasive, our approach allows monitoring of protein synthesis in single cells or tissues with intrinsically different protein synthesis rates. Furthermore, it can be readily implemented in other organisms or cell culture systems.

  10. THE MICROBIOLOGICAL MONITORING OF RECYCLED PAPER TISSUES

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    K. Imandel

    2000-08-01

    Full Text Available In order to investigate the microbiological safety of sanitary tissues made of recycled scrap papers in Iran, random samples were taken for one year with the cooperation of the Iranian Standard and Industrial Research Institute (Karaj unit, of 44 types of sanitary tissues, two samples of each type including tissues, toilet papers and dippers as well as a control sample and their probable contamination with microbiological elements (bacterial & fungal were assessed using proper ordinary and specific culture environments while also performing confirmation tests. Considering all aspects of this study including easy identification, high precision, simplicity of application, economic justification and observation of better results, the method which applies ringer 1/4 solution as the thinner environment was preferable to the saline peptone water solution. No contamination with Staphylococcus aureus, Streptococcus faecalis, Pseudomonas aeroginosa and E.coli bacteria was observed, but the excessive contamination with the mesophillic bacteria was confirmed. Among the 27 samples tested with the ringer 1/4 method, 8 cases (29.6% were excessively contaminated with the mesophillic bacteria and one case (3.7% with fungi. Meanwhile, out of the 43 samples that were tested with the saline peptone water solution, there was no excessive contamination with mesophillic bacteria and only one case (2.3% of fungal contamination was observed.

  11. MR elastography monitoring of tissue-engineered constructs.

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    Othman, Shadi F; Curtis, Evan T; Plautz, Sarah A; Pannier, Angela K; Butler, Stephanie D; Xu, Huihui

    2012-03-01

    The objective of tissue engineering (TE) is to create functional replacements for various tissues; the mechanical properties of these engineered constructs are critical to their function. Several techniques have been developed for the measurement of the mechanical properties of tissues and organs; however, current methods are destructive. The field of TE will benefit immensely if biomechanical models developed by these techniques could be combined with existing imaging modalities to enable noninvasive, dynamic assessment of mechanical properties during tissue growth. Specifically, MR elastography (MRE), which is based on the synchronization of a mechanical actuator with a phase contrast imaging pulse sequence, has the capacity to measure tissue strain generated by sonic cyclic displacement. The captured displacement is presented in shear wave images from which the complex shear moduli can be extracted or simplified by a direct measure, termed the shear stiffness. MRE has been extended to the microscopic scale, combining clinical MRE with high-field magnets, stronger magnetic field gradients and smaller, more sensitive, radiofrequency coils, enabling the interrogation of smaller samples, such as tissue-engineered constructs. The following topics are presented in this article: (i) current mechanical measurement techniques and their limitations in TE; (ii) a description of the MRE system, MRE theory and how it can be applied for the measurement of mechanical properties of tissue-engineered constructs; (iii) a summary of in vitro MRE work for the monitoring of osteogenic and adipogenic tissues originating from human adult mesenchymal stem cells (MSCs); (iv) preliminary in vivo studies of MRE of tissues originating from mouse MSCs implanted subcutaneously in immunodeficient mice with an emphasis on in vivo MRE challenges; (v) future directions to resolve current issues with in vivo MRE in the context of how to improve the future role of MRE in TE.

  12. Tissue-specific overexpression of lipoprotein lipase causes tissue-specific insulin resistance

    OpenAIRE

    Kim, Jason K.; Fillmore, Jonathan J.; Chen, Yan; Yu, Chunli; Moore, Irene K.; Pypaert, Marc; Lutz, E. Peer; Kako, Yuko; Velez-Carrasco, Wanda; Goldberg, Ira J.; Breslow, Jan L.; Shulman, Gerald I.

    2001-01-01

    Insulin resistance in skeletal muscle and liver may play a primary role in the development of type 2 diabetes mellitus, and the mechanism by which insulin resistance occurs may be related to alterations in fat metabolism. Transgenic mice with muscle- and liver-specific overexpression of lipoprotein lipase were studied during a 2-h hyperinsulinemic–euglycemic clamp to determine the effect of tissue-specific increase in fat on insulin action and signaling. Muscle–lipoprotein lipase mice had a 3...

  13. Real-time optoacoustic monitoring of temperature in tissues

    Energy Technology Data Exchange (ETDEWEB)

    Larina, Irina V [Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX 77555-0456 (United States); Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555-0456 (United States); Larin, Kirill V [Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX 77555-0456 (United States); Esenaliev, Rinat O [Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX 77555-0456 (United States); Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555-0456 (United States); Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX 77555-0456 (United States)

    2005-08-07

    To improve the safety and efficacy of thermal therapy, it is necessary to map tissue temperature in real time with submillimetre spatial resolution. Accurate temperature maps may provide the necessary control of the boundaries of the heated regions and minimize thermal damage to surrounding normal tissues. Current imaging modalities fail to monitor tissue temperature in real time with high resolution and accuracy. We investigated a non-invasive optoacoustic method for accurate, real-time monitoring of tissue temperature during thermotherapy. In this study, we induced temperature gradients in tissue and tissue-like samples and monitored the temperature distribution using the optoacoustic technique. The fundamental harmonic of a Q-switched Nd : YAG laser ({lambda} = 1064 nm) was used for optoacoustic wave generation and probing of tissue temperature. The tissue temperature was also monitored with a multi-sensor temperature probe inserted in the samples. Good agreement between optoacoustically measured and actual tissue temperatures was obtained. The accuracy of temperature monitoring was better than 1{sup 0}C, while the spatial resolution was about 1 mm. These data suggest that the optoacoustic technique has the potential to be used for non-invasive, real-time temperature monitoring during thermotherapy.

  14. Spectroscopic Monitoring of Kidney Tissue Ischemic Injury

    Energy Technology Data Exchange (ETDEWEB)

    Demos, S G; Fitzgerald, J T; Michalopoulou, A P; Troppmann, C

    2004-03-11

    Noninvasive evaluation of tissue viability of donor kidneys used for transplantation is an issue that current technology is not able to address. In this work, we explore optical spectroscopy for its potential to assess the degree of ischemic damage in kidney tissue. We hypothesized that ischemic damage to kidney tissue will give rise to changes in its optical properties which in turn may be used to asses the degree of tissue injury. The experimental results demonstrate that the autofluorescence intensity of the injured kidney is decreasing as a function of time exposed to ischemic injury. Changes were also observed in the NIR light scattering intensities most probably arising from changes due to injury and death of the tissue.

  15. Tissue specificity of endothelin binding sites

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    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.

  16. 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.

  17. Cost analysis of near-infrared spectroscopy tissue oximetry for monitoring autologous free tissue breast reconstruction.

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    Pelletier, Aaron; Tseng, Charles; Agarwal, Shailesh; Park, Julie; Song, David

    2011-10-01

    Free flap monitoring typically requires specialized nursing that can increase medical costs. This study uses near-infrared spectroscopy (NIRS) tissue oximetry to monitor free tissue breast reconstruction. We hypothesize this practice will reduce medical costs by eliminating the need for specialized nursing. From August 2006 to January 2010, women undergoing unilateral free tissue breast reconstruction were enrolled and admitted postoperatively to either the surgical intensive care unit (ICU) or floor. Each underwent continuous monitoring using NIRS tissue oximetry and intermittent clinical examination with surface Doppler ultrasonography. Patient demographics, comorbidities, perioperative details, and financial data were recorded. There were 50 patients studied, all with abdominal-based flaps (25 per group). There were no statistically significant differences in patient demographics, comorbidities, mean flap weight, ischemia time, or length of stay between the ICU and floor groups. Four flaps had vascular complications, all detected by NIRS tissue oximetry. Comparison of hospital costs showed an average reduction of $1937 per patient when monitored on the surgical floor (P = 0.036). NIRS tissue oximetry is a sensitive and reliable monitoring tool, eliminating the need for specialized nursing care. The effect is decreased cost structure and increased hospital contribution margin for autologous free tissue breast reconstruction.

  18. The Specifications for Monitoring of Acid Rain

    Institute of Scientific and Technical Information of China (English)

    Tang Jie

    2011-01-01

    Background Since China is a country seriously affected by acid rain pollution,it is a long-term fundamental work for acid rain pollution prevention and control in China by getting well informed of the characteristics of spatial and temporal changes in acid rain and long-term trends of these changes.In order to reach the national demand for acid rain monitoring data,the China Meteorological Administration (CMA) began to construct the network of acid rain monitoring stations in 1992.By the end of 2010,the total number of monitoring stations has exceeded 340.

  19. Tissue specific heterogeneity in effector immune cell response

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    Saba eTufail

    2013-08-01

    Full Text Available Post pathogen invasion, migration of effector T-cell subsets to specific tissue locations is of prime importance for generation of robust immune response. Effector T cells are imprinted with distinct ‘homing codes’ (adhesion molecules and chemokine receptors during activation which regulate their targeted trafficking to specific tissues. Internal cues in the lymph node microenvironment along with external stimuli from food (vitamin A and sunlight (vitamin D3 prime dendritic cells, imprinting them to play centrestage in the induction of tissue tropism in effector T cells. B cells as well, in a manner similar to effector T cells, exhibit tissue tropic migration. In this review, we have focused on the factors regulating the generation and migration of effector T cells to various tissues alongwith giving an overview of tissue tropism in B cells.

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

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    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.

  1. Photoacoustic monitoring and imaging of blood vessels in tissue

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    Kolkman, Roy G. M.; Pilatou, Magdalena C.; Steenbergen, Wiendelt; de Mul, Frits F. M.

    2002-06-01

    Using very sensitive photoacoustical detectors we localized and monitored the blood content in tissue. In these detectors a PVdF-layer has been used as piezo-electric material and also fibers for the illumination of the sample are integrated. The resolution is about 20micrometers in depth and about 50-100micrometers laterally. The wavelengths of the laser light were 532 and 1064 nm. With these colors we can measure at different depths in tissue. The measurements concerned blood perfusion in real tissue: vessels in chicken breast, in test animals at various positions and in the human arm.

  2. Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues

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    Blazie, Stephen M.; Geissel, Heather C.; Wilky, Henry; Joshi, Rajan; Newbern, Jason; Mangone, Marco

    2017-01-01

    mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3′untranslated region (3′UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3′UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3′UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis. PMID:28348061

  3. Impedance-based monitoring for tissue engineering applications

    DEFF Research Database (Denmark)

    Canali, Chiara; Heiskanen, Arto; Martinsen, Ø.G.

    2015-01-01

    Impedance is a promising technique for sensing the overall process of tissue engineering. Different electrode configurations can be used to characterize the scaffold that supports cell organization in terms of hydrogel polymerization and degree of porosity, monitoring cell loading, cell prolifera...

  4. DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns.

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    Lokk, Kaie; Modhukur, Vijayachitra; Rajashekar, Balaji; Märtens, Kaspar; Mägi, Reedik; Kolde, Raivo; Koltšina, Marina; Nilsson, Torbjörn K; Vilo, Jaak; Salumets, Andres; Tõnisson, Neeme

    2014-04-01

    DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.

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

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    Meagher, Richard B.; Balish, Rebecca S.; Tehryung, Kim; McKinney, Elizabeth C.

    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.

  6. 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...

  7. Transcription elongation and tissue-specific somatic CAG instability.

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    Agathi-Vasiliki Goula

    Full Text Available The expansion of CAG/CTG repeats is responsible for many diseases, including Huntington's disease (HD and myotonic dystrophy 1. CAG/CTG expansions are unstable in selective somatic tissues, which accelerates disease progression. The mechanisms underlying repeat instability are complex, and it remains unclear whether chromatin structure and/or transcription contribute to somatic CAG/CTG instability in vivo. To address these issues, we investigated the relationship between CAG instability, chromatin structure, and transcription at the HD locus using the R6/1 and R6/2 HD transgenic mouse lines. These mice express a similar transgene, albeit integrated at a different site, and recapitulate HD tissue-specific instability. We show that instability rates are increased in R6/2 tissues as compared to R6/1 matched-samples. High transgene expression levels and chromatin accessibility correlated with the increased CAG instability of R6/2 mice. Transgene mRNA and H3K4 trimethylation at the HD locus were increased, whereas H3K9 dimethylation was reduced in R6/2 tissues relative to R6/1 matched-tissues. However, the levels of transgene expression and these specific histone marks were similar in the striatum and cerebellum, two tissues showing very different CAG instability levels, irrespective of mouse line. Interestingly, the levels of elongating RNA Pol II at the HD locus, but not the initiating form of RNA Pol II, were tissue-specific and correlated with CAG instability levels. Similarly, H3K36 trimethylation, a mark associated with transcription elongation, was specifically increased at the HD locus in the striatum and not in the cerebellum. Together, our data support the view that transcription modulates somatic CAG instability in vivo. More specifically, our results suggest for the first time that transcription elongation is regulated in a tissue-dependent manner, contributing to tissue-selective CAG instability.

  8. 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.

  9. [Intraoperative monitoring of oxygen tissue pressure: Applications in vascular neurosurgery].

    Science.gov (United States)

    Arikan, Fuat; Vilalta, Jordi; Torne, Ramon; Chocron, Ivette; Rodriguez-Tesouro, Ana; Sahuquillo, Juan

    2014-01-01

    Ischemic lesions related to surgical procedures are a major cause of postoperative morbidity in patients with cerebral vascular disease. There are different systems of neuromonitoring to detect intraoperative ischemic events, including intraoperative monitoring of oxygen tissue pressure (PtiO2). The aim of this article was to describe, through the discussion of 4 cases, the usefulness of intraoperative PtiO2 monitoring during vascular neurosurgery. In presenting these cases, we demonstrate that monitoring PtiO2 is a reliable way to detect early ischemic events during surgical procedures. Continuous monitoring of PtiO2 in an area at risk allows the surgeon to resolve the cause of the ischemic event before it evolves to an established cerebral infarction. Copyright © 2014 Sociedad Española de Neurocirugía. Published by Elsevier España. All rights reserved.

  10. Bioprinting Cellularized Constructs Using a Tissue-specific Hydrogel Bioink.

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    Skardal, Aleksander; Devarasetty, Mahesh; Kang, Hyun-Wook; Seol, Young-Joon; Forsythe, Steven D; Bishop, Colin; Shupe, Thomas; Soker, Shay; Atala, Anthony

    2016-04-21

    Bioprinting has emerged as a versatile biofabrication approach for creating tissue engineered organ constructs. These constructs have potential use as organ replacements for implantation in patients, and also, when created on a smaller size scale as model "organoids" that can be used in in vitro systems for drug and toxicology screening. Despite development of a wide variety of bioprinting devices, application of bioprinting technology can be limited by the availability of materials that both expedite bioprinting procedures and support cell viability and function by providing tissue-specific cues. Here we describe a versatile hyaluronic acid (HA) and gelatin-based hydrogel system comprised of a multi-crosslinker, 2-stage crosslinking protocol, which can provide tissue specific biochemical signals and mimic the mechanical properties of in vivo tissues. Biochemical factors are provided by incorporating tissue-derived extracellular matrix materials, which include potent growth factors. Tissue mechanical properties are controlled combinations of PEG-based crosslinkers with varying molecular weights, geometries (linear or multi-arm), and functional groups to yield extrudable bioinks and final construct shear stiffness values over a wide range (100 Pa to 20 kPa). Using these parameters, hydrogel bioinks were used to bioprint primary liver spheroids in a liver-specific bioink to create in vitro liver constructs with high cell viability and measurable functional albumin and urea output. This methodology provides a general framework that can be adapted for future customization of hydrogels for biofabrication of a wide range of tissue construct types.

  11. Transient bioimpedance monitoring of mechanotransduction in artificial tissue during indentation

    Directory of Open Access Journals (Sweden)

    David Cheneler

    2014-09-01

    Full Text Available Mechanotransduction is of fundamental importance in cell physiology, facilitating sensing in touch and hearing as well as tissue development and wound healing. This study used an impedance sensor to monitor the effective resistance and permittivity of artificial tissues, alginate hydrogel with encapsulated fibroblasts, which were kept viable through the use of a bespoke microfluidic system. The observed transient impedance responses upon the application of identical compressive normal loads differed between acellular hydrogels and hydrogels in which fibroblasts were encapsulated. These differences resulted from changes in the conductivity and permeability of the hydrogel due to the presence of the encapsulated fibroblasts, and transient changes in ion concentrations due to mechanotransduction effects.

  12. 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.

  13. Predicting Tissue-Specific Enhancers in the Human Genome

    Energy Technology Data Exchange (ETDEWEB)

    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. Fracture of Human Femur Tissue Monitored by Acoustic Emission Sensors

    Directory of Open Access Journals (Sweden)

    Dimitrios. G. Aggelis

    2015-03-01

    Full Text Available The study describes the acoustic emission (AE activity during human femur tissue fracture. The specimens were fractured in a bending-torsion loading pattern with concurrent monitoring by two AE sensors. The number of recorded signals correlates well with the applied load providing the onset of micro-fracture at approximately one sixth of the maximum load. Furthermore, waveform frequency content and rise time are related to the different modes of fracture (bending of femur neck or torsion of diaphysis. The importance of the study lies mainly in two disciplines. One is that, although femurs are typically subjects of surgical repair in humans, detailed monitoring of the fracture with AE will enrich the understanding of the process in ways that cannot be achieved using only the mechanical data. Additionally, from the point of view of monitoring techniques, applying sensors used for engineering materials and interpreting the obtained data pose additional difficulties due to the uniqueness of the bone structure.

  15. Monitoring of tissue coagulation during thermotherapy using optoacoustic technique

    Energy Technology Data Exchange (ETDEWEB)

    Larin, Kirill V [Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX 77555 (United States); Larina, Irina V [Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX 77555 (United States); Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Esenaliev, Rinat O [Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX 77555 (United States); Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX 77555 (United States)

    2005-08-07

    In this paper we have applied the laser optoacoustic technique for real time noninvasive monitoring of thermal damage in tissues. Changes in tissue optical properties during coagulation were detected by measuring and analysing amplitude and temporal characteristics of optoacoustic signals. Coagulation of liver, myocardium and prostate was induced by interstitial continuous wave Nd : YAG laser irradiation of the samples or by conductive heating. Real time detection of thermally-induced changes in optical properties was performed with sensitive wide-band acoustic transducers. Combination of optoacoustic and diffuse reflectance technique was applied for determination of tissue optical properties: effective attenuation, total diffuse reflectance, reduced scattering coefficient and absorption coefficient. The optical properties did not change up to temperature of coagulation (about 53{sup 0}C) and sharply increased during heating up to 70{sup 0}C. Monitoring of the expansion of interstitial coagulation front within freshly excised canine tissues was performed in real time with spatial resolution of about 0.6 mm. The results of our study suggest that this technique can potentially be used for real time precise thermotherapy of malignant and benign lesions at depths of the order of the centimetre.

  16. Mesenchymal Stromal Cells and Tissue-Specific Progenitor Cells: Their Role in Tissue Homeostasis

    Directory of Open Access Journals (Sweden)

    Aleksandra Klimczak

    2016-01-01

    Full Text Available Multipotent mesenchymal stromal/stem cells (MSCs reside in many human organs and comprise heterogeneous population of cells with self-renewal ability. These cells can be isolated from different tissues, and their morphology, immunophenotype, and differentiation potential are dependent on their tissue of origin. Each organ contains specific population of stromal cells which maintain regeneration process of the tissue where they reside, but some of them have much more wide plasticity and differentiate into multiple cells lineage. MSCs isolated from adult human tissues are ideal candidates for tissue regeneration and tissue engineering. However, MSCs do not only contribute to structurally tissue repair but also MSC possess strong immunomodulatory and anti-inflammatory properties and may influence in tissue repair by modulation of local environment. This paper is presenting an overview of the current knowledge of biology of tissue-resident mesenchymal stromal and progenitor cells (originated from bone marrow, liver, skeletal muscle, skin, heart, and lung associated with tissue regeneration and tissue homeostasis.

  17. Analysis of methylation microarray for tissue specific detection.

    Science.gov (United States)

    Muangsub, Tachapol; Samsuwan, Jarunya; Tongyoo, Pumipat; Kitkumthorn, Nakarin; Mutirangura, Apiwat

    2014-12-10

    The role of human DNA methylation has been extensively studied in genomic imprinting, X-inactivation, and disease. However, studies of tissue-specific methylation remain limited. In this study, we use bioinformatics methods to analyze methylation data and reveal loci that are exclusively methylated or unmethylated in individual tissues. We collect 39 previously published DNA methylation profiles using an Illumina® HumanMethylation 27 BeadChip Kit containing 22 common tissues and involving 27,578 CpG loci across the human genome. We found 86 positions of tissue specific methylation CpG (TSM) that encompass 34 hypermethylated TSMs (31 genes) and 52 hypomethylated TSMs (47 genes). Tissues were found to contain 1 to 25 TSM loci, with the majority in the liver (25), testis (18), and brain (16). Fewer TSM loci were found in the muscle (8), ovary (7), adrenal gland (3), pancreas (2-4), kidney, spleen, and stomach (1 each). TSMs are predominantly located 0-300 base pairs in the 3' direction after the transcription start site. Similar to known promoters of methylation, hypermethylated TSM genes suppress transcription, while hypomethylated TSMs allow gene transcription. The majority of hypermethylated TSM genes encode membrane proteins and receptors, while hypomethylated TSM genes primarily encode signal peptides and tissue-specific proteins. In summary, the database of TSM loci produced herein is useful for the selection of tissue-specific DNA markers as diagnostic tools, as well as for the further study of the mechanisms and roles of TSM. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Gene expression analysis distinguishes tissue specific and gender related functions among adult Ascaris suum tissues

    Science.gov (United States)

    Wang, Zhengyuan; Gao, Xin; Martin, John; Yin, Yong; Abubucker, Sahar; Rash, Amy C.; Li, Ben-Wen; Nash, Bill; Hallsworth-Pepin, Kym; Jasmer, Douglas P.; Mitreva, Makedonka

    2013-01-01

    Over a billion people are infected by Ascaris spp. intestinal parasites. To clarify functional differences among tissues of adult A. suum, we compared gene expression by various tissues of these worms by expression microarray methods.. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender-specific elements were characterized in multiple non-reproductive tissues of female or male worms, with most prominence of gender differences in intestinal tissue. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine. Our results provide the most comprehensive assessment of gene expression among tissues of a parasitic nematode to date. PMID:23572074

  19. 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.

    2013-01-01

    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. PMID:23390599

  20. Monitoring free tissue transfer using laser speckle imaging

    Science.gov (United States)

    Winchester, Leonard W.; Chou, Nee-Yin

    2006-02-01

    Blood velocity information can be extracted by analyzing, either temporally or spatially, laser speckle (LS) patterns generated when a laser source illuminates the tissue. While a temporal analysis, such as that used for laser Doppler velocimetry (LDV), provides high spatial resolution, the time required to obtain flow data in vivo on large areas of tissue limits its utility. The LS imaging (LSI) technique combines the nonscanning, full-field, LS method and the modified multiple scattering algorithms developed for LDV analysis to retrieve blood velocity parameters. It provides a noninvasive means for realtime, quantitative measurements of subtle changes in the tissue vasculature. This paper describes the use of the LSI technique on free flap measurements of a swine model and compares the results with those obtained using an LDV probe. Both the LSI and the LDV measurements showed similar results - blood velocity and flow decreased about 10%-33% from the tip to the caudal base of the flap, respectively. The difference between the tip and the caudal base is a measure of flap ischemia. However, tissue pigmentation affects the blood flow parameters retrieved from the LDV measurements, it does not affect the blood velocity parameters retrieved from the LSI measurements. Both techniques were also used during free tissue transfer procedures in patients to demonstrate the utility of the LSI for monitoring the status of the graft.

  1. 46 CFR 162.050-25 - Cargo monitor: Design specification.

    Science.gov (United States)

    2010-10-01

    ..., AND MATERIALS: SPECIFICATIONS AND APPROVAL ENGINEERING EQUIPMENT Pollution Prevention Equipment § 162... cause formation of static electricity. (e) A monitor must be designed to operate in each plane that forms an angle of 22.5° with the plane of its normal operating position. (f) Each monitor must...

  2. Double Shell Tank (DST) Monitor and Control Subsystem Specification

    Energy Technology Data Exchange (ETDEWEB)

    BAFUS, R.R.

    2000-11-03

    This specification revises the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Monitor and Control Subsystem that supports the first phase of Waste Feed Delivery.

  3. Temperature-monitored optical treatment for radial tissue expansion.

    Science.gov (United States)

    Bak, Jinoh; Kang, Hyun Wook

    2017-07-01

    Esophageal stricture occurs in 7-23% of patients with gastroesophageal reflux disease. However, the current treatments including stent therapy, balloon dilation, and bougienage involve limitations such as stent migration, formation of the new strictures, and snowplow effect. The purpose of the current study was to investigate the feasibility of structural expansion in tubular tissue ex vivo during temperature-monitored photothermal treatment with a diffusing applicator for esophageal stricture. Porcine liver was used as an ex vivo tissue sample for the current study. A glass tube was used to maintain a constant distance between the diffuser and tissue surface and to evaluate any variations in the luminal area after 10-W 1470-nm laser irradiation for potential stricture treatment. The 3D goniometer measurements confirmed roughly isotropic distribution with less than 10% deviation from the average angular intensity over 2π (i.e., 0.86 ± 0.09 in arbitrary unit) from the diffusing applicator. The 30-s irradiation increased the tissue temperature up to 72.5 °C, but due to temperature feedback, the interstitial tissue temperature became saturated at 70 °C (i.e., steady-state error = ±0.4 °C). The irradiation times longer than 5 s presented area expansion index of 1.00 ± 0.04, signifying that irreversible tissue denaturation permanently deformed the lumen in a circular shape and secured the equivalent luminal area to that of the glass tube. Application of a temperature feedback controller for photothermal treatment with the diffusing applicator can regulate the degree of thermal denaturation to feasibly treat esophageal stricture in a tubular tissue.

  4. 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.

  5. 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

  6. Tissue-Specific Effects of Esophageal Extracellular Matrix.

    Science.gov (United States)

    Keane, Timothy J; DeWard, Aaron; Londono, Ricardo; Saldin, Lindsey T; Castleton, Arthur A; Carey, Lisa; Nieponice, Alejandro; Lagasse, Eric; Badylak, Stephen F

    2015-09-01

    Biologic scaffolds composed of extracellular matrix (ECM) have been used to facilitate repair or remodeling of numerous tissues, including the esophagus. The theoretically ideal scaffold for tissue repair is the ECM derived from the particular tissue to be treated, that is, site-specific or homologous ECM. The preference or potential advantage for the use of site-specific ECM remains unknown in the esophageal location. The objective of the present study was to characterize the in vitro cellular response and in vivo host response to a homologous esophageal ECM (eECM) versus nonhomologous ECMs derived from small intestinal submucosa and urinary bladder. The in vitro response of esophageal stem cells was characterized by migration, proliferation, and three-dimensional (3D) organoid formation assays. The in vivo remodeling response was evaluated in a rat model of esophageal mucosal resection. Results of the study showed that the eECM retains favorable tissue-specific characteristics that enhance the migration of esophageal stem cells and supports the formation of 3D organoids to a greater extent than heterologous ECMs. Implantation of eECM facilitates the remodeling of esophageal mucosa following mucosal resection, but no distinct advantage versus heterologous ECM could be identified.

  7. Tissue-specificity of proteoglycans expression in different cancers

    Directory of Open Access Journals (Sweden)

    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.

  8. Automated Synthesis of Assertion Monitors using Visual Specifications

    CERN Document Server

    Gadkari, Ambar A

    2011-01-01

    Automated synthesis of monitors from high-level properties plays a significant role in assertion-based verification. We present here a methodology to synthesize assertion monitors from visual specifications given in CESC (Clocked Event Sequence Chart). CESC is a visual language designed for specifying system level interactions involving single and multiple clock domains. It has well-defined graphical and textual syntax and formal semantics based on synchronous language paradigm enabling formal analysis of specifications. In this paper we provide an overview of CESC language with few illustrative examples. The algorithm for automated synthesis of assertion monitors from CESC specifications is described. A few examples from standard bus protocols (OCP-IP and AMBA) are presented to demonstrate the application of monitor synthesis algorithm.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. 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.

  11. 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.

  12. Double Shell Tank (DST) Monitor and Control Subsystem Specification

    Energy Technology Data Exchange (ETDEWEB)

    BAFUS, R.R.

    2000-04-27

    This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Monitor and Control Subsystem that supports the first phase of Waste Feed Delivery. This subsystem specification establishes the interface and performance requirements and provides references to the requisite codes and standards to be applied during the design of the Double-Shell Tank (DST) Monitor and Control Subsystem. The DST Monitor and Control Subsystem consists of the new and existing equipment that will be used to provide tank farm operators with integrated local monitoring and control of the DST systems to support Waste Feed Delivery (WFD). New equipment will provide automatic control and safety interlocks where required and provide operators with visibility into the status of DST subsystem operations (e.g., DST mixer pump operation and DST waste transfers) and the ability to manually control specified DST functions as necessary. This specification is intended to be the basis for new project/installations (W-521, etc.). This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

  13. Brain Tissue Oxygen: In Vivo Monitoring with Carbon Paste Electrodes

    Directory of Open Access Journals (Sweden)

    John P. Lowry

    2005-11-01

    Full Text Available In this communication we review selected experiments involving the use ofcarbon paste electrodes (CPEs to monitor and measure brain tissue O2 levels in awakefreely-moving animals. Simultaneous measurements of rCBF were performed using the H2clearance technique. Voltammetric techniques used include both differential pulse (O2 andconstant potential amperometry (rCBF. Mild hypoxia and hyperoxia produced rapidchanges (decrease and increase respectively in the in vivo O2 signal. Neuronal activation(tail pinch and stimulated grooming produced similar increases in both O2 and rCBFindicating that CPE O2 currents provide an index of increases in rCBF when such increasesexceed O2 utilization. Saline injection produced a transient increase in the O2 signal whilechloral hydrate produced slower more long-lasting changes that accompanied the behavioralchanges associated with anaesthesia. Acetazolamide increased O2 levels through an increasein rCBF.

  14. Tissue-specific insulin signaling mediates female sexual attractiveness.

    Science.gov (United States)

    Fedina, Tatyana Y; Arbuthnott, Devin; Rundle, Howard D; Promislow, Daniel E L; Pletcher, Scott D

    2017-08-01

    Individuals choose their mates so as to maximize reproductive success, and one important component of this choice is assessment of traits reflecting mate quality. Little is known about why specific traits are used for mate quality assessment nor about how they reflect it. We have previously shown that global manipulation of insulin signaling, a nutrient-sensing pathway governing investment in survival versus reproduction, affects female sexual attractiveness in the fruit fly, Drosophila melanogaster. Here we demonstrate that these effects on attractiveness derive from insulin signaling in the fat body and ovarian follicle cells, whose signals are integrated by pheromone-producing cells called oenocytes. Functional ovaries were required for global insulin signaling effects on attractiveness, and manipulations of insulin signaling specifically in late follicle cells recapitulated effects of global manipulations. Interestingly, modulation of insulin signaling in the fat body produced opposite effects on attractiveness, suggesting a competitive relationship with the ovary. Furthermore, all investigated tissue-specific insulin signaling manipulations that changed attractiveness also changed fecundity in the corresponding direction, pointing to insulin pathway activity as a reliable link between fecundity and attractiveness cues. The cues themselves, cuticular hydrocarbons, responded distinctly to fat body and follicle cell manipulations, indicating independent readouts of the pathway activity from these two tissues. Thus, here we describe a system in which female attractiveness results from an apparent connection between attractiveness cues and an organismal state of high fecundity, both of which are created by lowered insulin signaling in the fat body and increased insulin signaling in late follicle cells.

  15. Tissue electrical properties monitoring for the prevention of pressure sore.

    Science.gov (United States)

    Ching, Congo Tak-Shing; Chou, Mei-Yun; Jiang, Siou-Jhen; Huang, Su-Hua; Sun, Tai-Ping; Liu, Wei-Hao; Liu, Chia-Ming

    2011-12-01

    Pressure sores are a significant problem in the healthcare sector. Although they may cause considerable morbidity, they are preventable. The objectives of this study are to (1) investigate the electrical properties of a tissue close to and away from the pressure sore site, and (2) establish a new approach for objective, reliable, low-cost and noninvasive screening or detection of pressure sore in its early stage. Randomised controlled trial. Fifteen patients participated in this study. They all had stage I or stage II sacral pressure sores. Tiny surface electrodes in four-electrode configuration were used for all tissue electrical properties measurements recorded over the frequency range of 30-10 MHz. Intraclass correlation coefficient (ICC) showed that all measurements (ICC > 0.90 for all measurements) had good reliability and validity. The real part of impedance (R) and the imaginary part of impedance (X) of a tissue measured close to the pressure sore site was found to be significantly smaller (p pressure sore site at a specific frequency range (R: 30.00-38.55 Hz; X: 43.95-606.40 Hz). It was also found that the extracellular resistance (R(e)) and the ratio of extracellular resistance to intracellular resistance (R(e)/R(i)) of a tissue measured close to the pressure sore site were significantly smaller (p pressure sore site. Since the electrical properties (R, X, R(e), R(e)/R(i) ) of a tissue close to, and away from, the pressure sore site can be significantly distinguished, a potentially promising method for the screening of pressure sores at an early stage has been proposed.

  16. Cell type-specific properties and environment shape tissue specificity of cancer genes.

    Science.gov (United States)

    Schaefer, Martin H; Serrano, Luis

    2016-02-09

    One of the biggest mysteries in cancer research remains why mutations in certain genes cause cancer only at specific sites in the human body. The poor correlation between the expression level of a cancer gene and the tissues in which it causes malignant transformations raises the question of which factors determine the tissue-specific effects of a mutation. Here, we explore why some cancer genes are associated only with few different cancer types (i.e., are specific), while others are found mutated in a large number of different types of cancer (i.e., are general). We do so by contrasting cellular functions of specific-cancer genes with those of general ones to identify properties that determine where in the body a gene mutation is causing malignant transformations. We identified different groups of cancer genes that did not behave as expected (i.e., DNA repair genes being tissue specific, immune response genes showing a bimodal specificity function or strong association of generally expressed genes to particular cancers). Analysis of these three groups demonstrates the importance of environmental impact for understanding why certain cancer genes are only involved in the development of some cancer types but are rarely found mutated in other types of cancer.

  17. Monitoring microvascular free flaps with tissue oxygen measurement and PET.

    Science.gov (United States)

    Schrey, Aleksi R; Kinnunen, Ilpo A J; Grénman, Reidar A; Minn, Heikki R I; Aitasalo, Kalle M J

    2008-07-01

    Tissue oxygen measurement and positron emission tomography (PET) were evaluated as methods for predicting ischemia in microvascular free flaps of the head and neck. Ten patients with head and neck squamous cell cancer underwent resection of the tumour followed by microvascular reconstruction with a free flap. Tissue oxygenation of the flap (P(ti)O(2)) was continuously monitored for three postoperative (POP) days and the blood flow of the flap was assessed using oxygen-15 labelled water and PET. In three free flaps a perfusion problem was suspected due to a remarkable drop in P(ti)O(2)-values, due to two anastomosis problems and due to POP turgor. No flap losses occurred. During the blood flow measurements with PET [mean 8.5 mL 100 g(-1) min(-1 )(SD 2.5)], the mean P(ti)O(2) of the flaps [46.8 mmHg (SD 17.0)] appeared to correlate with each other in each patient (pmonitoring system of free flaps. The perfusion-study with PET correlates with P(ti)O(2)-measurement.

  18. Online monitoring of cartilage tissue in a novel bioreactor

    Science.gov (United States)

    von der Burg, E.; von Buttlar, M.; Grill, W.

    2011-04-01

    Standard techniques for the analysis of biological tissues like immunohistochemical staining are typically invasive and lead to mortification of cells. Non-invasive monitoring is an important element of regenerative medicine because implants and components of implants should be 100% quality-checked with non-invasive and therefore also marker-free methods. We report on a new bioreactor for the production of collagen scaffolds seeded with Mesenchymal Stem Cells (MSCs). It contains a computer controlled mechanical activation and ultrasonic online monitoring and has been constructed for the in situ determination of ultrasonic and rheological parameters. During the cultivation period of about two weeks the scaffold is periodically compressed by two movable pistons for improved differentiation of the MSCs. This periodic compression beneficially ensures the supply with nutrition even inside the sample. During the physiological stimuli, rheological properties are measured by means of highly sensitive load cells. In addition measurements of the speed of sound in the sample and in the culture medium, with frequencies up to 16 MHz, are performed continuously. Therefore piezoceramic transducers are attached to the pistons and emit and detect ultrasonic waves, travelling through the pistons, the sample and the culture medium. The time-of-flight (TOF) of the ultrasonic signals is determined in real time with the aid of chirped excitation and correlation procedures with a resolution of at least 10 ps. The implemented ultrasonic measurement scheme allows beside the speed of sound measurements the detection of the distance between the pistons with a resolution better than 100 nm. The developed monitoring delivers information on rigidity, fluid dynamics and velocity of sound in the sample and in the culture medium. The hermetically sealed bioreactor with its life support system provides a biocompatible environment for MSCs for long time cultivation.

  19. Tissue-specific Differentiation Potency of Mesenchymal Stromal Cells from Perinatal Tissues.

    Science.gov (United States)

    Kwon, Ahlm; Kim, Yonggoo; Kim, Myungshin; Kim, Jiyeon; Choi, Hayoung; Jekarl, Dong Wook; Lee, Seungok; Kim, Jung Min; Shin, Jong-Chul; Park, In Yang

    2016-04-05

    Human perinatal tissue is an abundant source of mesenchymal stromal cells(MSCs) and lacks the ethical concerns. Perinatal MSCs can be obtained from various tissues as like amnion, chorion, and umbilical cord. Still, little is known of the distinct nature of each MSC type. In this study, we successfully isolated and cultured MSCs from amnion(AMSCs), chorion(CMSCs), and umbilical cord(UC-MSCs). Proliferation potential was different among them, that AMSCs revealed the lowest proliferation rate due to increased Annexin V and senescence-associated β-galactosidase positive cells. We demonstrated distinct characteristic gene expression according to the source of the original tissue using microarray. In particular, genes associated with apoptosis and senescence including CDKN2A were up-regulated in AMSCs. In CMSCs, genes associated with heart morphogenesis and blood circulation including HTR2B were up-regulated. Genes associated with neurological system processes including NPY were up-regulated in UC-MSCs. Quantitative RT-PCR confirmed the gene expression data. And in vitro differentiation of MSCs demonstrated that CMSCs and UC-MSCs had a more pronounced ability to differentiate into cardiomyocyte and neural cells, respectively. This study firstly demonstrated the innate tissue-specific differentiation potency of perinatal MSCs which can be helpful in choosing more adequate cell sources for better outcome in a specific disease.

  20. Glow in the dark: fluorescent proteins as cell and tissue-specific markers in plants.

    Science.gov (United States)

    Ckurshumova, Wenzislava; Caragea, Adriana E; Goldstein, Rochelle S; Berleth, Thomas

    2011-09-01

    Since the hallmark discovery of Aequorea victoria's Green Fluorescent Protein (GFP) and its adaptation for efficient use in plants, fluorescent protein tags marking expression profiles or genuine proteins of interest have been used to recognize plant tissues and cell types, to monitor dynamic cell fate selection processes, and to obtain cell type-specific transcriptomes. Fluorescent tagging enabled visualization in living tissues and the precise recordings of dynamic expression pattern changes. The resulting accurate recording of cell fate acquisition kinetics in space and time has strongly stimulated mathematical modeling of self-organizing feedback mechanisms. In developmental studies, the use of fluorescent proteins has become critical, where morphological markers of tissues, cell types, or differentiation stages are either not known or not easily recognizable. In this review, we focus on the use of fluorescent markers to identify and illuminate otherwise invisible cell states in plant development.

  1. Glow in the Dark: Fluorescent Proteins as Cell and Tissue-Specific Markers in Plants

    Institute of Scientific and Technical Information of China (English)

    Wenzislava Ckurshumova; Adriana E. Caragea; Rochelle S. Goldstein; Thomas Berleth

    2011-01-01

    Since the hallmark discovery of Aequorea victoria's Green Fluorescent Protein (GFP) and its adaptation for efficient use in plants,fluorescent protein tags marking expression profiles or genuine proteins of interest have been used to recognize plant tissues and cell types,to monitor dynamic cell fate selection processes,and to obtain cell type-specific transcriptomes.Fluorescent tagging enabled visualization in living tissues and the precise recordings of dynamic expression pattern changes.The resulting accurate recording of cell fate acquisition kinetics in space and time has strongly stimulated mathematical modeling of self-organizing feedback mechanisms.In developmental studies,the use of fluorescent proteins has become critical,where morphological markers of tissues,cell types,or differentiation stages are either not known or not easily recognizable.In this review,we focus on the use of fluorescent markers to identify and illuminate otherwise invisible cell states in plant development.

  2. Reality monitoring impairment in schizophrenia reflects specific prefrontal cortex dysfunction

    Directory of Open Access Journals (Sweden)

    Jane R. Garrison

    2017-01-01

    Full Text Available Reality monitoring impairment is often reported in schizophrenia but the neural basis of this deficit is poorly understood. Difficulties with reality monitoring could be attributable to the same pattern of neural dysfunction as other cognitive deficits that characterize schizophrenia, or might instead represent a separable and dissociable impairment. This question was addressed through direct comparison of behavioral performance and neural activity associated with reality monitoring and working memory in patients with schizophrenia and matched healthy controls. Participants performed a word-pair reality monitoring task and a Sternberg working memory task while undergoing fMRI scanning. Distinct behavioral deficits were observed in the patients during performance of each task, which were associated with separable task- and region-specific dysfunction in the medial anterior prefrontal cortex for reality monitoring and dorsolateral prefrontal cortex for working memory. The results suggest that reality monitoring impairment is a distinct neurocognitive deficit in schizophrenia. The findings are consistent with the presence of a range of dissociable cognitive deficits in schizophrenia which may be associated with variable functional and structural dysconnectivity in underlying processing networks.

  3. A hierarchy of ECM-mediated signalling tissue-specific gene expression regulates tissue-specific gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Roskelley, Calvin D; Srebrow, Anabella; Bissell, Mina J

    1995-10-07

    A dynamic and reciprocal flow of information between cells and the extracellular matrix contributes significantly to the regulation of form and function in developing systems. Signals generated by the extracellular matrix do not act in isolation. Instead, they are processed within the context of global signalling hierarchies whose constituent inputs and outputs are constantly modulated by all the factors present in the cell's surrounding microenvironment. This is particularly evident in the mammary gland, where the construction and subsequent destruction of such a hierarchy regulates changes in tissue-specific gene expression, morphogenesis and apoptosis during each developmental cycle of pregnancy, lactation and involution.

  4. Tissue-specific insulin signaling mediates female sexual attractiveness.

    Directory of Open Access Journals (Sweden)

    Tatyana Y Fedina

    2017-08-01

    Full Text Available Individuals choose their mates so as to maximize reproductive success, and one important component of this choice is assessment of traits reflecting mate quality. Little is known about why specific traits are used for mate quality assessment nor about how they reflect it. We have previously shown that global manipulation of insulin signaling, a nutrient-sensing pathway governing investment in survival versus reproduction, affects female sexual attractiveness in the fruit fly, Drosophila melanogaster. Here we demonstrate that these effects on attractiveness derive from insulin signaling in the fat body and ovarian follicle cells, whose signals are integrated by pheromone-producing cells called oenocytes. Functional ovaries were required for global insulin signaling effects on attractiveness, and manipulations of insulin signaling specifically in late follicle cells recapitulated effects of global manipulations. Interestingly, modulation of insulin signaling in the fat body produced opposite effects on attractiveness, suggesting a competitive relationship with the ovary. Furthermore, all investigated tissue-specific insulin signaling manipulations that changed attractiveness also changed fecundity in the corresponding direction, pointing to insulin pathway activity as a reliable link between fecundity and attractiveness cues. The cues themselves, cuticular hydrocarbons, responded distinctly to fat body and follicle cell manipulations, indicating independent readouts of the pathway activity from these two tissues. Thus, here we describe a system in which female attractiveness results from an apparent connection between attractiveness cues and an organismal state of high fecundity, both of which are created by lowered insulin signaling in the fat body and increased insulin signaling in late follicle cells.

  5. Strategies for experiment-specific monitoring in the Grid

    CERN Document Server

    Mendez Lorenzo, Patricia; Campana, Simone; Santinelli, Roberto; Lanciotti, Elisa; Miccio, Enzo; Magini, Nicolo; Di Girolamo, Alessandro

    2008-01-01

    This contribution describes how the LHC experiments implement their own Grid resource monitoring, either by internally developed tools, or by reusing tools used for Grid operations, like the Service Availability Monitor (SAM) used for the EGEE operations. The LHC experiments perform most, if not all, of their computing activities on Grid resources. This requires an accurate and updated picture of the status of the Grid services used by them, and of the services which are specific to the experiment. To achieve this, a common method is to periodically execute tests on the services, where the functionalities tested may be different from a VO to another. The SAM framework, developed for the EGEE operations, can be easily used to run and publish the results of arbitrary tests, from basic functionality tests, to high-level operations from real production activities. This contribution describes in detail how the monitoring system of each LHC experiment has taken advantage of SAM. The work covered by this contributio...

  6. Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

    Directory of Open Access Journals (Sweden)

    Peter Smibert

    2012-03-01

    Full Text Available We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA in Drosophila melanogaster by using >1 billion reads of stranded mRNA-seq across a variety of dissected tissues. Beyond demonstrating that a majority of fly transcripts are subject to APA, we observed broad trends for 3′ untranslated region (UTR shortening in the testis and lengthening in the central nervous system (CNS; the latter included hundreds of unannotated extensions ranging up to 18 kb. Extensive northern analyses validated the accumulation of full-length neural extended transcripts, and in situ hybridization indicated their spatial restriction to the CNS. Genes encoding RNA binding proteins (RBPs and transcription factors were preferentially subject to 3′ UTR extensions. Motif analysis indicated enrichment of miRNA and RBP sites in the neural extensions, and their termini were enriched in canonical cis elements that promote cleavage and polyadenylation. Altogether, we reveal broad tissue-specific patterns of APA in Drosophila and transcripts with unprecedented 3′ UTR length in the nervous system.

  7. SLALOM: a Language for SLA specification and monitoring

    CERN Document Server

    Correia, Anacleto; Amaral, Vasco

    2011-01-01

    IT services provisioning is usually underpinned by service level agreements (SLAs), aimed at guaranteeing services quality. However, there is a gap between the customer perspective (business oriented) and that of the service provider (implementation oriented) that becomes more evident while defining and monitoring SLAs. This paper proposes a domain specific language (SLA Language for specificatiOn and Monitoring - SLALOM) to bridge the previous gap. The first step in SLALOM creation was factoring out common concepts, by composing the BPMN metamodel with that of the SLA life cycle, as described in ITIL. The derived metamodel expresses the SLALOM abstract syntax model. The second step was to write concrete syntaxes targeting different aims, such as SLA representation in process models. An example of SLALOM's concrete syntax model instantiation for an IT service sup-ported by self-service financial terminals is presented.

  8. Tissue viability monitoring: a multi-sensor wearable platform approach

    Science.gov (United States)

    Mathur, Neha; Davidson, Alan; Buis, Arjan; Glesk, Ivan

    2016-12-01

    Health services worldwide are seeking ways to improve patient care for amputees suffering from diabetes, and at the same time reduce costs. The monitoring of residual limb temperature, interface pressure and gait can be a useful indicator of tissue viability in lower limb amputees especially to predict the occurrence of pressure ulcers. This is further exacerbated by elevated temperatures and humid micro environment within the prosthesis which encourages the growth of bacteria and skin breakdown. Wearable systems for prosthetic users have to be designed such that the sensors are minimally obtrusive and reliable enough to faithfully record movement and physiological signals. A mobile sensor platform has been developed for use with the lower limb prosthetic users. This system uses an Arduino board that includes sensors for temperature, gait, orientation and pressure measurements. The platform transmits sensor data to a central health authority database server infrastructure through the Bluetooth protocol at a suitable sampling rate. The data-sets recorded using these systems are then processed using machine learning algorithms to extract clinically relevant information from the data. Where a sensor threshold is reached a warning signal can be sent wirelessly together with the relevant data to the patient and appropriate medical personnel. This knowledge is also useful in establishing biomarkers related to a possible deterioration in a patient's health or for assessing the impact of clinical interventions.

  9. Monitoring the marine environment using marine mammal tissue samples

    Energy Technology Data Exchange (ETDEWEB)

    Jones, P.D.; Hannah, D.J.; Day, P.J. [ESR:Environmental, Lower Hutt (New Zealand)] [and others

    1995-12-31

    Marine environments, both inshore and open ocean, receive numerous inputs of anthropogenic chemicals. Cetaceans provide a valuable resource for monitoring the low level contamination of marine environments with persistent organic contaminants. Comparative studies using inshore and offshore southern ocean cetaceans have revealed significant differences in the types of contamination in these two environments. The polychlorinated biphenyls (PCBs) deposited in the southern oceans are characterized by an abundance of lower chlorinated congeners. Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) are not present at significant concentrations in cetaceans from the open southern ocean. In contrast significant concentrations of PCDD/F congeners are detected in the blubber of the inshore living Hector`s dolphin. This species lives close to the shore and has a very small home range (approximately 30 km) for a cetacean. Analysis of tissue PCDD/F and PCB profiles from different populations and their food sources will be presented. The data are being used to determine if there are local variations in the contamination of the New Zealand inshore marine environment.

  10. Monitoring of Physicochemical Changes in Frozen Fish Muscle Tissue

    Directory of Open Access Journals (Sweden)

    František Ježek

    2011-10-01

    Full Text Available The aim of the study was to monitor physicochemical parameters (pH, nitrogen trimethylamine N-TMA, total volatile basic nitrogen TVBN, free fatty acids FFA, peroxide value and thiobarbituric acid assay TBA of postmortal changes in muscle tissue of silver carp (Hypophthalmichthys molitrix during a period of storage at -18°C. Fresh silver carp samples and samples aft er three, six, nine and 12 months of storage were tested. The degree of acidification during the experiment was insignificant (P > 0.05. Proteolytic changes were almost stopped and TVBN levels remained unchanged (P > 0.05, while N-TMA levels fluctuated significantly (P < 0.01 between months 3 and 12. The essential were lipid hydrolysis and oxidation, which caused a significant increase in FFA values (5.89 ± 0.99% total lipids as oleic acid, peroxides (9.90 ± 2.83 mekv O2.kg-1 and TBA values (50.76 ± 31.52 mg MDA.kg-1. The shelf life recommended for silver carp was set at three months.

  11. Monitoring of Physicochemical Changes in Frozen Fish Muscle Tissue

    Directory of Open Access Journals (Sweden)

    František Ježek

    2011-09-01

    Full Text Available The aim of the study was to monitor physicochemical parameters (pH, nitrogen trimethylamine N-TMA, total volatile basic nitrogen TVBN, free fatty acids FFA, peroxide value and thiobarbituric acid assay TBA of postmortal changes in muscle tissue of silver carp (Hypophthalmichthys molitrix during a period of storage at -18°C. Fresh silver carp samples and samples aft er three, six, nine and 12 months of storage were tested. The degree of acidification during the experiment was insignificant (P > 0.05. Proteolytic changes were almost stopped and TVBN levels remained unchanged (P > 0.05, while N-TMA levels fluctuated significantly (P < 0.01 between months 3 and 12. The essential were lipid hydrolysis and oxidation, which caused a significant increase in FFA values (5.89 ± 0.99% total lipids as oleic acid, peroxides (9.90 ± 2.83 mekv O2.kg-1 and TBA values (50.76 ± 31.52 mg MDA.kg-1. The shelf life recommended for silver carp was set at three months.

  12. Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq.

    Science.gov (United States)

    Zhu, Jinhang; Chen, Geng; Zhu, Sibo; Li, Suqing; Wen, Zhuo; Bin Li; Zheng, Yuanting; Shi, Leming

    2016-06-22

    Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions.

  13. Importance of good manufacturing practices in microbiological monitoring in processing human tissues for transplant.

    Science.gov (United States)

    Pianigiani, Elisa; Ierardi, Francesca; Fimiani, Michele

    2013-12-01

    Skin allografts represent an important therapeutic resource in the treatment of severe skin loss. The risk associated with application of processed tissues in humans is very low, however, human material always carries the risk of disease transmission. To minimise the risk of contamination of grafts, processing is carried out in clean rooms where air quality is monitored. Procedures and quality control tests are performed to standardise the production process and to guarantee the final product for human use. Since we only validate and distribute aseptic tissues, we conducted a study to determine what type of quality controls for skin processing are the most suitable for detecting processing errors and intercurrent contamination, and for faithfully mapping the process without unduly increasing production costs. Two different methods for quality control were statistically compared using the Fisher exact test. On the basis of the current study we selected our quality control procedure based on pre- and post-processing tissue controls, operator and environmental controls. Evaluation of the predictability of our control methods showed that tissue control was the most reliable method of revealing microbial contamination of grafts. We obtained 100 % sensitivity by doubling tissue controls, while maintaining high specificity (77 %).

  14. Sharing and Specificity of Co-expression Networks across 35 Human Tissues.

    Science.gov (United States)

    Pierson, Emma; Koller, Daphne; Battle, Alexis; Mostafavi, Sara; Ardlie, Kristin G; Getz, Gad; Wright, Fred A; Kellis, Manolis; Volpi, Simona; Dermitzakis, Emmanouil T

    2015-05-01

    To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes. However, a small number of samples are available for a majority of the tissues, and therefore statistical inference of networks in this setting is highly underpowered. To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related tissues. We show that this transfer learning approach increases the accuracy with which networks are learned. Analysis of these networks reveals that tissue-specific transcription factors are hubs that preferentially connect to genes with tissue specific functions. Additionally, we observe that genes with tissue-specific functions lie at the peripheries of our networks. We identify numerous modules enriched for Gene Ontology functions, and show that modules conserved across tissues are especially likely to have functions common to all tissues, while modules that are upregulated in a particular tissue are often instrumental to tissue-specific function. Finally, we provide a web tool, available at mostafavilab.stat.ubc.ca/GNAT, which allows exploration of gene function and regulation in a tissue-specific manner.

  15. Sharing and Specificity of Co-expression Networks across 35 Human Tissues.

    Directory of Open Access Journals (Sweden)

    Emma Pierson

    2015-05-01

    Full Text Available To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes. However, a small number of samples are available for a majority of the tissues, and therefore statistical inference of networks in this setting is highly underpowered. To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related tissues. We show that this transfer learning approach increases the accuracy with which networks are learned. Analysis of these networks reveals that tissue-specific transcription factors are hubs that preferentially connect to genes with tissue specific functions. Additionally, we observe that genes with tissue-specific functions lie at the peripheries of our networks. We identify numerous modules enriched for Gene Ontology functions, and show that modules conserved across tissues are especially likely to have functions common to all tissues, while modules that are upregulated in a particular tissue are often instrumental to tissue-specific function. Finally, we provide a web tool, available at mostafavilab.stat.ubc.ca/GNAT, which allows exploration of gene function and regulation in a tissue-specific manner.

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

    Science.gov (United States)

    Hench, Jürgen; Bratić Hench, Ivana; Pujol, Claire; Ipsen, Sabine; Brodesser, Susanne; Mourier, Arnaud; Tolnay, Markus; Frank, Stephan; Trifunović, Aleksandra

    2011-01-01

    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.

  18. A C++ framework for creating tissue specific segmentation-pipelines

    Science.gov (United States)

    Pfeifer, Bernhard; Hanser, Friedrich; Seger, Michael; Hintermueller, Christoph; Modre-Osprian, Robert; Fischer, Gerald; Muehlthaler, Hannes; Trieb, Thomas; Tilg, Bernhard

    2005-04-01

    For a clinical application of the inverse problem of electrocardiography, a flexible and fast generation of a patient's volume conductor model is essential. The volume conductor model includes compartments like chest, lungs, ventricles, atria and the associated blood masses. It is a challenging task to create an automatic or semi-automatic segmentation procedure for each compartment. For the extraction of the lungs, as one example, a region growing algorithm can be used, to extract the blood masses of the ventricles Active Appearance Models may succeed, and to construct the atrial myocardium a multiplicity of operations are necessary. These examples illustrate that there is no common method that will succeed for all compartments like a least common denominator. Another problem is the automatization of combining different methods and the origination of a segmentation pipeline in order to extract a compartment and, accordingly, the desired model - in our case the complete volume conductor model for estimating the spread of electrical excitation in the patient's heart. On account of this, we developed a C++ framework and a special application with the goal of creating tissue-specific segmentation pipelines. The C++ framework uses different standard frameworks like DCMTK for handling medical images (http://dicom.offis.de/dcmtk.php.en), ITK (http://www.itk.org/) for some segmentation methods, and Qt (http://www.trolltech.com/) for creating user interfaces. Our Medical Segmentation Toolkit (MST) enables to combine different segmentation techniques for each compartment. In addition, the framework enables to create user-defined compartment pipelines.

  19. Tissue-specific posttranslational modification allows functional targeting of thyrotropin.

    Science.gov (United States)

    Ikegami, Keisuke; Liao, Xiao-Hui; Hoshino, Yuta; Ono, Hiroko; Ota, Wataru; Ito, Yuka; Nishiwaki-Ohkawa, Taeko; Sato, Chihiro; Kitajima, Ken; Iigo, Masayuki; Shigeyoshi, Yasufumi; Yamada, Masanobu; Murata, Yoshiharu; Refetoff, Samuel; Yoshimura, Takashi

    2014-11-06

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. The development of power specific redlines for SSME safety monitoring

    Science.gov (United States)

    Maul, William A.; Bosch, Claudia M.

    1989-01-01

    Over the past several years, there has been an increased awareness in the necessity for rocket engine health monitoring because of the cost and complexity of present and future systems. A current rocket engine system, the Space Shuttle Main Engine (SSME), combines a limited redline system with closed-loop control of the engine's thrust level and mixture ratio. Despite these features, 27 tests of the SSME have resulted in major incidents. An SSME transient model was used to examine the effect of variations in high pressure turbopump performance on various engine parameters. Based on analysis of the responses, several new parameters are proposed for further investigation as power-level specific redlines.

  2. Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues.

    Science.gov (United States)

    Ghosh, Srimoyee; Yates, Allan J; Frühwald, Michael C; Miecznikowski, Jeffrey C; Plass, Christoph; Smiraglia, Dominic

    2010-08-16

    Although most CpG islands are generally thought to remain unmethylated in all adult somatic tissues, recent genome-wide approaches have found that some CpG islands have distinct methylation patterns in various tissues, with most differences being seen between germ cells and somatic tissues. Few studies have addressed this among human somatic tissues and fewer still have studied the same sets of tissues from multiple individuals. In the current study, we used Restriction Landmark Genomic Scanning to study tissue specific methylation patterns in a set of twelve human tissues collected from multiple individuals. We identified 34 differentially methylated CpG islands among these tissues, many of which showed consistent patterns in multiple individuals. Of particular interest were striking differences in CpG island methylation, not only among brain regions, but also between white and grey matter of the same region. These findings were confirmed for selected loci by quantitative bisulfite sequencing. Cluster analysis of the RLGS data indicated that several tissues clustered together, but the strongest clustering was in brain. Tissues from different brain regions clustered together, and, as a group, brain tissues were distinct from either mesoderm or endoderm derived tissues which demonstrated limited clustering. These data demonstrate consistent tissue specific methylation for certain CpG islands, with clear differences between white and grey matter of the brain. Furthermore, there was an overall pattern of tissue specifically methylated CpG islands that distinguished neural tissues from non-neural.

  3. De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies.

    Science.gov (United States)

    Leung, Priscilla T Y; Ip, Jack C H; Mak, Sarah S T; Qiu, Jian Wen; Lam, Paul K S; Wong, Chris K C; Chan, Leo L; Leung, Kenneth M Y

    2014-09-19

    The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome database from the tissues of adductor muscle, gills and the hepatopancreas of P. viridis in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses in this sentinel species. Illumina sequencing results yielded 544,272,542 high-quality filtered reads. After de novo assembly using Trinity, 233,257 contigs were generated with an average length of 1,264 bp and an N50 length of 2,868 bp; 192,879 assembled transcripts and 150,111 assembled unigenes were obtained after clustering. A total of 93,668 assembled transcripts (66,692 assembled genes) with putative functions for protein domains were predicted based on InterProScan analysis. Based on similarity searches, 44,713 assembled transcripts and 25,319 assembled unigenes were annotated with at least one BLAST hit. A total of 21,262 assembled transcripts (11,947 assembled genes) were annotated with at least one well-defined Gene Ontology (GO) and 5,131 assembled transcripts (3,181 assembled unigenes) were assigned to 329 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The quantity of assembled unigenes and transcripts obtained from male and female mussels were similar but varied among the three studied tissues, with the highest numbers recorded in the gills, followed by the hepatopancreas, and then the adductor muscle. Multivariate analyses revealed strong tissue-specific patterns among the three different tissues, but not between sexes in terms of expression profiles for annotated genes in various GO terms, and genes associated with stress responses and degradation of xenobiotics. The expression profiles of certain selected genes in each tissue type were further

  4. Specific expression of bioluminescence reporter gene in cardiomyocyte regulated by tissue specific promoter

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Vu Hong; Tae, Seong Ho; Le, Nguyen Uyen Chi; Min, Jung Joon [Chonnam National University Medical School, Gwangju (Korea, Republic of)

    2007-07-01

    As the human heart is not capable of regenerating the great numbers of cardiac cells that are lost after myocardial infarction, impaired cardiac function is the inevitable result of ischemic disease. Recently, human embryonic stem cells (hESCs) have gained popularity as a potentially ideal cell candidate for tissue regeneration. In particular, hESCs are capable of cardiac lineage-specific differentiation and confer improvement of cardiac function following transplantation into animal models. Although such data are encouraging, the specific strategy for in vivo and non-invasive detection of differentiated cardiac lineage is still limited. Therefore, in the present study, we established the gene construction in which the optical reporter gene Firefly luciferase was controlled by Myosin Heavy Chain promoter for specific expressing in heart cells. The vector consisting of - MHC promoter and a firefly luciferase coding sequence flanked by full-length bovine growth hormone (BGH) 3'-polyadenylation sequence based on pcDNA3.1- vector backbone. To test the specific transcription of this promoter in g of MHC-Fluc or CMV-Flue (for control) plasmid DNA in myocardial tissue, 20 phosphate-buffered saline was directly injected into mouse myocardium through a midline sternotomy and liver. After 1 week of injection, MHC-Fluc expression was detected from heart region which was observed under cooled CCD camera of in vivo imaging system but not from liver. In control group injected with CMV-Flue, the bioluminescence was detected from all these organs. The expression of Flue under control of Myosin Heavy Chain promoter may become a suitable optical reporter gene for stem cell-derived cardiac lineage differentiation study.

  5. Detection of tissue-specific effects by methotrexate on differentiating mouse embryonic stem cells.

    Science.gov (United States)

    Pellizzer, Cristian; Bello, Ezia; Adler, Sarah; Hartung, Thomas; Bremer, Susanne

    2004-10-01

    Pluripotent embryonic stem (ES) cells offer a unique possibility to monitor the differentiation of several cell types in vitro. This study attempts to identify marker genes during in vitro cell differentiation of murine ES cells and allow a prediction of chemical effects on cell differentiation of specific target tissues. The study focused on the expression pattern of key genes involved in cardiomyocyte and osteoblast differentiation: Oct-4, Brachyury, Nkx2.5, alpha myosin heavy chain, Cbfa1, and Osteocalcin. Methotrexate was selected due to its well-characterized teratogenic effects. Several in vivo studies have demonstrated the specific interactions of methotrexate with bone formation whereas the cardiovascular system is not specifically affected after exposure to low concentration. The capability of murine ES cells to differentiate in vitro into cardiomyocytes as well as into osteoblasts have been used to demonstrate the target cell specificity in vitro, at non-cytotoxic concentration. Exposure of differentiating ES cells did not result in any gene profile modification of the selected cardiomyocyte specific genes, whereas the expression of osteoblast specific key genes, Cbfa1 and Osteocalcin, decreased. At the latter stages of skeletal differentiation we observed a 30% decrease in gene expression for Cbfa1 and a 60% decrease for Osteocalcin, with reference to the control. Early marker genes for undifferentiated cells and mesodermal cells were not modified after methotrexate treatment. These results show the possibility to integrate specific in vitro tests for teratogenicity in a test strategy for developmental toxicity. 2004 Wiley-Liss, Inc.

  6. Tissue-specific designs of stem cell hierarchies

    NARCIS (Netherlands)

    Visvader, Jane E; Clevers, Hans

    Recent work in the field of stem cell biology suggests that there is no single design for an adult tissue stem cell hierarchy, and that different tissues employ distinct strategies to meet their self-renewal and repair requirements. Stem cells may be multipotent or unipotent, and can exist in

  7. Tissue-specific designs of stem cell hierarchies

    NARCIS (Netherlands)

    Visvader, Jane E; Clevers, Hans

    2016-01-01

    Recent work in the field of stem cell biology suggests that there is no single design for an adult tissue stem cell hierarchy, and that different tissues employ distinct strategies to meet their self-renewal and repair requirements. Stem cells may be multipotent or unipotent, and can exist in quiesc

  8. Tissue-specific stem cells: friend or foe?

    Institute of Scientific and Technical Information of China (English)

    Joerg Huelsken

    2009-01-01

    @@ In the face of a hostile environ-ment, the integrity of many tissues in the adult organism is maintained by a constant replacement of cells. This involves a hierarchical organization of the tissue with rare multi-potent stem cells giving rise to proliferating cells of limited proliferative capacity which in turn produce differentiating cells.

  9. Scrapie-specific pathology of sheep lymphoid tissues.

    Directory of Open Access Journals (Sweden)

    Gillian McGovern

    Full Text Available Transmissible spongiform encephalopathies (TSEs or prion diseases often result in accumulation of disease-associated PrP (PrP(d in the lymphoreticular system (LRS, specifically in association with follicular dendritic cells (FDCs and tingible body macrophages (TBMs of secondary follicles. We studied the effects of sheep scrapie on lymphoid tissue in tonsils and lymph nodes by light and electron microscopy. FDCs of sheep were grouped according to morphology as immature, mature or regressing. Scrapie was associated with FDC dendrite hypertrophy and electron dense deposit or vesicles. PrP(d was located using immunogold labelling at the plasmalemma of FDC dendrites and, infrequently, mature B cells. Abnormal electron dense deposits surrounding FDC dendrites were identified as immunoglobulins suggesting that excess immune complexes are retained and are indicative of an FDC dysfunction. Within scrapie-affected lymph nodes, macrophages outside the follicle and a proportion of germinal centre TBMs accumulated PrP(d within endosomes and lysosomes. In addition, TBMs showed PrP(d in association with the cell membrane, non-coated pits and vesicles, and also with discrete, large and random endoplasmic reticulum networks, which co-localised with ubiquitin. These observations suggest that PrP(d is internalised via the caveolin-mediated pathway, and causes an abnormal disease-related alteration in endoplasmic reticulum structure. In contrast to current dogma, this study shows that sheep scrapie is associated with cytopathology of germinal centres, which we attribute to abnormal antigen complex trapping by FDCs and abnormal endocytic events in TBMs. The nature of the sub-cellular changes in FDCs and TBMs differs from those of scrapie infected neurones and glial cells suggesting that different PrP(d/cell membrane interactions occur in different cell types.

  10. Measurement of tissue optical properties with optical coherence tomography: Implication for noninvasive blood glucose concentration monitoring

    Science.gov (United States)

    Larin, Kirill V.

    Approximately 14 million people in the USA and more than 140 million people worldwide suffer from diabetes mellitus. The current glucose sensing technique involves a finger puncture several times a day to obtain a droplet of blood for analysis. There have been enormous efforts by many scientific groups and companies to quantify glucose concentration noninvasively using different optical techniques. However, these techniques face limitations associated with low sensitivity, accuracy, and insufficient specificity of glucose concentrations over a physiological range. Optical coherence tomography (OCT), a new technology, is being applied for noninvasive imaging in tissues with high resolution. OCT utilizes sensitive detection of photons coherently scattered from tissue. The high resolution of this technique allows for exceptionally accurate measurement of tissue scattering from a specific layer of skin compared with other optical techniques and, therefore, may provide noninvasive and continuous monitoring of blood glucose concentration with high accuracy. In this dissertation work I experimentally and theoretically investigate feasibility of noninvasive, real-time, sensitive, and specific monitoring of blood glucose concentration using an OCT-based biosensor. The studies were performed in scattering media with stable optical properties (aqueous suspensions of polystyrene microspheres and milk), animals (New Zealand white rabbits and Yucatan micropigs), and normal subjects (during oral glucose tolerance tests). The results of these studies demonstrated: (1) capability of the OCT technique to detect changes in scattering coefficient with the accuracy of about 1.5%; (2) a sharp and linear decrease of the OCT signal slope in the dermis with the increase of blood glucose concentration; (3) the change in the OCT signal slope measured during bolus glucose injection experiments (characterized by a sharp increase of blood glucose concentration) is higher than that measured in

  11. Human keratin diseases: hereditary fragility of specific epithelial tissues.

    Science.gov (United States)

    Corden, L D; McLean, W H

    1996-12-01

    Keratins are heteropolymeric proteins which form the intermediate filament cytoskeleton in epithelial cells. Since 1991, mutations in several keratin genes have been found to cause a variety of human diseases affecting the epidermis and other epithelial structures. Epidermolysis bullosa simplex (EBS) was the first mechanobullous disease for which the underlying genetic lesion was found, with mutations in both the K5 and K14 genes rendering basal epidermal keratinocytes less resilient to trauma, resulting in skin fragility. The site of mutation in the keratin protein correlates with phenotypic severity in this disorder. Since mutations were identified in the basal cell keratins, the total number of keratin genes associated with diseases has risen to eleven. The rod domains of suprabasal keratins K1 and K10 are mutated in bullous congenital ichthyosiform erythroderma (BCIE; also called epidermolytic hyperkeratosis, EH) and mosaicism for K1/K10 mutations results in a nevoid distribution of EH. An unusual mutation in the VI domain of K1 has also been found to cause diffuse non-epidermolytic palmoplantar keratoderma (DNEPPK). Mutations in palmoplantar specific keratin K9 cause epidermolytic palmoplantar keratoderma (EPPK) and mutations in the late differentiation suprabasal keratin K2e cause ichthyosis bullosa of Siemens (IBS). In the last year or so, mutations were discovered in differentiation specific keratins K6a and K16 causing pachyonychia congenita type 1 and K17 mutations occur in pachyonychia congenita type 2. K16 and K17 mutations have also been reported to produce phenotypes with little or no nail changes: K16 mutations can present as focal non-epidermolytic palmoplantar keratoderma (NEPPK) and K17 mutations can result in a phenotype resembling steatocystoma multiplex. Recently, mutation of mucosal keratin pair K4 and K13 has been shown to underlie white sponge nevus (WSN). This year, the first mutations in a keratin-associated protein, plectin, were shown to

  12. Tissue-Specific Expression of the Chicken Calpain2 Gene

    Directory of Open Access Journals (Sweden)

    Zeng-Rong Zhang

    2010-01-01

    Full Text Available We quantified chicken calpain 2 (CAPN2 expression in two Chinese chicken breeds (mountainous black-bone chicken breed [MB] and a commercial meat type chicken breed [S01] to discern the tissue and ontogenic expression pattern and its effect on muscle metabolism. Real-time quantitative PCR assay was developed for accurate measurement of the CAPN2 mRNA expression in various tissues from chickens of different ages (0, 2, 4, 6, 8, 10, and 12 weeks. Results showed that the breast muscle and leg muscle tissues had the highest expression of CAPN2 compared to the other tissues from the same individual (P<.05. Overall, the CAPN2 mRNA level exhibited a “rise” developmental change in all tissues. The S01 chicken had a higher expression of the CAPN2 mRNA in all tissues than the MB chicken. Our results suggest that chicken CAPN2 expression may be related to chicken breeds and tissues.

  13. Dual perfluorocarbon method to noninvasively monitor dissolved oxygen concentration in tissue engineered constructs in vitro and in vivo.

    Science.gov (United States)

    Goh, Fernie; Long, Robert; Simpson, Nicholas; Sambanis, Athanassios

    2011-07-01

    Noninvasive in vivo monitoring of tissue implants provides important correlations between construct function and the observed physiologic effects. As oxygen is a key parameter affecting cell and tissue function, we established a monitoring method that utilizes (19) F nuclear magnetic resonance (NMR) spectroscopy, with perfluorocarbons (PFCs) as oxygen concentration markers, to noninvasively monitor dissolved oxygen concentration (DO) in tissue engineered implants. Specifically, we developed a dual PFC method capable of simultaneously measuring DO within a tissue construct and its surrounding environment, as the latter varies among animals and with physiologic conditions. In vitro studies using an NMR-compatible bioreactor demonstrated the feasibility of this method to monitor the DO within alginate beads containing metabolically active murine insulinoma βTC-tet cells, relative to the DO in the culture medium, under perfusion and static conditions. The DO profiles obtained under static conditions were supported by mathematical simulations of the system. In vivo, the dual PFC method was successful in tracking the oxygenation state of entrapped βTC-tet cells and the surrounding peritoneal DO over 16 days in normal mice. DO measurements correlated well with the extent of cell growth and host cell attachment examined postexplantation. The peritoneal oxygen environment was found to be variable and hypoxic, and significantly lower in the presence of metabolically active cells. The significance of the dual PFC system in providing critical DO measurements for entrapped cells and other tissue constructs, in vitro and in vivo, is discussed. Copyright © 2011 American Institute of Chemical Engineers (AIChE).

  14. 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.

  15. Tissue discrimination by uncorrected autofluorescence spectra: a proof-of-principle study for tissue-specific laser surgery.

    Science.gov (United States)

    Stelzle, Florian; Knipfer, Christian; Adler, Werner; Rohde, Maximilian; Oetter, Nicolai; Nkenke, Emeka; Schmidt, Michael; Tangermann-Gerk, Katja

    2013-10-11

    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.

  16. Tissue-Specific Effects of Bariatric Surgery Including Mitochondrial Function

    Directory of Open Access Journals (Sweden)

    Simon N. Dankel

    2011-01-01

    Full Text Available A better understanding of the molecular links between obesity and disease is potentially of great benefit for society. In this paper we discuss proposed mechanisms whereby bariatric surgery improves metabolic health, including acute effects on glucose metabolism and long-term effects on metabolic tissues (adipose tissue, skeletal muscle, and liver and mitochondrial function. More short-term randomized controlled trials should be performed that include simultaneous measurement of metabolic parameters in different tissues, such as tissue gene expression, protein profile, and lipid content. By directly comparing different surgical procedures using a wider array of metabolic parameters, one may further unravel the mechanisms of aberrant metabolic regulation in obesity and related disorders.

  17. Tissue viability assessment via laser-based fluorescence monitor

    Science.gov (United States)

    Curtis, Craig H.; Peyghambarian, Nasser; Dereniak, Eustace L.; Frink, Edward

    1996-04-01

    A preliminary study of the degree to which recently introduced inhalation anesthetics influence the intracellular energetic metabolism of isolated perfused rat livers is undertaken via NADH fluorometry. During liver transplantation, anesthesiologists desire to maintain a high level of metabolic energy status in newly transplanted liver tissue. Ischemic storage of donor liver tissue prior to transplantation is known to inhibit mitochondrial electron transfer, which results in decreased levels of ATP and increased levels of NADH in the stored tissue. The ability of transplanted liver tissue to regenerate ATP at normal levels is desirable for early post- operative recovery of liver function. Previous studies have examined the differential effects inhalation anesthetics have on the energetic metabolism of tissue at the cellular level; the trend of such agents is to induce a dose-dependent increase in NADH fluorescence in accordance with their strengths as general anesthetics. The present study evaluates the differential effects exhibited by new inhalation anesthetics on the return of function of energetic metabolism in liver tissue. The third-harmonic (355 nm) output of a Nd:YAG laser is spatially filtered and used as the excitation source for surface fluorometric measurements of isolated buffer-perfused rat livers. Lastly, maximum fluorescence emission versus spot-size are measured.

  18. [The clinical immunology laboratory in diagnosis and monitoring of systemic lupus erythematosus and connective tissue diseases].

    Science.gov (United States)

    Sinico, R A; Radice, A

    2005-01-01

    The laboratory and particularly clinical immunology laboratories have an essential role in diagnosing and monitoring systemic lupus erythematosus (SLE), as well as other connective tissue diseases. The role of the clinical immunology laboratory in these diseases is to confirm or exclude diagnosis, to monitor disease activity, and to identify subgroup of patients. To obtain the best results in terms of diagnostic performance and clinical usefulness, the following recommendations should be fulfilled: anti-nuclear antibodies (ANA) determination by indirect immunofluorescence on Hep-2 cells is an effective screening assay in patients with clinical features of SLE. A negative ANA test makes the diagnosis of SLE unlikely. Anti-dsDNA antibodies are highly specific for SLE and are associated with renal involvement. The method of choice for anti-dsDNA is the Farr assay; however, the necessity of using radioactive materials reduces its applicability. As an alternative, immunofluorescence on Crithidia Luciliae can be used in the diagnostic phase due to its high specificity. The detection of antibodies to extractable nuclear antigens (ENA) and to phospholipids (lupus anticoagulant and anti-cardiolipin antibodies) is useful in identifying subgroups of patients at risk for some clinical manifestations. Anti-dsDNA measurement with a quantitative assay (the Farr assay or ELISA) is currently the best method to monitor disease activity along with complement levels. New assays (anti-C1q and anti-nucleosome antibodies) have been recently proposed for the diagnosis (anti-nucleosome) and monitoring of SLE patients (anti-C1q and anti-nucleosome antibodies), with promising results.

  19. Tissue-specific splicing factor gene expression signatures

    NARCIS (Netherlands)

    A.R. Grosso; A.Q. Gomes (Anita); N.L. Barbosa-Morais (Nuno); S. Caldeira (Sandra); N.P. Thorne (Natalie); G. Grech (Godfrey); M.M. von Lindern (Marieke); M. Carmo-Fonseca (Maria)

    2008-01-01

    textabstractThe alternative splicing code that controls and coordinates the transcriptome in complex multicellular organisms remains poorly understood. It has long been argued that regulation of alternative splicing relies on combinatorial interactions between multiple proteins, and that tissue-spec

  20. Post-Surgical Clinical Monitoring of Soft Tissue Wound Healing in Periodontal and Implant Surgery.

    Science.gov (United States)

    Pippi, Roberto

    2017-01-01

    Clinical features of surgical soft tissue wound healing in dentistry have been rarely discussed in the international literature. The aim of the present paper is to highlight both the main clinical findings of surgical wound healing, especially in periodontal and implant dentistry, and the wound healing monitoring procedures which should be followed. Wound inspection after careful food and plaque debridement is the essential part of wound healing monitoring. Periodontal and peri-implant probing should be performed only after tissue healing has been completed and not on a weekly basis in peri-implant tissue monitoring. Telephone follow-up and patient self-assessment scales can also be used the days following surgery to monitor the most common surgical complications such as pain, swelling, bleeding, and bruising. Wound healing monitoring is an important concern in all surgical procedures since it allows to identify signs or/and symptoms possibly related to surgical complications.

  1. NAIL KERATIN AS MONITOR-TISSUE FOR SELENIUM EXPOSURE

    NARCIS (Netherlands)

    VANNOORD, PAH; MAAS, MJ; DEBRUIN, M

    1992-01-01

    Nail clippings might provide a way to monitor exposure to selenium in the recent past of an individual, since a clipping collected from a toe would reflect exposures months before actual clipping date. The relation between levels of exogenous selenium exposure and selenium levels in nail keratin was

  2. Tissue Oxygenation Monitoring using Resonance Raman Spectroscopy during Hemorrhage

    Science.gov (United States)

    2013-12-27

    by the fact that young swine are highly susceptible to iron-deficient anemia secondary to low tissue stores at birth and extremely rapid growth.40 The...venous oximetry and shock index in the emergency department: use in the evaluation of clinical shock. Am J Emerg Med. 1992;10:538 541. 38. Rivers EP

  3. Application of serum levels of pro-gastrin releasing peptide, tissue polypeptide specific antigen and neuron specific enolase in therapy monitoring in small cell lung cancer patients%血清ProGRP、TPS及NSE在小细胞肺癌患者治疗监测中的应用

    Institute of Scientific and Technical Information of China (English)

    王慜杰; 李学祥; 高佳; 韩彬彬; 付超; 王景智; 张春; 齐军

    2011-01-01

    Objective To evaluate the clinical significance of serum levels of ProGRP, TPS and NSE in diagnosis and therapy monitoring in small cell lung cancer patients. Methods The levels of serum ProGRP, TPS and NSE in 51 SCLC patients (SCLC group), 60 benign pulmonary disease patients (benign disease group ) and 60 healthy people (healthy group ) were determined using chemiluminescent immunoassay, ELISA and electrochemiluminescent immunoassay respectively. Blood samples were collected and detected prior to therapy, before the second course of chemotherapy and the third course of chemotherapy consecutively in all the 51 SCLC patients. Results The serum ProGRP, TPS and NSE concentrations prior to chemotherapy in limited stage SCLC (LSCLC) were 136. 9(22.8-631.7)ng/L, 78. 2(56.4-114.6) U/L and 28.1(20.9-46.1)μg/L, respectively; And in extensive stage SCLC patients (ESCLC) were 1 106.6(41.2-2161.1) ng/L, 230. 9( 143.5-259.0) U/L and 81.1 (34.3-140.0)μg/L, respectively. The serum concentrations of the 3 markers in benign disease group were 19. 7 ( 9. 5-29. 1 )ng/L, 48. 7 ( 17.9-95.4) U/L and 12. 1(1.2-13.9) μg/L; and in healthy group were 20.3(10.7-30.6) ng/L, 50.3(19.5-70.7) U/L and 11.7 (1.1-13.4)μg/L, respectively. The Kruskal-Wallis test showed significantly statistical difference in different groups of the 3 tumor markers, Chi-Square were 51. 368,36. 532 and 81. 645( P <0. 01 ). Significant statistically differences showed when the concentrations of the 3 marks of the 2 control group were compared with that of the LSCLC group ( U =491, 827, 609 and 476, 831, 585,respectively, P < 0. 05 ). Differences were also statistically significant when the 2 control group compared with that of the ESCLC group ( U = 314,532,456 and 302,553,430, respectively, P < 0. 01 ). The AUC of ProGRP was 0.832 +0.029(95% CI:0.774-0.890). When cutoff value of ProGRP set as 37.7 ng/L, the diagnostic sensitivity, specificity, positive predictive value, negative predictive value and Youden

  4. Selected Reaction Monitoring (SRM Analysis of Epidermal Growth Factor Receptor (EGFR in Formalin Fixed Tumor Tissue

    Directory of Open Access Journals (Sweden)

    Hembrough Todd

    2012-05-01

    Full Text Available Abstract Background Analysis of key therapeutic targets such as epidermal growth factor receptor (EGFR in clinical tissue samples is typically done by immunohistochemistry (IHC and is only subjectively quantitative through a narrow dynamic range. The development of a standardized, highly-sensitive, linear, and quantitative assay for EGFR for use in patient tumor tissue carries high potential for identifying those patients most likely to benefit from EGFR-targeted therapies. Methods A mass spectrometry-based Selected Reaction Monitoring (SRM assay for the EGFR protein (EGFR-SRM was developed utilizing the Liquid Tissue®-SRM technology platform. Tissue culture cells (n = 4 were analyzed by enzyme-linked immunosorbent assay (ELISA to establish quantitative EGFR levels. Matching formalin fixed cultures were analyzed by the EGFR-SRM assay and benchmarked against immunoassay of the non-fixed cultured cells. Xenograft human tumor tissue (n = 10 of non-small cell lung cancer (NSCLC origin and NSCLC patient tumor tissue samples (n = 23 were microdissected and the EGFR-SRM assay performed on Liquid Tissue lysates prepared from microdissected tissue. Quantitative curves and linear regression curves for correlation between immunoassay and SRM methodology were developed in Excel. Results The assay was developed for quantitation of a single EGFR tryptic peptide for use in FFPE patient tissue with absolute specificity to uniquely distinguish EGFR from all other proteins including the receptor tyrosine kinases, IGF-1R, cMet, Her2, Her3, and Her4. The assay was analytically validated against a collection of tissue culture cell lines where SRM analysis of the formalin fixed cells accurately reflects EGFR protein levels in matching non-formalin fixed cultures as established by ELISA sandwich immunoassay (R2 = 0.9991. The SRM assay was applied to a collection of FFPE NSCLC xenograft tumors where SRM data range from 305amol/μg to 12,860amol/μg and

  5. Monitoring of temperature-mediated adipose tissue phase transitions by refractive-index measurements

    Science.gov (United States)

    Yanina, I. Yu.; Popov, A. P.; Bykov, A. V.; Tuchin, V. V.

    2014-10-01

    Monitoring of temperature-mediated adipose tissue phase transitions were studied in vitro using an Abbe refractometer. The 1-2-mm thick porcine fat tissues slices were used in the experiments. The observed change in the tissue was associated with several phase transitions of lipid components of the adipose tissue. It was found that overall heating of a sample from the room to higher temperature led to more pronounced and tissue changes in refractive index if other experimental conditions were kept constant. We observed an abrupt change in the refractive index in the temperature range of 37-60 °C.

  6. Tissue-Specific Transcriptomics in the Field Cricket Teleogryllus oceanicus

    OpenAIRE

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

    2013-01-01

    This work was supported by a Natural Environment Research Council Junior Postdoctoral Fellowship (NE/G014906/1) and Pacific Rim Foundation funding (08-T-PRRP-05-0029) to N.W.B. 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 p...

  7. Magnetic resonance microscopy for monitoring osteogenesis in tissue-engineered construct in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Xu Huihui [Bioengineering Department (MC 063), University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7052 (United States); Othman, Shadi F [Bioengineering Department (MC 063), University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7052 (United States); Hong Liu [Bioengineering Department (MC 063), University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7052 (United States); Peptan, Ioana A [Bioengineering Department (MC 063), University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7052 (United States); Magin, Richard L [Bioengineering Department (MC 063), University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7052 (United States)

    2006-02-07

    Magnetic resonance microscopy (MRM) is used to monitor osteogenesis in tissue-engineered constructs. Measurements of the developing tissue's MR relaxation times (T{sub 1} and T{sub 2}), apparent diffusion coefficient (ADC) and elastic shear modulus were conducted over a 4-week growth period using an 11.74 T Bruker spectrometer with an imaging probe adapted for MR elastography (MRE). Both the relaxation times and the ADC show a statistically significant decrease after only one week of tissue development while the tissue stiffness increases progressively during the first two weeks of in vitro growth. The measured MR parameters are correlated with histologically monitored osteogenic tissue development. This study shows that MRM can provide quantitative data with which to characterize the growth and development of tissue-engineered bone.

  8. 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

    2015-02-18

    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.

  9. Scope and limitations of yeast as a model organism for studying human tissue-specific pathways.

    Science.gov (United States)

    Mohammadi, Shahin; Saberidokht, Baharak; Subramaniam, Shankar; Grama, Ananth

    2015-12-29

    Budding yeast, S. cerevisiae, has been used extensively as a model organism for studying cellular processes in evolutionarily distant species, including humans. However, different human tissues, while inheriting a similar genetic code, exhibit distinct anatomical and physiological properties. Specific biochemical processes and associated biomolecules that differentiate various tissues are not completely understood, neither is the extent to which a unicellular organism, such as yeast, can be used to model these processes within each tissue. We present a novel framework to systematically quantify the suitability of yeast as a model organism for different human tissues. To this end, we develop a computational method for dissecting the global human interactome into tissue-specific cellular networks. By individually aligning these networks with the yeast interactome, we simultaneously partition the functional space of human genes, and their corresponding pathways, based on their conservation both across species and among different tissues. Finally, we couple our framework with a novel statistical model to assess the conservation of tissue-specific pathways and infer the overall similarity of each tissue with yeast. We further study each of these subspaces in detail, and shed light on their unique biological roles in the human tissues. Our framework provides a novel tool that can be used to assess the suitability of the yeast model for studying tissue-specific physiology and pathophysiology in humans. Many complex disorders are driven by a coupling of housekeeping (universally expressed in all tissues) and tissue-selective (expressed only in specific tissues) dysregulated pathways. While tissue-selective genes are significantly associated with the onset and development of a number of tissue-specific pathologies, we show that the human-specific subset has even higher association. Consequently, they provide excellent candidates as drug targets for therapeutic interventions.

  10. Human Oral Mucosa Tissue-Engineered Constructs Monitored by Raman Fiber-Optic Probe

    OpenAIRE

    Khmaladze, Alexander; Kuo, Shiuhyang; Kim, Roderick Y; Matthews, Robert V.; Marcelo, Cynthia L.; Feinberg, Stephen E.; Morris, Michael D.

    2014-01-01

    In maxillofacial and oral surgery, there is a need for the development of tissue-engineered constructs. They are used for reconstructions due to trauma, dental implants, congenital defects, or oral cancer. A noninvasive monitoring of the fabrication of tissue-engineered constructs at the production and implantation stages done in real time is extremely important for predicting the success of tissue-engineered grafts. We demonstrated a Raman spectroscopic probe system, its design and applicati...

  11. 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

  12. 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

  13. Tissue-specific metabolic responses of Cyprinus flammans to copper.

    Science.gov (United States)

    Hu, Ming-Yan; Ye, Yang-Fang; Xue, Liang-Yi; Tang, Ze-Yuan

    2015-07-01

    Copper (Cu) contamination is serious in China, with ≤2.76 mg/L in some waters. Exposure to Cu causes a high toxicity to the aquatic organisms and subsequent ecological risk. To understand fish responses to Cu exposure, we analyzed the metabonomic changes in multiple tissues (gill, liver, and muscle) of Cyprinus flammans using an nuclear magnetic resonance-based metabonomic technique. Our results showed that metabolic alterations are dose-dependent. No significant metabolic alterations in three tissues of fish are caused by 0.25 mg/L Cu. However, 1.53 mg/L Cu caused changes of energy-related metabolites and amino acids, which we suggest are due to enhanced metabolic acidosis in gill and muscle, decreased tricarboxylic acid cycle activity in muscle, increased gluconeogenesis from amino acids in liver, and improved glycogenesis in liver and muscle. The Cori cycle between liver and muscle is concurrently triggered. Furthermore, high concentration of Cu resulted in the alteration of choline metabolism such that we hypothesize that Cu induces membrane damage and detoxification of CuSO4 in gill as well as altered osmoregulation in all three tissues. Choline-O-sulfate in gill may be used as a biomarker to provide an early warning of Cu exposure in C. flammans. Moreover, Cu exposure caused alterations of nucleoside and nucleotide metabolism in both gill and muscle. These findings provide a new insight into the metabolic effects of Cu exposure on C. flammans and highlight the value of metabonomics in the study of metabolic metal disturbance in fish.

  14. Dual-wavelength photoacoustic technique for monitoring tissue status during thermal treatments

    Science.gov (United States)

    Hsiao, Yi-Sing; Wang, Xueding; Deng, Cheri X.

    2013-06-01

    Photoacoustic (PA) techniques have been exploited for monitoring thermal treatments. However, PA signals depend not only on tissue temperature but also on tissue optical properties which indicate tissue status (e.g., native or coagulated). The changes in temperature and tissue status often occur simultaneously during thermal treatments, so both effects cause changes to PA signals. A new dual-wavelength PA technique to monitor tissue status independent of temperature is performed. By dividing the PA signal intensities obtained at two wavelengths at the same temperature, a ratio, which only depends on tissue optical properties, is obtained. Experiments were performed with two experimental groups, one with untreated tissue samples and the other with high-intensity focused ultrasound treated tissue samples including thermal coagulated lesion, using ex vivo porcine myocardium specimens to test the technique. The ratio of PA signal intensities obtained at 700 and 800 nm was constant for both groups from 25 to 43°C, but with distinct values for the two groups. Tissue alteration during thermal treatment was then studied using water bath heating of tissue samples from 35 to 60°C. We found that the ratio stayed constant before it exhibited a marked increase at around 55°C, indicating tissue changes at this temperature.

  15. Tissue-specific effects of acetylcholine in the canine heart

    DEFF Research Database (Denmark)

    Callø, Kirstine; Goodrow, Robert; Olesen, Søren-Peter

    2013-01-01

    INTRODUCTION: Acetylcholine (ACh) release from the vagus nerve slows heart rate and atrioventricular conduction. ACh stimulates a variety of receptors and channels, including an inward rectifying current (IK,ACh). The effect of ACh in ventricle is still debated. We compare the effect of ACh...... on action potentials in canine atria, Purkinje and ventricular tissue as well as on ionic currents in isolated cells. METHODS: Action potentials were recorded from ventricular slices, Purkinje fibers, and arterially perfused atrial preparations. Whole-cell currents were recorded under voltage...

  16. A heterogeneous human tissue mimicking phantom for RF heating and MRI thermal monitoring verification

    Science.gov (United States)

    Yuan, Yu; Wyatt, Cory; Maccarini, Paolo; Stauffer, Paul; Craciunescu, Oana; MacFall, James; Dewhirst, Mark; Das, Shiva K.

    2012-04-01

    This paper describes a heterogeneous phantom that mimics a human thigh with a deep-seated tumor, for the purpose of studying the performance of radiofrequency (RF) heating equipment and non-invasive temperature monitoring with magnetic resonance imaging (MRI). The heterogeneous cylindrical phantom was constructed with an outer fat layer surrounding an inner core of phantom material mimicking muscle, tumor and marrow-filled bone. The component materials were formulated to have dielectric and thermal properties similar to human tissues. The dielectric properties of the tissue mimicking phantom materials were measured with a microwave vector network analyzer and impedance probe over the frequency range of 80-500 MHz and at temperatures of 24, 37 and 45 °C. The specific heat values of the component materials were measured using a differential scanning calorimeter over the temperature range of 15-55 °C. The thermal conductivity value was obtained from fitting the curves obtained from one-dimensional heat transfer measurement. The phantom was used to verify the operation of a cylindrical four-antenna annular phased array extremity applicator (140 MHz) by examining the proton resonance frequency shift (PRFS) thermal imaging patterns for various magnitude/phase settings (including settings to focus heating in tumors). For muscle and tumor materials, MRI was also used to measure T1/T2* values (1.5 T) and to obtain the slope of the PRFS phase change versus temperature change curve. The dielectric and thermal properties of the phantom materials were in close agreement to well-accepted published results for human tissues. The phantom was able to successfully demonstrate satisfactory operation of the tested heating equipment. The MRI-measured thermal distributions matched the expected patterns for various magnitude/phase settings of the applicator, allowing the phantom to be used as a quality assurance tool. Importantly, the material formulations for the various tissue types

  17. 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

  18. HA novel approach to investigate tissue-specific trinucleotide repeat instability

    Directory of Open Access Journals (Sweden)

    Boily Marie-Josee

    2010-03-01

    Full Text Available Abstract Background In Huntington's disease (HD, an expanded CAG repeat produces characteristic striatal neurodegeneration. Interestingly, the HD CAG repeat, whose length determines age at onset, undergoes tissue-specific somatic instability, predominant in the striatum, suggesting that tissue-specific CAG length changes could modify the disease process. Therefore, understanding the mechanisms underlying the tissue specificity of somatic instability may provide novel routes to therapies. However progress in this area has been hampered by the lack of sensitive high-throughput instability quantification methods and global approaches to identify the underlying factors. Results Here we describe a novel approach to gain insight into the factors responsible for the tissue specificity of somatic instability. Using accurate genetic knock-in mouse models of HD, we developed a reliable, high-throughput method to quantify tissue HD CAG repeat instability and integrated this with genome-wide bioinformatic approaches. Using tissue instability quantified in 16 tissues as a phenotype and tissue microarray gene expression as a predictor, we built a mathematical model and identified a gene expression signature that accurately predicted tissue instability. Using the predictive ability of this signature we found that somatic instability was not a consequence of pathogenesis. In support of this, genetic crosses with models of accelerated neuropathology failed to induce somatic instability. In addition, we searched for genes and pathways that correlated with tissue instability. We found that expression levels of DNA repair genes did not explain the tissue specificity of somatic instability. Instead, our data implicate other pathways, particularly cell cycle, metabolism and neurotransmitter pathways, acting in combination to generate tissue-specific patterns of instability. Conclusion Our study clearly demonstrates that multiple tissue factors reflect the level of

  19. A comparative approach to understanding tissue-specific expression of uncoupling protein 1 expression in adipose tissue

    Directory of Open Access Journals (Sweden)

    Andrew eShore

    2013-01-01

    Full Text Available The thermoregulatory function of brown adipose tissue (BAT is due to the tissue-specific expression of uncoupling protein 1 (UCP1 which is thought to have evolved in early mammals. We report that a CpG island close to the UCP1 transcription start site is highly conserved in all 29 vertebrates examined apart from the mouse and xenopus. Using methylation sensitive restriction digest and bisulphite mapping we show that the CpG island in both the bovine and human is largely un-methylated and is not related to differences in UCP1 expression between white and brown adipose tissue. Tissue-specific expression of UCP1 has been proposed to be regulated by a conserved 5’ distal enhancer which has been reported to be absent in marsupials. We demonstrate that the enhancer, is also absent in 5 eutherians as well as marsupials, monotremes, amphibians and fish, is present in pigs despite UCP1 having become a pseudogene, and that absence of the enhancer element does not relate to brown adipose tissue-specific UCP1 expression. We identify an additional putative 5’ regulatory unit which is conserved in 14 eutherian species but absent in other eutherians and vertebrates, but again unrelated to UCP1 expression. We conclude that despite clear evidence of conservation of regulatory elements in the UCP1 5’ untranslated region, this does not appear to be related to species or tissues-specific expression of UCP1.

  20. 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.

  1. Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

    DEFF Research Database (Denmark)

    Börnigen, Daniela; Pers, Tune Hannes; Thorrez, Lieven

    2013-01-01

    Disease-causing variants in human genes usually lead to phenotypes specific to only a few tissues. Here, we present a method for predicting tissue specificity based on quantitative deregulation of protein complexes. The underlying assumption is that the degree of coordinated expression among...... proteins in a complex within a given tissue may pinpoint tissues that will be affected by a mutation in the complex and coordinated expression may reveal the complex to be active in the tissue. We identified known disease genes and their protein complex partners in a high-quality human interactome. Each...... susceptibility gene's tissue involvement was ranked based on coordinated expression with its interaction partners in a non-disease global map of human tissue-specific expression. The approach demonstrated high overall area under the curve (0.78) and was very successfully benchmarked against a random model...

  2. 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.

  3. Platelet subpopulation bearing leukocyte specific antigen and tissue factor.

    Science.gov (United States)

    Gabbasov, Z A; Saburova, O S; Antonova, O A; Golubeva, N V; Khaspekova, S G; Shustova, O N; Zyuryaev, I T; Ruda, M Ya; Mazurov, A V

    2016-11-01

    Platelets bearing leukocyte antigen CD45 were identified in the blood of patients with myocardial infarction (MI) and healthy donors by flow cytofluorimetry. Part of these platelets contained tissue factor (TF)-primary initiator of blood clotting. The number of CD45(+) and CD45(+)/TF(+) platelets in MI patients at the first day was comparable with their level in healthy donors, but was increased at 8-12 days after MI onset. At that time in some patients the amount of CD45(+) and CD45(+)/TF(+) platelets reached 5-6 and 2-3% of their total number. It is assumed that CD45(+)/TF(+) platelets could be formed as a result of platelet interaction with leukocytes or leukocyte produced membrane microparticles.

  4. GABA transporter 1 transcriptional starting site exhibiting tissue specific difference

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    GABA transporter 1(GAT1)takes important roles in multiple physiological processes through the uptake and release of GABA,but the regulation of GAT1 gene expression in different tissues is rarely known.To address the question,first,5' Rapid amplification of cDNA end(RACE)was used to determine GAT1 transcriptional starting sites in neonatal mouse cerebral cortex and intestine,adult mouse brain and adult rat testis.The products of 5'RACE were confirmed by DNA sequencing.We found that the transcript of GAT1 in neonatal mouse cerebral cortex and adult mouse brain starts at the same site(inside of exon 1),while in mouse intestine,GAT1 starts transcription in intron 1,and in rat testis,the transcript of GAT1 has an additional untranslation exon to the 5' direction.

  5. Initial experience with personal digital assistant-based reflectance photoplethysmograph for free tissue transfer monitoring.

    Science.gov (United States)

    Stack, Brendan C; Futran, Neal D; Zang, Billy; Scharf, John E

    2003-08-01

    Improved microsurgical technique has resulted in a high percentage of successful free tissue transfers. When a tissue transfer fails in the head and neck, however, the results are orocutaneous fistulas, carotid artery exposure, and deformity that adds morbidity, expense, and may delay adjuvant therapy. Postoperative monitoring of tissue perfusion can detect early problems in free tissue transfer that may allow for early intervention and salvage. The authors have demonstrated that reflectance photoplethysmography can detect perfusion changes in free tissue transfer within 5 minutes of a pedicle "insult" intraoperatively. Normative data for viable flaps from various donor sites have been established. The authors now report their initial experience with a newly developed reflectance photoplethysmograph based on a hand-held computer for routine clinical use. Their results are compared with a conventional surveillance protocol that included observation, bleeding to pin prick, and bedside duplex scanning of the vascular pedicle. In a series of 30 free tissue transfers (29 patients), there was one ischemic event (skin paddle loss only), which was detected by the monitor. The monitor was able to predict correctly (one flap) survival of a free tissue transfer even when duplex ultrasonic data were indicative of an absence of perfusion. Personal digital assistant-based photoplethysmography appears to be a promising device for bedside diagnosis of free tissue transfer viability or ischemia.

  6. Gene-specific correlation of RNA and protein levels in human cells and tissues.

    Science.gov (United States)

    Edfors, Fredrik; Danielsson, Frida; Hallström, Björn M; Käll, Lukas; Lundberg, Emma; Pontén, Fredrik; Forsström, Björn; Uhlén, Mathias

    2016-10-20

    An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.

  7. Localization of Legionella pneumophila in Tissue Using FITC-Conjugated Specific Antibody and a Background Stain

    Science.gov (United States)

    1982-05-01

    Pathologits P6 i U. S. A. Localization of Legionella pneumophila in Tissue Using FITC- Conjuga ted Specific Antibody and a Background Stain BARBARA S. LOWRY...LOWRY ET AL. A J ( P • 1982 Table I. Procedure to Localize Legionella white light alone, illuminating the pale blue to violet pneumophila in Tissue...tagged antibodies) (T)-tagged specific antibody. In searching for L. pneumophila in tissue in the fluorescent mode, back- ground autofluorescence

  8. Tissue and stage-specific distribution of Wolbachia in Brugia malayi.

    Directory of Open Access Journals (Sweden)

    Kerstin Fischer

    2011-05-01

    Full Text Available BACKGROUND: Most filarial parasite species contain Wolbachia, obligatory bacterial endosymbionts that are crucial for filarial development and reproduction. They are targets for alternative chemotherapy, but their role in the biology of filarial nematodes is not well understood. Light microscopy provides important information on morphology, localization and potential function of these bacteria. Surprisingly, immunohistology and in situ hybridization techniques have not been widely used to monitor Wolbachia distribution during the filarial life cycle. METHODS/PRINCIPAL FINDINGS: A monoclonal antibody directed against Wolbachia surface protein and in situ hybridization targeting Wolbachia 16S rRNA were used to monitor Wolbachia during the life cycle of B. malayi. In microfilariae and vector stage larvae only a few cells contain Wolbachia. In contrast, large numbers of Wolbachia were detected in the lateral chords of L4 larvae, but no endobacteria were detected in the genital primordium. In young adult worms (5 weeks p.i., a massive expansion of Wolbachia was observed in the lateral chords adjacent to ovaries or testis, but no endobacteria were detected in the growth zone of the ovaries, uterus, the growth zone of the testis or the vas deferens. Confocal laser scanning and transmission electron microscopy showed that numerous Wolbachia are aligned towards the developing ovaries and single endobacteria were detected in the germline. In inseminated females (8 weeks p.i. Wolbachia were observed in the ovaries, embryos and in decreasing numbers in the lateral chords. In young males Wolbachia were found in distinct zones of the testis and in large numbers in the lateral chords in the vicinity of testicular tissue but never in mature spermatids or spermatozoa. CONCLUSIONS: Immunohistology and in situ hybridization show distinct tissue and stage specific distribution patterns for Wolbachia in B. malayi. Extensive multiplication of Wolbachia occurs in the

  9. The differentiation of oral soft- and hard tissues using laser induced breakdown spectroscopy - a prospect for tissue specific laser surgery.

    Science.gov (United States)

    Rohde, Maximilian; Mehari, Fanuel; Klämpfl, Florian; Adler, Werner; Neukam, Friedrich-Wilhelm; Schmidt, Michael; Stelzle, Florian

    2016-11-22

    Compared to conventional techniques, Laser surgery procedures provide a number of advantages, but may be associated with an increased risk of iatrogenic damage to important anatomical structures. The type of tissue ablated in the focus spot is unknown. Laser-Induced Breakdown-Spectroscopy (LIBS) has the potential to gain information about the type of material that is being ablated by the laser beam. This may form the basis for tissue selective laser surgery. In the present study, 7 different porcine tissues (cortical and cancellous bone, nerve, mucosa, enamel, dentine and pulp) from 6 animals were analyzed for their qualitative and semiquantitative molecular composition using LIBS. The so gathered data was used to first differentiate between the soft- and hard-tissues using a Calcium-Carbon emission based classifier. The tissues were then further classified using emission-ratio based analysis, principal component analysis (PCA) and linear discriminant analysis (LDA). The relatively higher concentration of Calcium in the hard tissues allows for an accurate first differentiation of soft- and hard tissues (100% sensitivity and specificity). The ratio based statistical differentiation approach yields results in the range from 65% (enamel-dentine pair) to 100% (nerve-pulp, cancellous bone-dentine, cancellous bone-enamel pairs) sensitivity and specificity. Experimental LIBS measuring setup. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. The Roles of Mothers' Neighborhood Perceptions and Specific Monitoring Strategies in Youths' Problem Behavior

    Science.gov (United States)

    Byrnes, Hilary F.; Miller, Brenda A.; Chen, Meng-Jinn; Grube, Joel W.

    2011-01-01

    The neighborhood context can interfere with parents' abilities to effectively monitor their children, but may be related to specific monitoring strategies in different ways. The present study examines the importance of mothers' perceptions of neighborhood disorganization for the specific monitoring strategies they use and how each of these…

  11. Evaluation of a novel promoter from Populus trichocarpa for mature xylem tissue specific gene delivery.

    Science.gov (United States)

    Nguyen, Van Phap; Cho, Jin-Seong; Choi, Young-Im; Lee, Sang-Won; Han, Kyung-Hwan; Ko, Jae-Heung

    2016-07-01

    Wood (i.e., secondary xylem) is an important raw material for many industrial applications. Mature xylem (MX) tissue-specific genetic modification offers an effective means to improve the chemical and physical properties of the wood. Here, we describe a promoter that drives strong gene expression in a MX tissue-specific manner. Using whole-transcriptome genechip analyses of different tissue types of poplar, we identified five candidate genes that had strong expression in the MX tissue. The putative promoter sequences of the five MX-specific genes were evaluated for their promoter activity in both transgenic Arabidopsis and poplar. Among them, we found the promoter of Potri.013G007900.1 (called the PtrMX3 promoter) had the strongest activity in MX and thus was further characterized. In the stem and root tissues of transgenic Arabidopsis plants, the PtrMX3 promoter activity was found exclusively in MX tissue. MX-specific activity of the promoter was reproduced in the stem tissue of transgenic poplar plants. The PtrMX3 promoter activity was not influenced by abiotic stresses or exogenously applied growth regulators, indicating the PtrMX3 promoter is bona fide MX tissue-specific. Our study provides a strong MX-specific promoter for MX-specific modifications of woody biomass.

  12. Identification and target prediction of miRNAs specifically expressed in rat neural tissue

    Directory of Open Access Journals (Sweden)

    Tu Kang

    2009-05-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human, mouse and zebrafish tissues. For example, miR-1 and miR-133 are specifically expressed in muscles. Tissue-specific miRNAs may have particular functions. Although previous studies have reported the presence of human, mouse and zebrafish tissue-specific miRNAs, there have been no detailed reports of rat tissue-specific miRNAs. In this study, Home-made rat miRNA microarrays which established in our previous study were used to investigate rat neural tissue-specific miRNAs, and mapped their target genes in rat tissues. This study will provide information for the functional analysis of these miRNAs. Results In order to obtain as complete a picture of specific miRNA expression in rat neural tissues as possible, customized miRNA microarrays with 152 selected miRNAs from miRBase were used to detect miRNA expression in 14 rat tissues. After a general clustering analysis, 14 rat tissues could be clearly classified into neural and non-neural tissues based on the obtained expression profiles with p values Conclusion Our work provides a global view of rat neural tissue-specific miRNA profiles and a target map of miRNAs, which is expected to contribute to future investigations of miRNA regulatory mechanisms in neural systems.

  13. Specification of embryonic stem cell-derived tissues into eye fields by Wnt signaling using rostral diencephalic tissue-inducing culture.

    Science.gov (United States)

    Sakakura, Eriko; Eiraku, Mototsugu; Takata, Nozomu

    2016-08-01

    The eyes are subdivided from the rostral diencephalon in early development. How the neuroectoderm regulates this subdivision, however, is largely unknown. Taking advantage of embryonic stem cell (ESC) culture using a Rax reporter line to monitor rostral diencephalon formation, we found that ESC-derived tissues at day 7 grown in Glasgow Minimum Expression Media (GMEM) containing knockout serum replacement (KSR) exhibited higher levels of expression of axin2, a Wnt target gene, than those grown in chemically defined medium (CDM). Surprisingly, Wnt agonist facilitated eye field-like tissue specification in CDM. In contrast, the addition of Wnt antagonist diminished eye field tissue formation in GMEM+KSR. Furthermore, the morphological formation of the eye tissue anlage, including the optic vesicle, was accompanied by Wnt signaling activation. Additionally, using CDM culture, we developed an efficient method for generating Rax+/Chx10+ retinal progenitors, which could become fully stratified retina. Here we provide a new avenue for exploring the mechanisms of eye field specification in vitro.

  14. The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

    Directory of Open Access Journals (Sweden)

    Edgerton Mary E

    2003-05-01

    Full Text Available Abstract Background Tissue Microarrays (TMAs allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1 Header, containing the specification Dublin Core identifiers, 2 Block, describing the paraffin-embedded array of tissues, 3Slide, describing the glass slides produced from the Block, and 4 Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange

  15. 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

  16. Genome-wide de Novo Prediction of Proximal and Distal Tissue-Specific Enhancers

    Energy Technology Data Exchange (ETDEWEB)

    Loots, G G; Ovcharenko, I V

    2005-11-03

    Determining how transcriptional regulatory networks are encoded in the human genome is essential for understanding how cellular processes are directed. Here, we present a novel approach for systematically predicting tissue specific regulatory elements (REs) that blends genome-wide expression profiling, vertebrate genome comparisons, and pattern analysis of transcription factor binding sites. This analysis yields 4,670 candidate REs in the human genome with distinct tissue specificities, the majority of which reside far away from transcription start sites. We identify key transcription factors (TFs) for 34 distinct tissues and demonstrate that tissue-specific gene expression relies on multiple regulatory pathways employing similar, but different cohorts of interacting TFs. The methods and results we describe provide a global view of tissue specific gene regulation in humans, and propose a strategy for deciphering the transcriptional regulatory code in eukaryotes.

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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.

  19. Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Oded Magger

    Full Text Available The prioritization of candidate disease-causing genes is a fundamental challenge in the post-genomic era. Current state of the art methods exploit a protein-protein interaction (PPI network for this task. They are based on the observation that genes causing phenotypically-similar diseases tend to lie close to one another in a PPI network. However, to date, these methods have used a static picture of human PPIs, while diseases impact specific tissues in which the PPI networks may be dramatically different. Here, for the first time, we perform a large-scale assessment of the contribution of tissue-specific information to gene prioritization. By integrating tissue-specific gene expression data with PPI information, we construct tissue-specific PPI networks for 60 tissues and investigate their prioritization power. We find that tissue-specific PPI networks considerably improve the prioritization results compared to those obtained using a generic PPI network. Furthermore, they allow predicting novel disease-tissue associations, pointing to sub-clinical tissue effects that may escape early detection.

  20. An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction.

    Science.gov (United States)

    Piro, Rosario Michael; Ala, Ugo; Molineris, Ivan; Grassi, Elena; Bracco, Chiara; Perego, Gian Paolo; Provero, Paolo; Di Cunto, Ferdinando

    2011-11-01

    Gene coexpression relationships that are phylogenetically conserved between human and mouse have been shown to provide important clues about gene function that can be efficiently used to identify promising candidate genes for human hereditary disorders. In the past, such approaches have considered mostly generic gene expression profiles that cover multiple tissues and organs. The individual genes of multicellular organisms, however, can participate in different transcriptional programs, operating at scales as different as single-cell types, tissues, organs, body regions or the entire organism. Therefore, systematic analysis of tissue-specific coexpression could be, in principle, a very powerful strategy to dissect those functional relationships among genes that emerge only in particular tissues or organs. In this report, we show that, in fact, conserved coexpression as determined from tissue-specific and condition-specific data sets can predict many functional relationships that are not detected by analyzing heterogeneous microarray data sets. More importantly, we find that, when combined with disease networks, the simultaneous use of both generic (multi-tissue) and tissue-specific conserved coexpression allows a more efficient prediction of human disease genes than the use of generic conserved coexpression alone. Using this strategy, we were able to identify high-probability candidates for 238 orphan disease loci. We provide proof of concept that this combined use of generic and tissue-specific conserved coexpression can be very useful to prioritize the mutational candidates obtained from deep-sequencing projects, even in the case of genetic disorders as heterogeneous as XLMR.

  1. 40 CFR 75.14 - Specific provisions for monitoring opacity.

    Science.gov (United States)

    2010-07-01

    ... calendar year. (d) Diesel-fired units and dual-fuel reciprocating engine units. The owner or operator of an affected diesel-fired unit or a dual-fuel reciprocating engine unit is exempt from the opacity monitoring... unit by changing its fuel mix, the owner or operator shall install, operate, and certify a continuous...

  2. In situ fiber-optical monitoring of cytosolic calcium in tissue explant cultures

    CERN Document Server

    Ryser, Manuel; Geiser, Marianne; Frenz, Martin; Rička, Jaro

    2014-01-01

    We present a fluorescence-lifetime based method for monitoring cell and tissue activity in situ, during cell culturing and in the presence of a strong autofluorescence background. The miniature fiber-optic probes are easily incorporated in the tight space of a cell culture chamber or in an endoscope. As a first application we monitored the cytosolic calcium levels in porcine tracheal explant cultures using the Calcium Green-5N (CG5N) indicator. Despite the simplicity of the optical setup we are able to detect changes of calcium concentration as small as 2.5 nM, with a monitoring time resolution of less than 1 s.

  3. Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome.

    Science.gov (United States)

    Pérez-Montarelo, Dafne; Hudson, Nicholas J; Fernández, Ana I; Ramayo-Caldas, Yuliaxis; Dalrymple, Brian P; Reverter, Antonio

    2012-01-01

    The processes that drive tissue identity and differentiation remain unclear for most tissue types. So are the gene networks and transcription factors (TF) responsible for the differential structure and function of each particular tissue, and this is particularly true for non model species with incomplete genomic resources. To better understand the regulation of genes responsible for tissue identity in pigs, we have inferred regulatory networks from a meta-analysis of 20 gene expression studies spanning 480 Porcine Affymetrix chips for 134 experimental conditions on 27 distinct tissues. We developed a mixed-model normalization approach with a covariance structure that accommodated the disparity in the origin of the individual studies, and obtained the normalized expression of 12,320 genes across the 27 tissues. Using this resource, we constructed a network, based on the co-expression patterns of 1,072 TF and 1,232 tissue specific genes. The resulting network is consistent with the known biology of tissue development. Within the network, genes clustered by tissue and tissues clustered by site of embryonic origin. These clusters were significantly enriched for genes annotated in key relevant biological processes and confirm gene functions and interactions from the literature. We implemented a Regulatory Impact Factor (RIF) metric to identify the key regulators in skeletal muscle and tissues from the central nervous systems. The normalization of the meta-analysis, the inference of the gene co-expression network and the RIF metric, operated synergistically towards a successful search for tissue-specific regulators. Novel among these findings are evidence suggesting a novel key role of ERCC3 as a muscle regulator. Together, our results recapitulate the known biology behind tissue specificity and provide new valuable insights in a less studied but valuable model species.

  4. Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome.

    Directory of Open Access Journals (Sweden)

    Dafne Pérez-Montarelo

    Full Text Available The processes that drive tissue identity and differentiation remain unclear for most tissue types. So are the gene networks and transcription factors (TF responsible for the differential structure and function of each particular tissue, and this is particularly true for non model species with incomplete genomic resources. To better understand the regulation of genes responsible for tissue identity in pigs, we have inferred regulatory networks from a meta-analysis of 20 gene expression studies spanning 480 Porcine Affymetrix chips for 134 experimental conditions on 27 distinct tissues. We developed a mixed-model normalization approach with a covariance structure that accommodated the disparity in the origin of the individual studies, and obtained the normalized expression of 12,320 genes across the 27 tissues. Using this resource, we constructed a network, based on the co-expression patterns of 1,072 TF and 1,232 tissue specific genes. The resulting network is consistent with the known biology of tissue development. Within the network, genes clustered by tissue and tissues clustered by site of embryonic origin. These clusters were significantly enriched for genes annotated in key relevant biological processes and confirm gene functions and interactions from the literature. We implemented a Regulatory Impact Factor (RIF metric to identify the key regulators in skeletal muscle and tissues from the central nervous systems. The normalization of the meta-analysis, the inference of the gene co-expression network and the RIF metric, operated synergistically towards a successful search for tissue-specific regulators. Novel among these findings are evidence suggesting a novel key role of ERCC3 as a muscle regulator. Together, our results recapitulate the known biology behind tissue specificity and provide new valuable insights in a less studied but valuable model species.

  5. Non-invasive chemically specific measurement of subsurface temperature in biological tissues using surface-enhanced spatially offset Raman spectroscopy.

    Science.gov (United States)

    Gardner, Benjamin; Stone, Nicholas; Matousek, Pavel

    2016-06-23

    Here we demonstrate for the first time the viability of characterising non-invasively the subsurface temperature of SERS nanoparticles embedded within biological tissues using spatially offset Raman spectroscopy (SORS). The proposed analytical method (T-SESORS) is applicable in general to diffusely scattering (turbid) media and features high sensitivity and high chemical selectivity. The method relies on monitoring the Stokes and anti-Stokes bands of SERS nanoparticles in depth using SORS. The approach has been conceptually demonstrated using a SORS variant, transmission Raman spectroscopy (TRS), by measuring subsurface temperatures within a slab of porcine tissue (5 mm thick). Root-mean-square errors (RMSEs) of 0.20 °C were achieved when measuring temperatures over ranges between 25 and 44 °C. This unique capability complements the array of existing, predominantly surface-based, temperature monitoring techniques. It expands on a previously demonstrated SORS temperature monitoring capability by adding extra sensitivity stemming from SERS to low concentration analytes. The technique paves the way for a wide range of applications including subsurface, chemical-specific, non-invasive temperature analysis within turbid translucent media including: the human body, subsurface monitoring of chemical (e.g. catalytic) processes in manufacture quality and process control and research. Additionally, the method opens prospects for control of thermal treatment of cancer in vivo with direct non-invasive feedback on the temperature of mediating plasmonic nanoparticles.

  6. Cell Microenvironment Engineering and Monitoring for Tissue Engineering and Regenerative Medicine: The Recent Advances

    Science.gov (United States)

    Barthes, Julien; Özçelik, Hayriye; Hindié, Mathilde; Ndreu-Halili, Albana; Hasan, Anwarul

    2014-01-01

    In tissue engineering and regenerative medicine, the conditions in the immediate vicinity of the cells have a direct effect on cells' behaviour and subsequently on clinical outcomes. Physical, chemical, and biological control of cell microenvironment are of crucial importance for the ability to direct and control cell behaviour in 3-dimensional tissue engineering scaffolds spatially and temporally. In this review, we will focus on the different aspects of cell microenvironment such as surface micro-, nanotopography, extracellular matrix composition and distribution, controlled release of soluble factors, and mechanical stress/strain conditions and how these aspects and their interactions can be used to achieve a higher degree of control over cellular activities. The effect of these parameters on the cellular behaviour within tissue engineering context is discussed and how these parameters are used to develop engineered tissues is elaborated. Also, recent techniques developed for the monitoring of the cell microenvironment in vitro and in vivo are reviewed, together with recent tissue engineering applications where the control of cell microenvironment has been exploited. Cell microenvironment engineering and monitoring are crucial parts of tissue engineering efforts and systems which utilize different components of the cell microenvironment simultaneously can provide more functional engineered tissues in the near future. PMID:25143954

  7. Tissue-specific Regulation of Porcine Prolactin Receptor Expression by Estrogen, Progesterone and Prolactin

    Science.gov (United States)

    Prolactin (PRL) acts through its receptor (PRLR) via both endocrine and local paracrine/autocrine pathways to regulate biological processes including reproduction and lactation. We analyzed the tissue and stage of gestation-specific regulation of PRL and PRLR expression in various tissues of pigs. ...

  8. A tissue and developmental specific enhancer is located downstream from the human β-globin gene.

    NARCIS (Netherlands)

    G. Kollias (George); J. Hurst; E. de Boer (Ernie); F.G. Grosveld (Frank)

    1987-01-01

    textabstractThe human P-globin gene is part of a multigene family and is expressed specifically in adult human erythroid tissue (for review, 1). When the human P-globin is introduced into fertilized mouse eggs, it is first activated in foetal liver and remains expressed in adult erythroid tissues

  9. Tissue specific DNA methylation in normal human breast epithelium and in breast cancer.

    Science.gov (United States)

    Avraham, Ayelet; Cho, Sean Soonweng; Uhlmann, Ronit; Polak, Mia Leonov; Sandbank, Judith; Karni, Tami; Pappo, Itzhak; Halperin, Ruvit; Vaknin, Zvi; Sella, Avishay; Sukumar, Saraswati; Evron, Ella

    2014-01-01

    Cancer is a heterogeneous and tissue-specific disease. Thus, the tissue of origin reflects on the natural history of the disease and dictates the therapeutic approach. It is suggested that tissue differentiation, mediated mostly by epigenetic modifications, could guide tissue-specific susceptibility and protective mechanisms against cancer. Here we studied breast specific methylation in purified normal epithelium and its reflection in breast cancers. We established genome wide methylation profiles of various normal epithelial tissues and identified 110 genes that were differentially methylated in normal breast epithelium. A number of these genes also showed methylation alterations in breast cancers. We elaborated on one of them, TRIM29 (ATDC), and showed that its promoter was hypo-methylated in normal breast epithelium and heavily methylated in other normal epithelial tissues. Moreover, in breast carcinomas methylation increased and expression decreased whereas the reverse was noted for multiple other carcinomas. Interestingly, TRIM29 regulation in breast tumors clustered according to the PAM50 classification. Thus, it was repressed in the estrogen receptor positive tumors, particularly in the more proliferative luminal B subtype. This goes in line with previous reports indicating tumor suppressive activity of TRIM29 in estrogen receptor positive luminal breast cells in contrast to oncogenic function in pancreatic and lung cancers. Overall, these findings emphasize the linkage between breast specific epigenetic regulation and tissue specificity of cancer.

  10. Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs

    Science.gov (United States)

    Pihlajamaa, Päivi; Sahu, Biswajyoti; Lyly, Lauri; Aittomäki, Viljami; Hautaniemi, Sampsa; Jänne, Olli A

    2014-01-01

    Androgen receptor (AR) binds male sex steroids and mediates physiological androgen actions in target tissues. ChIP-seq analyses of AR-binding events in murine prostate, kidney and epididymis show that in vivo AR cistromes and their respective androgen-dependent transcription programs are highly tissue specific mediating distinct biological pathways. This high order of tissue specificity is achieved by the use of exclusive collaborating factors in the three androgen-responsive tissues. We find two novel collaborating factors for AR signaling in vivo—Hnf4α (hepatocyte nuclear factor 4α) in mouse kidney and AP-2α (activating enhancer binding protein 2α) in mouse epididymis—that define tissue-specific AR recruitment. In mouse prostate, FoxA1 serves for the same purpose. FoxA1, Hnf4α and AP-2α motifs are over-represented within unique AR-binding loci, and the cistromes of these factors show substantial overlap with AR-binding events distinct to each tissue type. These licensing or pioneering factors are constitutively bound to chromatin and guide AR to specific genomic loci upon hormone exposure. Collectively, liganded receptor and its DNA-response elements are required but not sufficient for establishment of tissue-specific transcription programs. PMID:24451200

  11. Monitoring of tissue optical properties using OCT: application for blood glucose analysis

    Science.gov (United States)

    Larin, Kirill V.; Eledrisi, Mohsen S.; Ashitkov, Taras V.; Motamedi, Massoud; Esenaliev, Rinat O.

    2002-07-01

    Noninvasive monitoring of tissue optical properties in real time could significantly improve diagnostics and management of various diseases. Recently we proposed to use high- resolution Optical Coherence Tomography (OCT) technique for measurement of tissue scattering coefficient at the depth of up to 1mm. Our pilot studies performed in vitro and in vivo demonstrated that measurement of tissue scattering with this technique can potentially be applied for noninvasive monitoring of blood glucose concentration. High resolution and coherent photon detection of the OCT technique allowed detection of glucose-induced changes in the scattering coefficient. In this paper we report results of in vivo studies performed in dog, New Zealand rabbits, and first human subjects. OCT system with the wavelength of 1300 nm was used in our experiments. OCT signal slope was measured and compared with actual blood glucose concentration. Bolus glucose injections and glucose clamping administrations were used in animal studies. OCT signals were recorded form human subjects during oral glucose tolerance test. Results obtained form both animal and human studies show good correlation between slope of the OCT signals and actual blood glucose concentration measured using standard glucometesr. Sensitivity and accuracy of blood glucose concentrations monitoring with the OCT is discussed. Obtained result suggest that OCT is a promising technique for noninvasive monitoring of tissue analytes including glucose.

  12. Computational detection and functional analysis of human tissue-specific A-to-I RNA editing.

    Directory of Open Access Journals (Sweden)

    Tao He

    Full Text Available A-to-I RNA editing is a widespread post-transcriptional modification event in vertebrates. It could increase transcriptome and proteome diversity through recoding the genomic information and cross-linking other regulatory events, such as those mediated by alternative splicing, RNAi and microRNA (miRNA. Previous studies indicated that RNA editing can occur in a tissue-specific manner in response to the requirements of the local environment. We set out to systematically detect tissue-specific A-to-I RNA editing sites in 43 human tissues using bioinformatics approaches based on the Fisher's exact test and the Benjamini & Hochberg false discovery rate (FDR multiple testing correction. Twenty-three sites in total were identified to be tissue-specific. One of them resulted in an altered amino acid residue which may prevent the phosphorylation of PARP-10 and affect its activity. Eight and two tissue-specific A-to-I RNA editing sites were predicted to destroy putative exonic splicing enhancers (ESEs and exonic splicing silencers (ESSs, respectively. Brain-specific and ovary-specific A-to-I RNA editing sites were further verified by comparing the cDNA sequences with their corresponding genomic templates in multiple cell lines from brain, colon, breast, bone marrow, lymph, liver, ovary and kidney tissue. Our findings help to elucidate the role of A-to-I RNA editing in the regulation of tissue-specific development and function, and the approach utilized here can be broadened to study other types of tissue-specific substitution editing.

  13. Monitoring temporal microstructural variations of skeletal muscle tissues by multispectral Mueller matrix polarimetry

    Science.gov (United States)

    Dong, Yang; He, Honghui; He, Chao; Ma, Hui

    2017-02-01

    Mueller matrix polarimetry is a powerful tool for detecting microscopic structures, therefore can be used to monitor physiological changes of tissue samples. Meanwhile, spectral features of scattered light can also provide abundant microstructural information of tissues. In this paper, we take the 2D multispectral backscattering Mueller matrix images of bovine skeletal muscle tissues, and analyze their temporal variation behavior using multispectral Mueller matrix parameters. The 2D images of the Mueller matrix elements are reduced to the multispectral frequency distribution histograms (mFDHs) to reveal the dominant structural features of the muscle samples more clearly. For quantitative analysis, the multispectral Mueller matrix transformation (MMT) parameters are calculated to characterize the microstructural variations during the rigor mortis and proteolysis processes of the skeletal muscle tissue samples. The experimental results indicate that the multispectral MMT parameters can be used to judge different physiological stages for bovine skeletal muscle tissues in 24 hours, and combining with the multispectral technique, the Mueller matrix polarimetry and FDH analysis can monitor the microstructural variation features of skeletal muscle samples. The techniques may be used for quick assessment and quantitative monitoring of meat qualities in food industry.

  14. Evaluation of tissue oxygen measurements for flap monitoring in an animal model

    DEFF Research Database (Denmark)

    Bonde, Christian; Elberg, Jens; Holstein-Rathlou, N.-H.

    2008-01-01

    Tissue oxygen tension (p(ti)O(2)) measurements are common in neurosurgery but uncommon in plastic surgery. We examined this technique as a monitoring method with probe placement in the subcutaneous tissue and addressed the importance of probe placement. Myocutaneous flaps were raised in an animal......) was 18 minutes. We found no significant relation between initial levels of p(ti)O(2) and T(1/2). Location of the probe and absolute p(ti)O(2) value is of little relevance for flap monitoring. It is the relative change in p(ti)O(2) that is important. The p(ti)O(2) technique is well suited for monitoring...

  15. Multimode near-field microwave monitoring of free water content of skin and imaging of tissue

    Energy Technology Data Exchange (ETDEWEB)

    Lofland, S E [Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028 (United States); Mazzatenta, J D [Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028 (United States); Croman, J [Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028 (United States); Tyagi, S D [Department of Physics, Drexel University, 34th and Chestnut Sts., Philadelphia, PA 19104 (United States)

    2007-03-07

    We have used the near-field scanning microwave microscopy (NSMM) technique in the 1-10 GHz range to monitor the free water content of skin. The water content is interpreted from the measured dielectric properties of the epidermis. The finger skin was first hydrated by soaking in water at 37 {sup 0}C for 30 min followed by monitoring of water content as the free water evaporated under ambient conditions. The same technique has also been employed to image a 1 cm x 1 cm sample of chicken skin. It has been shown that variations exist in the resonant frequencies and quality factors of tissue under varying physical parameters. The samples analysed were as-received and thermally dehydrated or damaged chicken tissue samples. We contrast between the dielectric properties with the optical images. We also discuss possible application of our imaging technique in clinical monitoring of the wound healing process.

  16. Long ncRNA expression associates with tissue-specific enhancers.

    Science.gov (United States)

    Vučićević, Dubravka; Corradin, Olivia; Ntini, Evgenia; Scacheri, Peter C; Ørom, Ulf Andersson

    2015-01-01

    Long non-coding RNAs (ncRNA) have recently been demonstrated to be expressed from a subset of enhancers and to be required for the distant regulation of gene expression. Several approaches to predict enhancers have been developed based on various chromatin marks and occupancy of enhancer-binding proteins. Despite the rapid advances in the field, no consensus how to define tissue specific enhancers yet exists. Here, we identify 2,695 long ncRNAs annotated by ENCODE (corresponding to 28% of all ENCODE annotated long ncRNAs) that overlap tissue-specific enhancers. We use a recently developed algorithm to predict tissue-specific enhancers, PreSTIGE, that is based on the H3K4me1 mark and tissue specific expression of mRNAs. The expression of the long ncRNAs overlapping enhancers is significantly higher when the enhancer is predicted as active in a specific cell line, suggesting a general interdependency of active enhancers and expression of long ncRNAs. This dependency is not identified using previous enhancer prediction algorithms that do not account for expression of their downstream targets. The predicted enhancers that overlap annotated long ncRNAs generally have a lower ratio of H3K4me1 to H3K4me3, suggesting that enhancers expressing long ncRNAs might be associated with specific epigenetic marks. In conclusion, we demonstrate the tissue-specific predictive power of PreSTIGE and provide evidence for thousands of long ncRNAs that are expressed from active tissue-specific enhancers, suggesting a particularly important functional relationship between long ncRNAs and enhancer activity in determining tissue-specific gene expression.

  17. 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

  18. 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.

  19. Pathway-specific differences between tumor cell lines and normal and tumor tissue cells

    Directory of Open Access Journals (Sweden)

    Tozeren Aydin

    2006-11-01

    Full Text Available Abstract Background Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue. Methods This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM. Results Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs, and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways. Conclusion Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative

  20. Tension of knotted surgical sutures shows tissue specific rapid loss in a rodent model

    Directory of Open Access Journals (Sweden)

    Klink Christian D

    2011-12-01

    Full Text Available Abstract Background Every surgical suture compresses the enclosed tissue with a tension that depends from the knotting force and the resistance of the tissue. The aim of this study was to identify the dynamic change of applied suture tension with regard to the tissue specific cutting reaction. Methods In rabbits we placed single polypropylene sutures (3/0 in skin, muscle, liver, stomach and small intestine. Six measurements for each single organ were determined by tension sensors for 60 minutes. We collected tissue specimens to analyse the connective tissue stability by measuring the collagen/protein content. Results We identified three phases in the process of suture loosening. The initial rapid loss of the first phase lasts only one minute. It can be regarded as cutting through damage of the tissue. The percentage of lost tension is closely related to the collagen content of the tissue (r = -0.424; p = 0.016. The second phase is characterized by a slower decrease of suture tension, reflecting a tissue specific plastic deformation. Phase 3 is characterized by a plateau representing the remaining structural stability of the tissue. The ratio of remaining tension to initial tension of phase 1 is closely related to the collagen content of the tissue (r = 0.392; p = 0.026. Conclusions Knotted non-elastic monofilament sutures rapidly loose tension. The initial phase of high tension may be narrowed by reduction of the surgeons' initial force of the sutures' elasticity to those of the tissue. Further studies have to confirm, whether reduced tissue compression and less local damage permits improved wound healing.

  1. Stable microwave radiometry system for long term monitoring of deep tissue temperature

    Science.gov (United States)

    Stauffer, Paul R.; Rodriques, Dario B.; Salahi, Sara; Topsakal, Erdem; Oliveira, Tiago R.; Prakash, Aniruddh; D'Isidoro, Fabio; Reudink, Douglas; Snow, Brent W.; Maccarini, Paolo F.

    2013-02-01

    Background: There are numerous clinical applications for non-invasive monitoring of deep tissue temperature. We present the design and experimental performance of a miniature radiometric thermometry system for measuring volume average temperature of tissue regions located up to 5cm deep in the body. Methods: We constructed a miniature sensor consisting of EMI-shielded log spiral microstrip antenna with high gain onaxis and integrated high-sensitivity 1.35GHz total power radiometer with 500 MHz bandwidth. We tested performance of the radiometry system in both simulated and experimental multilayer phantom models of several intended clinical measurement sites: i) brown adipose tissue (BAT) depots within 2cm of the skin surface, ii) 3-5cm deep kidney, and iii) human brain underlying intact scalp and skull. The physical models included layers of circulating tissue-mimicking liquids controlled at different temperatures to characterize our ability to quantify small changes in target temperature at depth under normothermic surface tissues. Results: We report SAR patterns that characterize the sense region of a 2.6cm diameter receive antenna, and radiometric power measurements as a function of deep tissue temperature that quantify radiometer sensitivity. The data demonstrate: i) our ability to accurately track temperature rise in realistic tissue targets such as urine refluxed from prewarmed bladder into kidney, and 10°C drop in brain temperature underlying normothermic scalp and skull, and ii) long term accuracy and stability of +0.4°C over 4.5 hours as needed for monitoring core body temperature over extended surgery or monitoring effects of brown fat metabolism over an extended sleep/wake cycle. Conclusions: A non-invasive sensor consisting of 2.6cm diameter receive antenna and integral 1.35GHz total power radiometer has demonstrated sufficient sensitivity to track clinically significant changes in temperature of deep tissue targets underlying normothermic surface

  2. TISSUE POLYPEPTIDE-SPECIFIC ANTIGEN - A DISCRIMINATIVE PARAMETER BETWEEN PROSTATE-CANCER AND BENIGN PROSTATIC HYPERTROPHY

    NARCIS (Netherlands)

    MARRINK, J; OOSTEROM, R; BONFRER, HMG; SCHRODER, FH; MENSINK, HJA

    1993-01-01

    The serum concentration of the cell proliferation marker TPS (tissue polypeptide-specific antigen) was compared with the tumour marker PSA (prostate specific antigen). PSA was found elevated in 50% of the benign prostatic hypertrophy (BPH) patients, in 88% of the patients with active prostate cancer

  3. TISSUE POLYPEPTIDE-SPECIFIC ANTIGEN - A DISCRIMINATIVE PARAMETER BETWEEN PROSTATE-CANCER AND BENIGN PROSTATIC HYPERTROPHY

    NARCIS (Netherlands)

    MARRINK, J; OOSTEROM, R; BONFRER, HMG; SCHRODER, FH; MENSINK, HJA

    1993-01-01

    The serum concentration of the cell proliferation marker TPS (tissue polypeptide-specific antigen) was compared with the tumour marker PSA (prostate specific antigen). PSA was found elevated in 50% of the benign prostatic hypertrophy (BPH) patients, in 88% of the patients with active prostate cancer

  4. Non-destructive monitoring of viability in an ex vivo organ culture model of osteochondral tissue

    Directory of Open Access Journals (Sweden)

    KM Elson

    2015-06-01

    Full Text Available Organ culture is an increasingly important tool in research, with advantages over monolayer cell culture due to the inherent natural environment of tissues. Successful organ cultures must retain cell viability. The aim of this study was to produce viable and non-viable osteochondral organ cultures, to assess the accumulation of soluble markers in the conditioned medium for predicting tissue viability. Porcine femoral osteochondral plugs were cultured for 20 days, with the addition of Triton X-100 on day 6 (to induce necrosis, camptothecin (to induce apoptosis or no toxic additives. Tissue viability was assessed by the tissue destructive XTT (2,3-bis[2-methoxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxyanilide tetrazolium salt assay method and LIVE/DEAD® staining of the cartilage at days 0, 6 and 20. Tissue structure was assessed by histological evaluation using haematoxylin & eosin and safranin O. Conditioned medium was assessed every 3-4 days for glucose depletion, and levels of lactate dehydrogenase (LDH, alkaline phosphatase (AP, glycosaminoglycans (GAGs, and matrix metalloproteinase (MMP-2 and MMP-9. Necrotic cultures immediately showed a reduction in glucose consumption, and an immediate increase in LDH, GAG, MMP-2 and MMP-9 levels. Apoptotic cultures showed a delayed reduction in glucose consumption and delayed increase in LDH, a small rise in MMP-2 and MMP-9, but no significant effect on GAGs released into the conditioned medium. The data showed that tissue viability could be monitored by assessing the conditioned medium for the aforementioned markers, negating the need for tissue destructive assays. Physiologically relevant whole- or part-joint organ culture models, necessary for research and pre-clinical assessment of therapies, could be monitored this way, reducing the need to sacrifice tissues to determine viability, and hence reducing the sample numbers necessary.

  5. Tissue-Specific Immune Gene Expression in the Migratory Locust, Locusta Migratoria

    Directory of Open Access Journals (Sweden)

    Tamara Pulpitel

    2015-04-01

    Full Text Available The ability of hosts to respond to infection involves several complex immune recognition pathways. Broadly conserved pathogen-associated molecular patterns (PAMPs allow individuals to target a range of invading microbes. Recently, studies on insect innate immunity have found evidence that a single pathogen can activate different immune pathways across species. In this study, expression changes in immune genes encoding peptidoglycan-recognition protein SA (PGRP-SA, gram-negative binding protein 1 (GNBP1 and prophenoloxidase (ProPO were investigated in Locusta migratoria, following an immune challenge using injected lipopolysaccharide (LPS solution from Escherichia coli. Since immune activation might also be tissue-specific, gene expression levels were followed across a range of tissue types. For PGRP-SA, expression increased in response to LPS within all seven of the tissue-types assayed and differed significantly between tissues. Expression of GNBP1 similarly varied across tissue types, yet showed no clear expression difference between LPS-injected and uninfected locusts. Increases in ProPO expression in response to LPS, however, could only be detected in the gut sections. This study has revealed tissue-specific immune response to add a new level of complexity to insect immune studies. In addition to variation in recognition pathways identified in previous works, tissue-specificity should be carefully considered in similar works.

  6. 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.

  7. Using swept source optical coherence tomography to monitor wound healing in tissue engineered skin

    Science.gov (United States)

    Smith, L. E.; Lu, Z.; Bonesi, M.; Smallwood, R.; Matcher, S. J.; MacNeil, S.

    2010-02-01

    There is an increasing need for a robust simple to use non-invasive imaging technology for monitoring tissue engineered constructs as they develop. We have applied optical coherence tomography (OCT), a relatively new optical technique, to image tissue engineered constructs. Our aim was to evaluate the use of swept-source optical coherence tomography (SSOCT) to non-invasively image reconstructed skin as it developed over several weeks. The epidermis of the reconstructed skin was readily distinguished from the neodermis when examined with standard histology - a destructive imaging technique - of samples. The development of reconstructed skin based on deepithelialised acellular dermis (DED) was accurately monitored with SS-OCT over three weeks and confirmed with conventional histology. It was also possible to image changes in the epidermis due to the presence of melanoma and the healing of these 3D models after wounding with a scalpel, with or without the addition of a fibrin clot. SS-OCT is proving to be a valuable tool in tissue engineering, showing great promise for the non-invasive imaging of optically turbid tissue engineered constructs, including tissue engineered skin.

  8. Precision of multiple reaction monitoring mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue.

    Science.gov (United States)

    Sprung, Robert W; Martinez, Misti A; Carpenter, Kristen L; Ham, Amy-Joan L; Washington, Mary Kay; Arteaga, Carlos L; Sanders, Melinda E; Liebler, Daniel C

    2012-06-01

    We compared the reproducibility of multiple reaction monitoring (MRM) mass spectrometry-based peptide quantitation in tryptic digests from formalin-fixed, paraffin-embedded (FFPE) and frozen clear cell renal cell carcinoma tissues. The analyses targeted a candidate set of 114 peptides previously identified in shotgun proteomic analyses, of which 104 were detectable in FFPE and frozen tissue. Although signal intensities for MRM of peptides from FFPE tissue were on average 66% of those in frozen tissue, median coefficients of variation (CV) for measurements in FFPE and frozen tissues were nearly identical (18-20%). Measurements of lysine C-terminal peptides and arginine C-terminal peptides from FFPE tissue were similarly reproducible (19.5% and 18.3% median CV, respectively). We further evaluated the precision of MRM-based quantitation by analysis of peptides from the Her2 receptor in FFPE and frozen tissues from a Her2 overexpressing mouse xenograft model of breast cancer and in human FFPE breast cancer specimens. We obtained equivalent MRM measurements of HER2 receptor levels in FFPE and frozen mouse xenografts derived from HER2-overexpressing BT474 cells and HER2-negative Sum159 cells. MRM analyses of 5 HER2-positive and 5 HER-negative human FFPE breast tumors confirmed the results of immunohistochemical analyses, thus demonstrating the feasibility of HER2 protein quantification in FFPE tissue specimens. The data demonstrate that MRM analyses can be performed with equal precision on FFPE and frozen tissues and that lysine-containing peptides can be selected for quantitative comparisons, despite the greater impact of formalin fixation on lysine residues. The data further illustrate the feasibility of applying MRM to quantify clinically important tissue biomarkers in FFPE specimens.

  9. Mercury monitoring in fish using a non-lethal tissue biopsy method

    Science.gov (United States)

    Ackerson, J; Schmitt, Christopher J.; McKee, J; Brumbaugh, W. G.

    2010-01-01

    The occurrence of mercury in fish is well-known and often occurs at levels that warrant restricted consumption by sensitive human populations. Because of this, local wildlife and health agencies have developed monitoring programs to identify the magnitude of fish contamination and changes through time. Monitoring mercury levels in fish typically requires killing fish for removal of a fillet. Recently, researchers have proposed the use of a non-lethal tissue biopsy plug method as a surrogate for analysis of the entire fillet.

  10. In situ monitoring of brain tissue reaction of chronically implanted electrodes with an optical coherence tomography fiber system

    Science.gov (United States)

    Xie, Yijing; Hassler, Christina; Stieglitz, Thomas; Seifert, Andreas; Hofmann, Ulrich G.

    2014-03-01

    Neural microelectrodes are well established tools for delivering therapeutic electrical pulses, and recording neural electrophysiological signals. However, long term implanted neural probes often become functionally impaired by tissue encapsulation. At present, analyzing this immune reaction is only feasible with post-mortem histology; currently no means for specific in vivo monitoring exist and most applicable imaging modalities provide no sufficient resolution for a cellular measurement in deep brain regions. Optical coherence tomography (OCT) is a well developed imaging modality, providing cellular resolution and up to 1.2 mm imaging depth in brain tissue. Further more, a fiber based spectral domain OCT was shown to be capable of minimally invasive brain intervention. In the present study, we propose to use a fiber based spectral domain OCT to monitor the the progression of the tissue's immune response and scar encapsulation of microprobes in a rat animal model. We developed an integrated OCT fiber catheter consisting of an implantable ferrule based fiber cannula and a fiber patch cable. The fiber cannula was 18.5 mm long, including a 10.5 mm ceramic ferrule and a 8.0 mm long, 125 μm single mode fiber. A mating sleeve was used to fix and connect the fiber cannula to the OCT fiber cable. Light attenuation between the OCT fiber cable and the fiber cannula through the mating sleeve was measured and minimized. The fiber cannula was implanted in rat brain together with a microelectrode in sight used as a foreign body to induce the brain tissue immune reaction. Preliminary data showed a significant enhancement of the OCT backscattering signal during the brain tissue scarring process, while the OCT signal of the flexible microelectrode was getting weaker consequentially.

  11. Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

    Directory of Open Access Journals (Sweden)

    States David

    2007-01-01

    Full Text Available Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcription factor sites with previously uncharacterized function in gene expression. Coupled with the complexity underlying tissue-specific gene expression, there are several motifs that are putatively responsible for expression in a certain cell type. This has important implications in understanding fundamental biological processes such as development and disease progression. In this work, we present an approach to the identification of motifs (not necessarily transcription factor sites and examine its application to some questions in current bioinformatics research. These motifs are seen to discriminate tissue-specific gene promoter or regulatory regions from those that are not tissue-specific. There are two main contributions of this work. Firstly, we propose the use of directed information for such classification constrained motif discovery, and then use the selected features with a support vector machine (SVM classifier to find the tissue specificity of any sequence of interest. Such analysis yields several novel interesting motifs that merit further experimental characterization. Furthermore, this approach leads to a principled framework for the prospective examination of any chosen motif to be discriminatory motif for a group of coexpressed/coregulated genes, thereby integrating sequence and expression perspectives. We hypothesize that the discovery of these motifs would enable the large-scale investigation for the tissue-specific regulatory role of any conserved sequence element identified from genome-wide studies.

  12. А new Gal/GalNAc-specific lectin from the mussel Mytilus trossulus: Structure, tissue specificity, antimicrobial and antifungal activity.

    Science.gov (United States)

    Chikalovets, Irina V; Kovalchuk, Svetlana N; Litovchenko, Alina P; Molchanova, Valentina I; Pivkin, Mikhail V; Chernikov, Oleg V

    2016-03-01

    In the present study, a new Gal/GalNAc specific lectin from the mussel Mytilus trossulus (designated as MTL) was identified, and its expression levels, both in tissues and toward pathogen stimulation, were then characterized. The MTL primary structure was determined via cDNA sequencing. Deduced sequence of 150 amino acid residues showed 89% similarity to lectins from the mussels Crenomytilus grayanus and Mytilus galloprovincialis that were the first members of a new family of zoolectins. The results indicated that the MTL might be involved in immune response toward pathogen infection, and it might perform different recognition specificity toward bacteria or fungi.

  13. Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice.

    Science.gov (United States)

    Hu, Zhan; Ding, Xuezhi; Hu, Shengbiao; Sun, Yunjun; Xia, Liqiu

    2013-12-01

    Marker-free, genetically-modified rice was created by the tissue-specifically regulated Cre/loxP system, in which the Cre recombinase gene and hygromycin phosphotransferase gene (hpt) were flanked by two directly oriented loxP sites. Cre expression was activated by the tissue-specific promoter OsMADS45 in flower or napin in seed, resulting in simultaneous excision of the recombinase and marker genes. Segregation of T1 progeny was performed to select recombined plants. The excision was confirmed by PCR, Southern blot and sequence analyses indicating that efficiency varied from 10 to 53 % for OsMADS45 and from 12 to 36 % for napin. The expression of cry1Ac and vip3A was detected by RT-PCR analysis in marker-free transgenic rice. These results suggested that our tissue-specifically regulated Cre/loxP system could auto-excise marker genes from transgenic rice and alleviate public concerns about the security of GM crops.

  14. Linear Elastic Properties of the Facial Soft Tissues Using an Aspiration Device: Towards Patient Specific Characterization.

    OpenAIRE

    Luboz, Vincent; Promayon, Emmanuel; Payan, Yohan

    2014-01-01

    International audience; Biomechanical modeling of the facial soft tissue behavior is needed in aesthetic or maxillo-facial surgeries where the simulation of the bone displacements cannot accurately predict the visible outcome on the patient's face. Because these tissues have different nature and elastic properties across the face, depending on their thickness, and their content in fat or muscle, individualizing their mechanical parameters could increase the simulation accuracy. Using a specif...

  15. 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.

    2016-01-01

    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. PMID:27821729

  16. Simultaneous Monitoring of Vascular Oxygenation and Tissue Oxygen Tension of Breast Tumors Under Hyperbaric Oxygen Exposure

    Science.gov (United States)

    2008-04-01

    biological tissue, and allow for detection of specific light-absorbing chromophores in human in vivo, such as oxygenated and deoxygenated hemoglobin...spectra from tumor tissue. Briefly, continuous wave (CW) light from a 20 W tungsten-halogen light source (HL-2000HP, ocean optics, FL) is coupled...spectrometer (USB2000, Ocean optics, FL). The broadband light diffuse spectrometer provides reflectance spectra from 400 to 900 nm. According to

  17. Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.

    Science.gov (United States)

    Mei, Hao; Li, Lianna; Liu, Shijian; Jiang, Fan; Griswold, Michael; Mosley, Thomas

    2017-01-21

    We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

  18. 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.

  19. 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.

  20. The Role of the Endocrine System in Feeding-Induced Tissue-Specific Circadian Entrainment

    Directory of Open Access Journals (Sweden)

    Miho Sato

    2014-07-01

    Full Text Available 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.

  1. Photoacoustic a-scanning and monitoring of blood content in tissue

    Science.gov (United States)

    Kolkman, Roy G. M.; Pilatou, Magdalena C.; Hondebrink, Erwin; de Mul, Frits F. M.

    2000-05-01

    To localize and monitor the blood content in tissue we developed a very sensitive double-ring photo-acoustical detector. PvdF has been used as piezo-electric material. In this detector also a fiber for illumination of the sample is integrated. This detector has the advantage that it is very sensitive in the forward direction. A ratio of FWHM to depth of 1:70 can be obtained with this detector.

  2. Application of new optical coherence elastography to monitor the mineralization processing in bone tissue engineering constructs

    Science.gov (United States)

    Guan, Guangying; Song, Shaozhen; Huang, Zhihong; Yang, Ying

    2015-03-01

    Generation of functional tissue in vitro through tissue engineering technique is a promising direction to repair and replace malfunctioned organ and tissue in the modern medicine for various diseases which could not been treated well by conventional therapy. Similar to the embryo development, the generation of tissue in vitro is a highly dynamic processing. Obtaining the feedback of the processing real time is highly demanded. In this study, a new methodology has been explored aiming to monitor the morphological and mechanical property alteration of bone tissue engineering constructs simultaneously. Optical coherence elastography (OCE) equipped with a LDS V201 permanent magnet shaker and a modulated acoustic radiation force (ARF) to provide a vibration signal, has been used for the real time and non-destructive monitoring. A phantom construct system has been used to optimize the measurement conditions in which agar hydrogel with concentration from 0, 0.75 to 2% with/without hydroxyappatite particles have been injected to 3D porous poly (lactic acid) scaffolds to simulate the collagenous extracellular matrix (ECM) and mineralized ECM. The structural and elastography images of the constructs have clearly demonstrated the linear relation with the increased mechanical property versus the increase of agar concentration within the pores of the scaffolds. The MG63 bone cells seeded in the scaffolds and cultured for 4 weeks have been monitored by the established protocol exhibiting the increased mechanical strength in the pore wall where the ECM or mineralized ECM was assumed to be formed in comparison to empty pores. This study confirms that OCE-ARF could become a valuable tool in regenerative medicine to assess the biological events during in vitro culture and conditioning.

  3. Online Image-based Monitoring of Soft-tissue Displacements for Radiation Therapy of the Prostate

    Energy Technology Data Exchange (ETDEWEB)

    Schlosser, Jeffrey [Department of Mechanical Engineering, Stanford University, Stanford, CA (United States); Department of Bioengineering, Stanford University, Stanford, CA (United States); Salisbury, Kenneth [Department of Computer Science, Stanford University, Stanford, CA (United States); Department of Surgery, Stanford University, Stanford, CA (United States); Hristov, Dimitre, E-mail: dhristov@stanford.edu [Department of Radiation Oncology, Stanford University, Stanford, CA (United States)

    2012-08-01

    Purpose: Emerging prolonged, hypofractionated radiotherapy regimens rely on high-dose conformality to minimize toxicity and thus can benefit from image guidance systems that continuously monitor target position during beam delivery. To address this need we previously developed, as a potential add-on device for existing linear accelerators, a novel telerobotic ultrasound system capable of real-time, soft-tissue imaging. Expanding on this capability, the aim of this work was to develop and characterize an image-based technique for real-time detection of prostate displacements. Methods and Materials: Image processing techniques were implemented on spatially localized ultrasound images to generate two parameters representing prostate displacements in real time. In a phantom and five volunteers, soft-tissue targets were continuously imaged with a customized robotic manipulator while recording the two tissue displacement parameters (TDPs). Variations of the TDPs in the absence of tissue displacements were evaluated, as was the sensitivity of the TDPs to prostate translations and rotations. Robustness of the approach to probe force was also investigated. Results: With 95% confidence, the proposed method detected in vivo prostate displacements before they exceeded 2.3, 2.5, and 2.8 mm in anteroposterior, superoinferior, and mediolateral directions. Prostate pitch was detected before exceeding 4.7 Degree-Sign at 95% confidence. Total system time lag averaged 173 ms, mostly limited by ultrasound acquisition rate. False positives (FPs) (FP) in the absence of displacements did not exceed 1.5 FP events per 10 min of continuous in vivo imaging time. Conclusions: The feasibility of using telerobotic ultrasound for real-time, soft-tissue-based monitoring of target displacements was confirmed in vivo. Such monitoring has the potential to detect small clinically relevant intrafractional variations of the prostate position during beam delivery.

  4. Limbal Stromal Tissue Specific Stem Cells and Their Differentiation Potential to Corneal Epithelial Cells.

    Science.gov (United States)

    Katikireddy, Kishore Reddy; Jurkunas, Ula V

    2016-01-01

    From the derivation of the first human embryonic stem (hES) cell line to the development of induced pluripotent stem (iPS) cells; it has become evident that tissue specific stem cells are able to differentiate into a specific somatic cell types. The understanding of key processes such as the signaling pathways and the role of the microenvironment in epidermal/epithelial development has provided important clues for the derivation of specific epithelial cell types.Various differentiation protocols/methods were used to attain specific epithelial cell types. Here, we describe in detail the procedure to follow for isolation of tissue specific stem cells, mimicking their microenvironment to attain stem cell characteristics, and their potential differentiation to corneal epithelial cells.

  5. Coat protein promoter from cotton leaf curl virus is not a tissue-specifically expressed promoter

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Geminivirus is a kind of single-stranded DNA virus. Experimental results from tomato golden mosaic virus (TGMV) showed that expression pattern of coat protein gene (cp) promoter was phloem specifically expressed. In this note, the studies on cp promoter of cotton leaf curl virus (CLCuV) which is found and identified recently suggest that the promoter is not phloem specifically expressed. The expressing activity of gus gene driven by the promoter exists not only in phloem but also in mesophyll tissues and root tip meristem. Transient expression suggests that cp promoter transactivated by AC2 shows expressing activity in mesophyll and vascular tissue of leaf vein.

  6. Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns

    DEFF Research Database (Denmark)

    Lundby, Alicia; Hansen, Kasper Lage; Weinert, Brian Tate;

    2012-01-01

    ,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals...... that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle...

  7. Monitoring late radiation damage in normal muscle tissue with electrical impedance spectroscopy

    Science.gov (United States)

    Osterman, Kendra Sunshine

    During radiation treatment for cancer, normal tissue will be exposed to radiation and it is the response of this tissue and the risk of complications that limits the prescribed dose and the efficacy of treatment. The response to radiation exposure is dose, time and tissue-type dependent and has been studied extensively in animal and human systems. However, there remains significant heterogeneity among individuals. Systematic and quantitative monitoring of tissue response with electrical impedance spectroscopy (EIS) might providing insight into early warning signs of late effects which could be used to alter the course of therapy on an individual patient basis. The implementation of EIS in three clinically relevant radiation settings is described. A kilovolt unit (orthovoltage, x-ray), a linear accelerator (x-ray), and an implantable radionuclide source (high dose rate, iridium-192 seed) were employed for the irradiation of muscle in the hind leg of rats. Doses of 70 Gy, 90 Gy, and 150 Gy were delivered with orthovoltage, nominal doses of 70 and 90 Gy which translate to doses of approximately 50 and 63 Gy at a 5mm distance from the center were employed with the linear accelerator, and doses of 26 and 52 Gy, at 5mm, were employed with the HDR system. The responses were monitored from 1--4 months post-irradiation. In all cases, EIS was capable of detecting a dose and time response, suggesting that EIS may indeed have a role to play in three of the most common irradiation procedures.

  8. Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression.

    Science.gov (United States)

    Dean, Rebecca; Mank, Judith E

    2016-09-01

    Genetic correlations between males and females are often thought to constrain the evolution of sexual dimorphism. However, sexually dimorphic traits and the underlying sexually dimorphic gene expression patterns are often rapidly evolving. We explore this apparent paradox by measuring the genetic correlation in gene expression between males and females (Cmf) across broad evolutionary timescales, using two RNA-sequencing data sets spanning multiple populations and multiple species. We find that unbiased genes have higher Cmf than sex-biased genes, consistent with intersexual genetic correlations constraining the evolution of sexual dimorphism. However, we found that highly sex-biased genes (both male and female biased) also had higher tissue specificity, and unbiased genes had greater expression breadth, suggesting that pleiotropy may constrain the breakdown of intersexual genetic correlations. Finally, we show that genes with high Cmf showed some degree of sex-specific changes in gene expression in males and females. Together, our results suggest that genetic correlations between males and females may be less important in constraining the evolution of sex-biased gene expression than pleiotropy. Sex-specific regulatory variation and tissue specificity may resolve the paradox of widespread sex bias within a largely shared genome.

  9. Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.

    Science.gov (United States)

    Blazie, Stephen M; Babb, Cody; Wilky, Henry; Rawls, Alan; Park, Jin G; Mangone, Marco

    2015-01-20

    Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. Here we developed a new method, polyA-tagging and sequencing (PAT-Seq) to isolate high-quality tissue-specific mRNA from Caenorhabditis elegans intestine, pharynx and body muscle tissues and study changes in their tissue-specific transcriptomes and 3'UTRomes. We have identified thousands of novel genes and isoforms differentially expressed between these three tissues. The intestine transcriptome is expansive, expressing over 30% of C. elegans mRNAs, while muscle transcriptomes are smaller but contain characteristic unique gene signatures. Active promoter regions in all three tissues reveal both known and novel enriched tissue-specific elements, along with putative transcription factors, suggesting novel tissue-specific modes of transcription initiation. We have precisely mapped approximately 20,000 tissue-specific polyadenylation sites and discovered that about 30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3'UTR isoforms significantly enriched with microRNA targets. For the first time, PAT-Seq allowed us to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment. We pinpoint precise tissue-specific transcriptome rearrangements and for the first time link tissue-specific alternative polyadenylation to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.

  10. Sensitivity and Specificity of Cardiac Tissue Discrimination Using Fiber-Optics Confocal Microscopy.

    Science.gov (United States)

    Huang, Chao; Sachse, Frank B; Hitchcock, Robert W; Kaza, Aditya K

    2016-01-01

    Disturbances of the cardiac conduction system constitute a major risk after surgical repair of complex cases of congenital heart disease. Intraoperative identification of the conduction system may reduce the incidence of these disturbances. We previously developed an approach to identify cardiac tissue types using fiber-optics confocal microscopy and extracellular fluorophores. Here, we applied this approach to investigate sensitivity and specificity of human and automated classification in discriminating images of atrial working myocardium and specialized tissue of the conduction system. Two-dimensional image sequences from atrial working myocardium and nodal tissue of isolated perfused rodent hearts were acquired using a fiber-optics confocal microscope (Leica FCM1000). We compared two methods for local application of extracellular fluorophores: topical via pipette and with a dye carrier. Eight blinded examiners evaluated 162 randomly selected images of atrial working myocardium (n = 81) and nodal tissue (n = 81). In addition, we evaluated the images using automated classification. Blinded examiners achieved a sensitivity and specificity of 99.2 ± 0.3% and 98.0 ± 0.7%, respectively, with the dye carrier method of dye application. Sensitivity and specificity was similar for dye application via a pipette (99.2 ± 0.3% and 94.0 ± 2.4%, respectively). Sensitivity and specificity for automated methods of tissue discrimination were similarly high. Human and automated classification achieved high sensitivity and specificity in discriminating atrial working myocardium and nodal tissue. We suggest that our findings facilitate clinical translation of fiber-optics confocal microscopy as an intraoperative imaging modality to reduce the incidence of conduction disturbances during surgical correction of congenital heart disease.

  11. Sensitivity and Specificity of Cardiac Tissue Discrimination Using Fiber-Optics Confocal Microscopy

    Science.gov (United States)

    Huang, Chao; Sachse, Frank B.; Hitchcock, Robert W.; Kaza, Aditya K.

    2016-01-01

    Disturbances of the cardiac conduction system constitute a major risk after surgical repair of complex cases of congenital heart disease. Intraoperative identification of the conduction system may reduce the incidence of these disturbances. We previously developed an approach to identify cardiac tissue types using fiber-optics confocal microscopy and extracellular fluorophores. Here, we applied this approach to investigate sensitivity and specificity of human and automated classification in discriminating images of atrial working myocardium and specialized tissue of the conduction system. Two-dimensional image sequences from atrial working myocardium and nodal tissue of isolated perfused rodent hearts were acquired using a fiber-optics confocal microscope (Leica FCM1000). We compared two methods for local application of extracellular fluorophores: topical via pipette and with a dye carrier. Eight blinded examiners evaluated 162 randomly selected images of atrial working myocardium (n = 81) and nodal tissue (n = 81). In addition, we evaluated the images using automated classification. Blinded examiners achieved a sensitivity and specificity of 99.2±0.3% and 98.0±0.7%, respectively, with the dye carrier method of dye application. Sensitivity and specificity was similar for dye application via a pipette (99.2±0.3% and 94.0±2.4%, respectively). Sensitivity and specificity for automated methods of tissue discrimination were similarly high. Human and automated classification achieved high sensitivity and specificity in discriminating atrial working myocardium and nodal tissue. We suggest that our findings facilitate clinical translation of fiber-optics confocal microscopy as an intraoperative imaging modality to reduce the incidence of conduction disturbances during surgical correction of congenital heart disease. PMID:26808149

  12. Sensitivity and Specificity of Cardiac Tissue Discrimination Using Fiber-Optics Confocal Microscopy.

    Directory of Open Access Journals (Sweden)

    Chao Huang

    Full Text Available Disturbances of the cardiac conduction system constitute a major risk after surgical repair of complex cases of congenital heart disease. Intraoperative identification of the conduction system may reduce the incidence of these disturbances. We previously developed an approach to identify cardiac tissue types using fiber-optics confocal microscopy and extracellular fluorophores. Here, we applied this approach to investigate sensitivity and specificity of human and automated classification in discriminating images of atrial working myocardium and specialized tissue of the conduction system. Two-dimensional image sequences from atrial working myocardium and nodal tissue of isolated perfused rodent hearts were acquired using a fiber-optics confocal microscope (Leica FCM1000. We compared two methods for local application of extracellular fluorophores: topical via pipette and with a dye carrier. Eight blinded examiners evaluated 162 randomly selected images of atrial working myocardium (n = 81 and nodal tissue (n = 81. In addition, we evaluated the images using automated classification. Blinded examiners achieved a sensitivity and specificity of 99.2 ± 0.3% and 98.0 ± 0.7%, respectively, with the dye carrier method of dye application. Sensitivity and specificity was similar for dye application via a pipette (99.2 ± 0.3% and 94.0 ± 2.4%, respectively. Sensitivity and specificity for automated methods of tissue discrimination were similarly high. Human and automated classification achieved high sensitivity and specificity in discriminating atrial working myocardium and nodal tissue. We suggest that our findings facilitate clinical translation of fiber-optics confocal microscopy as an intraoperative imaging modality to reduce the incidence of conduction disturbances during surgical correction of congenital heart disease.

  13. Visualizing Oxazine 4 nerve-specific fluorescence ex vivo in frozen tissue sections

    Science.gov (United States)

    Barth, Connor W.; Gibbs, Summer L.

    2016-03-01

    Nerve damage plagues surgical outcomes and remains a major burden for patients, surgeons, and the healthcare system. Fluorescence image-guided surgery using nerve specific small molecule fluorophores offers a solution to diminish surgical nerve damage through improved intraoperative nerve identification and visualization. Oxazine 4 has shown superior nerve specificity in initial testing in vivo, while exhibiting a red shifted excitation and emission spectra compared to other nerve-specific fluorophores. However, Oxazine 4 does not exhibit near-infrared (NIR) excitation and emission, which would be ideal to improve penetration depth and nerve signal to background ratios for in vivo imaging. Successful development of a NIR nerve-specific fluorophore will require understanding of the molecular target of fluorophore nerve specificity. While previous small molecule nerve-specific fluorophores have demonstrated excellent ex vivo nerve specificity, Oxazine 4 ex vivo nerve specific fluorescence has been difficult to visualize. In the present study, we examined each step of the ex vivo fluorescence microscopy sample preparation procedure to discover how in vivo nerve-specific fluorescence is changed during ex vivo tissue sample preparation. Through step-by-step examination we found that Oxazine 4 fluorescence was significantly diminished by washing and mounting tissue sections for microscopy. A method to preserve Oxazine 4 nerve specific fluorescence ex vivo was determined, which can be utilized for visualization by fluorescence microscopy.

  14. Tissue-specific alterations in expression and function of P-glycoprotein in streptozotocininduced diabetic rats

    Institute of Scientific and Technical Information of China (English)

    Lu-lu ZHANG; Guang-ji WANG; Lin XIE; Liang LU; Shi JIN; Xin-yue JING; Dan YAO; Nan HU; Li LIU; Ru DUAN; Xiao-dong LIU

    2011-01-01

    Aim: To investigate the changes of expression and function of P-glycoprotein (P-GP) in cerebral cortex, hippocampus, liver, intestinal mucosa and kidney of streptozocin-induced diabetic rats.Methods: Diabetic rats were prepared via a single dose of streptozocin (65 mg/kg, ip). Abcb1/P-GP mRNA and protein expression levels in tissues were evaluated using quantitative real time polymerase chain reaction (QRT-PCR) analysis and Western blot, respectively.P-GP function was investigated via measuring tissue-to-plasma concentration ratios and body fluid excretion percentages of rhodamine 123.Results: In 5- and 8-week diabetic rats, Abcb1a mRNA levels were significantly decreased in cerebral cortices and intestinal mucosa,but dramatically increased in hippocampus and kidney. In liver, the level was increased in 5-week diabetic rats, and decreased in 8-week diabetic rats. Abcb1b mRNA levels were increased in cerebral cortex, hippocampus and kidney, but reduced in liver and intestinal mucosa in the diabetic rats. Western blot results were in accordance with the alterations of Abcb1a mRNA levels in most tissues examined. P-GP activity was markedly decreased in most tissues of diabetic rats, except kidney tissues.Conclusion: Alterations in the expression and function of Abcb1/P-GP under diabetic conditions are tissue specific, Abcb1 specific and diabetic duration-dependent.

  15. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Maria D Chikina

    2009-06-01

    Full Text Available Tissue-specific gene expression plays a fundamental role in metazoan biology and is an important aspect of many complex diseases. Nevertheless, an organism-wide map of tissue-specific expression remains elusive due to difficulty in obtaining these data experimentally. Here, we leveraged existing whole-animal Caenorhabditis elegans microarray data representing diverse conditions and developmental stages to generate accurate predictions of tissue-specific gene expression and experimentally validated these predictions. These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues. We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues. We also investigate the role of tissue context in gene function through tissue-specific functional interaction networks. To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.

  16. Lipodystrophy and severe metabolic dysfunction in mice with adipose tissue-specific insulin receptor ablation.

    Science.gov (United States)

    Qiang, Guifen; Whang Kong, Hyerim; Xu, Shanshan; Pham, Hoai An; Parlee, Sebastian D; Burr, Aaron A; Gil, Victoria; Pang, Jingbo; Hughes, Amy; Gu, Xuejiang; Fantuzzi, Giamila; MacDougald, Ormond A; Liew, Chong Wee

    2016-07-01

    Insulin signaling plays pivotal roles in the development and metabolism of many tissues and cell types. A previous study demonstrated that ablation of insulin receptor (IR) with aP2-Cre markedly reduced adipose tissues mass and protected mice from obesity. However, multiple studies have demonstrated widespread non-adipocyte recombination of floxed alleles in aP2-Cre mice. These findings underscore the need to re-evaluate the role of IR in adipocyte and systemic metabolism with a more adipose tissue-specific Cre mouse line. We generated and phenotyped a new adipose tissue-specific IR mouse model using the adipose tissue-specific Adipoq-Cre line. Here we show that the Adipoq-Cre-mediated IR KO in mice leads to lipodystrophy and metabolic dysfunction, which is in stark contrast to the previous study. In contrast to white adipocytes, absence of insulin signaling does not affect development of marrow and brown adipocytes, but instead is required for lipid accumulation particularly for the marrow adipocytes. Lipodystrophic IR KO mice have profound insulin resistance, hyperglycemia, organomegaly, and impaired adipokine secretion. Our results demonstrate differential roles for insulin signaling for white, brown, and marrow adipocyte development and metabolic regulation.

  17. Tissue-specific patterning of host innate immune responses by Staphylococcus aureus α-toxin.

    Science.gov (United States)

    Becker, Russell E N; Berube, Bryan J; Sampedro, Georgia R; DeDent, Andrea C; Bubeck Wardenburg, Juliane

    2014-01-01

    Immunomodulatory cytotoxins are prominent virulence factors produced by Staphylococcus aureus, a leading cause of bacterial sepsis, skin infection, and pneumonia. S. aureus α-toxin is a pore-forming toxin that utilizes a widely expressed receptor, ADAM10, to injure the host epithelium, endothelium, and immune cells. As each host tissue is characterized by a unique composition of resident cells and recruited immune cells, the outcome of α-toxin-mediated injury may depend on the infected tissue environment. Utilizing myeloid lineage-specific Adam10 knockout mice, we show that α-toxin exerts tissue-specific effects on innate immunity to staphylococcal infection. Loss of ADAM10 expression exacerbates skin infection, yet affords protection against lethal pneumonia. These diverse outcomes are not related to altered immune cell recruitment, but rather correlate with a defect in toxin-induced IL-1β production. Extension of these studies through analysis of ADAM10 double-knockout mice affecting both the myeloid lineage and either the skin or lung epithelium highlight the prominence of toxin-induced injury to the epithelium in governing the outcome of infection. Together, these studies provide evidence of tissue specificity of pore-forming cytotoxin action in the modulation of host immunity, and illustrate that the outcome of infection is a collective manifestation of all effects of the toxin within the tissue microenvironment.

  18. Tissue-specific deletion patterns of the mitochondrial genome with advancing age.

    Science.gov (United States)

    Meissner, Christoph; Bruse, Petra; Oehmichen, Manfred

    2006-05-01

    Aging is a multifactorial process and a lot of theories have been put forward to explain the deterioration of organ function with advancing age. The free radical hypothesis developed by Harman is amongst the most prominent today and has been focused on mitochondrial aging in the last decades. Applying a long PCR approach we screened human skeletal muscle, heart, caudate nucleus and cerebellum of 50 individuals for large-scale deletions of mitochondrial DNA (mtDNA). The most important observation of our study was the detection of age dependent tissue specific deletion patterns of mtDNA. The pattern of the same tissue of different individuals was more similar than the pattern of different tissues of the same individuals. Whereas deletions were barely detectable in cerebellar tissue, in caudate nucleus a specific banding pattern with deletions of 4-8 kb was already observed around the age of thirty. However, the increase of these large-scale deletions in number and variety over lifetime was more pronounced in skeletal muscle or heart. Our data support the notion that different tissues accumulate mtDNA damage in a specific manner. Although functional consequences of mitochondrial deletions are clearly supported by experimental data on the single-cell level in model organisms and mammals, their role regarding impaired function of organs with advancing age in humans remains unresolved.

  19. A tissue-specific role for intraflagellar transport genes during craniofacial development

    Science.gov (United States)

    Williams, Trevor J.; Snedeker, John; Brugmann, Samantha A.

    2017-01-01

    Primary cilia are nearly ubiquitous, cellular projections that function to transduce molecular signals during development. Loss of functional primary cilia has a particularly profound effect on the developing craniofacial complex, causing several anomalies including craniosynostosis, micrognathia, midfacial dysplasia, cleft lip/palate and oral/dental defects. Development of the craniofacial complex is an intricate process that requires interactions between several different tissues including neural crest cells, neuroectoderm and surface ectoderm. To understand the tissue-specific requirements for primary cilia during craniofacial development we conditionally deleted three separate intraflagellar transport genes, Kif3a, Ift88 and Ttc21b with three distinct drivers, Wnt1-Cre, Crect and AP2-Cre which drive recombination in neural crest, surface ectoderm alone, and neural crest, surface ectoderm and neuroectoderm, respectively. We found that tissue-specific conditional loss of ciliary genes with different functions produces profoundly different facial phenotypes. Furthermore, analysis of basic cellular behaviors in these mutants suggests that loss of primary cilia in a distinct tissue has unique effects on development of adjacent tissues. Together, these data suggest specific spatiotemporal roles for intraflagellar transport genes and the primary cilium during craniofacial development. PMID:28346501

  20. 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

  1. Equal modulation of endothelial cell function by four distinct tissue-specific mesenchymal stem cells.

    Science.gov (United States)

    Lin, Ruei-Zeng; Moreno-Luna, Rafael; Zhou, Bin; Pu, William T; Melero-Martin, Juan M

    2012-09-01

    Mesenchymal stem cells (MSCs) can generate multiple end-stage mesenchymal cell types and constitute a promising population of cells for regenerative therapies. Additionally, there is increasing evidence supporting other trophic activities of MSCs, including the ability to enable formation of vasculature in vivo. Although MSCs were originally isolated from the bone marrow, the presence of these cells in the stromal vascular fraction of multiple adult tissues has been recently recognized. However, it is unknown whether the capacity to modulate vasculogenesis is ubiquitous to all MSCs regardless of their tissue of origin. Here, we demonstrated that tissue-resident MSCs isolated from four distinct tissues have equal capacity to modulate endothelial cell function, including formation of vascular networks in vivo. MSCs were isolated from four murine tissues, including bone marrow, white adipose tissue, skeletal muscle, and myocardium. In culture, all four MSC populations secreted a plethora of pro-angiogenic factors that unequivocally induced proliferation, migration, and tube formation of endothelial colony-forming cells (ECFCs). In vivo, co-implantation of MSCs with ECFCs into mice generated an extensive network of blood vessels with ECFCs specifically lining the lumens and MSCs occupying perivascular positions. Importantly, there were no differences among all four MSCs evaluated. Our studies suggest that the capacity to modulate the formation of vasculature is a ubiquitous property of all MSCs, irrespective of their original anatomical location. These results validate multiple tissues as potential sources of MSCs for future cell-based vascular therapies.

  2. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

    Science.gov (United States)

    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.

  3. Wagging the dogma; tissue-specific cell cycle control in the mouse embryo.

    Science.gov (United States)

    Pagano, Michele; Jackson, Peter K

    2004-09-03

    The family of cyclin-dependent kinases (Cdks) lies at the core of the machinery that drives the cell division cycle. Studies in cultured mammalian cells have provided insight into the cellular functions of many Cdks. Recent Cdk and cyclin knockouts in the mouse show that the functions of G1 cell cycle regulatory genes are often essential only in specific cell types, pointing to our limited understanding of tissue-specific expression, redundancy, and compensating mechanisms in the Cdk network.

  4. Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species.

    Directory of Open Access Journals (Sweden)

    Chrysa Pantzartzi

    Full Text Available The mechanisms of stress tolerance in sessile animals, such as molluscs, can offer fundamental insights into the adaptation of organisms for a wide range of environmental challenges. One of the best studied processes at the molecular level relevant to stress tolerance is the heat shock response in the genus Mytilus. We focus on the upstream region of Mytilus galloprovincialis Hsp90 genes and their structural and functional associations, using comparative genomics and network inference. Sequence comparison of this region provides novel evidence that the transcription of Hsp90 is regulated via a dense region of transcription factor binding sites, also containing a region with similarity to the Gamera family of LINE-like repetitive sequences and a genus-specific element of unknown function. Furthermore, we infer a set of gene networks from tissue-specific expression data, and specifically extract an Hsp class-associated network, with 174 genes and 2,226 associations, exhibiting a complex pattern of expression across multiple tissue types. Our results (i suggest that the heat shock response in the genus Mytilus is regulated by an unexpectedly complex upstream region, and (ii provide new directions for the use of the heat shock process as a biosensor system for environmental monitoring.

  5. 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.

    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 genes

  6. 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

  7. Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

    NARCIS (Netherlands)

    Limpens, E.H.M.; Moling, S.; Hooiveld, G.J.; Pereira, P.A.; Bisseling, T.; Becker, J.D.; Küster, H.

    2013-01-01

    Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the mod

  8. Gene-specific correlation of RNA and protein levels in human cells and tissues

    DEFF Research Database (Denmark)

    Edfors, Fredrik; Danielsson, Frida; Hallström, Björn M.

    2016-01-01

    to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP...

  9. Tissue-specific 5' heterogeneity of PPARα transcripts and their differential regulation by leptin.

    Science.gov (United States)

    Garratt, Emma S; Vickers, Mark H; Gluckman, Peter D; Hanson, Mark A; Burdge, Graham C; Lillycrop, Karen A

    2013-01-01

    The genes encoding nuclear receptors comprise multiple 5'untranslated exons, which give rise to several transcripts encoding the same protein, allowing tissue-specific regulation of expression. Both human and mouse peroxisome proliferator activated receptor (PPAR) α genes have multiple promoters, although their function is unknown. Here we have characterised the rat PPARα promoter region and have identified three alternative PPARα transcripts, which have different transcription start sites owing to the utilisation of distinct first exons. Moreover these alternative PPARα transcripts were differentially expressed between adipose tissue and liver. We show that while the major adipose (P1) and liver (P2) transcripts were both induced by dexamethasone, they were differentially regulated by the PPARα agonist, clofibric acid, and leptin. Leptin had no effect on the adipose-specific P1 transcript, but induced liver-specific P2 promoter activity via a STAT3/Sp1 mechanism. Moreover in Wistar rats, leptin treatment between postnatal day 3-13 led to an increase in P2 but not P1 transcription in adipose tissue which was sustained into adulthood. This suggests that the expression of the alternative PPARα transcripts are in part programmed by early life exposure to leptin leading to persistent change in adipose tissue fatty acid metabolism through specific activation of a quiescent PPARα promoter. Such complexity in the regulation of PPARα may allow the expression of PPARα to be finely regulated in response to environmental factors.

  10. Tissue-specific alternative splicing and expression of ATP1B2 gene ...

    African Journals Online (AJOL)

    Tissue-specific alternative splicing and expression of ATP1B2 gene. ... It also balances metabolism and body temperature. ... In the study, ATP1B2-AS2 showed that many of the amino acid residues were in an unfavorable energy environment.

  11. Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models.

    Science.gov (United States)

    Amaral, Andreia J; Brito, Francisco F; Chobanyan, Tamar; Yoshikawa, Seiko; Yokokura, Takakazu; Van Vactor, David; Gama-Carvalho, Margarida

    2014-01-01

    RNA-sequencing (RNA-seq) is rapidly emerging as the technology of choice for whole-transcriptome studies. However, RNA-seq is not a bias free technique. It requires large amounts of RNA and library preparation can introduce multiple artifacts, compounded by problems from later stages in the process. Nevertheless, RNA-seq is increasingly used in multiple studies, including the characterization of tissue-specific transcriptomes from invertebrate models of human disease. The generation of samples in this context is complex, involving the establishment of mutant strains and the delicate contamination prone process of dissecting the target tissue. Moreover, in order to achieve the required amount of RNA, multiple samples need to be pooled. Such datasets pose extra challenges due to the large variability that may occur between similar pools, mostly due to the presence of cells from surrounding tissues. Therefore, in addition to standard quality control of RNA-seq data, analytical procedures for control of "biological quality" are critical for successful comparison of gene expression profiles. In this study, the transcriptome of the central nervous system (CNS) of a Drosophila transgenic strain with neuronal-specific RNAi of an ubiquitous gene was profiled using RNA-seq. After observing the existence of an unusual variance in our dataset, we showed that the expression profile of a small panel of marker genes, including GAL4 under control of a tissue specific driver, can identify libraries with low levels of contamination from neighboring tissues, enabling the selection of a robust dataset for differential expression analysis. We further analyzed the potential of profiling a complex tissue to identify cell-type specific changes in response to target gene down-regulation. Finally, we showed that trimming 5' ends of reads decreases nucleotide frequency biases, increasing the coverage of protein coding genes with a potential positive impact in the incurrence of systematic

  12. Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models

    Directory of Open Access Journals (Sweden)

    Andreia J Amaral

    2014-03-01

    Full Text Available RNA-sequencing (RNA-seq is rapidly emerging as the technology of choice for whole-transcriptome studies. However, RNA-seq is not a bias free technique. It requires large amounts of RNA and library preparation can introduce multiple artifacts, compounded by problems from later stages in the process. Nevertheless, RNA-seq is increasingly used in multiple studies, including the characterization of tissue-specific transcriptomes from invertebrate models of human disease. The generation of samples in this context is complex, involving the establishment of mutant strains and the delicate contamination prone process of dissecting the target tissue. Moreover, in order achieve the required amount of RNA, multiple samples need to be pooled. Such datasets pose extra challenges due to the large variability that may occur between similar pools, mostly due to the presence of cells from surrounding tissues. Therefore, in addition to standard quality control of RNA-seq data, analytical procedures for control of 'biological quality’ are critical for successful comparison of gene expression profiles. In this study, the transcriptome of the central nervous system of a Drosophila transgenic strain with neuronal-specific RNAi of an ubiquitous gene was profiled using RNA-seq. After observing the existence of an unusual variance in our dataset, we showed that the expression profile of a small panel of marker genes, including GAL4 under control of a tissue specific driver, can identify libraries with low levels of contamination from neighboring tissues, enabling the selection of a robust dataset for differential expression analysis. We further analyzed the potential of profiling a complex tissue to identify cell-type specific changes in response to target gene down-regulation. Finally, we showed that trimming 5’ ends of reads decreases nucleotide frequency biases, increasing the coverage of protein coding genes and decreasing the occurrence of systematic technical

  13. Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA.

    Science.gov (United States)

    Fox, Rebecca M; Vaishnavi, Aria; Maruyama, Rika; Andrew, Deborah J

    2013-05-01

    FoxA transcription factors play major roles in organ-specific gene expression, regulating, for example, glucagon expression in the pancreas, GLUT2 expression in the liver, and tyrosine hydroxylase expression in dopaminergic neurons. Organ-specific gene regulation by FoxA proteins is achieved through cooperative regulation with a broad array of transcription factors with more limited expression domains. Fork head (Fkh), the sole Drosophila FoxA family member, is required for the development of multiple distinct organs, yet little is known regarding how Fkh regulates tissue-specific gene expression. Here, we characterize Sage, a bHLH transcription factor expressed exclusively in the Drosophila salivary gland (SG). We show that Sage is required for late SG survival and normal tube morphology. We find that many Sage targets, identified by microarray analysis, encode SG-specific secreted cargo, transmembrane proteins, and the enzymes that modify these proteins. We show that both Sage and Fkh are required for the expression of Sage target genes, and that co-expression of Sage and Fkh is sufficient to drive target gene expression in multiple cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage-Fkh targets, and Sage, Fkh and Sens colocalize on SG chromosomes. Importantly, expression of Sage-Fkh target genes appears to simply add to the tissue-specific gene expression programs already established in other cell types, and Sage and Fkh cannot alter the fate of most embryonic cell types even when expressed early and continuously.

  14. In-situ photopolymerization and monitoring device for controlled shaping of tissue fillers, replacements, or implants

    Science.gov (United States)

    Schmocker, Andreas M.; Khoushabi, Azadeh; Bourban, Pierre-Etienne; Schizas, Constantin; Pioletti, Dominique; Moser, Christophe

    2015-03-01

    Photopolymerization is a common tool to harden materials initially in a liquid state. A surgeon can directly trigger the solidification of a dental implant or a bone or tissue filler simply by illumination. Traditionally, photopolymerization has been used mainly in dentistry. Over the last decade advances in material development including a wide range of biocompatible gel- and cement-systems open up a new avenue for in-situ photopolymerization. However, at the device level, surgical endoscopic probes are required. We present a miniaturized light probe where a photoactive material can be 1) mixed, pressurized and injected 2) photopolymerized or photoactivated and 3) monitored during the chemical reaction. The device enables surgeries to be conducted through a hole smaller than 1 mm in diameter. Beside basic injection mechanics, the tool consists of an optical fiber guiding the light required for photopolymerization and for chemical analysis. Combining photorheology and fluorescence spectroscopy, the current state of the photopolymerization is inferred and monitored in real time. Biocompatible and highly tuneable Poly-Ethylene-Glycol (PEG) hydrogels were used as the injection material. The device was tested on a model for intervertebral disc replacement. Gels were successfully implanted into a bovine caudal model and mechanically tested in-vitro during two weeks. The photopolymerized gel was evaluated at the tissue level (adherence and mechanical properties of the implant), at the cellular level (biocompatibility and cytotoxicity) and ergonomic level (sterilization procedure and feasibility study). This paper covers the monitoring aspect of the device.

  15. Raman fiberoptic probe for monitoring human tissue engineered oral mucosa constructs

    Science.gov (United States)

    Khmaladze, Alexander; Kuo, Shiuhyang; Okagbare, Paul; Marcelo, Cynthia L.; Feinberg, Stephen E.; Morris, Michael D.

    2013-02-01

    In oral and maxillofacial surgery, there is a need for tissue engineered constructs for dental implants, reconstructions due to trauma, oral cancer or congenital defects. A non-invasive quality monitoring of the fabrication of tissue engineered constructs during their production and implantation is a required component of any successful tissue engineering technique. We demonstrate the design and application of a Raman spectroscopic probe for rapid and noninvasive monitoring of Ex Vivo Produced Oral Mucosa Equivalent constructs (EVPOMEs). We conducted in vivo studies to identify Raman spectroscopic failure indicators for EVPOMEs (already developed in vitro), and found that Raman spectra of EVPOMEs exposed to thermal stress showed correlation of the band height ratio of CH2 deformation to phenylalanine ring breathing modes, providing a Raman metric to distinguish between viable and nonviable constructs. This is the first step towards the ultimate goal to design a stand-alone system, which will be usable in a clinical setting, as the data processing and analysis will be performed with minimal user intervention, based on already established and tested Raman spectroscopic indicators for EVPOMEs.

  16. Human oral mucosa tissue-engineered constructs monitored by Raman fiber-optic probe.

    Science.gov (United States)

    Khmaladze, Alexander; Kuo, Shiuhyang; Kim, Roderick Y; Matthews, Robert V; Marcelo, Cynthia L; Feinberg, Stephen E; Morris, Michael D

    2015-01-01

    In maxillofacial and oral surgery, there is a need for the development of tissue-engineered constructs. They are used for reconstructions due to trauma, dental implants, congenital defects, or oral cancer. A noninvasive monitoring of the fabrication of tissue-engineered constructs at the production and implantation stages done in real time is extremely important for predicting the success of tissue-engineered grafts. We demonstrated a Raman spectroscopic probe system, its design and application, for real-time ex vivo produced oral mucosa equivalent (EVPOME) constructs noninvasive monitoring. We performed in vivo studies to find Raman spectroscopic indicators for postimplanted EVPOME failure and determined that Raman spectra of EVPOMEs preexposed to thermal stress during manufacturing procedures displayed correlation of the band height ratio of CH2 deformation to phenylalanine ring breathing modes, giving a Raman metric to distinguish between healthy and compromised postimplanted constructs. This study is the step toward our ultimate goal to develop a stand-alone system, to be used in a clinical setting, where the data collection and analysis are conducted on the basis of these spectroscopic indicators with minimal user intervention.

  17. Tissue-specific mutation accumulation in human adult stem cells during life

    Science.gov (United States)

    Blokzijl, Francis; de Ligt, Joep; Jager, Myrthe; Sasselli, Valentina; Roerink, Sophie; Sasaki, Nobuo; Huch, Meritxell; Boymans, Sander; Kuijk, Ewart; Prins, Pjotr; Nijman, Isaac J.; Martincorena, Inigo; Mokry, Michal; Wiegerinck, Caroline L.; Middendorp, Sabine; Sato, Toshiro; Schwank, Gerald; Nieuwenhuis, Edward E. S.; Verstegen, Monique M. A.; van der Laan, Luc J. W.; de Jonge, Jeroen; Ijzermans, Jan N. M.; Vries, Robert G.; van de Wetering, Marc; Stratton, Michael R.; Clevers, Hans; Cuppen, Edwin; van Boxtel, Ruben

    2016-10-01

    The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life is associated with various age-related diseases, including cancer. Extreme variation in cancer risk across tissues was recently proposed to depend on the lifetime number of ASC divisions, owing to unavoidable random mutations that arise during DNA replication. However, the rates and patterns of mutations in normal ASCs remain unknown. Here we determine genome-wide mutation patterns in ASCs of the small intestine, colon and liver of human donors with ages ranging from 3 to 87 years by sequencing clonal organoid cultures derived from primary multipotent cells. Our results show that mutations accumulate steadily over time in all of the assessed tissue types, at a rate of approximately 40 novel mutations per year, despite the large variation in cancer incidence among these tissues. Liver ASCs, however, have different mutation spectra compared to those of the colon and small intestine. Mutational signature analysis reveals that this difference can be attributed to spontaneous deamination of methylated cytosine residues in the colon and small intestine, probably reflecting their high ASC division rate. In liver, a signature with an as-yet-unknown underlying mechanism is predominant. Mutation spectra of driver genes in cancer show high similarity to the tissue-specific ASC mutation spectra, suggesting that intrinsic mutational processes in ASCs can initiate tumorigenesis. Notably, the inter-individual variation in mutation rate and spectra are low, suggesting tissue-specific activity of common mutational processes throughout life.

  18. Linear elastic properties of the facial soft tissues using an aspiration device: towards patient specific characterization.

    Science.gov (United States)

    Luboz, V; Promayon, E; Payan, Y

    2014-11-01

    Biomechanical modeling of the facial soft tissue behavior is needed in aesthetic or maxillo-facial surgeries where the simulation of the bone displacements cannot accurately predict the visible outcome on the patient's face. Because these tissues have different nature and elastic properties across the face, depending on their thickness, and their content in fat or muscle, individualizing their mechanical parameters could increase the simulation accuracy. Using a specifically designed aspiration device, the facial soft tissues deformation is measured at four different locations (cheek, cheekbone, forehead, and lower lip) on 16 young subjects. The stiffness is estimated from the deformations generated by a set of negative pressures using an inverse analysis based on a Neo Hookean model. The initial Young's modulus of the cheek, cheekbone, forehead, and lower lip are respectively estimated to be 31.0 kPa±4.6, 34.9 kPa±6.6, 17.3 kPa±4.1, and 33.7 kPa±7.3. Significant intra-subject differences in tissue stiffness are highlighted by these estimations. They also show important inter-subject variability for some locations even when mean stiffness values show no statistical difference. This study stresses the importance of using a measurement device capable of evaluating the patient specific tissue stiffness during an intervention.

  19. Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma

    Directory of Open Access Journals (Sweden)

    Kern Rei Chng

    2016-06-01

    Full Text Available Cholangiocarcinoma (CCA is the primary cancer of the bile duct system. The role of bile duct tissue microbiomes in CCA tumorigenesis is unestablished. To address this, sixty primary CCA tumors and matched normals, from both liver fluke (Opisthorchis viverrini associated (OVa, n = 28 and non-O. viverrini associated (non-OVa, n = 32 cancers, were profiled using high-throughput 16S rRNA sequencing. A distinct, tissue-specific microbiome dominated by the bacterial families Dietziaceae, Pseudomonadaceae and Oxalobacteraceae was observed in bile duct tissues. Systemic perturbation of the microbiome was noted in tumor and paired normal samples (vs non-cancer normals for several bacterial families with a significant increase in Stenotrophomonas species distinguishing tumors vs paired normals. Comparison of parasite associated (OVa vs non-associated (non-OVa groups identified enrichment for specific enteric bacteria (Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae. One of the enriched families, Bifidobacteriaceae, was found to be dominant in the O. viverrini microbiome, providing a mechanistic link to the parasite. Functional analysis and comparison of CCA microbiomes revealed higher potential for producing bile acids and ammonia in OVa tissues, linking the altered microbiota to carcinogenesis. These results define how the unique microbial communities resident in the bile duct, parasitic infections and the tissue microenvironment can influence each other, and contribute to cancer.

  20. Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma.

    Science.gov (United States)

    Chng, Kern Rei; Chan, Sock Hoai; Ng, Amanda Hui Qi; Li, Chenhao; Jusakul, Apinya; Bertrand, Denis; Wilm, Andreas; Choo, Su Pin; Tan, Damien Meng Yew; Lim, Kiat Hon; Soetinko, Roy; Ong, Choon Kiat; Duda, Dan G; Dima, Simona; Popescu, Irinel; Wongkham, Chaisiri; Feng, Zhu; Yeoh, Khay Guan; Teh, Bin Tean; Yongvanit, Puangrat; Wongkham, Sopit; Bhudhisawasdi, Vajaraphongsa; Khuntikeo, Narong; Tan, Patrick; Pairojkul, Chawalit; Ngeow, Joanne; Nagarajan, Niranjan

    2016-06-01

    Cholangiocarcinoma (CCA) is the primary cancer of the bile duct system. The role of bile duct tissue microbiomes in CCA tumorigenesis is unestablished. To address this, sixty primary CCA tumors and matched normals, from both liver fluke (Opisthorchis viverrini) associated (OVa, n=28) and non-O. viverrini associated (non-OVa, n=32) cancers, were profiled using high-throughput 16S rRNA sequencing. A distinct, tissue-specific microbiome dominated by the bacterial families Dietziaceae, Pseudomonadaceae and Oxalobacteraceae was observed in bile duct tissues. Systemic perturbation of the microbiome was noted in tumor and paired normal samples (vs non-cancer normals) for several bacterial families with a significant increase in Stenotrophomonas species distinguishing tumors vs paired normals. Comparison of parasite associated (OVa) vs non-associated (non-OVa) groups identified enrichment for specific enteric bacteria (Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae). One of the enriched families, Bifidobacteriaceae, was found to be dominant in the O. viverrini microbiome, providing a mechanistic link to the parasite. Functional analysis and comparison of CCA microbiomes revealed higher potential for producing bile acids and ammonia in OVa tissues, linking the altered microbiota to carcinogenesis. These results define how the unique microbial communities resident in the bile duct, parasitic infections and the tissue microenvironment can influence each other, and contribute to cancer.

  1. Facial soft tissue depths in French adults: variability, specificity and estimation.

    Science.gov (United States)

    Guyomarc'h, Pierre; Santos, Frédéric; Dutailly, Bruno; Coqueugniot, Hélène

    2013-09-10

    Facial soft tissue depths (FSTD) are used in facial approximation to render the shape of the face, and are traditionally published specifically to population, corpulence, and sex amongst other factors. This paper investigates the variability of FSTD collected at 37 landmarks on 500 CT (computed tomography) scans of French living individuals. The specificity of the sample is evaluated by comparing values with six published datasets of various populations and recording techniques. Apart from a significant influence of the corpulence, FSTD show negligible variations with age and sex. The differences between the French sample and other datasets contradict the hypothesis of major influence of population, and underline sample specificity linked with technique and methodology of data measurement. Regression equations were computed to estimate FSTD using age, sex, facial build, and craniometrics, leading to more accurate results if such factors are known. Nevertheless, application of the pooled T-table (Tallied-Facial-Soft-Tissue-Depth-Data) has been validated according to the French sample.

  2. In vitro measurements of temperature-dependent specific heat of liver tissue.

    Science.gov (United States)

    Haemmerich, Dieter; dos Santos, Icaro; Schutt, David J; Webster, John G; Mahvi, David M

    2006-03-01

    We measured the specific heat of liver tissue in vitro by uniformly heating liver samples between two electrodes. We insulated the samples by expanded polystyrene, and corrected for heat loss and water loss. The specific heat of the liver is temperature-dependent, and increases by 17% at 83.5 degrees C (p specific heat was 3411 J kg(-1)K(-1) at 25 degrees C, and 4187 J kg(-1)K(-1) at 83.5 degrees C. Water loss from the samples was significant above 70 degrees C, with approximately 20% of reduction in sample mass at 90 degrees C.

  3. Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

    Directory of Open Access Journals (Sweden)

    Nadezda Kryuchkova-Mostacci

    Full Text Available Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

  4. Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

    Science.gov (United States)

    Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

    2016-03-01

    The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

  5. Identification of novel tissue-specific genes by analysis of microarray databases: a human and mouse model.

    Science.gov (United States)

    Song, Yan; Ahn, Jinsoo; Suh, Yeunsu; Davis, Michael E; Lee, Kichoon

    2013-01-01

    Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI's Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved.

  6. Formal specification and animation of a water level monitoring system. Research report No. INFO-0428

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, P.S.; Stokes, P.A.

    1993-01-01

    This report describes the Vienna Development Method (VDM), a formal method for software specification and development, and its use for a real-time application where it is used to formally specify the requirements of a water level monitoring system. The procedure and techniques used to produce an executable form (animation) of the specification are covered.

  7. 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...

  8. Non-invasive monitoring of tissue oxygenation during laparoscopic donor nephrectomy

    Directory of Open Access Journals (Sweden)

    Kirk Allan D

    2008-04-01

    Full Text Available Abstract Background Standard methods for assessment of organ viability during surgery are typically limited to visual cues and tactile feedback in open surgery. However, during laparoscopic surgery, these processes are impaired. This is of particular relevance during laparoscopic renal donation, where the condition of the kidney must be optimized despite considerable manipulation. However, there is no in vivo methodology to monitor renal parenchymal oxygenation during laparoscopic surgery. Methods We have developed a method for the real time, in vivo, whole organ assessment of tissue oxygenation during laparoscopic nephrectomy to convey meaningful biological data to the surgeon during laparoscopic surgery. We apply the 3-CCD (charge coupled device camera to monitor qualitatively renal parenchymal oxygenation with potential real-time video capability. Results We have validated this methodology in a porcine model across a range of hypoxic conditions, and have then applied the method during clinical laparoscopic donor nephrectomies during clinically relevant pneumoperitoneum. 3-CCD image enhancement produces mean region of interest (ROI intensity values that can be directly correlated with blood oxygen saturation measurements (R2 > 0.96. The calculated mean ROI intensity values obtained at the beginning of the laparoscopic nephrectomy do not differ significantly from mean ROI intensity values calculated immediately before kidney removal (p > 0.05. Conclusion Here, using the 3-CCD camera, we qualitatively monitor tissue oxygenation. This means of assessing intraoperative tissue oxygenation may be a useful method to avoid unintended ischemic injury during laparoscopic surgery. Preliminary results indicate that no significant changes in renal oxygenation occur as a result of pneumoperitoneum.

  9. Adipose tissue-specific dysregulation of angiotensinogen by oxidative stress in obesity.

    Science.gov (United States)

    Okada, Sadanori; Kozuka, Chisayo; Masuzaki, Hiroaki; Yasue, Shintaro; Ishii-Yonemoto, Takako; Tanaka, Tomohiro; Yamamoto, Yuji; Noguchi, Michio; Kusakabe, Toru; Tomita, Tsutomu; Fujikura, Junji; Ebihara, Ken; Hosoda, Kiminori; Sakaue, Hiroshi; Kobori, Hiroyuki; Ham, Mira; Lee, Yun Sok; Kim, Jae Bum; Saito, Yoshihiko; Nakao, Kazuwa

    2010-09-01

    Adipose tissue expresses all components of the renin-angiotensin system including angiotensinogen (AGT). Recent studies have highlighted a potential role of AGT in adipose tissue function and homeostasis. However, some controversies surround the regulatory mechanisms of AGT in obese adipose tissue. In this context, we here demonstrated that the AGT messenger RNA (mRNA) level in human subcutaneous adipose tissue was significantly reduced in obese subjects as compared with nonobese subjects. Adipose tissue AGT mRNA level in obese mice was also lower as compared with their lean littermates; however, the hepatic AGT mRNA level remained unchanged. When 3T3-L1 adipocytes were cultured for a long period, the adipocytes became hypertrophic with a marked increase in the production of reactive oxygen species. Expression and secretion of AGT continued to decrease during the course of adipocyte hypertrophy. Treatment of the 3T3-L1 and primary adipocytes with reactive oxygen species (hydrogen peroxide) or tumor necrosis factor alpha caused a significant decrease in the expression and secretion of AGT. On the other hand, treatment with the antioxidant N-acetyl cysteine suppressed the decrease in the expression and secretion of AGT in the hypertrophied 3T3-L1 adipocytes. Finally, treatment of obese db/db mice with N-acetyl cysteine augmented the expression of AGT in the adipose tissue, but not in the liver. The present study demonstrates for the first time that oxidative stress dysregulates AGT in obese adipose tissue, providing a novel insight into the adipose tissue-specific interaction between the regulation of AGT and oxidative stress in the pathophysiology of obesity. Copyright 2010 Elsevier Inc. All rights reserved.

  10. Development of a spherical tissue equivalent proportional counter for neutron monitoring

    Institute of Scientific and Technical Information of China (English)

    姜志刚; 袁永刚; 王和义; 陈华

    2015-01-01

    A spherical tissue equivalent proportional counter (TEPC) for neutron monitoring has been developed. It was properly designed to produce a uniform electric field intensity around the anode wire. An internal 241Am alpha source was adopted for lineal energy calibration. The TEPC was characterized in terms of dose equivalent response in a standard 252Cf neutron field, and was tested with 2.45 MeV neutrons. Microdosimetric spec-tra, frequency mean lineal energy and dose-average mean lineal energy of 2.45 MeV neutrons were obtained and compared with FLUKA Monte Carlo simulation results. The measurement and simulation results agreed well. The mean quality factor and dose equivalent values evaluated from the 2.45 MeV neutron measurement were in good agreement with the recommended effective quality factor and ambient dose equivalent H∗(10), respectively. Preliminary results have proved the availability of the developed TEPC for neutron monitoring.

  11. Engineered hybrid cardiac patches with multifunctional electronics for online monitoring and regulation of tissue function

    Science.gov (United States)

    Feiner, Ron; Engel, Leeya; Fleischer, Sharon; Malki, Maayan; Gal, Idan; Shapira, Assaf; Shacham-Diamand, Yosi; Dvir, Tal

    2016-01-01

    In cardiac tissue engineering approaches to treat myocardial infarction, cardiac cells are seeded within three-dimensional porous scaffolds to create functional cardiac patches. However, current cardiac patches do not allow for online monitoring and reporting of engineered-tissue performance, and do not interfere to deliver signals for patch activation or to enable its integration with the host. Here, we report an engineered cardiac patch that integrates cardiac cells with flexible, free-standing electronics and a 3D nanocomposite scaffold. The patch exhibited robust electronic properties, enabling the recording of cellular electrical activities and the on-demand provision of electrical stimulation for synchronizing cell contraction. We also show that electroactive polymers containing biological factors can be deposited on designated electrodes to release drugs in the patch microenvironment on-demand. We expect that the integration of complex electronics within cardiac patches will eventually provide therapeutic control and regulation of cardiac function. PMID:26974408

  12. Monitoring cerebral tissue oxygen saturation at frontal and parietal regions during carotid artery stenting.

    Science.gov (United States)

    Meng, Lingzhong; Hall, Melanie; Settecase, Fabio; Higashida, Randall T; Gelb, Adrian W

    2016-04-01

    Cerebral oximetry is normally placed on the upper forehead to monitor the frontal lobe cerebral tissue oxygen saturation (SctO2). We present a case in which the SctO2 was simultaneously monitored at both frontal and parietal regions during internal carotid artery (ICA) stenting. Our case involves a 79-year-old man who presented after a sudden fall and was later diagnosed with a watershed ischemic stroke in the distal fields perfused by the left middle cerebral artery. He had diffuse atherosclerotic occlusive lesions in the carotid and cerebral arterial systems including an 85 % stenotic lesion in the left distal cervical ICA. The brain territory perfused by the left ICA was devoid of collateral flow from anterior and posterior communicating arteries due to an abnormal circle of Willis. During stenting, the SctO2 monitored at both frontal and parietal regions tracked the procedure-induced acute flow change. However, the baseline SctO2 values of frontal and parietal regions differed. The SctO2-MAP correlation was more consistent on the stroked hemisphere than the non-stroked hemisphere. This case showed that SctO2 can be reliably monitored at the parietal region, which is primarily perfused by the ICA. SctO2 of the stroked brain is more pressure dependent than the non-stroked brain.

  13. A novel instrumented retractor to monitor tissue-disruptive forces during lateral thoracotomy.

    Science.gov (United States)

    Bolotin, Gil; Buckner, Gregory D; Jardine, Nicholas J; Kiefer, Aaron J; Campbell, Nigel B; Kocherginsky, Masha; Raman, Jai; Jeevanandam, Valluvan

    2007-04-01

    Acute and chronic pain after thoracotomy, post-thoracotomy pain syndrome, is well documented. The mechanical retractors used for the thoracotomy exert significant forces on the skeletal cage. Our hypothesis was that instrumented retractors could be developed to enable real-time monitoring and control of retraction forces. This would provide equivalent exposure with significantly reduced forces and tissue damage and thus less post-thoracotomy pain. A novel instrumented retractor was designed and fabricated to enable real-time force monitoring during surgical retraction. Eight mature sheep underwent bilateral thoracotomy. One lateral thoracotomy was retracted at a standard clinical pace of 5.93 +/- 0.80 minutes to 7.5 cm without real-time monitoring of retraction forces. The other lateral thoracotomy was retracted to the same exposure with real-time visual force feedback and a consequently more deliberate pace of 9.87 +/- 1.89 minutes (P = .006). Retraction forces, blood pressure, and heart rate were monitored throughout the procedure. Full lateral retraction resulted in an average force of 102.88 +/- 50.36 N at the standard clinical pace, versus 77.88 +/- 38.85 N with force feedback (a 24.3% reduction, P = .006). Standard retraction produced peak forces of 450.01 +/- 129.58 N, whereas force feedback yielded peak forces of 323.99 +/- 127.79 N (a 28.0% reduction, P = .009). Systolic blood pressure was significantly higher during standard clinical retraction (P = .0097), and rib fracture occurrences were reduced from 5 to 1 with force feedback (P = .04). Use of the novel instrumented retractor resulted in significantly lower average and peak retraction forces during lateral thoracotomy. Moreover, these reduced retraction forces were correlated with reductions in animal stress and tissue damage, as documented by lower systolic blood pressures and fewer rib fractures.

  14. Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies.

    Science.gov (United States)

    Hwang, Pei-Ing; Wu, Huan-Bin; Wang, Chin-Di; Lin, Bai-Ling; Chen, Cheng-Tao; Yuan, Shinsheng; Wu, Guani; Li, Ker-Chau

    2011-09-01

    To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue. By analyzing three independent microarray datasets on normal human tissues, we established a quantitative molecular model GET, which consists of 24 tissue-specific Gene Expression Templates constructed from a set of 56 genes, for predicting 24 distinct tissue types under disease-free condition. 99.2% correctness was reached when a large-scale validation was performed on 61 new datasets to test the tissue-prediction power of GET. Network analysis based on molecular interactions suggests a potential role of these 56 genes in tissue differentiation and carcinogenesis.Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages. Cancerous tissues and cell lines yielded significantly lower correlation with GET than the normal tissues. GET distinguished melanoma from normal skin tissue or benign skin tumor with 96% sensitivity and 89% specificity. These results strongly suggest that a normal tissue or cell may uphold its normal functioning and morphology by maintaining specific chemical stoichiometry among genes. The state of stoichiometry can be depicted by a compact set of representative genes such as the 56 genes obtained here. A significant deviation from normal stoichiometry may result in malfunction or abnormal growth of the cells.

  15. Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies

    Directory of Open Access Journals (Sweden)

    Yuan Shinsheng

    2011-09-01

    Full Text Available Abstract Background To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue. Results By analyzing three independent microarray datasets on normal human tissues, we established a quantitative molecular model GET, which consists of 24 tissue-specific Gene Expression Templates constructed from a set of 56 genes, for predicting 24 distinct tissue types under disease-free condition. 99.2% correctness was reached when a large-scale validation was performed on 61 new datasets to test the tissue-prediction power of GET. Network analysis based on molecular interactions suggests a potential role of these 56 genes in tissue differentiation and carcinogenesis. Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages. Cancerous tissues and cell lines yielded significantly lower correlation with GET than the normal tissues. GET distinguished melanoma from normal skin tissue or benign skin tumor with 96% sensitivity and 89% specificity. Conclusions These results strongly suggest that a normal tissue or cell may uphold its normal functioning and morphology by maintaining specific chemical stoichiometry among genes. The state of stoichiometry can be depicted by a compact set of representative genes such as the 56 genes obtained here. A significant deviation from normal stoichiometry may result in malfunction or abnormal growth of the cells.

  16. 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.

  17. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

    DEFF Research Database (Denmark)

    Hansen, Kasper Lage; Hansen, Niclas Tue; Karlberg, Erik, Olof, Linnart

    2008-01-01

    Heritable diseases are caused by germ-line mutations that, despite tissuewide presence, often lead to tissue-specific pathology. Here, we make a systematic analysis of the link between tissue-specific gene expression and pathological manifestations in many human diseases and cancers. Diseases were...... to be overexpressed in the normal tissues where defects cause pathology. In contrast, cancer genes and complexes were not overexpressed in the tissues from which the tumors emanate. We specifically identified a complex involved in XY sex reversal that is testis-specific and down-regulated in ovaries. We also...... identified complexes in Parkinson disease, cardiomyopathies, and muscular dystrophy syndromes that are similarly tissue specific. Our method represents a conceptual scaffold for organism-spanning analyses and reveals an extensive list of tissue-specific draft molecular pathways, both known and unexpected...

  18. Development of a quantitative PCR assay for monitoring Streptococcus agalactiae colonization and tissue tropism in experimentally infected tilapia.

    Science.gov (United States)

    Su, Y-L; Feng, J; Li, Y-W; Bai, J-S; Li, A-X

    2016-02-01

    Streptococcus agalactiae has become one of the most important emerging pathogens in the aquaculture industry and has resulted in large economic losses for tilapia farms in China. In this study, three pairs of specific primers were designed and tested for their specificities and sensitivities in quantitative real-time polymerase chain reactions (qPCRs) after optimization of the annealing temperature. The primer pair IGS-s/IGS-a, which targets the 16S-23S rRNA intergenic spacer region, was finally chosen, having a detection limit of 8.6 copies of S. agalactiae DNA in a 20 μL reaction mixture. Bacterial tissue tropism was demonstrated by qPCR in Oreochromis niloticus 5 days post-injection with a virulent S. agalactiae strain. Bacterial loads were detected at the highest level in brain, followed by moderately high levels in kidney, heart, spleen, intestines, and eye. Significantly lower bacterial loads were observed in muscle, gill and liver. In addition, significantly lower bacterial loads were observed in the brain of convalescent O. niloticus 14 days post-injection with several different S. agalactiae strains. The qPCR for the detection of S. agalactiae developed in this study provides a quantitative tool for investigating bacterial tissue tropism in infected fish, as well as for monitoring bacterial colonization in convalescent fish.

  19. Rapid expression of transgenes driven by seed-specific constructs in leaf tissue: DHA production

    Directory of Open Access Journals (Sweden)

    Zhou Xue-Rong

    2010-03-01

    Full Text Available Abstract Background Metabolic engineering of seed biosynthetic pathways to diversify and improve crop product quality is a highly active research area. The validation of genes driven by seed-specific promoters is time-consuming since the transformed plants must be grown to maturity before the gene function can be analysed. Results In this study we demonstrate that genes driven by seed-specific promoters contained within complex constructs can be transiently-expressed in the Nicotiana benthamiana leaf-assay system by co-infiltrating the Arabidopsis thaliana LEAFY COTYLEDON2 (LEC2 gene. A real-world case study is described in which we first assembled an efficient transgenic DHA synthesis pathway using a traditional N. benthamiana Cauliflower Mosaic Virus (CaMV 35S-driven leaf assay before using the LEC2-extended assay to rapidly validate a complex seed-specific construct containing the same genes before stable transformation in Arabidopsis. Conclusions The LEC2-extended N. benthamiana assay allows the transient activation of seed-specific promoters in leaf tissue. In this study we have used the assay as a rapid preliminary screen of a complex seed-specific transgenic construct prior to stable transformation, a feature that will become increasingly useful as genetic engineering moves from the manipulation of single genes to the engineering of complex pathways. We propose that the assay will prove useful for other applications wherein rapid expression of transgenes driven by seed-specific constructs in leaf tissue are sought.

  20. The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.

    Directory of Open Access Journals (Sweden)

    Da Cheng Hao

    Full Text Available BACKGROUND: Illumina second generation sequencing is now an efficient route for generating enormous sequence collections that represent expressed genes and quantitate expression level. Taxus is a world-wide endangered gymnosperm genus and forms an important anti-cancer medicinal resource, but the large and complex genomes of Taxus have hindered the development of genomic resources. The research of its tissue-specific transcriptome is absent. There is also no study concerning the association between the plant transcriptome and metabolome with respect to the plant tissue type. METHODOLOGY/PRINCIPAL FINDINGS: We performed the de novo assembly of Taxus mairei transcriptome using Illumina paired-end sequencing technology. In a single run, we produced 13,737,528 sequencing reads corresponding to 2.03 Gb total nucleotides. These reads were assembled into 36,493 unique sequences. Based on similarity search with known proteins, 23,515 Unigenes were identified to have the Blast hit with a cut-off E-value above 10⁻⁵. Furthermore, we investigated the transcriptome difference of three Taxus tissues using a tag-based digital gene expression system. We obtained a sequencing depth of over 3.15 million tags per sample and identified a large number of genes associated with tissue specific functions and taxane biosynthetic pathway. The expression of the taxane biosynthetic genes is significantly higher in the root than in the leaf and the stem, while high activity of taxane-producing pathway in the root was also revealed via metabolomic analyses. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and enriched metabolic pathways with regard to the differentially expressed genes were revealed for the first time. CONCLUSIONS/SIGNIFICANCE: Our data provides the most comprehensive sequence resource available for Taxus study and will help define mechanisms of tissue

  1. Tissue-specific regulation of the mouse Pkhd1 (ARPKD) gene promoter

    Science.gov (United States)

    Williams, Scott S.; Cobo-Stark, Patricia; Hajarnis, Sachin; Aboudehen, Karam; Shao, Xinli; Richardson, James A.; Patel, Vishal

    2014-01-01

    Autosomal recessive polycystic kidney disease, an inherited disorder characterized by the formation of cysts in renal collecting ducts and biliary dysgenesis, is caused by mutations of the polycystic kidney and hepatic disease 1 (PKHD1) gene. Expression of PKHD1 is tissue specific and developmentally regulated. Here, we show that a 2.0-kb genomic fragment containing the proximal promoter of mouse Pkhd1 directs tissue-specific expression of a lacZ reporter gene in transgenic mice. LacZ is expressed in renal collecting ducts beginning during embryonic development but is not expressed in extrarenal tissues. The Pkhd1 promoter contains a binding site for the transcription factor hepatocyte nuclear factor (HNF)-1β, which is required for activity in transfected cells. Mutation of the HNF-1β-binding site abolishes the expression of the lacZ reporter gene in renal collecting ducts. Transgenes containing the 2.0-kb promoter and 2.7 kb of additional genomic sequence extending downstream to the second exon are expressed in the kidney, intrahepatic bile ducts, and male reproductive tract. This pattern overlaps with the endogenous expression of Pkhd1 and coincides with sites of expression of HNF-1β. We conclude that the proximal 2.0-kb promoter is sufficient for tissue-specific expression of Pkhd1 in renal collecting ducts in vivo and that HNF-1β is required for Pkhd1 promoter activity in collecting ducts. Additional genomic sequences located from exons 1-2 or elsewhere in the gene locus are required for expression in extrarenal tissues. PMID:24899057

  2. Tissue-specific genetic control of splicing: implications for the study of complex traits.

    Directory of Open Access Journals (Sweden)

    Erin L Heinzen

    2008-12-01

    Full Text Available Numerous genome-wide screens for polymorphisms that influence gene expression have provided key insights into the genetic control of transcription. Despite this work, the relevance of specific polymorphisms to in vivo expression and splicing remains unclear. We carried out the first genome-wide screen, to our knowledge, for SNPs that associate with alternative splicing and gene expression in human primary cells, evaluating 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. We identified 23 high confidence associations with total expression and 80 with alternative splicing as reflected by expression levels of specific exons. Fewer than 50% of the implicated SNPs however show effects in both tissue types, reflecting strong evidence for distinct genetic control of splicing and expression in the two tissue types. The data generated here also suggest the possibility that splicing effects may be responsible for up to 13 out of 84 reported genome-wide significant associations with human traits. These results emphasize the importance of establishing a database of polymorphisms affecting splicing and expression in primary tissue types and suggest that splicing effects may be of more phenotypic significance than overall gene expression changes.

  3. Age-dependent tissue-specific exposure of cell phone users

    Energy Technology Data Exchange (ETDEWEB)

    Christ, Andreas; Gosselin, Marie-Christine; Kuehn, Sven; Kuster, Niels [Foundation for Research on Information Technologies in Society (IT' IS), Zeughausstr. 43, 8004 Zuerich (Switzerland); Christopoulou, Maria [National Technical University of Athens, School of Electrical and Computer Engineering, 9 Iroon Polytechniou Str., 15780 Athens (Greece)], E-mail: christ@itis.ethz.ch

    2010-04-07

    The peak spatial specific absorption rate (SAR) assessed with the standardized specific anthropometric mannequin head phantom has been shown to yield a conservative exposure estimate for both adults and children using mobile phones. There are, however, questions remaining concerning the impact of age-dependent dielectric tissue properties and age-dependent proportions of the skull, face and ear on the global and local absorption, in particular in the brain tissues. In this study, we compare the absorption in various parts of the cortex for different magnetic resonance imaging-based head phantoms of adults and children exposed to different models of mobile phones. The results show that the locally induced fields in children can be significantly higher (>3 dB) in subregions of the brain (cortex, hippocampus and hypothalamus) and the eye due to the closer proximity of the phone to these tissues. The increase is even larger for bone marrow (>10 dB) as a result of its significantly high conductivity. Tissues such as the pineal gland show no increase since their distances to the phone are not a function of age. This study, however, confirms previous findings saying that there are no age-dependent changes of the peak spatial SAR when averaged over the entire head.

  4. Immunohistochemical identification of mast cells in formaldehyde-fixed tissue using monoclonal antibodies specific for tryptase.

    Science.gov (United States)

    Walls, A F; Jones, D B; Williams, J H; Church, M K; Holgate, S T

    1990-10-01

    An avidin-biotin enhanced immunoperoxidase procedure using monoclonal antibodies (AA1, AA3, and AA5) prepared against human mast cell tryptase resulted in intense staining of mast cells in paraffin-embedded tissue. The distribution of mast cells observed was similar to that seen when adjacent serial sections were stained using a standard procedure with toluidine blue, though the immunoperoxidase technique permitted the identification of significantly more mast cells. With monoclonal antibody AA1, immunostaining was entirely specific for mast cell granules, and there was negligible background staining in a range of tissues including lung, tonsil, colon, gastric mucosa, skin, and pituitary. There was no staining of antibody on basophils or on any other normal blood leukocyte. The technique was effective with tissue fixed in either Carnoy's or neutral buffered formalin, though the internal mast cell structure was better preserved with formaldehyde fixation. The immunoperoxidase staining procedure with monoclonal antibody AA1 is a highly specific and sensitive means for the detection of mast cells in routinely processed tissues.

  5. The modification of specific absorption rates in interstitial microwave hyperthermia via tissue-equivalent material bolus.

    Science.gov (United States)

    Sundararaman, S; Denman, D L; Legorreta, R A; Foster, A E; Redmond, K P; Elson, H R; Born, A M; Samaratunga, R C; Lewis, G C; Kereiakes, J G

    1990-09-01

    Patterns of specific absorption rates generated by interstitial, microwave antenna arrays must be experimentally ascertained and quantified to facilitate their clinical incorporation. Phantom studies involved the use of four single-gap, coaxial antennas oriented in a 2 cm square array. These dipoles were driven in phase by a microwave generator at a frequency of 915 MHz. The inherent limitations in modifying the specific absorption rate patterns were addressed with the addition of bolus to the phantom. These additions of Guy's muscle tissue-equivalent material were made either proximal or distal to the phantom proper. Experiments conducted in the presence and absence of tissue-equivalent material bolus showed the ability to achieve broader bands of 50% power deposition in certain bolus conditions. These heating patterns were sufficiently reproducible and predictable to warrant clinical application of the bolus addition. A through-and-through method of catheter implantation allowed for bolus addition when deemed necessary. Treatments with veterinary and human patients using the bolus method to modify heating patterns yielded augmented patterns of power deposition. The effective length of the antennas that would radiate efficiently was essentially broadened via introduction of a microwave-interacting medium. As a result of the tissue equivalent material's ability to absorb microwave power, it was necessary to interpose minimally-interactive styrofoam spacers to limit heat transfer effects at the tissue-bolus interfaces.

  6. Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation.

    Science.gov (United States)

    Vragović, Kristina; Sela, Ayala; Friedlander-Shani, Lilach; Fridman, Yulia; Hacham, Yael; Holland, Neta; Bartom, Elizabeth; Mockler, Todd C; Savaldi-Goldstein, Sigal

    2015-01-20

    The mechanisms ensuring balanced growth remain a critical question in developmental biology. In plants, this balance relies on spatiotemporal integration of hormonal signaling pathways, but the understanding of the precise contribution of each hormone is just beginning to take form. Brassinosteroid (BR) hormone is shown here to have opposing effects on root meristem size, depending on its site of action. BR is demonstrated to both delay and promote onset of stem cell daughter differentiation, when acting in the outer tissue of the root meristem, the epidermis, and the innermost tissue, the stele, respectively. To understand the molecular basis of this phenomenon, a comprehensive spatiotemporal translatome mapping of Arabidopsis roots was performed. Analyses of wild type and mutants featuring different distributions of BR revealed autonomous, tissue-specific gene responses to BR, implying its contrasting tissue-dependent impact on growth. BR-induced genes were primarily detected in epidermal cells of the basal meristem zone and were enriched by auxin-related genes. In contrast, repressed BR genes prevailed in the stele of the apical meristem zone. Furthermore, auxin was found to mediate the growth-promoting impact of BR signaling originating in the epidermis, whereas BR signaling in the stele buffered this effect. We propose that context-specific BR activity and responses are oppositely interpreted at the organ level, ensuring coherent growth.

  7. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Rebecca Lyons

    Full Text Available Some of the most devastating agricultural diseases are caused by root-infecting pathogens, yet the majority of studies on these interactions to date have focused on the host responses of aerial tissues rather than those belowground. Fusarium oxysporum is a root-infecting pathogen that causes wilt disease on several plant species including Arabidopsis thaliana. To investigate and compare transcriptional changes triggered by F. oxysporum in different Arabidopsis tissues, we infected soil-grown plants with F. oxysporum and subjected root and leaf tissue harvested at early and late timepoints to RNA-seq analyses. At least half of the genes induced or repressed by F. oxysporum showed tissue-specific regulation. Regulators of auxin and ABA signalling, mannose binding lectins and peroxidases showed strong differential expression in root tissue. We demonstrate that ARF2 and PRX33, two genes regulated in the roots, promote susceptibility to F. oxysporum. In the leaves, defensins and genes associated with the response to auxin, cold and senescence were strongly regulated while jasmonate biosynthesis and signalling genes were induced throughout the plant.

  8. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.

    Science.gov (United States)

    Lyons, Rebecca; Stiller, Jiri; Powell, Jonathan; Rusu, Anca; Manners, John M; Kazan, Kemal

    2015-01-01

    Some of the most devastating agricultural diseases are caused by root-infecting pathogens, yet the majority of studies on these interactions to date have focused on the host responses of aerial tissues rather than those belowground. Fusarium oxysporum is a root-infecting pathogen that causes wilt disease on several plant species including Arabidopsis thaliana. To investigate and compare transcriptional changes triggered by F. oxysporum in different Arabidopsis tissues, we infected soil-grown plants with F. oxysporum and subjected root and leaf tissue harvested at early and late timepoints to RNA-seq analyses. At least half of the genes induced or repressed by F. oxysporum showed tissue-specific regulation. Regulators of auxin and ABA signalling, mannose binding lectins and peroxidases showed strong differential expression in root tissue. We demonstrate that ARF2 and PRX33, two genes regulated in the roots, promote susceptibility to F. oxysporum. In the leaves, defensins and genes associated with the response to auxin, cold and senescence were strongly regulated while jasmonate biosynthesis and signalling genes were induced throughout the plant.

  9. Metabolic profiling of the tissue-specific responses in mussel Mytilus galloprovincialis towards Vibrio harveyi challenge.

    Science.gov (United States)

    Liu, Xiaoli; Ji, Chenglong; Zhao, Jianmin; Wang, Qing; Li, Fei; Wu, Huifeng

    2014-08-01

    Mussel Mytilus galloprovincialis is a marine aquaculture shellfish distributing widely along the coast in north China. In this work, we studied the differential metabolic responses induced by Vibrio harveyi in digestive gland and gill tissues from M. galloprovincialis using NMR-based metabolomics. The differential metabolic responses in the two tissue types were detected, except the similarly altered taurine and betaine. These metabolic responses suggested that V. harveyi mainly induced osmotic disruption and reduced energy demand via the metabolic pathways of glucose synthesis and ATP/AMP conversion in mussel digestive gland. In mussel gill tissues, V. harveyi basically caused osmotic stress and possible reduced energy demand as shown by the elevated phosphocholine that is involved in one of the metabolic pathways of ATP synthesis from ADP and phosphocholine. The altered mRNA expression levels of related genes (superoxide dismutase with copper and zinc, heat shock protein 90, defensin and lysozyme) suggested that V. harveyi induced clear oxidative and immune stresses in both digestive gland and gill tissues. However, the mRNA expression levels of both lysozyme and defensin in digestive gland were more significantly up-regulated than those in gill from V. harveyi-challenged mussel M. galloprovincialis, meaning that the immune organ, digestive gland, was more sensitive than gill. Overall, our results indicated that V. harveyi could induce tissue-specific metabolic responses in mussel M. galloprovincialis.

  10. Specificity of circulating and tissue-bound autoantibodies in Goodpasture syndrome.

    Science.gov (United States)

    Kalluri, R; Melendez, E; Rumpf, K W; Sattler, K; Müller, G A; Strutz, F; Neilson, E G

    1996-03-01

    Goodpasture syndrome is an often fatal autoimmune disease associated with glomerulonephritis and/or pulmonary hemorrhage. The clinical manifestations of this disease correlate well with the presence of circulating antiglomerular basement membrane (GBM) autoantibodies. The primary target antigen in glomerular and alveolar basement membranes is thought to be the alpha 3 chain of type IV collagen. Nearly all that is known about anti-GBM antibodies in humans comes from work on unbound circulating antibody. We recently had the unique and rare opportunity to obtain early postmortem antibody and tissues from a patient who died with catastrophic Goodpasture syndrome. The specificity of circulating, kidney-bound and lung-bound autoantibodies from this patient was evaluated against a variety of purified basement membrane constituents. The results indicate that the primary target for the circulating and tissue-bound autoantibodies is the NC1 domain of the alpha 3(IV) chain of type IV collagen. Additionally, all the antibodies recognize a cryptic epitope/s on the alpha 3(IV)NC1 hexamer. Furthermore, tissue-bound and circulating antibodies compete with one another for overlapping epitopes on the antigen. These findings demonstrate that circulating autoantibodies in Goodpasture syndrome are highly representative of those bound to organ tissues, strengthening the notion that pathogenic autoantibodies are targeted to the alpha 3(IV)NC1 collagen, and that previous reports of findings in the circulation may be applicable to tissue injury.

  11. Assessing allele-specific expression across multiple tissues from RNA-seq read data

    Science.gov (United States)

    Pirinen, Matti; Lappalainen, Tuuli; Zaitlen, Noah A.; Dermitzakis, Emmanouil T.; Donnelly, Peter; McCarthy, Mark I.; Rivas, Manuel A.

    2015-01-01

    Motivation: RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data. Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally. Availability and implementation: http://www.well.ox.ac.uk/~rivas/mamba/. R-sources and data examples http://www.iki.fi/mpirinen/ Contact: matti.pirinen@helsinki.fi or rivas@well.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25819081

  12. 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 genes...... involved in the Mendelian disorder long QT syndrome (LOTS). We integrated the LOTS network with GWAS loci from the corresponding common complex trait, QT-interval variation, to identify candidate genes that were subsequently confirmed in Xenopus laevis oocytes and zebrafish. We used the LOTS protein...... to propose candidates in GWAS loci for functional studies and to systematically filter subtle association signals using tissue-specific quantitative interaction proteomics....

  13. Screening of tissue-specific genes and promoters in tomato by comparing genome wide expression profiles of Arabidopsis orthologues.

    Science.gov (United States)

    Lim, Chan Ju; Lee, Ha Yeon; Kim, Woong Bom; Lee, Bok-Sim; Kim, Jungeun; Ahmad, Raza; Kim, Hyun A; Yi, So Young; Hur, Cheol-Goo; Kwon, Suk-Yoon

    2012-07-01

    Constitutive overexpression of transgenes occasionally interferes with normal growth and developmental processes in plants. Thus, the development of tissue-specific promoters that drive transgene expression has become agriculturally important. To identify tomato tissue-specific promoters, tissue-specific genes were screened using a series of in silico-based and experimental procedures, including genome-wide orthologue searches of tomato and Arabidopsis databases, isolation of tissue-specific candidates using an Arabidopsis microarray database, and validation of tissue specificity by reverse transcription-polymerase chain reaction (RT-PCR) analysis and promoter assay. Using these procedures, we found 311 tissue-specific candidate genes and validated 10 tissue-specific genes by RT-PCR. Among these identified genes, histochemical analysis of five isolated promoter::GUS transgenic tomato and Arabidopsis plants revealed that their promoters have different but distinct tissue-specific activities in anther, fruit, and root, respectively. Therefore, it appears these in silico-based screening approaches in addition to the identification of new tissue-specific genes and promoters will be helpful for the further development of tailored crop development.

  14. Deconstructing autofluorescence: non-invasive detection and monitoring of biochemistry in cells and tissues (Conference Presentation)

    Science.gov (United States)

    Goldys, Ewa M.; Gosnell, Martin E.; Anwer, Ayad G.; Cassano, Juan C.; Sue, Carolyn M.; Mahbub, Saabah B.; Pernichery, Sandeep M.; Inglis, David W.; Adhikary, Partho P.; Jazayeri, Jalal A.; Cahill, Michael A.; Saad, Sonia; Pollock, Carol; Sutton-Mcdowall, Melanie L.; Thompson, Jeremy G.

    2016-03-01

    Automated and unbiased methods of non-invasive cell monitoring able to deal with complex biological heterogeneity are fundamentally important for biology and medicine. Label-free cell imaging provides information about endogenous fluorescent metabolites, enzymes and cofactors in cells. However extracting high content information from imaging of native fluorescence has been hitherto impossible. Here, we quantitatively characterise cell populations in different tissue types, live or fixed, by using novel image processing and a simple multispectral upgrade of a wide-field fluorescence microscope. Multispectral intrinsic fluorescence imaging was applied to patient olfactory neurosphere-derived cells, cell model of a human metabolic disease MELAS (mitochondrial myopathy, encephalomyopathy, lactic acidosis, stroke-like syndrome). By using an endogenous source of contrast, subtle metabolic variations have been detected between living cells in their full morphological context which made it possible to distinguish healthy from diseased cells before and after therapy. Cellular maps of native fluorophores, flavins, bound and free NADH and retinoids unveiled subtle metabolic signatures and helped uncover significant cell subpopulations, in particular a subpopulation with compromised mitochondrial function. The versatility of our method is further illustrated by detecting genetic mutations in cancer, non-invasive monitoring of CD90 expression, label-free tracking of stem cell differentiation, identifying stem cell subpopulations with varying functional characteristics, tissue diagnostics in diabetes, and assessing the condition of preimplantation embryos. Our optimal discrimination approach enables statistical hypothesis testing and intuitive visualisations where previously undetectable differences become clearly apparent.

  15. An electrochemical approach to monitor pH change in agar media during plant tissue culture.

    Science.gov (United States)

    Wang, Min; Ha, Yang

    2007-05-15

    In this work, metal oxide microelectrodes were developed to monitor pH change in agar media during plant tissue culture. An antimony wire was produced by a new approach "capillary melt method". The surface of the obtained antimony wire was oxidized in a potassium nitrate melt to fabricate an antimony oxide film for pH sensing. Characterization results show that the oxide layer grown on the wire surface consists of Sb(2)O(3) crystal phase. The sensing response, open-circuit potential, of the electrode has a good linear relationship (R(2)=1.00) with pH value of the test solution. Adding organic compounds into the test media would not affect the linear relationship, although the slope of the lines varied with different ingredients added. The antimony oxide electrodes were employed to continuously monitor pH change of agar culture media during a 2-week plant tissue culture of Dendrobium candidum. The antimony oxide electrode fabricated this way has the advantages of low cost, easy fabrication, fast response, and almost no contamination introduced into the system. It would be suitable for in situ and continuous pH measurement in many bio applications.

  16. 17β-Estradiol suppresses visceral adipogenesis and activates brown adipose tissue-specific gene expression.

    Science.gov (United States)

    Al-Qahtani, Saad Misfer; Bryzgalova, Galyna; Valladolid-Acebes, Ismael; Korach-André, Marion; Dahlman-Wright, Karin; Efendić, Suad; Berggren, Per-Olof; Portwood, Neil

    2017-01-01

    Both functional ovaries and estrogen replacement therapy (ERT) reduce the risk of type 2 diabetes (T2D). Understanding the mechanisms underlying the antidiabetic effects of 17β-estradiol (E2) may permit the development of a molecular targeting strategy for the treatment of metabolic disease. This study examines how the promotion of insulin sensitivity and weight loss by E2 treatment in high-fat-diet (HFD)-fed mice involve several anti-adipogenic processes in the visceral adipose tissue. Magnetic resonance imaging (MRI) revealed specific reductions in visceral adipose tissue volume in HFD+E2 mice, compared with HFD mice. This loss of adiposity was associated with diminished visceral adipocyte size and reductions in expression of lipogenic genes, adipokines and of the nuclear receptor nr2c2/tr4. Meanwhile, expression levels of adipose triglyceride lipase/pnpla2 and leptin receptor were increased. As mRNA levels of stat3, a transcription factor involved in brown adipose tissue differentiation, were also increased in visceral adipose, the expression of other brown adipose-specific markers was assessed. Both expression and immunohistochemical staining of ucp-1 were increased, and mRNA levels of dio-2, and of adrβ3, a regulator of ucp-1 expression during the thermogenic response, were increased. Furthermore, expression of cpt-1b, a brown adipose-specific gene involved in fatty acid utilization, was also increased. Methylation studies demonstrated that the methylation status of both dio-2 and adrβ3 was significantly reduced. These results show that improved glycemic control and weight loss due to E2 involve anti-adipogenic mechanisms which include suppressed lipogenesis and augmented fatty acid utilization, and in addition, the activation of brown adipose tissue-specific gene expression in association with E2-dependent epigenetic modifications in these genes.

  17. A tissue-specific landscape of sense/antisense transcription in the mouse intestine

    Directory of Open Access Journals (Sweden)

    Sina Christian

    2011-06-01

    Full Text Available Abstract Background The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the analysis of the RNA sequence space, the level of detail on the global architecture of the transcriptome reached a new order of magnitude compared to microarrays. Results We report the ultra-deep characterization of the polyadenylated transcriptome in two closely related, yet distinct regions of the mouse intestinal tract (small intestine and colon. We assessed tissue-specific transcriptomal architecture and the presence of novel transcriptionally active regions (nTARs. In the first step, signatures of 20,541 NCBI RefSeq transcripts could be identified in the intestine (74.1% of annotated genes, thereof 16,742 are common in both tissues. Although the majority of reads could be linked to annotated genes, 27,543 nTARs not consistent with current gene annotations in RefSeq or ENSEMBL were identified. By use of a second independent strand-specific RNA-Seq protocol, 20,966 of these nTARs were confirmed, most of them in vicinity of known genes. We further categorized our findings by their relative adjacency to described exonic elements and investigated regional differences of novel transcribed elements in small intestine and colon. Conclusions The current study demonstrates the complexity of an archetypal mammalian intestinal mRNA transcriptome in high resolution and identifies novel transcriptionally active regions at strand-specific, single base resolution. Our analysis for the first time shows a strand-specific comparative picture of nTARs in two tissues and represents a resource for further investigating the transcriptional processes that contribute to tissue identity.

  18. A Tissue-Specific Approach to the Analysis of Metabolic Changes in Caenorhabditis elegans

    OpenAIRE

    Jürgen Hench; Ivana Bratić Hench; Claire Pujol; Sabine Ipsen; Susanne Brodesser; Arnaud Mourier; Markus Tolnay; Stephan Frank; Aleksandra Trifunović

    2011-01-01

    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...

  19. Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data

    Science.gov (United States)

    Badr, Eman; ElHefnawi, Mahmoud; Heath, Lenwood S.

    2016-01-01

    Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors that bind to specific sequences called splicing regulatory elements (SREs). Here, we report a genome-wide analysis to study alternative splicing on multiple tissues, including brain, heart, liver, and muscle. We propose a pipeline to identify differential exons across tissues and hence tissue-specific SREs. In our pipeline, we utilize the DEXSeq package along with our previously reported algorithms. Utilizing the publicly available RNA-Seq data set from the Human BodyMap project, we identified 28,100 differentially used exons across the four tissues. We identified tissue-specific exonic splicing enhancers that overlap with various previously published experimental and computational databases. A complicated exonic enhancer regulatory network was revealed, where multiple exonic enhancers were found across multiple tissues while some were found only in specific tissues. Putative combinatorial exonic enhancers and silencers were discovered as well, which may be responsible for exon inclusion or exclusion across tissues. Some of the exonic enhancers are found to be co-occurring with multiple exonic silencers and vice versa, which demonstrates a complicated relationship between tissue-specific exonic enhancers and silencers. PMID:27861625

  20. Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo

    Directory of Open Access Journals (Sweden)

    Hyun Cheol Roh

    2017-01-01

    Full Text Available Epigenomic mechanisms direct distinct gene expression programs for different cell types. Various in vivo tissues have been subjected to epigenomic analysis; however, these studies have been limited by cellular heterogeneity, resulting in composite gene expression and epigenomic profiles. Here, we introduce “NuTRAP,” a transgenic mouse that allows simultaneous isolation of cell-type-specific translating mRNA and chromatin from complex tissues. Using NuTRAP, we successfully characterize gene expression and epigenomic states of various adipocyte populations in vivo, revealing significant differences compared to either whole adipose tissue or in vitro adipocyte cell lines. We find that chromatin immunoprecipitation sequencing (ChIP-seq using NuTRAP is highly efficient, scalable, and robust with even limited cell input. We further demonstrate the general utility of NuTRAP by analyzing hepatocyte-specific epigenomic states. The NuTRAP mouse is a resource that provides a powerful system for cell-type-specific gene expression and epigenomic profiling.

  1. cell- and tissue-specific transcriptome analyses of Medicago truncatula root nodules.

    Directory of Open Access Journals (Sweden)

    Erik Limpens

    Full Text Available Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur and proximal region (where symbiosomes are mainly differentiating, as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital "in situ". This digital "in situ" offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies.

  2. Tissue-specific effects of hypothyroidism on postnatal muscle development in the barnacle goose.

    Science.gov (United States)

    Deaton, K E; Bishop, C M; Butler, P J

    1998-03-01

    The hypothesis that tissue-specific levels of thyroid hormones may be required for normal locomotor muscle development was investigated in the barnacle goose Branta leucopsis. Hypothyroidism was induced in goslings by treatment with methimazole from either 3 days or 2 weeks of age, and birds were killed at 7 weeks of age. The masses of the pectoralis, iliofibularis, semimembranosus and cardiac ventricle muscles were measured, and samples from these tissues were analysed for the mass-specific activity of the mitochondrial enzyme citrate synthase (CS). An ultrastructural electron micrograph analysis of the pectoralis was also carried out. No significant differences were found between the two hypothyroid groups except for the effect on the relative mass of the iliofibularis muscle. Developmental responses to hypothyroidism were found to be tissue-specific. Hypothyroidism resulted in a significantly lower relative cardiac ventricle mass (by 17 %) and CS activity of the leg muscles (by 34 %), while absolute leg muscle mass was not affected. The relative mass of the pectoralis was significantly lower (by 57 %) in hypothyroid birds and showed a significant, uniformly lower CS activity (by 60-83 %) as a result of a lower mitochondrial fractional volume. Haematocrit and capillary-to-fibre ratio in the pectoralis were also significantly lower in hypothyroid birds, and skeletal growth and plumage development were affected.

  3. Multidimensional Monitoring of Keratin Intermediate Filaments in Cultured Cells and Tissues.

    Science.gov (United States)

    Schwarz, Nicole; Moch, Marcin; Windoffer, Reinhard; Leube, Rudolf E

    2016-01-01

    Keratin filaments are a hallmark of epithelial differentiation. Their cell type-specific spatial organization and dynamic properties reflect and support epithelial function. To study this interdependency, imaging of fluorescently tagged keratins is a widely used method by which the temporospatial organization and behavior of the keratin intermediate filament network can be analyzed in living cells. Here, we describe methods that have been adapted and optimized to dissect and quantify keratin intermediate filament network dynamics in vital cultured cells and functional tissues.

  4. Specifications and applications of the technical code for monitoring of building and bridge structures in China

    Directory of Open Access Journals (Sweden)

    Y Yang

    2016-12-01

    Full Text Available Recently, the exclusive compulsory technical code (GB 50982-2014 for structural health monitoring of buildings and bridges in China has been developed and implemented. This code covers the majority of the field monitoring methods and stipulates the corresponding technical parameters for monitoring of high-rise structures, large-span spatial structures, bridges and base-isolated structures. This article first presents the comprehensive review and linear comparison of existing structural health monitoring codes and standards. Subsequently, the progress of the codification of GB 50982-2014 is imparted and its main features and specifications are summarized. Finally, in accordance with GB50982-2014, several representative structural health monitoring practical applications of large-scale infrastructures in China are exemplified to illustrate how this national code can bridge the gap between theory and practical applications of structural health monitoring. This technical code is an important milestone in the application of well-established structural health monitoring techniques into the realistic and complex engineering projects. Also, it can provide abundant and authoritative information for practitioners and researchers involving the structural health monitoring techniques.

  5. Tissue transglutaminase is the target in both rodent and primate tissues for celiac disease-specific autoantibodies.

    Science.gov (United States)

    Korponay-Szabó, I R; Sulkanen, S; Halttunen, T; Maurano, F; Rossi, M; Mazzarella, G; Laurila, K; Troncone, R; Mäki, M

    2000-11-01

    Endomysial antibodies have recently been shown to react with tissue transglutaminase. This study was undertaken to investigate whether the tissue distribution of transglutaminase is also compatible with reticulin, jejunal, and fibroblast autoantibody binding patterns. Sera from patients with and without celiac disease, monoclonal tissue transglutaminase antibodies, and sera from mice parenterally immunized against commercially available tissue transglutaminase, transglutaminase complexed with gliadin, or gliadin were used in indirect immunofluorescence and double-staining studies using both rodent and primate tissues as substrates. Also, antibody competition, affinity chromatography, and potassium thiocyanate extraction studies were undertaken. Tissue transglutaminase antibody binding patterns were identical with the extracellular binding patterns seen with celiac patient sera. Human umbilical cord-derived fibroblasts exhibited both cytoplasmic and extracellular matrix staining. Double staining with patients' sera and tissue transglutaminase antibodies showed complete overlapping. Tissue transglutaminase effectively absorbed reticulin-endomysial antibodies from celiac sera, and patients' sera blocked the staining of the monoclonal tissue transglutaminase antibodies. Potassium thiocyanate extraction abolished the staining patterns, but they were elicited again after readdition of tissue transglutaminase. Reticulin, endomysial, and jejunal antibodies detect transglutaminase in both rodent and primate tissues, indicating that these tissue autoantibodies are identical.

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

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    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.

  7. Multi-channel electrical impedance tomography for regional tissue hydration monitoring.

    Science.gov (United States)

    Chen, Xiaohui; Kao, Tzu-Jen; Ashe, Jeffrey M; Boverman, Gregory; Sabatini, James E; Davenport, David M

    2014-06-01

    Poor assessment of hydration status during hemodialysis can lead to under- or over-hydration in patients with consequences of increased morbidity and mortality. In current practice, fluid management is largely based on clinical assessments to estimate dry weight (normal hydration body weight). However, hemodialysis patients usually have co-morbidities that can make the signs of fluid status ambiguous. Therefore, achieving normal hydration status remains a major challenge for hemodialysis therapy. Electrical impedance technology has emerged as a promising method for hydration monitoring due to its non-invasive nature, low cost and ease-of-use. Conventional electrical impedance-based hydration monitoring systems employ single-channel current excitation (either 2-electrode or 4-electrode methods) to perturb and extract averaged impedance from bulk tissue and use generalized models from large populations to derive hydration estimates. In the present study, a prototype, single-frequency electrical impedance tomography (EIT) system with simultaneous multi-channel current excitation was used to enable regional hydration change detection. We demonstrated the capability to detect a difference in daily impedance change between left leg and right leg in healthy human subjects, who wore a compression sock only on one leg to reduce daily gravitational fluid accumulation. The impedance difference corresponded well with the difference of lower leg volume change between left leg and right leg measured by volumetry, which on average is ~35 ml, accounting for 0.7% of the lower leg volume. We have demonstrated the feasibility of using multi-channel EIT to extract hydration information in different tissue layers with minimal skin interference. Our simultaneous, multi-channel current excitation approach provides an effective method to separate electrode contact impedance and skin condition artifacts from hydration signals. The prototype system has the potential to be used in clinical

  8. Ultrasound and photoacoustic imaging to monitor ocular stem cell delivery and tissue regeneration (Conference Presentation)

    Science.gov (United States)

    Kubelick, Kelsey; Snider, Eric; Yoon, Heechul; Ethier, C. Ross; Emelianov, Stanislav Y.

    2017-03-01

    Glaucoma is associated with dysfunction of the trabecular meshwork (TM), a fluid drainage tissue in the anterior eye. A promising treatment involves delivery of stem cells to the TM to restore tissue function. Currently histology is the gold standard for tracking stem cell delivery and differentiation. To expedite clinical translation, non-invasive longitudinal monitoring in vivo is desired. Our current research explores a technique combining ultrasound (US) and photoacoustic (PA) imaging to track mesenchymal stem cells (MSCs) after intraocular injection. Adipose-derived MSCs were incubated with gold nanospheres to label cells (AuNS-MSCs) for PA imaging. Successful labeling was first verified with in vitro phantom studies. Next, MSC delivery was imaged ex vivo in porcine eyes, while intraocular pressure was hydrostatically clamped to maintain a physiological flow rate through the TM. US/PA imaging was performed before, during, and after AuNS-MSC delivery. Additionally, spectroscopic PA imaging was implemented to isolate PA signals from AuNS-MSCs. In vitro cell imaging showed AuNS-MSCs produce strong PA signals, suggesting that MSCs can be tracked using PA imaging. While the cornea, sclera, iris, and TM region can be visualized with US imaging, pigmented tissues also produce PA signals. Both modalities provide valuable anatomical landmarks for MSC localization. During delivery, PA imaging can visualize AuNS-MSC motion and location, creating a unique opportunity to guide ocular cell delivery. Lastly, distinct spectral signatures of AuNS-MSCs allow unmixing, with potential for quantitative PA imaging. In conclusion, results show proof-of-concept for monitoring MSC ocular delivery, raising opportunities for in vivo image-guided cell delivery.

  9. Interstitial fluid pressure: A novel biomarker to monitor photo-induced drug uptake in tumor and normal tissues.

    Science.gov (United States)

    Cavin, Sabrina; Wang, Xingyu; Zellweger, Matthieu; Gonzalez, Michel; Bensimon, Michaël; Wagnières, Georges; Krueger, Thorsten; Ris, Hans-Beat; Gronchi, Fabrizio; Perentes, Jean Y

    2017-10-01

    Low-dose photodynamic therapy PDT (photoinduction) can modulate tumor vessels and enhance the uptake of liposomal cisplatin (Lipoplatin®) in pleural malignancies. However, the photo-induction conditions must be tightly controlled as overtreatment shuts down tumor vessels and enhances normal tissue drug uptake. In a pleural sarcoma and adenocarcinoma rat model (n = 12/group), we applied photoinduction (0.0625 mg/kg Visudyne®, 10 J/cm(2) ) followed by intravenous Lipoplatin® (5 mg/kg) administration. Tumor and normal tissue IFP were assessed before and up to 1 hour following photoinduction. Lipoplatin® uptake was determined 60 minutes following photoinduction. We then treated the pleura of tumor-free minipigs with high dose photodynamic therapy (PDT) (0.0625 mg/kg Visudyne®, 30 J/cm(2) , n = 5) followed by Lipoplatin (5 mg/kg) administration. In rodents, photoinduction resulted in a significant decrease of IFP (P parabola. In minipigs, high dose photodynamic treatment resulted in pleural IFP increase of some animals which predicted higher Lipoplatin® uptake levels. Normal and tumor vasculatures react differently to PDT. Continuous IFP monitoring in normal and tumor tissues is a promising biomarker of vessel photoinduction. Moderate drop in tumor with no change in normal tissue IFP are predictive of specific Lipoplatin® uptake by cancer following PDT. Lasers Surg. Med. 49:773-780, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  10. Micro-Raman spectroscopy of tissue samples for oral pathology follow-up monitoring

    Science.gov (United States)

    Delfino, I.; Camerlingo, C.; Zenone, F.; Perna, G.; Capozzi, V.; Cirillo, N.; Gaeta, G. M.; Lepore, M.

    2010-04-01

    An "in vitro" study of Raman spectra from oral human tissues is reported in order to the develop a diagnostic method suitable for "in vivo" oral pathology follow-up. The investigated pathology is Pemphigus Vulgaris (PV) for which new techniques for guiding and monitoring therapy would be particularly useful. Raman spectra were obtained in the wavenumber regions from 1000 to 1800 cm-1 and 2700 to 3200 cm-1 from tissues from patients at different stages of pathology (active PV, under therapy and in PV remission stage) as confirmed by histopathological and immunofluorescence analysis. Differences in the spectra depending on tissue illness stage arise in 1150-1250 cm-1 (amide III) and 1420-1450 cm-1 (CH3 deformation) regions and around 1650 cm-1 (amide I) and 2930 cm-1 (CH3 symmetric stretch). A wavelet deconvolution procedure was applied to the spectra for better discriminating among the three different stages of illness and a linear regression analysis was used to fully exploit the content of information of Raman spectra.

  11. Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

    Directory of Open Access Journals (Sweden)

    Tobias Wagner

    Full Text Available ApoE deficiency in mice (Apoe-/- results in severe hypercholesterolemia and atherosclerosis. In diet-induced obesity, Apoe-/- display steatohepatitis but reduced accumulation of triacylglycerides and enhanced insulin sensitivity in white adipose tissue (WAT. Although the vast majority of apoE is expressed by hepatocytes apoE is also abundantly expressed in WAT. As liver and adipose tissue play important roles for metabolism, this study aims to outline functions of both hepatocyte- and adipocyte-derived apoE separately by investigating a novel mouse model of tissue-specific apoE deficiency. Therefore we generated transgenic mice carrying homozygous floxed Apoe alleles. Mice lacking apoE either in hepatocytes (ApoeΔHep or in adipose tissue (ApoeΔAT were fed experimental diets. ApoeΔHep exhibited slightly higher body weights, adiposity and liver weights on diabetogenic high fat diet (HFD. Accordingly, hepatic steatosis and markers of inflammation were more pronounced compared to controls. Hypercholesterolemia evoked by lipoprotein remnant accumulation was present in ApoeΔHep mice fed a Western type diet (WTD. Lipidation of VLDL particles and tissue uptake of VLDL were disturbed in ApoeΔHep while the plasma clearance rate remained unaltered. ApoeΔAT did not display any detectable phenotype, neither on HFD nor on WTD. In conclusion, our novel conditional apoE deletion model has proven here the role of hepatocyte apoE for VLDL production and diet-induced dyslipidemia. Specific deletion of apoE in adipocytes cannot reproduce the adipose phenotype of global Apoe-/- mice, suggesting that apoE produced in other cell types than hepatocytes or adipocytes explains the lean and insulin-sensitive phenotype described for Apoe-/- mice.

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

    Science.gov (United States)

    Rocha, Thiago Lopes; Gomes, Tânia; Mestre, Nélia C; Cardoso, Cátia; Bebianno, Maria João

    2015-12-01

    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(-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, indicating nano-specific effects possibly associated to oxidative stress and changes in redox homeostasis.

  13. 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.

  14. Hole Burning Imaging Studies of Cancerous and Analogous Normal Ovarian Tissues Utilizing Organelle Specific Dyes

    Energy Technology Data Exchange (ETDEWEB)

    Matsuzaki, Satoshi [Iowa State Univ., Ames, IA (United States)

    2004-01-01

    Presented in this dissertation is the successful demonstration that nonphotochemical hole burning (NPWB) imaging can be used to study in vitro tissue cellular systems for discerning differences in cellular ultrastructures due to cancer development. This has been accomplished with the surgically removed cancerous ovarian and analogous normal peritoneal tissues from the same patient and the application of a fluorescent mitochondrion specific dye, Molecular Probe MitoFluor Far Red 680 (MF680), commonly known as rhodamine 800, that has been proven to exhibit efficient NPHB. From the results presented in Chapters 4 and 5 , and Appendix B, the following conclusions were made: (1) fluorescence excitation spectra of MF680 and confocal microscopy images of thin sliced tissues incubated with MF680 confirm the site-specificity of the probe molecules in the cellular systems. (2) Tunneling parameters, {lambda}{sub 0} and σΛ, as well as the standard hole burning parameters (namely, γ and S), have been determined for the tissue samples by hole growth kinetics (HGK) analyses. Unlike the preliminary cultured cell studies, these parameters have not shown the ability to distinguish tissue cellular matrices surrounding the chromophores. (3) Effects of an external electric (Stark) field on the nonphotochemical holes have been used to determine the changes in permanent dipole moment (fΔμ) for MF680 in tissue samples when burn laser polarization is parallel to the Stark field. Differences are detected between fΔμs in the two tissue samples, with the cancerous tissue exhibiting a more pronounced change (1.35-fold increase) in permanent dipole moment change relative to the normal analogs. It is speculated that the difference may be related to differences in mitochondrial membrane potentials in these tissue samples. (4) In the HGK mode, hole burning imaging (HBI) of cells adhered to coverslips and cooled to liquid helium temperatures in the complete absence of

  15. Hole Burning Imaging Studies of Cancerous and Analogous Normal Ovarian Tissues Utilizing Organelle Specific Dyes

    Energy Technology Data Exchange (ETDEWEB)

    Satoshi Matsuzaki

    2004-12-19

    Presented in this dissertation is the successful demonstration that nonphotochemical hole burning (NPWB) imaging can be used to study in vitro tissue cellular systems for discerning differences in cellular ultrastructures due to cancer development. This has been accomplished with the surgically removed cancerous ovarian and analogous normal peritoneal tissues from the same patient and the application of a fluorescent mitochondrion specific dye, Molecular Probe MitoFluor Far Red 680 (MF680), commonly known as rhodamine 800, that has been proven to exhibit efficient NPHB. From the results presented in Chapters 4 and 5 , and Appendix B, the following conclusions were made: (1) fluorescence excitation spectra of MF680 and confocal microscopy images of thin sliced tissues incubated with MF680 confirm the site-specificity of the probe molecules in the cellular systems. (2) Tunneling parameters, {lambda}{sub 0} and {sigma}{sub {lambda}}, as well as the standard hole burning parameters (namely, {gamma} and S), have been determined for the tissue samples by hole growth kinetics (HGK) analyses. Unlike the preliminary cultured cell studies, these parameters have not shown the ability to distinguish tissue cellular matrices surrounding the chromophores. (3) Effects of an external electric (Stark) field on the nonphotochemical holes have been used to determine the changes in permanent dipole moment (f{Delta}{mu}) for MF680 in tissue samples when burn laser polarization is parallel to the Stark field. Differences are detected between f{Delta}{mu}s in the two tissue samples, with the cancerous tissue exhibiting a more pronounced change (1.35-fold increase) in permanent dipole moment change relative to the normal analogs. It is speculated that the difference may be related to differences in mitochondrial membrane potentials in these tissue samples. (4) In the HGK mode, hole burning imaging (HBI) of cells adhered to coverslips and cooled to liquid helium temperatures in the

  16. Tissue- Specific Expression Analysis of Anthocyanin Biosynthetic Genes in White- and Red-Fleshed Grape Cultivars

    Directory of Open Access Journals (Sweden)

    Sha Xie

    2015-12-01

    Full Text Available Yan73, a teinturier (dyer grape variety in China, is one of the few Vitis vinifera cultivars with red-coloured berry flesh. To examine the tissue-specific expression of genes associated with berry colour in Yan73, we analysed the differential accumulation of anthocyanins in the skin and flesh tissues of two red-skinned grape varieties with either red (Yan73 or white flesh (Muscat Hamburg based on HPLC-MS analysis, as well as the differential expression of 18 anthocyanin biosynthesis genes in both varieties by quantitative RT-PCR. The results revealed that the transcripts of GST, OMT, AM3, CHS3, UFGT, MYBA1, F3′5′H, F3H1 and LDOX were barely detectable in the white flesh of Muscat Hamburg. In particular, GST, OMT, AM3, CHS3 and F3H1 showed approximately 50-fold downregulation in the white flesh of Muscat Hamburg compared to the red flesh of Yan73. A correlation analysis between the accumulation of different types of anthocyanins and gene expression indicated that the cumulative expression of GST, F3′5′H, LDOX and MYBA1 was more closely associated with the acylated anthocyanins and the 3′5′-OH anthocyanins, while OMT and AM3 were more closely associated with the total anthocyanins and methoxylated anthocyanins. Therefore, the transcripts of OMT, AM3, GST, F3′5′H, LDOX and MYBA1 explained most of the variation in the amount and composition of anthocyanins in skin and flesh of Yan73. The data suggest that the specific localization of anthocyanins in the flesh tissue of Yan73 is most likely due to the tissue-specific expression of OMT, AM3, GST, F3′5′H, LDOX and MYBA1 in the flesh.

  17. 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

  18. Genome-wide Transcription Factor Gene Prediction and their Expressional Tissue-Specificities in Maize

    Institute of Scientific and Technical Information of China (English)

    Yi Jiang; Biao Zeng; Hainan Zhao; Mei Zhang; Shaojun Xie; Jinsheng Lai

    2012-01-01

    Transcription factors (TFs) are important regulators of gene expression.To better understand TFencoding genes in maize (Zea mays L.),a genome-wide TF prediction was performed using the updated B73 reference genome.A total of 2 298 TF genes were identified,which can be classified into 56 families.The largest family,known as the MYB superfamily,comprises 322 MYB and MYB-related TF genes.The expression patterns of 2014 (87.64%) TF genes were examined using RNA-seq data,which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues (including root,shoot,leaf,ear,tassel and kernel).Similarly,98 kernel-specific TF genes were further analyzed,and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage,while 69 of the genes were expressed in the late kernel developmental stage.Identification of these TFs,particularly the tissue-specific ones,provides important information for the understanding of development and transcriptional regulation of maize.

  19. Mitochondrial dysfunction: bench-to-bedside optical monitoring of tissue vitality

    Science.gov (United States)

    Mayevsky, Avraham; Dekel, Nava; Oren, Levi; Deutsch, Assaf; Pewzner, Eliyahu

    2008-02-01

    In normal cell the mitochondria are the major source of energy for cellular functions. They serve as biosensors for oxidative stress and involved also in termination of cell function by apoptosis. The involvement of mitochondria in pathological states such as neurodegenerative diseases, sepsis, stroke and cancer are well documented. The involvement of mitochondrial respiration and function in cancer development, proliferation and possible therapy were initiated 75 years ago by Otto Warburg. Monitoring of NADH fluorescence in vivo as an intracellular oxygen indicator was established in the 1950-1970 by Britton Chance and collaborators. In the last 20 years we developed and used a multiparametric monitoring system enabling real time assessment of mitochondria NADH, microcirculatory blood flow and volume as well as HbO II oxygenation. In order to use this technology in clinical practice the commercial developed device-the "CritiView" was tested in animal models as well as in patients hospitalized in the critical care departments. In patients we tested the viability of the urethral wall (a less-vital tissue) by a 3 way Foley urinary catheter that contains the optical probe. The catheter was introduced to patients underwent open heart by-pass surgery or abdominal aorta aneurysm (AAA) operations. The monitoring started immediately after the insertion of the catheter to the patient and was stopped when the patient was discharged from the operation room. The results show that monitoring of the vitality of the Urethral wall provides information in correlation to the surgical procedure performed. In the AAA patients the occlusion of the aorta led to severe ischemia developed in the urethral wall and recovery of signals were recorded after the reopening of the aorta. In patients under went heart bypass surgery the urethra vitality was decreased dramatically during the operation and recovery was noted in most patients after the discharge of the patient from the operation room.

  20. Pilot study of laser induced breakdown spectroscopy for tissue differentiation by monitoring the plume created during laser surgery — An approach on a feedback Laser control mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Kanawade, Rajesh, E-mail: Rajesh.Kanawade@aot.uni-erlangen.de [Clinical Photonics Lab, Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052 Erlangen (Germany); Institute of Photonics Technologies, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen (Germany); Mehari, Fanuel [Master Programme in Advanced Optical Technologies (MAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052 Erlangen (Germany); Knipfer, Christian; Rohde, Maximilian [Department of Oral and Maxillofacial Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Glueckstrasse 11, 91054 Erlangen (Germany); Tangermann-Gerk, Katja [Bayerisches Laserzentrum GmbH, Konrad-Zuse-Strasse 2-6, 91052 Erlangen (Germany); Schmidt, Michael [Clinical Photonics Lab, Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052 Erlangen (Germany); Institute of Photonics Technologies, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen (Germany); Bayerisches Laserzentrum GmbH, Konrad-Zuse-Strasse 2-6, 91052 Erlangen (Germany); and others

    2013-09-01

    This study focuses on tissue differentiation using ‘Laser Induced Breakdown Spectroscopy’ (LIBS) by monitoring the plasma plume created during laser surgery processes. This technique is aimed at controlling a laser surgery feedback system in real time. An Excimer laser (Ar-F 193 nm) was used for the ablation of tissue samples. Fat, muscle, nerve and skin tissue samples of bisected ex-vivo pig heads were prepared as test objects for the ablation procedure. A single fiber was used to collect emissions and deliver them to a spectrometer. The obtained LIBS spectra in the measured emissions were analyzed to determine each tissue type according to their chemical composition. The elements found in the samples and their emission spectra were in agreement with those described in literature. The collected LIBS spectra were analyzed to differentiate the tissues using statistical data analysis: Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and Receiver Operating Characteristics (ROC). The obtained preliminary results suggest a successful differentiation of the target tissues with high sensitivity and specificity. The main goal of this study was to qualitatively identify tissue types during laser ablation, which will provide a real time feedback mechanism for clinical Laser surgery applications to significantly improve the accuracy and safety of laser surgery procedures. - Graphical abstract: Skin, fat, muscle and nerve tissue differentiation. - Highlights: • Methods to differentiate tissues for the application in a laser surgery feedback control system • Successful differentiation of the target tissues with high sensitivity and specificity for laser surgery application • Real time feedback mechanism for clinical Laser surgery applications • Laser surgery requirements • Biomedical applications of LIBS.

  1. 40 CFR 75.71 - Specific provisions for monitoring NOX and heat input for the purpose of calculating NOX mass...

    Science.gov (United States)

    2010-07-01

    ... MONITORING NOX Mass Emissions Provisions § 75.71 Specific provisions for monitoring NOX and heat input for... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Specific provisions for monitoring NOX and heat input for the purpose of calculating NOX mass emissions. 75.71 Section 75.71 Protection...

  2. Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar.

    Science.gov (United States)

    Cribbin, Kayla M; Quackenbush, Corey R; Taylor, Kyle; Arias-Rodriguez, Lenin; Kelley, Joanna L

    2017-04-07

    The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and increasing concerns about overexploitation and habitat degradation, basic genetic information on the tropical gar is lacking. Determining genetic information on the tropical gar is important for the sustainable management of wild populations, implementation of best practices in aquaculture settings, evolutionary studies of ancient lineages, and an understanding of sex-specific gene expression. In this study, the transcriptome of the tropical gar was sequenced and assembled de novo using tissues from three males and three females using Illumina sequencing technology. Sex-specific and highly differentially expressed transcripts in brain and muscle tissues between adult males and females were subsequently identified. The transcriptome was assembled de novo resulting in 80,611 transcripts with a contig N50 of 3,355 base pairs and over 168 kilobases in total length. Male muscle, brain, and gonad as well as female muscle and brain were included in the assembly. The assembled transcriptome was annotated to identify the putative function of expressed transcripts using Trinotate and SwissProt, a database of well-annotated proteins. The brain and muscle datasets were then aligned to the assembled transcriptome to identify transcripts that were differentially expressed between males and females. The contrast between male and female brain identified 109 transcripts from 106 genes that were significantly differentially expressed. In the muscle comparison, 82 transcripts from 80 genes were identified with evidence for significant differential expression. Almost all genes identified as differentially expressed were sex-specific. The differentially expressed transcripts were enriched for genes involved in

  3. Monitoring the effect of magnetically aligned collagen scaffolds on tendon tissue engineering by PSOCT

    Science.gov (United States)

    Yang, Ying; Ahearne, Mark; Wimpenny, Ian; Torbet, Jim

    2009-02-01

    As the repair of injured or degenerated tendon is often compromised by the shortage of suitable donor tissue, other procedures need to be developed. The application of a functional tissue engineered tendon could prove to be a promising alternative therapy. Due to their good biocompatibility, collagen hydrogel based scaffolds have been considered to be potentially suitable for engineering tendon tissue in vitro. One of the major limitations of collagen hydrogels for engineering tissues is the difficulty in controlling their architecture and collagen concentration which results in poor mechanical strength. This study aims to overcome these limitations by creating a highly biocompatible scaffold that is both mechanically robust and aligned. Collagen fibers were pre-aligned under a high magnetic field then concentrated using plastic compression. Primary tenocytes cultured from rats were seeded on the aligned scaffolds. Following a protocol in public domain, thick cultured collagen constructs were rolled up into a spiral after undergoing plastic compressed. Both a light microscopy and a polarization sensitive optical coherence tomography (PSOCT) with central beam at 1300 nm were used to monitor the birefringence in the constructs. Conventional light microscopy showed that the tenocytes aligned along the pre-organized collagen bundles in contrast to the random distributed observed on unaligned scaffolds. PSOCT only revealed weak birefringence from aligned but uncompressed constructs. However, PSOCT images showed contrast band structures in the spiral constructs which suggests that the birefringence signal depends on the density of aligned collagen fibers. The effect of aligned cells, neo-formed matrix and the plastic compression on the birefringence signals are discussed in this paper briefly.

  4. Differential Effects of Tissue-Specific Deletion of BOSS on Feeding Behaviors and Energy Metabolism.

    Directory of Open Access Journals (Sweden)

    Ayako Kohyama-Koganeya

    Full Text Available Food intake and energy metabolism are tightly controlled to maintain stable energy homeostasis and healthy states. Thus, animals detect their stored energy levels, and based on this, they determine appropriate food intake and meal size. Drosophila melanogaster putative G protein-coupled receptor, Bride of sevenless (BOSS is a highly evolutionarily conserved protein that responds to extracellular glucose levels in order to regulate energy homeostasis. To address how BOSS regulates energy homeostasis, we characterized a boss mutant by assessing its food intake and stored energy levels. Boss mutants exhibited increased food intake but decreased stored triacylglyceride levels. Using boss-GAL4 drivers, we found that boss is expressed in select tissues that are involved in nutrient sensing and food intake, in a subset of neurons in brain and chemosensory organs, in fat body, and in endocrine cells in gut (enteroendocrine cells. Flies with tissue-specific boss knockdowns in these tissues had abnormal stored energy levels and abnormal food intake. These results suggest that BOSS in either neurons or peripheral nutrient-sensing tissues affects energy homeostasis in ways that relate to the sensing of nutrients and regulation of food intake.

  5. Modified oleic cottonseeds show altered content, composition and tissue-specific distribution of triacylglycerol molecular species.

    Science.gov (United States)

    Horn, Patrick J; Sturtevant, Drew; Chapman, Kent D

    2014-01-01

    Targeted increases in monounsaturated (oleic acid) fatty acid content of refined cottonseed oil could support improved human nutrition and cardiovascular health. Genetic modifications of cottonseed fatty acid composition have been accomplished using several different molecular strategies. Modification of oleic acid content in cottonseed embryos using a dominant-negative protein approach, while successful in effecting change in the desired fatty acid composition, resulted in reduced oil content and seed viability. Here these changes in fatty acid composition were associated with changes in dominant molecular species of triacylglycerols (TAGs) and their spatial distributions within embryo tissues. A combination of mass spectrometry (MS)-based lipidomics approaches, including MS imaging of seed cryo-sections, revealed that cotton embryos expressing a non-functional allele of a Brassica napus delta-12 desaturase showed altered accumulation of TAG species, especially within cotyledonary tissues. While lipid analysis of seed extracts could demonstrate detailed quantitative changes in TAG species in transgenics, the spatial contribution of metabolite compartmentation could only be visualized by MS imaging. Our results suggest tissue-specific differences in TAG biosynthetic pathways within cotton embryos, and indicate the importance of considering the location of metabolites in tissues in addition to their identification and quantification when developing a detailed view of cellular metabolism.

  6. Isolation and functional analysis of a strong specific promoter in photosynthetic tissues

    Institute of Scientific and Technical Information of China (English)

    YANG; Yutao; (杨予涛); YANG; Guodong; (杨国栋); LIU; Shijuan; (刘石娟); GUO; Xingqi; (郭兴启); ZHENG; Chengchao; (郑成超)

    2003-01-01

    PNZIP gene promoter has been cloned from Pharbitis nil by adaptor PCR, which conforms to eukaryotic promoter characteristic. Primer extension analysis showed that the transcription start site was located 122 nucleotides upstream of the translation start site of PNZIP gene. According to the characteristic of PNZIP promoter, a series of deletions were purposely made by PCR. Five deletion fragments were fused to upstream of GUS gene and transferred into tobacco. Fluorometric GUS assay showed that five different length promoters all could specifically drive GUS gene expression in photosynthetic tissues and their activities decreased along with the gradual deletion of PNZIP promoter. In addition, the activity of full-length promoter was 9 times higher than that of CaMV 35S in leaf. PNZIP promoter may have two putative cis-elements, GAAATA and GATACT, which relate to gene expression in photosynthetic tissues. GATACT may determine the gene specific expression in photosynthetic tissues, while GAAATA, perhaps, as an enhancer, increases the intensity of gene expression.

  7. Chicken FTO gene: tissue-specific expression, brain distribution, breed difference and effect of fasting.

    Science.gov (United States)

    Wang, Yufeng; Rao, Kaiqing; Yuan, Lixia; Everaert, Nadia; Buyse, Johan; Grossmann, Roland; Zhao, Ruqian

    2012-11-01

    Fat mass and obesity-associated (FTO) gene is widely expressed in central and peripheral tissues of mammals, and exhibits a range of functions, especially in energy balance. However, basic knowledge of FTO in the chicken is lacking. Therefore, we studied the tissue distribution, age and breed dependent changes, brain localization, as well as the impact of fasting on FTO mRNA expression in the chicken. FTO mRNA was expressed in all the tissues studied, and generally, with high expression in hypothalamus, liver, visceral fat and cerebellum. However it exhibited breed-specific patterns: in broilers, the highest expression was seen in the liver, while in layers, hypothalamus and cerebellum showed relatively higher FTO mRNA expression. One-week-old broilers expressed markedly higher FTO mRNA in liver compared with the layers of the same age (Pbreed difference was reversed in visceral fat and cerebellum (PBreed-specific expression of FTO mRNA was shown in PVN, but not in VMN, with higher abundance in broilers compared to layers. The decrease in FTO mRNA levels after 24h of fasting was seen only in VMN of layer chickens. These results may provide some intriguing hints for further investigation of FTO function in the chicken. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. 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

  9. Tissue-Specific Suppression of Thyroid Hormone Signaling in Various Mouse Models of Aging.

    Directory of Open Access Journals (Sweden)

    W Edward Visser

    Full Text Available DNA damage contributes to the process of aging, as underscored by premature aging syndromes caused by defective DNA repair. Thyroid state changes during aging, but underlying mechanisms remain elusive. Since thyroid hormone (TH is a key regulator of metabolism, changes in TH signaling have widespread effects. Here, we reveal a significant common transcriptomic signature in livers from hypothyroid mice, DNA repair-deficient mice with severe (Csbm/m/Xpa-/- or intermediate (Ercc1-/Δ-7 progeria and naturally aged mice. A strong induction of TH-inactivating deiodinase D3 and decrease of TH-activating D1 activities are observed in Csbm/m/Xpa-/- livers. Similar findings are noticed in Ercc1-/Δ-7, in naturally aged animals and in wild-type mice exposed to a chronic subtoxic dose of DNA-damaging agents. In contrast, TH signaling in muscle, heart and brain appears unaltered. These data show a strong suppression of TH signaling in specific peripheral organs in premature and normal aging, probably lowering metabolism, while other tissues appear to preserve metabolism. D3-mediated TH inactivation is unexpected, given its expression mainly in fetal tissues. Our studies highlight the importance of DNA damage as the underlying mechanism of changes in thyroid state. Tissue-specific regulation of deiodinase activities, ensuring diminished TH signaling, may contribute importantly to the protective metabolic response in aging.

  10. Inter-specific coral chimerism: Genetically distinct multicellular structures associated with tissue loss in Montipora capitata

    Science.gov (United States)

    Work, Thierry M.; Forsman, Zac H.; Szabo, Zoltan; Lewis, Teresa D.; Aeby, Greta S.; Toonen, Robert J.

    2011-01-01

    Montipora white syndrome (MWS) results in tissue-loss that is often lethal to Montipora capitata, a major reef building coral that is abundant and dominant in the Hawai'ian Archipelago. Within some MWS-affected colonies in Kane'ohe Bay, Oahu, Hawai'i, we saw unusual motile multicellular structures within gastrovascular canals (hereafter referred to as invasive gastrovascular multicellular structure-IGMS) that were associated with thinning and fragmentation of the basal body wall. IGMS were in significantly greater densities in coral fragments manifesting tissue-loss compared to paired normal fragments. Mesenterial filaments from these colonies yielded typical M. capitata mitochondrial haplotypes (CO1, CR), while IGMS from the same colony consistently yielded distinct haplotypes previously only found in a different Montipora species (Montipora flabellata). Protein profiles showed consistent differences between paired mesenterial filaments and IGMS from the same colonies as did seven microsatellite loci that also exhibited an excess of alleles per locus inconsistent with a single diploid organism. We hypothesize that IGMS are a parasitic cellular lineage resulting from the chimeric fusion between M. capitata and M. flabellata larvae followed by morphological reabsorption of M. flabellata and subsequent formation of cell-lineage parasites. We term this disease Montiporaiasis. Although intra-specific chimerism is common in colonial animals, this is the first suspected inter-specific example and the first associated with tissue loss.

  11. Inter-specific coral chimerism: genetically distinct multicellular structures associated with tissue loss in Montipora capitata.

    Directory of Open Access Journals (Sweden)

    Thierry M Work

    Full Text Available Montipora white syndrome (MWS results in tissue-loss that is often lethal to Montipora capitata, a major reef building coral that is abundant and dominant in the Hawai'ian Archipelago. Within some MWS-affected colonies in Kane'ohe Bay, Oahu, Hawai'i, we saw unusual motile multicellular structures within gastrovascular canals (hereafter referred to as invasive gastrovascular multicellular structure-IGMS that were associated with thinning and fragmentation of the basal body wall. IGMS were in significantly greater densities in coral fragments manifesting tissue-loss compared to paired normal fragments. Mesenterial filaments from these colonies yielded typical M. capitata mitochondrial haplotypes (CO1, CR, while IGMS from the same colony consistently yielded distinct haplotypes previously only found in a different Montipora species (Montipora flabellata. Protein profiles showed consistent differences between paired mesenterial filaments and IGMS from the same colonies as did seven microsatellite loci that also exhibited an excess of alleles per locus inconsistent with a single diploid organism. We hypothesize that IGMS are a parasitic cellular lineage resulting from the chimeric fusion between M. capitata and M. flabellata larvae followed by morphological reabsorption of M. flabellata and subsequent formation of cell-lineage parasites. We term this disease Montiporaiasis. Although intra-specific chimerism is common in colonial animals, this is the first suspected inter-specific example and the first associated with tissue loss.

  12. Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

    Directory of Open Access Journals (Sweden)

    Alicia Lundby

    2012-08-01

    Full Text Available Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.

  13. Taproot promoters cause tissue specific gene expression within the storage root of sugar beet.

    Science.gov (United States)

    Oltmanns, Heiko; Kloos, Dorothee U; Briess, Waltraud; Pflugmacher, Maike; Stahl, Dietmar J; Hehl, Reinhard

    2006-08-01

    The storage root (taproot) of sugar beet (Beta vulgaris L.) originates from hypocotyl and primary root and contains many different tissues such as central xylem, primary and secondary cambium, secondary xylem and phloem, and parenchyma. It was the aim of this work to characterize the promoters of three taproot-expressed genes with respect to their tissue specificity. To investigate this, promoters for the genes Tlp, His1-r, and Mll were cloned from sugar beet, linked to reporter genes and transformed into sugar beet and tobacco. Reporter gene expression analysis in transgenic sugar beet plants revealed that all three promoters are active in the storage root. Expression in storage root tissues is either restricted to the vascular zone (Tlp, His1-r) or is observed in the whole organ (Mll). The Mll gene is highly organ specific throughout different developmental stages of the sugar beet. In tobacco, the Tlp and Mll promoters drive reporter gene expression preferentially in hypocotyl and roots. The properties of the Mll promoter may be advantageous for the modification of sucrose metabolism in storage roots.

  14. Pattern specification and immune response transcriptional signatures of pericardial and subcutaneous adipose tissue.

    Directory of Open Access Journals (Sweden)

    Frank H Lau

    Full Text Available Cardiovascular disease (CVD remains the leading cause of morbidity and mortality in the United States. Recent studies suggest that pericardial adipose tissue (PCAT secretes inflammatory factors that contribute to the development of CVD. To better characterize the role of PCAT in the pathogenesis of disease, we performed a large-scale unbiased analysis of the transcriptional differences between PCAT and subcutaneous adipose tissue, analysing 53 microarrays across 19 individuals. As it was unknown whether PCAT-secreted factors are produced by adipocytes or cells in the supporting stromal fraction, we also sought to identify differentially expressed genes in isolated pericardial adipocytes vs. isolated subcutaneous adipocytes. Using microarray analysis, we found that: 1 pericardial adipose tissue and isolated pericardial adipocytes both overexpress atherosclerosis-promoting chemokines and 2 pericardial and subcutaneous fat depots, as well as isolated pericardial adipocytes and subcutaneous adipocytes, express specific patterns of homeobox genes. In contrast, a core set of lipid processing genes showed no significant overlap with differentially expressed transcripts. These depot-specific homeobox signatures and transcriptional profiles strongly suggest different functional roles for the pericardial and subcutaneous adipose depots. Further characterization of these inter-depot differences should be a research priority.

  15. Pattern specification and immune response transcriptional signatures of pericardial and subcutaneous adipose tissue.

    Science.gov (United States)

    Lau, Frank H; Deo, Rahul C; Mowrer, Gregory; Caplin, Joshua; Ahfeldt, Tim; Kaplan, Adam; Ptaszek, Leon; Walker, Jennifer D; Rosengard, Bruce R; Cowan, Chad A

    2011-01-01

    Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality in the United States. Recent studies suggest that pericardial adipose tissue (PCAT) secretes inflammatory factors that contribute to the development of CVD. To better characterize the role of PCAT in the pathogenesis of disease, we performed a large-scale unbiased analysis of the transcriptional differences between PCAT and subcutaneous adipose tissue, analysing 53 microarrays across 19 individuals. As it was unknown whether PCAT-secreted factors are produced by adipocytes or cells in the supporting stromal fraction, we also sought to identify differentially expressed genes in isolated pericardial adipocytes vs. isolated subcutaneous adipocytes. Using microarray analysis, we found that: 1) pericardial adipose tissue and isolated pericardial adipocytes both overexpress atherosclerosis-promoting chemokines and 2) pericardial and subcutaneous fat depots, as well as isolated pericardial adipocytes and subcutaneous adipocytes, express specific patterns of homeobox genes. In contrast, a core set of lipid processing genes showed no significant overlap with differentially expressed transcripts. These depot-specific homeobox signatures and transcriptional profiles strongly suggest different functional roles for the pericardial and subcutaneous adipose depots. Further characterization of these inter-depot differences should be a research priority.

  16. 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.

  17. Functional characterization of tissue-specific enhancers in the DLX5/6 locus.

    Science.gov (United States)

    Birnbaum, Ramon Y; Everman, David B; Murphy, Karl K; Gurrieri, Fiorella; Schwartz, Charles E; Ahituv, Nadav

    2012-11-15

    Disruption of distaless homeobox 5 and 6 (Dlx5/6) in mice results in brain, craniofacial, genital, ear and limb defects. In humans, chromosomal aberrations in the DLX5/6 region, some of which do not encompass DLX5/6, are associated with split hand/foot malformation 1 (SHFM1) as well as intellectual disability, craniofacial anomalies and hearing loss, suggesting that the disruption of DLX5/6 regulatory elements could lead to these abnormalities. Here, we characterized enhancers in the DLX5/6 locus whose tissue-specific expression and genomic location along with previously characterized enhancers correlate with phenotypes observed in individuals with chromosomal abnormalities. By analyzing chromosomal aberrations at 7q21, we refined the minimal SHFM1 critical region and used comparative genomics to select 26 evolutionary conserved non-coding sequences in this critical region for zebrafish enhancer assays. Eight of these sequences were shown to function as brain, olfactory bulb, branchial arch, otic vesicle and fin enhancers, recapitulating dlx5a/6a expression. Using a mouse enhancer assay, several of these zebrafish enhancers showed comparable expression patterns in the branchial arch, otic vesicle, forebrain and/or limb at embryonic day 11.5. Examination of the coordinates of various chromosomal rearrangements in conjunction with the genomic location of these tissue-specific enhancers showed a correlation with the observed clinical abnormalities. Our findings suggest that chromosomal abnormalities that disrupt the function of these tissue-specific enhancers could be the cause of SHFM1 and its associated phenotypes. In addition, they highlight specific enhancers in which mutations could lead to non-syndromic hearing loss, craniofacial defects or limb malformations.

  18. Monitoring phthalates in the tissues of broiler chicks with feedstuffs different phthalate contents

    Directory of Open Access Journals (Sweden)

    Alžbeta Jarošová

    2010-01-01

    Full Text Available For the monitoring of distribution and accumulation of phthalic acid esters (PAE in animal tissues, samples of muscle, mesenteric fat (fat, skin and liver from broiler chicks ROSS 308 were used. The chicks were divided into 4 groups (50 chicks each. All the chicks were given commercial diets (complete feed, KKS for broiler chicks (starter – BR1; grower – BR2 and finisher – BR3. The experimental diets were supplemented with vegetable oil (RO with low (group N or high (group V phthalate contents, or animal fat with a high phthalate content (group Z. Neither the control diets (K, nor the grower (BR1 diets contained vegetable oils or animal fat. The N chicks were given the grower (BR2 and finisher (BR3 diets supplemented with 5% and 3% vegetable oil, respectively. The V chicks were given BR2 and BR3 diets with 5% and 3% vegetable oil, respectively. The Z chicks were given BR2 and BR3 diets with 5% and 3% animal fat, respectively. Di-n-butyl phthalate (DBP and di-(2-ethylhexyl phthalate (DEHP were found in the tissues of chicks in all the experimental groups. The DBP content in the muscle ranged from 0.03 to 0.55 mg . kg−1, in the adipose tissue from < 0.20 to 2.56 mg . kg−1, in the skin from < 0.20 to 1.49 mg . kg−1, and in the liver from 0.03 to 0.13 mg . kg−1. The content of DEHP in the muscle ranged from 0.03 to 1.15 mg . kg−1, in the adipose tissue from 0.25 to 9.85 mg . kg−1, in the skin from < 0.20 to 4.68 mg . kg−1, and in the liver from 0.16 to 0.24 mg . kg−1. The highest concentrations of DBP of 1.28 ± 1.00 mg . kg−1 of fresh sample (an average value from 8 chicks was determined in the adipose tissue of V chicks. The highest concentration of DEHP of 3.27 ± 2.87 mg . kg−1 of fresh sample (mean of 8 chicks was also determined in the V group. The accumulation of DEHP was 3.2; 2.6 and 2.9 times higher than that of DBP in the muscle, adipose tissue and skin

  19. Systematic review of clinical applications of monitoring muscle tissue oxygenation with near-infrared spectroscopy in vascular disease.

    Science.gov (United States)

    Boezeman, Reinout P E; Moll, Frans L; Ünlü, Çağdaş; de Vries, Jean-Paul P M

    2016-03-01

    The use of wavelengths of the near-infrared region by near-infrared spectroscopy (NIRS) has been studied for several applications in vascular disease. This systematic review aims to explore the clinical relevance of monitoring muscle tissue oxygenation in vascular disease with NIRS. A systematic search in PubMed, EMBASE, CINAHL and Cochrane databases was performed to identify clinical NIRS studies, published until April 2015, involving muscle tissue oxygenation in vascular disease. After screening 183 manuscripts, 38 studies (n=2010) were included. Studies concerned peripheral arterial disease (PAD) (twelve studies, n=848), compartment syndrome of lower extremities (seven studies, n=205), deep vein thrombosis (DVT) (six studies, n=429), buttock and lower extremity ischaemia in abdominal aortic aneurysm repair (six studies, n=139), free flap failure (five studies, n=354), and spinal cord ischaemia in thoracoabdominal aortic aneurysm repair (two studies, n=35). Nine studies compared NIRS with gold standards and provided cut-off values. Four studies regarding chronic compartment syndrome and DVT determined higher sensitivity (78%-97%) than specificity (56%-76%). Two studies regarding PAD and buttock claudication determined higher specificity (87%-95%) than sensitivity (33%-88%). Three studies regarding free flap failure determined sensitivity and specificity of 100%. We found sufficient evidence to use NIRS in clinical setting for assessment of chronic compartment syndrome of lower extremities, and as surveillance tool for detection of free flap failure. So far, clinical relevance of routine use of NIRS in other vascular applications is less clear. Cut-off values to discriminate are not yet unanimous and better validation has to be awaited for. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Progress report:Specifications and design criteria for innovative corrosion monitoring and (downhole) sensor systems

    NARCIS (Netherlands)

    Zhang, X.; Akemu, A.

    2010-01-01

    The objective of this sub-project is to establish specifications and design criteria for corrosion monitoring and corrosion sensor systems used in CO2 storage wells; this includes sensitivity analysis and an evaluation of technological maturity. In the Year 1 programme, we review the tools deployed

  1. Magnetization Transfer MR Imaging to Monitor Muscle Tissue Formation during Myogenic in Vivo Differentiation of Muscle Precursor Cells.

    Science.gov (United States)

    Rottmar, Markus; Haralampieva, Deana; Salemi, Souzan; Eberhardt, Christian; Wurnig, Moritz C; Boss, Andreas; Eberli, Daniel

    2016-11-01

    Purpose To determine whether magnetization transfer (MT) magnetic resonance (MR) imaging may serve as a quantitative measure of the degree of fiber formation during differentiation of muscle precursor cells into engineered muscle tissue as a potential noninvasive monitoring tool in mice. Materials and Methods The study was approved by the local ethics committee (no. StV 01/2008) and the local Veterinary Office (license no. 99/2013). Human muscle progenitor cells (hMPCs) derived from rectus abdominis muscles were subcutaneously injected into CD-1 nude mice (CD-1 nude mice, Crl:CD1-Foxn1(nu); Charles River Laboratories, Wilmington, Mass) for development of muscle tissue. The mice underwent MR imaging examinations at 4.7 T at days 1, 3, 7, 14, 21, and 28 after cell transplantation by using a gradient-echo sequence with an MT prepulse and systematic variation of the off-resonance frequency (50-37 500 Hz) at an amplitude of 800°. Direct saturation was estimated from a Bloch equation simulation. The MT ratio (MTR) was correlated to immunohistochemistry findings, Western blot results, and results of myography. Data were analyzed by using one-way or two-way analysis of variance with the Sidak or Tukey multiple comparisons test. Results In the reference skeletal muscle, highest MT was found for 2500 Hz off-resonance frequency with an MTR ± standard deviation of 57.5% ± 3.5. The developing muscle tissue exhibited increasing MT values during the 28 days of myogenic in vivo differentiation and did not reach the values of native skeletal muscle. Mean values of MTR (2500 Hz) for hMPCs were 27.6% ± 6.3 (day 1), 24.7% ± 8.7 (day 3), 28.2% ± 5.7 (day 7), 35.9% ± 5.0 (day 14), 37.0% ± 7.9 (day 21), and 39.9% ± 8.1 (day 28). The results from MT MR imaging correlated qualitatively well with muscle tissue expression of specific skeletal markers, as well as muscle contractility. Conclusion MT MR imaging may be used to noninvasively monitor the process of myogenic in vivo

  2. Gender and obesity specific MicroRNA expression in adipose tissue from lean and obese pigs

    DEFF Research Database (Denmark)

    Mentzel, Caroline M. Junker; Anthon, Christian; Jacobsen, Mette Juul

    2015-01-01

    Obesity is a complex condition that increases the risk of life threatening diseases such as cardiovascular disease and diabetes. Studying the gene regulation of obesity is important for understanding the molecular mechanisms behind the obesity derived diseases and may lead to better intervention...... expressed miRNAs in subcutaneous adipose tissue by RNA sequencing (RNAseq). Both male and female pigs are included to explore gender differences. The RNAseq study shows that the most highly expressed miRNAs are in accordance with comparable studies in pigs and humans. A total of six mi......RNAs are differentially expressed in subcutaneous adipose tissue between the lean and obese group of pigs, and in addition gender specific significant differential expression is observed for a number of miRNAs. The differentially expressed miRNAs have been verified using qPCR. The results of these studies in general...

  3. Gender and obesity specific MicroRNA expression in adipose tissue from lean and obese pigs

    DEFF Research Database (Denmark)

    Mentzel, Caroline M. Junker; Anthon, Christian; Jacobsen, Mette Juul;

    2015-01-01

    Obesity is a complex condition that increases the risk of life threatening diseases such as cardiovascular disease and diabetes. Studying the gene regulation of obesity is important for understanding the molecular mechanisms behind the obesity derived diseases and may lead to better intervention ...... expressed miRNAs in subcutaneous adipose tissue by RNA sequencing (RNAseq). Both male and female pigs are included to explore gender differences. The RNAseq study shows that the most highly expressed miRNAs are in accordance with comparable studies in pigs and humans. A total of six mi......RNAs are differentially expressed in subcutaneous adipose tissue between the lean and obese group of pigs, and in addition gender specific significant differential expression is observed for a number of miRNAs. The differentially expressed miRNAs have been verified using qPCR. The results of these studies in general...

  4. Photoperiod sensitivity of the Arabidopsis circadian clock is tissue-specific.

    Science.gov (United States)

    Shimizu, Hanako; Araki, Takashi; Endo, Motomu

    2015-01-01

    Tissue-specific functions of the circadian clock in Arabidopsis have recently been revealed. The vasculature clock shows distinctive gene expression profiles compared to the clock in other tissues under light-dark cycles. However, it has not yet been established whether the vasculature clock also shows unique gene expression patterns that correlate with temperature cycles, another important environmental cue. Here, we detected diel phase of TIMING OF CAB EXPRESSION 1 (TOC1) expression in the vasculature and whole leaf under long-day light-dark cycles and temperature cycles. We found that the vasculature clock had advanced TOC1 phase under light-dark cycles but not under temperature cycles, suggesting that the vasculature clock has lower sensitivity against temperature signals. Furthermore, the phase advancement of TOC1 was seen only under long-day condition but not under short-day condition. These results support our previous conclusion that the circadian clock in vasculature preferentially senses photoperiodic signals.

  5. Investigation of tissue-specific human orthologous alternative splice events in pig

    DEFF Research Database (Denmark)

    Hillig, Ann-Britt Nygaard; Jørgensen, Claus Bøttcher; Salicio, Susanna Cirera

    2010-01-01

    Alternative splicing of pre-mRNA can contribute to differences between tissues or cells either by regulating gene expression or creating proteins with various functions encoded by one gene. The number of investigated alternative splice events in pig has so far been limited. In this study we have......-specific primers in 19 different tissues. The same splice variants as reported in humans were detected in 15 orthologous pig genes, however, the expression pattern predicted in the in silico analyses was only experimentally verified in a few cases. The results support the findings that splice events resulting...... in preservation of open reading frame are indicative of a functional significance of the splice variants of the gene....

  6. Cell-specific dysregulation of microRNA expression in obese white adipose tissue.

    Science.gov (United States)

    Oger, Frédérik; Gheeraert, Celine; Mogilenko, Denis; Benomar, Yacir; Molendi-Coste, Olivier; Bouchaert, Emmanuel; Caron, Sandrine; Dombrowicz, David; Pattou, François; Duez, Hélène; Eeckhoute, Jérome; Staels, Bart; Lefebvre, Philippe

    2014-08-01

    Obesity is characterized by the excessive accumulation of dysfunctional white adipose tissue (WAT), leading to a strong perturbation of metabolic regulations. However, the molecular events underlying this process are not fully understood. MicroRNAs (miRNAs) are small noncoding RNAs acting as posttranscriptional regulators of gene expression in multiple tissues and organs. However, their expression and roles in WAT cell subtypes, which include not only adipocytes but also immune, endothelial, and mesenchymal stem cells as well as preadipocytes, have not been characterized. Design/Results: By applying differential miRNome analysis, we demonstrate that the expression of several miRNAs is dysregulated in epididymal WAT from ob/ob and high-fat diet-fed mice. Adipose tissue-specific down-regulation of miR-200a and miR-200b and the up-regulation of miR-342-3p, miR-335-5p, and miR-335-3p were observed. Importantly, a similarly altered expression of miR-200a and miR-200b was observed in obese diabetic patients. Furthermore, cell fractionation of mouse adipose tissue revealed that miRNAs are differentially expressed in adipocytes and in subpopulations from the stromal vascular fraction. Finally, integration of transcriptomic data showed that bioinformatically predicted miRNA target genes rarely showed anticorrelated expression with that of targeting miRNA, in contrast to experimentally validated target genes. Taken together, our data indicate that the dysregulated expression of miRNAs occurs in distinct cell types and is likely to affect cell-specific function(s) of obese WAT.

  7. Effects of fixation and tissue processing on immunohistochemical demonstration of specific antigens.

    Science.gov (United States)

    Arnold, M M; Srivastava, S; Fredenburgh, J; Stockard, C R; Myers, R B; Grizzle, W E

    1996-09-01

    Identification of biomarkers in archival tissues using immunochemistry is becoming increasingly important for determining the diagnosis and prognosis of tumors, for characterizing preinvasive neoplastic changes in glandular tissues such as prostate, for evaluating the response of tumors and preinvasive neoplastic changes to certain therapies (i.e., as a surrogate intermediate end point), for selecting patients who are candidates for specific therapies (e.g., immunotherapy) and for retrospective studies. For detecting specific biomarkers it is important to understand the limitations imposed by the fixation methods and processing of the tissues. This study was designed to determine the effects of fixation on the detection in archival paraffin blocks of selected antigens postulated to be important in tumor biology. We evaluated the antigens TGF alpha, p185erbB-2, broad spectrum keratins, p53, and TAG-72 (B72.3). Fixatives evaluated included standard preparations of neutral buffered formalin, acid formalin, zinc formalin, alcoholic formalin, ethanol, methanol, and Bouin's fixative. We found that in general neutral buffered formalin is the poorest fixative for maintaining antigen recognition by immunohistochemistry and that no single fixative was best for all antigens. The dehydrating (coagulant) fixatives (e.g., ethanol and methanol) preserved immunorecognition of p53 and broad spectrum keratins best while the slow cross-linking fixatives (e.g., unbuffered zinc formalin) were best for demonstrating TGF alpha and p185erbB-2. Fixatives other than neutral buffered formalin produced equivalent recognition of the epitope of TAG-72 by B72.3. In formalin fixed archival tissues, only a portion of the antigen signal can be detected by routine immunohistologic methods.

  8. Nesprins: tissue-specific expression of epsilon and other short isoforms.

    Directory of Open Access Journals (Sweden)

    Nguyen Thuy Duong

    Full Text Available Nesprin-1-giant and nesprin-2-giant regulate nuclear positioning by the interaction of their C-terminal KASH domains with nuclear membrane SUN proteins and their N-terminal calponin-homology domains with cytoskeletal actin. A number of short isoforms lacking the actin-binding domains are produced by internal promotion. We have evaluated the significance of these shorter isoforms using quantitative RT-PCR and western blotting with site-specific monoclonal antibodies. Within a complete map of nesprin isoforms, we describe two novel nesprin-2 epsilon isoforms for the first time. Epsilon isoforms are similar in size and structure to nesprin-1-alpha. Expression of nesprin isoforms was highly tissue-dependent. Nesprin-2-epsilon-1 was found in early embryonic cells, while nesprin-2-epsilon-2 was present in heart and other adult tissues, but not skeletal muscle. Some cell lines lack shorter isoforms and express only one of the two nesprin genes, suggesting that either of the giant nesprins is sufficient for basic cell functions. For the first time, localisation of endogenous nesprin away from the nuclear membrane was shown in cells where removal of the KASH domain by alternative splicing occurs. By distinguishing between degradation products and true isoforms on western blots, it was found that previously-described beta and gamma isoforms are expressed either at only low levels or with a limited tissue distribution. Two of the shortest alpha isoforms, nesprin-1-alpha-2 and nesprin-2-alpha-1, were found almost exclusively in cardiac and skeletal muscle and a highly conserved and alternatively-spliced exon, available in both nesprin genes, was always included in these tissues. These "muscle-specific" isoforms are thought to form a complex with emerin and lamin A/C at the inner nuclear membrane and mutations in all three proteins cause Emery-Dreifuss muscular dystrophy and/or inherited dilated cardiomyopathy, disorders in which only skeletal muscle and

  9. 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.

  10. 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.

  11. Tissue-specific epigenetic modifications in root apical meristem cells of Hordeum vulgare.

    Directory of Open Access Journals (Sweden)

    Agnieszka J Braszewska-Zalewska

    Full Text Available Epigenetic modifications of chromatin structure are essential for many biological processes, including growth and reproduction. Patterns of DNA and histone modifications have recently been widely studied in many plant species, although there is virtually no data on the spatial and temporal distribution of epigenetic markers during plant development. Accordingly, we have used immunostaining techniques to investigate epigenetic modifications in the root apical meristem of Hordeum vulgare. Histone H4 acetylation (H4K5ac, histone H3 dimethylation (H3K4me2, H3K9me2 and DNA methylation (5mC patterns were established for various root meristem tissues. Distinct levels of those modifications were visualised in the root cap, epidermis, cortex and vascular tissues. The lateral root cap cells seem to display the highest level of H3K9me2 and 5mC. In the epidermis, the highest level of 5mC and H3K9me2 was detected in the nuclei from the boundary of the proximal meristem and the elongation zone, while the vascular tissues were characterized by the highest level of H4K5ac. Some of the modified histones were also detectable in the cytoplasm in a highly tissue-specific manner. Immunolocalisation of epigenetic modifications of chromatin carried out in this way, on longitudinal or transverse sections, provides a unique topographic context within the organ, and will provide some answers to the significant biological question of tissue differentiation processes during root development in a monocotyledon plant species.

  12. 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

  13. Tissue-Specific Epigenetic Modifications in Root Apical Meristem Cells of Hordeum vulgare

    Science.gov (United States)

    Braszewska-Zalewska, Agnieszka J.; Wolny, Elzbieta A.; Smialek, Lukasz; Hasterok, Robert

    2013-01-01

    Epigenetic modifications of chromatin structure are essential for many biological processes, including growth and reproduction. Patterns of DNA and histone modifications have recently been widely studied in many plant species, although there is virtually no data on the spatial and temporal distribution of epigenetic markers during plant development. Accordingly, we have used immunostaining techniques to investigate epigenetic modifications in the root apical meristem of Hordeum vulgare. Histone H4 acetylation (H4K5ac), histone H3 dimethylation (H3K4me2, H3K9me2) and DNA methylation (5mC) patterns were established for various root meristem tissues. Distinct levels of those modifications were visualised in the root cap, epidermis, cortex and vascular tissues. The lateral root cap cells seem to display the highest level of H3K9me2 and 5mC. In the epidermis, the highest level of 5mC and H3K9me2 was detected in the nuclei from the boundary of the proximal meristem and the elongation zone, while the vascular tissues were characterized by the highest level of H4K5ac. Some of the modified histones were also detectable in the cytoplasm in a highly tissue-specific manner. Immunolocalisation of epigenetic modifications of chromatin carried out in this way, on longitudinal or transverse sections, provides a unique topographic context within the organ, and will provide some answers to the significant biological question of tissue differentiation processes during root development in a monocotyledon plant species. PMID:23935955

  14. Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids.

    Directory of Open Access Journals (Sweden)

    Sara L Svahn

    Full Text Available Dietary polyunsaturated fatty acids (PUFA are suggested to modulate immune function, but the effects of dietary fatty acids composition on gene expression patterns in immune organs have not been fully characterized. In the current study we investigated how dietary fatty acids composition affects the total transcriptome profile, and especially, immune related genes in two immune organs, spleen (SPL and bone marrow cells (BMC. Four tissues with metabolic function, skeletal muscle (SKM, white adipose tissue (WAT, brown adipose tissue (BAT, and liver (LIV, were investigated as a comparison. Following 8 weeks on low fat diet (LFD, high fat diet (HFD rich in saturated fatty acids (HFD-S, or HFD rich in PUFA (HFD-P, tissue transcriptomics were analyzed by microarray and metabolic health assessed by fasting blood glucose level, HOMA-IR index, oral glucose tolerance test as well as quantification of crown-like structures in WAT. HFD-P corrected the metabolic phenotype induced by HFD-S. Interestingly, SKM and BMC were relatively inert to the diets, whereas the two adipose tissues (WAT and BAT were mainly affected by HFD per se (both HFD-S and HFD-P. In particular, WAT gene expression was driven closer to that of the immune organs SPL and BMC by HFDs. The LIV exhibited different responses to both of the HFDs. Surprisingly, the spleen showed a major response to HFD-P (82 genes differed from LFD, mostly immune genes, while it was not affected at all by HFD-S (0 genes differed from LFD. In conclusion, the quantity and composition of dietary fatty acids affected the transcriptome in distinct manners in different organs. Remarkably, dietary PUFA, but not saturated fat, prompted a specific regulation of immune related genes in the spleen, opening the possibility that PUFA can regulate immune function by influencing gene expression in this organ.

  15. Surgical technique for the implantation of tissue engineered vascular grafts and subsequent in vivo monitoring.

    Science.gov (United States)

    Koobatian, Maxwell T; Koenigsknecht, Carmon; Row, Sindhu; Andreadis, Stelios; Swartz, Daniel

    2015-04-03

    The development of Tissue Engineered Vessels (TEVs) is advanced by the ability to routinely and effectively implant TEVs (4-5 mm in diameter) into a large animal model. A step by-step protocol for inter-positional placement of the TEV and real-time digital assessment of the TEV and native carotid arteries is described here. In vivo monitoring is made possible by the implantation of flow probes, catheters and ultrasonic crystals (capable of recording dynamic diameter changes of implanted TEVs and native carotid arteries) at the time of surgery. Once implanted, researchers can calculate arterial blood flow patterns, invasive blood pressure and artery diameter yielding parameters such as pulse wave velocity, augmentation index, pulse pressures and compliance. Data acquisition is accomplished using a single computer program for analysis throughout the duration of the experiment. Such invaluable data provides insight into TEV matrix remodeling, its resemblance to native/sham controls and overall TEV performance in vivo.

  16. The Effect of Patient-Specific Cerebral Oxygenation Monitoring on Postoperative Cognitive Function: A Multicenter Randomized Controlled Trial

    Science.gov (United States)

    Ellis, Lucy; Murphy, Gavin J; Culliford, Lucy; Dreyer, Lucy; Clayton, Gemma; Downes, Richard; Nicholson, Eamonn; Stoica, Serban; Reeves, Barnaby C

    2015-01-01

    Background Indices of global tissue oxygen delivery and utilization such as mixed venous oxygen saturation, serum lactate concentration, and arterial hematocrit are commonly used to determine the adequacy of tissue oxygenation during cardiopulmonary bypass (CPB). However, these global measures may not accurately reflect regional tissue oxygenation and ischemic organ injury remains a common and serious complication of CPB. Near-infrared spectroscopy (NIRS) is a noninvasive technology that measures regional tissue oxygenation. NIRS may be used alongside global measures to optimize regional perfusion and reduce organ injury. It may also be used as an indicator of the need for red blood cell transfusion in the presence of anemia and tissue hypoxia. However, the clinical benefits of using NIRS remain unclear and there is a lack of high-quality evidence demonstrating its efficacy and cost effectiveness. Objective The aim of the patient-specific cerebral oxygenation monitoring as part of an algorithm to reduce transfusion during heart valve surgery (PASPORT) trial is to determine whether the addition of NIRS to CPB management algorithms can prevent cognitive decline, postoperative organ injury, unnecessary transfusion, and reduce health care costs. Methods Adults aged 16 years or older undergoing valve or combined coronary artery bypass graft and valve surgery at one of three UK cardiac centers (Bristol, Hull, or Leicester) are randomly allocated in a 1:1 ratio to either a standard algorithm for optimizing tissue oxygenation during CPB that includes a fixed transfusion threshold, or a patient-specific algorithm that incorporates cerebral NIRS monitoring and a restrictive red blood cell transfusion threshold. Allocation concealment, Internet-based randomization stratified by operation type and recruiting center, and blinding of patients, ICU and ward care staff, and outcome assessors reduce the risk of bias. The primary outcomes are cognitive function 3 months after

  17. Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes

    Directory of Open Access Journals (Sweden)

    Dasgupta Dipayan

    2005-05-01

    Full Text Available Abstract Background Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group. Results In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes. Conclusion The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome.

  18. A mathematical model for bone tissue regeneration inside a specific type of scaffold.

    Science.gov (United States)

    Sanz-Herrera, J A; Garcia-Aznar, J M; Doblare, M

    2008-10-01

    Bone tissue regeneration using scaffolds is receiving an increasing interest in orthopedic surgery and tissue engineering applications. In this study, we present the geometrical characterization of a specific family of scaffolds based on a face cubic centered (FCC) arrangement of empty pores leading to analytical formulae of porosity and specific surface. The effective behavior of those scaffolds, in terms of mechanical properties and permeability, is evaluated through the asymptotic homogenization theory applied to a representative volume element identified with the unit cell FCC. Bone growth into the scaffold is estimated by means of a phenomenological model that considers a macroscopic effective stress as the mechanical stimulus that regulates bone formation. Cell migration within the scaffold is modeled as a diffusion process based on Fick's law which allows us to estimate the cell invasion into the scaffold microstructure. The proposed model considers that bone growth velocity is proportional to the concentration of cells and regulated by the mechanical stimulus. This model allows us to explore what happens within the scaffold, the surrounding bone and their interaction. The mathematical model has been numerically implemented and qualitatively compared with previous experimental results found in the literature for a scaffold implanted in the femoral condyle of a rabbit. Specifically, the model predicts around 19 and 23% of bone regeneration for non-grafted and grafted scaffolds, respectively, both with an initial porosity of 76%.

  19. Tissue-specific mRNA expression profiles of human solute carrier 35 transporters.

    Science.gov (United States)

    Nishimura, Masuhiro; Suzuki, Satoshi; Satoh, Tetsuo; Naito, Shinsaku

    2009-01-01

    Pairs of forward and reverse primers and TaqMan probes specific to each of 23 human solute carrier 35 (SLC35) transporters were prepared. The mRNA expression level of each target transporter was analyzed in total RNA from single and pooled specimens of adult human tissues (adipose tissue, adrenal gland, bladder, bone marrow, brain, cerebellum, colon, heart, kidney, liver, lung, mammary gland, ovary, pancreas, peripheral leukocytes, placenta, prostate, retina, salivary gland, skeletal muscle, small intestine, smooth muscle, spinal cord, spleen, stomach, testis, thymus, thyroid gland, tonsil, trachea, and uterus), from pooled specimens of fetal human tissues (brain, heart, kidney, liver, spleen, and thymus), and from three human cell lines (HeLa cell line ATCC#: CCL-2, human cell line Hep G2, and human breast carcinoma cell line MDA-435) by real-time reverse transcription PCR using an Applied Biosystems 7500 Fast Real-Time PCR System. The mRNA expression of SLC35As, SLC35Bs, SLC35Cs, SLC35D1, SLC35D2, SLC35Es, and SLC35F5 was found to be ubiquitous in both adult and fetal tissues. SLC35D3 mRNA was expressed at the highest levels in the adult retina. SLC35F1 mRNA was expressed at high levels in the adult and fetal brain. SLC35F2 mRNA was expressed at the highest levels in the adult salivary gland. Both SLC35F3 and SLC35F4 mRNAs were expressed at the highest levels in the adult cerebellum. Further, individual differences in the mRNA expression levels of human SLC35 transporters in the liver were also evaluated. Our newly determined expression profiles were used to study the gene expression in 31 adult human tissues, 6 fetal human tissues, and 3 cell lines, and tissues with high transcriptional activity for human SLC35 transporters were identified. These results are expected to be valuable for research concerning the clinical diagnosis of disease.

  20. Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

    Science.gov (United States)

    Erceg, Jelena; Saunders, Timothy E.; Girardot, Charles; Devos, Damien P.; Hufnagel, Lars; Furlong, Eileen E. M.

    2014-01-01

    Deciphering the specific contribution of individual motifs within cis-regulatory modules (CRMs) is crucial to understanding how gene expression is regulated and how this process is affected by sequence variation. But despite vast improvements in the ability to identify where transcription factors (TFs) bind throughout the genome, we are limited in our ability to relate information on motif occupancy to function from sequence alone. Here, we engineered 63 synthetic CRMs to systematically assess the relationship between variation in the content and spacing of motifs within CRMs to CRM activity during development using Drosophila transgenic embryos. In over half the cases, very simple elements containing only one or two types of TF binding motifs were capable of driving specific spatio-temporal patterns during development. Different motif organizations provide different degrees of robustness to enhancer activity, ranging from binary on-off responses to more subtle effects including embryo-to-embryo and within-embryo variation. By quantifying the effects of subtle changes in motif organization, we were able to model biophysical rules that explain CRM behavior and may contribute to the spatial positioning of CRM activity in vivo. For the same enhancer, the effects of small differences in motif positions varied in developmentally related tissues, suggesting that gene expression may be more susceptible to sequence variation in one tissue compared to another. This result has important implications for human eQTL studies in which many associated mutations are found in cis-regulatory regions, though the mechanism for how they affect tissue-specific gene expression is often not understood. PMID:24391522

  1. Tissue- and species-specific differences in cytochrome c oxidase assembly induced by SURF1 defects.

    Science.gov (United States)

    Kovářová, Nikola; Pecina, Petr; Nůsková, Hana; Vrbacký, Marek; Zeviani, Massimo; Mráček, Tomáš; Viscomi, Carlo; Houštěk, Josef

    2016-04-01

    Mitochondrial protein SURF1 is a specific assembly factor of cytochrome c oxidase (COX), but its function is poorly understood. SURF1 gene mutations cause a severe COX deficiency manifesting as the Leigh syndrome in humans, whereas in mice SURF1(-/-) knockout leads only to a mild COX defect. We used SURF1(-/-) mouse model for detailed analysis of disturbed COX assembly and COX ability to incorporate into respiratory supercomplexes (SCs) in different tissues and fibroblasts. Furthermore, we compared fibroblasts from SURF1(-/-) mouse and SURF1 patients to reveal interspecies differences in kinetics of COX biogenesis using 2D electrophoresis, immunodetection, arrest of mitochondrial proteosynthesis and pulse-chase metabolic labeling. The crucial differences observed are an accumulation of abundant COX1 assembly intermediates, low content of COX monomer and preferential recruitment of COX into I-III2-IVn SCs in SURF1 patient fibroblasts, whereas SURF1(-/-) mouse fibroblasts were characterized by low content of COX1 assembly intermediates and milder decrease in COX monomer, which appeared more stable. This pattern was even less pronounced in SURF1(-/-) mouse liver and brain. Both the control and SURF1(-/-) mice revealed only negligible formation of the I-III2-IVn SCs and marked tissue differences in the contents of COX dimer and III2-IV SCs, also less noticeable in liver and brain than in heart and muscle. Our studies support the view that COX assembly is much more dependent on SURF1 in humans than in mice. We also demonstrate markedly lower ability of mouse COX to form I-III2-IVn supercomplexes, pointing to tissue-specific and species-specific differences in COX biogenesis.

  2. Enhanced Soft Tissue Attachment and Fixation Using a Mechanically-Stimulated Cytoselective Tissue-Specific ECM Coating

    Science.gov (United States)

    2013-01-01

    appropriate scaffold for the tendon to bone interface, characterizing the co-culture behavior on the selected scaffold, developing a mechanical bioreactor to...correlate data. Finally, a customizable bioreactor was designed to selectively mechanically stimulate tendon-to-bone tissue engineering co-cultured...scaffolds. 15. SUBJECT TERMS Scaffold, Tissue Engineering, Bioreactor , Tendon, Bone, Biomaterial, Extracellular Matrix, Animal model 16. SECURITY

  3. Selection of a breast cancer subpopulation-specific antibody using phage display on tissue sections

    DEFF Research Database (Denmark)

    Larsen, Simon Asbjørn; Meldgaard, Theresa; Fridriksdottir, Agla J

    2015-01-01

    Breast cancer tumors are composed of heterogeneous cell populations. These populations display a high variance in morphology, growth and metastatic propensity. They respond differently to therapeutic interventions, and some may be more prone to cause recurrence. Studying individual subpopulations...... stem cells. We isolated an antibody fragment LH 7, which in immunohistochemistry experiments demonstrates specific binding to breast cancer subpopulations. The selection of antibody fragments directly on small defined areas within a larger section of malignant tissue is a novel approach by which...... has the potential to provide new insight and treatment strategies for breast cancer....

  4. The mouse Eb meiotic recombination hotspot contains a tissue-specific transcriptional enhancer.

    Science.gov (United States)

    Ling, X; Shenkar, R; Sakai, D; Arnheim, N

    1993-01-01

    A meiotic recombination hotspot exists within the second intron of the mouse major histocompatibility complex (MHC) gene, Eb. In the present study, a small fragment from the intron which contains two potential transcriptional regulatory elements was cloned into an expression vector and its effect on transcription was tested. This fragment was found to contain tissue-specific transcriptional enhancer activity. An octamer-like sequence and a B motif may contribute to this enhancer activity. Similar regulatory sequences with the same orientation and distance from one another are found in another mouse MHC recombination hotspot.

  5. Biotransformation of tissue-specific hormone tibolone with fungal culture Trichothecium roseum

    Science.gov (United States)

    Shah, Syed Adnan Ali; Sultan, Sadia; Zaimi bin Mohd Noor, M.

    2013-06-01

    Whole cells based biotransformation is an important tool for bioconversion of steroids. It can be used to synthesize biologically potent compounds with diverse structures. Biotransformation of tissue-specific hormone tibolone (1) with Trichothecium roseum (ATCC 13411) has being carried out for the first time. Two new and three known metabolites 2-6 were isolated from fermentation of tibolone (1) with Trichothecium roseum and their structures were characterized by 2D NMR spectroscopy and mass spectrometry. The relative stereochemistry of new metabolites 5 and 6 was deduced by 2D NOESY experiments. The effect of cultures on tibolone structural modifications and time-course studies has also been conducted.

  6. Pilot study of laser induced breakdown spectroscopy for tissue differentiation by monitoring the plume created during laser surgery — An approach on a feedback Laser control mechanism

    Science.gov (United States)

    Kanawade, Rajesh; Mehari, Fanuel; Knipfer, Christian; Rohde, Maximilian; Tangermann-Gerk, Katja; Schmidt, Michael; Stelzle, Florian

    2013-09-01

    This study focuses on tissue differentiation using 'Laser Induced Breakdown Spectroscopy' (LIBS) by monitoring the plasma plume created during laser surgery processes. This technique is aimed at controlling a laser surgery feedback system in real time. An Excimer laser (Ar-F 193 nm) was used for the ablation of tissue samples. Fat, muscle, nerve and skin tissue samples of bisected ex-vivo pig heads were prepared as test objects for the ablation procedure. A single fiber was used to collect emissions and deliver them to a spectrometer. The obtained LIBS spectra in the measured emissions were analyzed to determine each tissue type according to their chemical composition. The elements found in the samples and their emission spectra were in agreement with those described in literature. The collected LIBS spectra were analyzed to differentiate the tissues using statistical data analysis: Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and Receiver Operating Characteristics (ROC). The obtained preliminary results suggest a successful differentiation of the target tissues with high sensitivity and specificity. The main goal of this study was to qualitatively identify tissue types during laser ablation, which will provide a real time feedback mechanism for clinical Laser surgery applications to significantly improve the accuracy and safety of laser surgery procedures.

  7. Monitoring heat-induced changes in soft tissues with 1D transient elastography

    Energy Technology Data Exchange (ETDEWEB)

    Benech, Nicolas; Negreira, Carlos A [Laboratorio de Acustica Ultrasonora, Facultad de Ciencias, Igua 4225, 11400, Montevideo (Uruguay)

    2010-03-21

    In this paper 1D transient elastography was employed in fresh bovine skeletal muscle samples to assess the shear elastic modulus {mu} while the tissue was locally heated by means of an electrical resistance. The investigation is based on the study of the time shift of the shear wave propagation produced by the local temperature variation. The experiments show that the thermal expansion contribution to the time shift is negligible when compared with the shear wave speed variation. In such a case, the quantification of {mu} as a function of temperature becomes possible. Repeated experiments in different samples lead to a reproducible behavior of {mu} as a function of temperature. Irreversible elasticity changes are produced when the temperature exceeds a certain critical value T{sub c}. The proposed method allows estimating this value as well as the spatial extension of the resulting thermal lesion. This point is important when considering applications in monitoring focused ultrasound surgery (FUS) because the surrounding normal tissue should remain unaffected.

  8. A method for monitoring of oxygen saturation changes in brain tissue using diffuse reflectance spectroscopy.

    Science.gov (United States)

    Rejmstad, Peter; Johansson, Johannes D; Haj-Hosseini, Neda; Wårdell, Karin

    2017-03-01

    Continuous measurement of local brain oxygen saturation (SO2 ) can be used to monitor the status of brain trauma patients in the neurocritical care unit. Currently, micro-oxygen-electrodes are considered as the "gold standard" in measuring cerebral oxygen pressure (pO2 ), which is closely related to SO2 through the oxygen dissociation curve (ODC) of hemoglobin, but with the drawback of slow in response time. The present study suggests estimation of SO2 in brain tissue using diffuse reflectance spectroscopy (DRS) for finding an analytical relation between measured spectra and the SO2 for different blood concentrations. The P3 diffusion approximation is used to generate a set of spectra simulating brain tissue for various levels of blood concentrations in order to estimate SO2 . The algorithm is evaluated on optical phantoms mimicking white brain matter (blood volume of 0.5-2%) where pO2 and temperature is controlled and on clinical data collected during brain surgery. The suggested method is capable of estimating the blood fraction and oxygen saturation changes from the spectroscopic signal and the hemoglobin absorption profile.

  9. The estimated sensitivity and specificity of compartment pressure monitoring for acute compartment syndrome.

    Science.gov (United States)

    McQueen, Margaret M; Duckworth, Andrew D; Aitken, Stuart A; Court-Brown, Charles M

    2013-04-17

    The aim of our study was to document the estimated sensitivity and specificity of continuous intracompartmental pressure monitoring for the diagnosis of acute compartment syndrome. From our prospective trauma database, we identified all patients who had sustained a tibial diaphyseal fracture over a ten-year period. A retrospective analysis of 1184 patients was performed to record and analyze the documented use of continuous intracompartmental pressure monitoring and the use of fasciotomy. A diagnosis of acute compartment syndrome was made if there was escape of muscles at fasciotomy and/or color change in the muscles or muscle necrosis intraoperatively. A diagnosis of acute compartment syndrome was considered incorrect if it was possible to close the fasciotomy wounds primarily at forty-eight hours. The absence of acute compartment syndrome was confirmed by the absence of neurological abnormality or contracture at the time of the latest follow-up. Of 979 monitored patients identified, 850 fit the inclusion criteria with a mean age of thirty-eight years (range, twelve to ninety-four years), and 598 (70.4%) were male (p compartment syndrome: 141 had acute compartment syndrome (true positives), six did not have it (false positives), and five underwent fasciotomy despite having a normal differential pressure reading, with subsequent operative findings consistent with acute compartment syndrome (false negatives). Of the 698 patients (82.1%) who did not undergo fasciotomy, 689 had no evidence of any late sequelae of acute compartment syndrome (true negatives) at a mean follow-up time of fifty-nine weeks. The estimated sensitivity of intracompartmental pressure monitoring for suspected acute compartment syndrome was 94%, with an estimated specificity of 98%, an estimated positive predictive value of 93%, and an estimated negative predictive value of 99%. The estimated sensitivity and specificity of continuous intracompartmental pressure monitoring for the diagnosis of

  10. An Arabidopsis tissue-specific RNAi method for studying genes essential to mitosis.

    Directory of Open Access Journals (Sweden)

    Brunilís Burgos-Rivera

    Full Text Available A large fraction of the genes in plants can be considered essential in the sense that when absent the plant fails to develop past the first few cell divisions. The fact that angiosperms pass through a haploid gametophyte stage can make it challenging to propagate such mutants even in the heterozygous condition. Here we describe a tissue-specific RNAi method that allows us to visualize cell division phenotypes in petals, which are large dispensable organs. Portions of the APETALA (AP3 and PISTILLATA (PI promoters confer early petal-specific expression. We show that when either promoter is used to drive the expression of a beta-glucuronidase (GUS RNAi transgene in plants uniformly expressing GUS, GUS expression is knocked down specifically in petals. We further tested the system by targeting the essential kinetochore protein CENPC and two different components of the Spindle Assembly Checkpoint (MAD2 and BUBR1. Plant lines expressing petal-specific RNAi hairpins targeting these genes exhibited an array of petal phenotypes. Cytological analyses of the affected flower buds confirmed that CENPC knockdown causes cell cycle arrest but provided no evidence that either MAD2 or BUBR1 are required for mitosis (although both genes are required for petal growth by this assay. A key benefit of the petal-specific RNAi method is that the phenotypes are not expressed in the lineages leading to germ cells, and the phenotypes are faithfully transmitted for at least four generations despite their pronounced effects on growth.

  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. Polarization second harmonic generation microscopy provides quantitative enhanced molecular specificity for tissue diagnostics.

    Science.gov (United States)

    Kumar, Rajesh; Grønhaug, Kirsten M; Romijn, Elisabeth I; Finnøy, Andreas; Davies, Catharina L; Drogset, Jon O; Lilledahl, Magnus B

    2015-09-01

    Due to specific structural organization at the molecular level, several biomolecules (e.g., collagen, myosin etc.) which are strong generators of second harmonic generation (SHG) signals, exhibit unique responses depending on the polarization of the excitation light. By using the polarization second harmonic generation (p-SHG) technique, the values of the second order susceptibility components can be used to differentiate the types of molecule, which cannot be done by the use of a standard SHG intensity image. In this report we discuss how to implement p-SHG on a commercial multiphoton microscope and overcome potential artifacts in susceptibility (χ) image. Furthermore we explore the potential of p-SHG microscopy by applying the technique to different types of tissue in order to determine corresponding reference values of the ratio of second-order χ tensor elements. These values may be used as a bio-marker to detect any structural alterations in pathological tissue for diagnostic purposes. The SHG intensity image (red) in (a) shows the distribution of collagen fibers in ovary tissue but cannot determine the type of collagen fiber. However, the histogram distribution (b) for the values of the χ tensor element ratio can be used to quantitatively identify the types of collagen fibers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Preventing tissue fibrosis by local biomaterials interfacing of specific cryptic extracellular matrix information

    Science.gov (United States)

    Horejs, Christine-Maria; St-Pierre, Jean-Philippe; Ojala, Juha R. M.; Steele, Joseph A. M.; da Silva, Patricia Barros; Rynne-Vidal, Angela; Maynard, Stephanie A.; Hansel, Catherine S.; Rodríguez-Fernández, Clara; Mazo, Manuel M.; You, Amanda Y. F.; Wang, Alex J.; von Erlach, Thomas; Tryggvason, Karl; López-Cabrera, Manuel; Stevens, Molly M.

    2017-06-01

    Matrix metalloproteinases (MMPs) contribute to the breakdown of tissue structures such as the basement membrane, promoting tissue fibrosis. Here we developed an electrospun membrane biofunctionalized with a fragment of the laminin β1-chain to modulate the expression of MMP2 in this context. We demonstrate that interfacing of the β1-fragment with the mesothelium of the peritoneal membrane via a biomaterial abrogates the release of active MMP2 in response to transforming growth factor β1 and rescues tissue integrity ex vivo and in vivo in a mouse model of peritoneal fibrosis. Importantly, our data demonstrate that the membrane inhibits MMP2 expression. Changes in the expression of epithelial-to-mesenchymal transition (EMT)-related molecules further point towards a contribution of the modulation of EMT. Biomaterial-based presentation of regulatory basement membrane signals directly addresses limitations of current therapeutic approaches by enabling a localized and specific method to counteract MMP2 release applicable to a broad range of therapeutic targets.

  14. Tissue-specific methylation differences and cognitive function in fragile X premutation females

    Energy Technology Data Exchange (ETDEWEB)

    Allingham-Hawkins, D.J.; Babul, R.; Chitayat, D. [Hospital for Sick Children, Toronto (Canada)] [and others

    1996-08-09

    Tissue-specific variation in (CGG){sub n} repeat size and methylation status of the FMR1 gene was investigated in 17 female premutation carriers. Minor variation in premutation repeat size among leukocyte, lymphoblast, and fibroblast tissues was noted in some subjects. One subject exhibited a premutation size allele of (CGG){sub 64} in leukocyte and fibroblast tissues by polymerase chain reaction analysis but a normal-size allele of (CGG){sub 46} in lymphoblast cells, suggesting low-level mosaicism in blood and clonality of the lymphoblast cell line. Six subjects exhibited differences in methylation pattern between leukocytes and lymphoblasts but not between leukocytes and fibroblasts, whereas 2 subjects showed large differences in methylation pattern between leukocytes and fibroblasts. Cognitive function was studied in 14 subjects using the Wechsler Adult Intelligence Scale-Revised. Mean Verbal and Performance IQs were well within the average range as was the mean Full Scale IQ; nevertheless, a trend toward lower Performance IQ compared with Verbal IQ was observed. No significant correlation was apparent between Full Scale IQ and (CGG){sub n} repeat size; however, a significant positive correlation was observed between Full Scale IQ and the proportion of the active X carrying the normal FMR1 allele in fibroblasts but not in leukocytes or lymphoblasts. 24 refs., 1 fig., 2 tabs.

  15. 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.

  16. 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.

  17. 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.

  18. Dendroctonus armandi (Curculionidae: Scolytinae) cytochrome P450s display tissue specificity and responses to host terpenoids.

    Science.gov (United States)

    Dai, Lulu; Ma, Mingyuan; Gao, Guanqun; Chen, Hui

    2016-11-01

    Bark beetles oxidize the defensive allelochemicals of their host trees both to detoxify them and convert them into components of their pheromone systems which were catalyzed by cytochrome P450 enzymes (CYPs) and occur in different tissues of the insect. We study P450 genes in the Chinese white pine beetle (Dendroctonus armandi), and some bio-information analysis was done for the full-length deduced amino acid sequences. The tissue specificity of these P450 genes was determined in three tissues (antenna, gut and reproductive organs). Differential expression of the P450 genes was observed between sexes, and within these significant differences exposed to stimuli (α-pinene (1:1 racemic mix), (S)-(-)-α-pinene, (S)-(-)-β-pinene, (+)-3-carene, (±)-limonene and turpentine oil) at 24h. Increased expression of P450 genes suggested that they play a role in the detoxification of monoterpenes released by the host trees. The different transcript accumulation patterns of these bark beetle P450 genes provided insight into ecological interactions of D. armandi with its host pine.

  19. Preliminary observation of genes specifically expressed in brain tissues during stroke-like episodes in rats

    Institute of Scientific and Technical Information of China (English)

    WANG Xian-mei; ZHAO Bin; ZHU Shan-jun; ZHU Zhi-ming; ZHANG Qian; HUI Ru-tai

    2001-01-01

    Objective: To observe the difference of gene expressions of brain tissues during apoplectic episodes and those of normal brain in Wistar rats in order to study the pathological mechanism of apoplexy. Methods: A rat model of hypertension was established with the administration of cold stimulus and high salt intake as the environmental risk factors.Apoplexy occurred in the rats because of hypertension. Suppression subtractive hybridization(SSH) was used to identify and analyze the differential genes specifically expressed in cerebral tissues of stoke group and control rats. Results: A total of 226 genes out of the 228 were usable and analyzed. The average length of the 226 genes was (286.6±120.3) bp with a range from 50 bp to 619 bp. And 126 clones out of the 226 showed a sequence with significant identity to the known genes; 78 clones demonstrated homogenous sequences to the existing ESTs ofdbEST, but no one of the 78 showed sequence with identity to that of known genes; and remaining 22 were novel transrcipts exhibiting no similarity to any known sequences. All the clones which were highly homogenous to the known genes were categorized on the basis of their function. It was found that 26.5% of the mitochodrial genes in brain tissues underwent changes after apoplexy and the changes showed a twofold relationship of cause and effect. Conclusion: Environmental factors are able to induce changes of gene expression, which may increase the sensitivity to apoplectic stroke.

  20. Specificity Evaluation and Disease Monitoring in Arthritis Imaging with Complement Receptor of the Ig superfamily targeting Nanobodies

    Science.gov (United States)

    Zheng, Fang; Perlman, Harris; Matthys, Patrick; Wen, Yurong; Lahoutte, Tony; Muyldermans, Serge; Lu, Shemin; De Baetselier, Patrick; Schoonooghe, Steve; Devoogdt, Nick; Raes, Geert

    2016-01-01

    Single-photon emission computed tomography combined with micro-CT (SPECT/μCT) imaging using Nanobodies against complement receptor of the Ig superfamily (CRIg), found on tissue macrophages such as synovial macrophages, has promising potential to visualize joint inflammation in experimental arthritis. Here, we further addressed the specificity and assessed the potential for arthritis monitoring. Signals obtained with 99mTc-labelled NbV4m119 Nanobody were compared in joints of wild type (WT) versus CRIg−/− mice with collagen-induced arthritis (CIA) or K/BxN serum transfer-induced arthritis (STIA). In addition, SPECT/μCT imaging was used to investigate arthritis development in STIA and in CIA under dexamethasone treatment. 99mTc-NbV4m119 accumulated in inflamed joints of WT, but not CRIg−/− mice with CIA and STIA. Development and spontaneous recovery of symptoms in STIA was reflected in initially increased and subsequently reduced joint accumulation of 99mTc-NbV4m119. Dexamethasone treatment of CIA mice reduced 99mTc-NbV4m119 accumulation as compared to saline control in most joints except knees. SPECT/μCT imaging with 99mTc-NbV4m119 allows specific assessment of inflammation in different arthritis models and provides complementary information to clinical scoring for quantitatively and non-invasively monitoring the pathological process and the efficacy of arthritis treatment. PMID:27779240

  1. Celiac Disease in Adult Patients: Specific Autoantibodies in the Diagnosis, Monitoring, and Screening

    Directory of Open Access Journals (Sweden)

    Evagelia Trigoni

    2014-01-01

    Full Text Available The increasing prevalence of celiac disease (CD, especially in adults, its atypical clinical presentation, and the strict, lifelong adherence to gluten-free diet (GFD as the only option for healthy state create an imperative need for noninvasive methods that can effectively diagnose CD and monitor GFD. Aim. Evaluation of anti-endomysium (EmA and anti-tissue transglutaminase IgA (tTG-A antibodies in CD diagnosis, GFD monitoring, and first degree relatives screening in CD adult patients. Methods. 70 newly diagnosed Greek adult patients, 70 controls, and 47 first degree relatives were tested for the presence of EmA and tTG-A. The CD patients were monitored during a 3-year period. Results. EmA predictive ability for CD diagnosis was slightly better compared to tTG-A (P=0.043. EmA could assess compliance with GFD already from the beginning of the diet, while both EmA and tTG-A had an equal ability to discriminate between strictly and partially compliant patients after the first semester and so on. Screening of first degree relatives resulted in the identification of 2 undiagnosed CD cases. Conclusions. Both EmA and tTG-A are suitable markers in the CD diagnosis, in the screening of CD among first degree relatives, having also an equal performance in the long term monitoring.

  2. Celiac disease in adult patients: specific autoantibodies in the diagnosis, monitoring, and screening.

    Science.gov (United States)

    Trigoni, Evagelia; Tsirogianni, Alexandra; Pipi, Elena; Mantzaris, Gerassimos; Papasteriades, Chryssa

    2014-01-01

    The increasing prevalence of celiac disease (CD), especially in adults, its atypical clinical presentation, and the strict, lifelong adherence to gluten-free diet (GFD) as the only option for healthy state create an imperative need for noninvasive methods that can effectively diagnose CD and monitor GFD. Aim. Evaluation of anti-endomysium (EmA) and anti-tissue transglutaminase IgA (tTG-A) antibodies in CD diagnosis, GFD monitoring, and first degree relatives screening in CD adult patients. Methods. 70 newly diagnosed Greek adult patients, 70 controls, and 47 first degree relatives were tested for the presence of EmA and tTG-A. The CD patients were monitored during a 3-year period. Results. EmA predictive ability for CD diagnosis was slightly better compared to tTG-A (P = 0.043). EmA could assess compliance with GFD already from the beginning of the diet, while both EmA and tTG-A had an equal ability to discriminate between strictly and partially compliant patients after the first semester and so on. Screening of first degree relatives resulted in the identification of 2 undiagnosed CD cases. Conclusions. Both EmA and tTG-A are suitable markers in the CD diagnosis, in the screening of CD among first degree relatives, having also an equal performance in the long term monitoring.

  3. Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.▿†

    Science.gov (United States)

    Bogdanove, Adam J.; Koebnik, Ralf; Lu, Hong; Furutani, Ayako; Angiuoli, Samuel V.; Patil, Prabhu B.; Van Sluys, Marie-Anne; Ryan, Robert P.; Meyer, Damien F.; Han, Sang-Wook; Aparna, Gudlur; Rajaram, Misha; Delcher, Arthur L.; Phillippy, Adam M.; Puiu, Daniela; Schatz, Michael C.; Shumway, Martin; Sommer, Daniel D.; Trapnell, Cole; Benahmed, Faiza; Dimitrov, George; Madupu, Ramana; Radune, Diana; Sullivan, Steven; Jha, Gopaljee; Ishihara, Hiromichi; Lee, Sang-Won; Pandey, Alok; Sharma, Vikas; Sriariyanun, Malinee; Szurek, Boris; Vera-Cruz, Casiana M.; Dorman, Karin S.; Ronald, Pamela C.; Verdier, Valérie; Dow, J. Maxwell; Sonti, Ramesh V.; Tsuge, Seiji; Brendel, Volker P.; Rabinowicz, Pablo D.; Leach, Jan E.; White, Frank F.; Salzberg, Steven L.

    2011-01-01

    Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity. PMID:21784931

  4. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

    Science.gov (United States)

    Bogdanove, Adam J; Koebnik, Ralf; Lu, Hong; Furutani, Ayako; Angiuoli, Samuel V; Patil, Prabhu B; Van Sluys, Marie-Anne; Ryan, Robert P; Meyer, Damien F; Han, Sang-Wook; Aparna, Gudlur; Rajaram, Misha; Delcher, Arthur L; Phillippy, Adam M; Puiu, Daniela; Schatz, Michael C; Shumway, Martin; Sommer, Daniel D; Trapnell, Cole; Benahmed, Faiza; Dimitrov, George; Madupu, Ramana; Radune, Diana; Sullivan, Steven; Jha, Gopaljee; Ishihara, Hiromichi; Lee, Sang-Won; Pandey, Alok; Sharma, Vikas; Sriariyanun, Malinee; Szurek, Boris; Vera-Cruz, Casiana M; Dorman, Karin S; Ronald, Pamela C; Verdier, Valérie; Dow, J Maxwell; Sonti, Ramesh V; Tsuge, Seiji; Brendel, Volker P; Rabinowicz, Pablo D; Leach, Jan E; White, Frank F; Salzberg, Steven L

    2011-10-01

    Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.

  5. Raising an Antibody Specific to Breast Cancer Subpopulations Using Phage Display on Tissue Sections

    DEFF Research Database (Denmark)

    Larsen, Simon Asbjørn; Meldgaard, Theresa; Fridriksdottir, Agla Jael Rubner

    2016-01-01

    BACKGROUND/AIM: Primary tumors display a great level of intra-tumor heterogeneity in breast cancer. The current lack of prognostic and predictive biomarkers limits accurate stratification and the ability to predict response to therapy. The aim of the present study was to select recombinant antibody...... fragments specific against breast cancer subpopulations, aiding the discovery of novel biomarkers. MATERIALS AND METHODS: Recombinant antibody fragments were selected by phage display. A novel shadowstick technology enabled the direct selection using tissue sections of antibody fragments specific against...... small subpopulations of breast cancer cells. Selections were performed against a subpopulation of breast cancer cells expressing CD271(+), as these previously have been indicated to be potential breast cancer stem cells. The selected antibody fragments were screened by phage ELISA on both breast cancer...

  6. Aequorin-Based Luminescence Imaging Reveals Stimulus- and Tissue-Specific Ca2+ Dynamics in Arabidopsis Plants

    Institute of Scientific and Technical Information of China (English)

    Xiaohong Zhu; Ying Feng; Gaimei Liang; Na Liu; Jian-Kang Zhu

    2013-01-01

    Calcium ion is a versatile second messenger for diverse cell signaling in response to developmental and environmental cues.The specificity of Ca2+-mediated signaling is defined by stimulus-elicited Ca2+ signature and down-stream decoding processes.Here,an Aequorin-based luminescence recording system was developed for monitoring Ca2+ in response to various stimuli in Arabidopsis.With the simple,highly sensitive,and robust Ca2+ recording,this system revealed stimulus-and tissue-specific Ca2+ signatures in seedlings.Cellular Ca2+ dynamics and relationship to Aequorin-based Ca2+ recording were explored using a GFP-based Ca2+ indicator,which suggested that a synchronous cellular Ca2+ signal is responsible for cold-induced Ca2+ response in seedlings,whereas asynchronous Ca2+ oscillation contributes to osmotic stress-induced Ca2+ increase in seedlings.The optimized recording system would be a powerful tool for the identification and characterization of novel components in Ca2+-mediated stress-signaling pathways.

  7. The tissue micro-array data exchange specification: a web based experience browsing imported data

    Directory of Open Access Journals (Sweden)

    Ayers Leona W

    2005-08-01

    Full Text Available Abstract Background The AIDS and Cancer Specimen Resource (ACSR is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI Division of Cancer Treatment and Diagnosis (DCTD. The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API extensible mark-up language (XML TMA data exchange specification (TMA DES proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT scripts that convert XML data into Hyper-Text Mark-up Language (HTML web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core

  8. Cooperative activation of tissue-specific genes by pRB and E2F1.

    Science.gov (United States)

    Flowers, Stephen; Xu, Fuhua; Moran, Elizabeth

    2013-04-01

    The retinoblastoma tumor suppressor protein pRB is conventionally regarded as an inhibitor of the E2F family of transcription factors. Conversely, pRB is also recognized as an activator of tissue-specific gene expression along various lineages including osteoblastogenesis. During osteoblast differentiation, pRB directly targets Alpl and Bglap, which encode the major markers of osteogenesis alkaline phosphatase and osteocalcin. Surprisingly, p130 and repressor E2Fs were recently found to cooccupy and repress Alpl and Bglap in proliferating osteoblast precursors before differentiation. This raises the further question of whether these genes convert to E2F activation targets when differentiation begins, which would constitute a remarkable situation wherein pRB and E2F would be cotargeting genes for activation. Chromatin immunoprecipitation analysis in an osteoblast differentiation model shows that Alpl and Bglap are indeed targeted by an activator E2F, i.e., is E2F1. Promoter occupation of Alpl and Bglap by E2F1 occurs specifically during activation, and depletion of E2F1 severely impairs their induction. Mechanistically, promoter occupation by E2F1 and pRB is mutually dependent, and without this cooperative effect, activation steps previously shown to be dependent on pRB, including recruitment of RNA polymerase II, are impaired. Myocyte- and adipocyte-specific genes are also cotargeted by E2F1 and pRB during differentiation along their respective lineages. The finding that pRB and E2F1 cooperate to activate expression of tissue-specific genes is a paradigm distinct from the classical concept of pRB as an inhibitor of E2F1, but is consistent with the observed roles of these proteins in physiological models.

  9. Depot- and sex-specific effects of maternal obesity in offspring's adipose tissue.

    Science.gov (United States)

    Lecoutre, Simon; Deracinois, Barbara; Laborie, Christine; Eberlé, Delphine; Guinez, Céline; Panchenko, Polina E; Lesage, Jean; Vieau, Didier; Junien, Claudine; Gabory, Anne; Breton, Christophe

    2016-07-01

    According to the Developmental Origin of Health and Disease (DOHaD) concept, alterations of nutrient supply in the fetus or neonate result in long-term programming of individual body weight (BW) setpoint. In particular, maternal obesity, excessive nutrition, and accelerated growth in neonates have been shown to sensitize offspring to obesity. The white adipose tissue may represent a prime target of metabolic programming induced by maternal obesity. In order to unravel the underlying mechanisms, we have developed a rat model of maternal obesity using a high-fat (HF) diet (containing 60% lipids) before and during gestation and lactation. At birth, newborns from obese dams (called HF) were normotrophs. However, HF neonates exhibited a rapid weight gain during lactation, a key period of adipose tissue development in rodents. In males, increased BW at weaning (+30%) persists until 3months of age. Nine-month-old HF male offspring was normoglycemic but showed mild glucose intolerance, hyperinsulinemia, and hypercorticosteronemia. Despite no difference in BW and energy intake, HF adult male offspring was predisposed to fat accumulation showing increased visceral (gonadal and perirenal) depots weights and hyperleptinemia. However, only perirenal adipose tissue depot exhibited marked adipocyte hypertrophy and hyperplasia with elevated lipogenic (i.e. sterol-regulated element binding protein 1 (Srebp1), fatty acid synthase (Fas), and leptin) and diminished adipogenic (i.e. peroxisome proliferator-activated receptor gamma (Pparγ), 11β-hydroxysteroid dehydrogenase type 1 (11β-Hds1)) mRNA levels. By contrast, very few metabolic variations were observed in HF female offspring. Thus, maternal obesity and accelerated growth during lactation program offspring for higher adiposity via transcriptional alterations of visceral adipose tissue in a depot- and sex-specific manner. © 2016 Society for Endocrinology.

  10. Liver-targeting of interferon-alpha with tissue-specific domain antibodies.

    Science.gov (United States)

    Coulstock, Edward; Sosabowski, Jane; Ovečka, Milan; Prince, Rob; Goodall, Laura; Mudd, Clare; Sepp, Armin; Davies, Marie; Foster, Julie; Burnet, Jerome; Dunlevy, Gráinne; Walker, Adam

    2013-01-01

    Interferon alpha (IFNα) is used for the treatment of hepatitis C infection and whilst efficacious it is associated with multiple adverse events including reduced leukocyte, erythrocyte, and platelet counts, fatigue, and depression. These events are most likely caused by systemic exposure to interferon. We therefore hypothesise that targeting the therapeutic directly to the intended site of action in the liver would reduce exposure in blood and peripheral tissue and hence improve the safety and tolerability of IFNα therapy. We genetically fused IFN to a domain antibody (dAb) specific to a hepatocyte restricted antigen, asialoglycoprotein receptor (ASGPR). Our results show that the murine IFNα2 homolog (mIFNα2) fused to an ASGPR specific dAb, termed DOM26h-196-61, could be expressed in mammalian tissue culture systems and retains the desirable biophysical properties and activity of both fusion partners when measured in vitro. Furthermore a clear increase in in vivo targeting of the liver by mIFNα2-ASGPR dAb fusion protein, compared to that observed with either unfused mIFNα2 or mIFNα2 fused to an isotype control dAb VHD2 (which does not bind ASGPR) was demonstrated using microSPECT imaging. We suggest that these findings may be applicable in the development of a liver-targeted human IFN molecule with improved safety and patient compliance in comparison to the current standard of care, which could ultimately be used as a treatment for human hepatitis virus infections.

  11. Sensitive and specific KRAS somatic mutation analysis on whole-genome amplified DNA from archival tissues.

    Science.gov (United States)

    van Eijk, Ronald; van Puijenbroek, Marjo; Chhatta, Amiet R; Gupta, Nisha; Vossen, Rolf H A M; Lips, Esther H; Cleton-Jansen, Anne-Marie; Morreau, Hans; van Wezel, Tom

    2010-01-01

    Kirsten RAS (KRAS) is a small GTPase that plays a key role in Ras/mitogen-activated protein kinase signaling; somatic mutations in KRAS are frequently found in many cancers. The most common KRAS mutations result in a constitutively active protein. Accurate detection of KRAS mutations is pivotal to the molecular diagnosis of cancer and may guide proper treatment selection. Here, we describe a two-step KRAS mutation screening protocol that combines whole-genome amplification (WGA), high-resolution melting analysis (HRM) as a prescreen method for mutation carrying samples, and direct Sanger sequencing of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue, from which limited amounts of DNA are available. We developed target-specific primers, thereby avoiding amplification of homologous KRAS sequences. The addition of herring sperm DNA facilitated WGA in DNA samples isolated from as few as 100 cells. KRAS mutation screening using high-resolution melting analysis on wgaDNA from formalin-fixed, paraffin-embedded tissue is highly sensitive and specific; additionally, this method is feasible for screening of clinical specimens, as illustrated by our analysis of pancreatic cancers. Furthermore, PCR on wgaDNA does not introduce genotypic changes, as opposed to unamplified genomic DNA. This method can, after validation, be applied to virtually any potentially mutated region in the genome.

  12. Tissue-specific expression of a splicing mutation in the IKBKAP gene causes familial dysautonomia.

    Science.gov (United States)

    Slaugenhaupt, S A; Blumenfeld, A; Gill, S P; Leyne, M; Mull, J; Cuajungco, M P; Liebert, C B; Chadwick, B; Idelson, M; Reznik, L; Robbins, C; Makalowska, I; Brownstein, M; Krappmann, D; Scheidereit, C; Maayan, C; Axelrod, F B; Gusella, J F

    2001-03-01

    Familial dysautonomia (FD; also known as "Riley-Day syndrome"), an Ashkenazi Jewish disorder, is the best known and most frequent of a group of congenital sensory neuropathies and is characterized by widespread sensory and variable autonomic dysfunction. Previously, we had mapped the FD gene, DYS, to a 0.5-cM region on chromosome 9q31 and had shown that the ethnic bias is due to a founder effect, with >99.5% of disease alleles sharing a common ancestral haplotype. To investigate the molecular basis of FD, we sequenced the minimal candidate region and cloned and characterized its five genes. One of these, IKBKAP, harbors two mutations that can cause FD. The major haplotype mutation is located in the donor splice site of intron 20. This mutation can result in skipping of exon 20 in the mRNA of patients with FD, although they continue to express varying levels of wild-type message in a tissue-specific manner. RNA isolated from lymphoblasts of patients is primarily wild-type, whereas only the deleted message is seen in RNA isolated from brain. The mutation associated with the minor haplotype in four patients is a missense (R696P) mutation in exon 19, which is predicted to disrupt a potential phosphorylation site. Our findings indicate that almost all cases of FD are caused by an unusual splice defect that displays tissue-specific expression; and they also provide the basis for rapid carrier screening in the Ashkenazi Jewish population.

  13. CELLULAR LOCALIZATION OF IMMUNOGLOBULINS WITH DIFFERENT ALLOTYPIC SPECIFICITIES IN RABBIT LYMPHOID TISSUES

    Science.gov (United States)

    Pernis, Benvenuto; Chiappino, Gerolamo; Kelus, Andrew S.; Gell, Philip G. H.

    1965-01-01

    The cellular localization of allotypes in rabbit lymphoid tissues has been studied by immunofluorescence. In heterozygous animals the double staining for two allotypes controlled by allelic genes (A1 and A2; A4 and A5; A4 and A6) has shown the existence of two populations of plasma cells, one containing one allotype and the other the alternative one. The localization in different cells of immunoglobulins marked by allelic allotypic specificities has been confirmed by microspectrography of single cells. An exception to this rule was given by the presence in the germinal centers of lymphoid follicles of apparently uniform mixtures of products of the two allelic genes. Double staining for two allotypes controlled by genes at different loci showed, instead, the presence of many cells containing both allotypes; the number of these cells was highest in doubly homozygotes, in the other it was consistent with random association of non-allelic specificities. In addition double staining for one allotype and gamma G globulins in the lymphoid tissues of rabbits homozygous at the a or at the b locus, has shown the presence of cells containing immunoglobulins that lack one allotype. PMID:4159057

  14. GATA transcription factors as tissue-specific master regulators for induced responses.

    Science.gov (United States)

    Block, Dena Hs; Shapira, Michael

    2015-01-01

    GATA transcription factors play important roles in directing developmental genetic programs and cell differentiation, and are conserved in animals, plants and fungi. C. elegans has 11 GATA-type transcription factors that orchestrate development of the gut, epidermis and vulva. However, the expression of certain GATA proteins persists into adulthood, where their function is less understood. Accumulating evidence demonstrates contributions of 2 terminal differentiation GATA transcription factors, ELT-2 and ELT-3, to epithelial immune responses in the adult intestine and epidermis (hypodermis), respectively. Involvement in other stress responses has also been documented. We recently showed that ELT-2 acted as a tissue-specific master regulator, cooperating with 2 transcription factors activated by the p38 pathway, ATF-7 and SKN-1, to control immune responses in the adult C. elegans intestine. Here, we discuss the broader implications of these findings for understanding the involvement of GATA transcription factors in adult stress responses, and draw parallels between ELT-2 and ELT-3 to speculate that the latter may fulfill similar tissue-specific functions in the epidermis.

  15. Tissue specificity of enhancer and promoter activities of a HERV-K(HML-2) LTR.

    Science.gov (United States)

    Ruda, V M; Akopov, S B; Trubetskoy, D O; Manuylov, N L; Vetchinova, A S; Zavalova, L L; Nikolaev, L G; Sverdlov, E D

    2004-08-01

    Transient expression of a luciferase reporter gene was used to evaluate tissue-specific promoter and enhancer activities of a solitary extraviral long terminal repeat (LTR) of the human endogenous retrovirus K (HERV-K) in several human and CHO cell lines. The promoter activity of the LTR varied from virtually not detectable (GS and Jurkat cells) to as high as that of the SV40 early promoter (Tera-1 human testicular embryonal carcinoma cells). The negative regulatory element (NRE) of the LTR retained its activity in all cell lines where the LTR could act as a promoter, and was also capable of binding host cell nuclear proteins. The enhancer activity of the LTR towards the SV40 early promoter was detected only in Tera-1 cells and was not observed in a closely related human testicular embryonal carcinoma cell line of different origin, NT2/D1. A comparison of proteins bound to central part of the LTR in nuclear extracts from Tera-1 and NT2/D1 by electrophoretic mobility shift assay revealed striking differences that could be determined by different LTR enhancer activities in these cells. Tissue specificity of the SV40 early promoter activity was also revealed.

  16. Depot-specific Regulation of the Conversion of Cortisone to Cortisol in Human Adipose Tissue

    Science.gov (United States)

    Lee, Mi-Jeong; Fried, Susan K.; Mundt, Steven S.; Wang, Yanxin; Sullivan, Sean; Stefanni, Alice; Daugherty, Bruce L.; Hermanowski-Vosatka, Anne

    2015-01-01

    Objective Our main objective was to compare the regulation of cortisol production within omental (Om) and abdominal subcutaneous (Abd sc) human adipose tissue. Methods and Procedures Om and Abd sc adipose tissue were obtained at surgery from subjects with a wide range of BMI. Hydroxysteroid dehydrogenase (HSD) activity (3H-cortisone and 3H-cortisol interconversion) and expression were measured before and after organ culture with insulin and/or dexamethasone. Results Type 1 HSD (HSD1) mRNA and reductase activity were mainly expressed within adipocytes and tightly correlated with adipocyte size within both depots. There was no depot difference in HSD1 expression or reductase activity, while cortisol inactivation and HSD2 mRNA expression (expressed in stromal cells) were higher in Om suggesting higher cortisol turnover in this depot. Culture with insulin decreased HSD reductase activity in both depots. Culture with dexamethasone plus insulin compared to insulin alone increased HSD reductase activity only in the Om depot. This depot-specific increase in reductase activity could not be explained by an alteration in HSD1 mRNA or protein, which was paradoxically decreased. However, in Om only, hexose-6-phosphate dehydrogenase (H6PDH) mRNA levels were increased by culture with dexamethasone plus insulin compared to insulin alone, suggesting that higher nicotinamide adenine dinucleotide phosphate-oxidase (NADPH) production within the endoplasmic reticulum (ER) contributed to the higher HSD reductase activity. Discussion We conclude that in the presence of insulin, glucocorticoids cause a depot-specific increase in the activation of cortisone within Om adipose tissue, and that this mechanism may contribute to adipocyte hypertrophy and visceral obesity. PMID:18388900

  17. Tissue-specific expression and functional role of dehydrins in heat tolerance of sugarcane (Saccharum officinarum).

    Science.gov (United States)

    Galani, Saddia; Wahid, Abdul; Arshad, Muhammad

    2013-04-01

    Studies on the functional roles of dehydrins (DHNs) in heat tolerance of plants are scarce. This study was conducted to immunohistolocalize DHNs in leaves of heat-tolerant (CP-4333) and heat-sensitive (HSF-240) sugarcane (Saccharum officinarum L.) clones at three phenological stages in order to elucidate their putative roles under heat stress. CP-4333 indicated greater amounts of heat-stable proteins than HSF-240 under heat stress. Western blotting revealed the expression of three DHNs in CP-4333 (13- and 15-kDa peptides at 48 h and an additional 18-kDa band at 72 h) and two (13 and 15 kDa at 48 h) in HSF-240 at formative stage; two DHNs in CP-4333 (20 and 25 kDa) and one in HSF-240 (20 kDa) at grand growth stage, while two DHNs in CP-4333 (20 and 22 kDa) and one in HSF-240 (20 kDa) at maturity stage. Tissue-specific immunohistolocalization showed that DHNs were expressed in stele particularly the phloem and the cells intervening bundle sheath and vascular bundles. Furthermore, DHNs were also found scattered along the epidermal and parenchymatous cells. Recovery of sugarcane from heat stress manifested a gradual disappearance of DHNs in both the clones, being quicker in sensitive clone (HSF-240). Results suggested specific implications for DHNs synthesis. Their synthesis in epidermis appears to protect the mesophyll tissues from heat injury. When associated to vascular tissue, they tend to ensure the normal photoassimilate loading into the sieve element-companion cell complex. DHNs diminution during recovery suggested that their expression was transitory. However, prolonged retention of DHNs by tolerant clone appears to be an adaptive advantage of sugarcane to withstand heat stress.

  18. Chronic social isolation is associated with metabolic gene expression changes specific to mammary adipose tissue.

    Science.gov (United States)

    Volden, Paul A; Wonder, Erin L; Skor, Maxwell N; Carmean, Christopher M; Patel, Feenalie N; Ye, Honggang; Kocherginsky, Masha; McClintock, Martha K; Brady, Matthew J; Conzen, Suzanne D

    2013-07-01

    Chronic social isolation is linked to increased mammary tumor growth in rodent models of breast cancer. In the C3(1)/SV40 T-antigen FVB/N (TAg) mouse model of "triple-negative" breast cancer, the heightened stress response elicited by social isolation has been associated with increased expression of metabolic genes in the mammary gland before invasive tumors develop (i.e., during the in situ carcinoma stage). To further understand the mechanisms underlying how accelerated mammary tumor growth is associated with social isolation, we separated the mammary gland adipose tissue from adjacent ductal epithelial cells and analyzed individual cell types for changes in metabolic gene expression. Specifically, increased expression of the key metabolic genes Acaca, Hk2, and Acly was found in the adipocyte, rather than the epithelial fraction. Surprisingly, metabolic gene expression was not significantly increased in visceral adipose depots of socially isolated female mice. As expected, increased metabolic gene expression in the mammary adipocytes of socially isolated mice coincided with increased glucose metabolism, lipid synthesis, and leptin secretion from this adipose depot. Furthermore, application of media that had been cultured with isolated mouse mammary adipose tissue (conditioned media) resulted in increased proliferation of mammary cancer cells relative to group-housed-conditioned media. These results suggest that exposure to a chronic stressor (social isolation) results in specific metabolic reprogramming in mammary gland adipocytes that in turn contributes to increased proliferation of adjacent preinvasive malignant epithelial cells. Metabolites and/or tumor growth-promoting proteins secreted from adipose tissue could identify biomarkers and/or targets for preventive intervention in breast cancer.

  19. Tissue-specific expression and regulatory networks of pig microRNAome.

    Directory of Open Access Journals (Sweden)

    Paolo Martini

    Full Text Available BACKGROUND: Despite the economic and medical importance of the pig, knowledge about its genome organization, gene expression regulation, and molecular mechanisms involved in physiological processes is far from that achieved for mouse and rat, the two most used model organisms in biomedical research. MicroRNAs (miRNAs are a wide class of molecules that exert a recognized role in gene expression modulation, but only 280 miRNAs in pig have been characterized to date. RESULTS: We applied a novel computational approach to predict species-specific and conserved miRNAs in the pig genome, which were then subjected to experimental validation. We experimentally identified candidate miRNAs sequences grouped in high-confidence (424 and medium-confidence (353 miRNAs according to RNA-seq results. A group of miRNAs was also validated by PCR experiments. We established the subtle variability in expression of isomiRs and miRNA-miRNA star couples supporting a biological function for these molecules. Finally, miRNA and mRNA expression profiles produced from the same sample of 20 different tissue of the animal were combined, using a correlation threshold to filter miRNA-target predictions, to identify tissue-specific regulatory networks. CONCLUSIONS: Our data represent a significant progress in the current understanding of miRNAome in pig. The identification of miRNAs, their target mRNAs, and the construction of regulatory circuits will provide new insights into the complex biological networks in several tissues of this important animal model.

  20. Unconventional microarray design reveals the response to obesity is largely tissue specific: analysis of common and divergent responses to diet-induced obesity in insulin-sensitive tissues.

    Science.gov (United States)

    Lee, Robyn K; Hittel, Dustin S; Nyamandi, Vongai Z; Kang, Li; Soh, Jung; Sensen, Christoph W; Shearer, Jane

    2012-04-01

    Obesity is a chronic condition involving the excessive accumulation of adipose tissue that adversely affects all systems in the body. The aim of the present study was to employ an unbiased, genome-wide assessment of transcript abundance in order to identify common gene expression pathways within insulin-sensitive tissues in response to dietary-induced diabetes. Following 20 weeks of chow or high-fat feeding (60% kcal), age-matched mice underwent a euglycemic-hyperinsulinemic clamp to assess insulin sensitivity. High-fat-fed animals were obese and highly insulin resistant, disposing of ∼75% less glucose compared with their chow-fed counterparts. Tissues were collected, and gene expression was examined by microarray in 4 tissues known to exhibit obesity-related metabolic disturbances: white adipose tissue, skeletal muscle, liver, and heart. A total of 463 genes were differentially expressed between diets. Analysis of individual tissues showed skeletal muscle to exhibit the largest number of differentially expressed genes (191) in response to high-fat feeding, followed by adipose tissue (169), liver (115), and heart (65). Analyses revealed that the response of individual genes to obesity is distinct and largely tissue specific, with less than 10% of transcripts being shared among tissues. Although transcripts are largely tissue specific, a systems approach shows numerous commonly activated pathways, including those involved in signal transduction, inflammation, oxidative stress, substrate transport, and metabolism. This suggests a coordinated attempt by tissues to limit metabolic perturbations occurring in early-stage obesity. Many identified genes were associated with a variety of disorders, thereby serving as potential links between obesity and its related health risks.

  1. High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice.

    Science.gov (United States)

    Hageman, Rachael S; Wagener, Asja; Hantschel, Claudia; Svenson, Karen L; Churchill, Gary A; Brockmann, Gudrun A

    2010-06-01

    The aim of this study was to characterize the responses of individual tissues to high-fat feeding as a function of mass, fat composition, and transcript abundance. We examined a panel of eight tissues [5 white adipose tissues (WAT), brown adipose tissue (BAT), liver, muscle] obtained from DBA/2J mice on either a standard breeding diet (SBD) or a high-fat diet (HFD). HFD led to weight gain, decreased insulin sensitivity, and tissue-specific responses, including inflammation, in these mice. The dietary fatty acids were partially metabolized and converted in both liver and fat tissues. Saturated fatty acids (SFA) were converted in the liver to monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA), and oleic acid (C18:1) was the preferred MUFA for storage of excess energy in all tissues of HFD-fed mice. Transcriptional changes largely reflected the tissue-specific fat deposition. SFA were negatively correlated with genes in the collagen family and processes involving the extracellular matrix. We propose a novel role of the tryptophan hydroxylase 2 (Tph2) gene in adipose tissues of diet-induced obesity. Tissue-specific responses to HFD were identified. Liver steatosis was evident in HFD-fed mice. Gonadal, retroperitoneal and subcutaneous adipose tissue and BAT exhibited severe inflammatory and immune responses. Mesenteric adipose tissue was the most metabolically active adipose tissue. Gluteal adipose tissue had the highest mass gain but was sluggish in its metabolism. In HFD conditions, BAT functioned largely like WAT in its role as a depot for excess energy, whereas WAT played a role in thermogenesis.

  2. 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.

  3. 5'-heterogeneity of glucocorticoid receptor messenger RNA is tissue specific: differential regulation of variant transcripts by early-life events.

    Science.gov (United States)

    McCormick, J A; Lyons, V; Jacobson, M D; Noble, J; Diorio, J; Nyirenda, M; Weaver, S; Ester, W; Yau, J L; Meaney, M J; Seckl, J R; Chapman, K E

    2000-04-01

    Glucocorticoid receptor (GR) gene expression is regulated in a complex tissue-specific manner, notably by early-life environmental events that program tissue GR levels. We have identified and characterized several new rat GR mRNAs. All encode a common protein, but differ in their 5'-leader sequences as a consequence of alternate splicing of, potentially, 11 different exon 1 sequences. Most are located in a 3-kb CpG island, upstream of exon 2, that exhibits substantial promoter activity in transfected cells. Ribonuclease (RNase) protection analysis demonstrated significant levels of six alternate exons 1 in vivo in rat, with differences between liver, hippocampus, and thymus reflecting tissue-specific differences in promoter activity. Two of the alternate exons 1 (exons 1(6) and 1(10)) were expressed in all tissues examined, together present in 77-87% of total GR mRNA. The remaining GR transcripts contained tissue-specific alternate first exons. Importantly, tissue-specific first exon usage was altered by perinatal environmental manipulations. Postnatal handling, which permanently increases GR in the hippocampus, causing attenuation of stress responses, selectively elevated GR mRNA containing the hippocampus-specific exon 1(7). Prenatal glucocorticoid exposure, which increases hepatic GR expression and produces adult hyperglycemia, decreased the proportion of hepatic GR mRNA containing the predominant exon 1(10), suggesting an increase in a minor exon 1 variant. Such tissue specificity of promoter usage allows differential GR regulation and programming.

  4. A novel method for monitoring functional lesion-specific recruitment of repair proteins in live cells

    Energy Technology Data Exchange (ETDEWEB)

    Woodrick, Jordan; Gupta, Suhani; Khatkar, Pooja; Dave, Kalpana; Levashova, Darya; Choudhury, Sujata; Elias, Hadi; Saha, Tapas; Mueller, Susette; Roy, Rabindra, E-mail: rr228@georgetown.edu

    2015-05-15

    Highlights: • A method of monitoring lesion-specific recruitment of proteins in vivo is described. • Recruitment of repair enzymes to abasic sites is monitored by co-localization. • Repair protein recruitment is consistent with known protein–protein relationships. • Cells demonstrated complete repair of abasic sites by 90 min. - Abstract: DNA–protein relationships have been studied by numerous methods, but a particular gap in methodology lies in the study of DNA adduct-specific interactions with proteins in vivo, which particularly affects the field of DNA repair. Using the repair of a well-characterized and ubiquitous adduct, the abasic (AP) site, as a model, we have developed a comprehensive method of monitoring DNA lesion-specific recruitment of proteins in vivo over time. We utilized a surrogate system in which a Cy3-labeled plasmid containing a single AP-site was transfected into cells, and the interaction of the labeled DNA with BER enzymes, including APE1, Polβ, LIG1, and FEN1, was monitored by immunofluorescent staining of the enzymes by Alexafluor-488-conjugated secondary antibody. The recruitment of enzymes was characterized by quantification of Cy3-Alexafluor-488 co-localization. To validate the microscopy-based method, repair of the transfected AP-site DNA was also quantified at various time points post-transfection using a real time PCR-based method. Notably, the recruitment time kinetics for each enzyme were consistent with AP-site repair time kinetics. This microscopy-based methodology is reliable in detecting the recruitment of proteins to specific DNA substrates and can be extended to study other in vivo DNA–protein relationships in any DNA sequence and in the context of any DNA structure in transfectable proliferating or quiescent cells. The method may be applied to a variety of disciplines of nucleic acid transaction pathways, including repair, replication, transcription, and recombination.

  5. 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

  6. Highly interactive nature of flower-specific enhancers and promoters, and its potential impact on tissue-specific expression and engineering of multiple genes or agronomic traits.

    Science.gov (United States)

    Wen, Zhifeng; Yang, Yazhou; Zhang, Jinjin; Wang, Xiping; Singer, Stacy; Liu, Zhongchi; Yang, Yingjun; Yan, Guohua; Liu, Zongrang

    2014-09-01

    Molecular stacking enables multiple traits to be effectively engineered in crops using a single vector. However, the co-existence of distinct plant promoters in the same transgenic unit might, like their mammalian counterparts, interfere with one another. In this study, we devised a novel approach to investigate enhancer-promoter and promoter-promoter interactions in transgenic plants and demonstrated that three of four flower-specific enhancer/promoters were capable of distantly activating a pollen- and stigma-specific Pps promoter (fused to the cytotoxic DT-A gene) in other tissues, as revealed by novel tissue ablation phenotypes in transgenic plants. The NtAGI1 enhancer exclusively activated stamen- and carpel-specific DT-A expression, thus resulting in tissue ablation in an orientation-independent manner; this activation was completely abolished by the insertion of an enhancer-blocking insulator (EXOB) between the NtAGI1 enhancer and Pps promoter. Similarly, AGL8 and AP1Lb1, but not AP1La, promoters also activated distinct tissue-specific DT-A expression and ablation, with the former causing global growth retardation and the latter ablating apical inflorescences. While the tissue specificity of the enhancer/promoters generally defined their activation specificities, the strength of their activity in particular tissues or developmental stages appeared to determine whether activation actually occurred. Our findings provide the first evidence that plant-derived enhancer/promoters can distantly interact/interfere with one another, which could pose potential problems for the tissue-specific engineering of multiple traits using a single-vector stacking approach. Therefore, our work highlights the importance of adopting enhancer-blocking insulators in transformation vectors to minimize promoter-promoter interactions. The practical and fundamental significance of these findings will be discussed.

  7. Monitoring of organochlorine pesticide residue levels in adipose tissue of Veracruz, Mexico inhabitants.

    Science.gov (United States)

    Waliszewski, Stefan M; Caba, M; Herrero-Mercado, M; Saldariaga-Noreña, H; Meza, E; Zepeda, R; Martínez-Valenzuela, C; Infanzon, R; Hernández-Chalate, F

    2011-11-01

    The objective of the present study was to monitor the levels of organochlorine pesticides HCB, α-β-γ-HCH, pp'DDE, op'DDT and pp'DDT in 150 adipose tissue samples of Veracruz, Mexico inhabitants. In analyzed samples, the following pesticides were detected: p,p'-DDE in 100% of the samples at mean 1.643 mg/kg; p,p'-DDT in 99.3.% of the samples at mean 0.227 mg/kg; β-HCH in 97.3% of the samples at mean 0.063 mg/kg; and op'DDT in 93.3% of the samples at mean 0.022 mg/kg. Comparing mean, median and geometric mean concentrations of organochlorine pesticides shows a decrease in values from mean to median and to geometric mean which points out a prevalence of lower concentrations among the total samples and the existence of occasional cases of extreme exposure expressed in range values. The pooled samples divided according to sex, showed only significant differences of pp'DDE median concentrations between sexes. The other organochlorine pesticides indicated no statistical differences between sexes, including the pp'DDE/pp'DDT ratio. The samples grouped according to age, showed that the third tertile was more contaminated for both sexes, indicating age as a positively associated factor with organochlorine pesticide levels in adipose tissue of Veracruz inhabitants. Comparing organochlorine pesticide levels between 2008 and 2010 years, a decreased tendency for β-HCH, pp'DDE, Σ-DDT and pp'DDE/pp'DDT ratio levels was observed.

  8. Biochemistry of Short-Chain Alkanes (Tissue-Specific Biosynthesis of n-Heptane in Pinus jeffreyi).

    Science.gov (United States)

    Savage, T. J.; Hamilton, B. S.; Croteau, R.

    1996-01-01

    Short-chain (C7-C11) alkanes accumulate as the volatile component of oleoresin (pitch) in several pine species native to western North America. To establish the tissue most amenable for use in detailed studies of short-chain alkane biosynthesis, we examined the tissue specificity of alkane accumulation and biosynthesis in Pinus jeffreyi Grev. & Balf. Short-chain alkane accumulation was highly tissue specific in both 2-year-old saplings and mature trees; heart-wood xylem accumulated alkanes up to 7.1 mg g-1 dry weight, whereas needles and other young green tissue contained oleoresin with monoterpenoid, rather than paraffinic, volatiles. These tissue-specific differences in oleoresin composition appear to be a result of tissue-specific rates of alkane and monoterpene biosynthesis; incubation of xylem tissue with [14C]sucrose resulted in accumulation of radiolabel in alkanes but not monoterpenes, whereas incubation of foliar tissue with 14CO2 resulted in the accumulation of radiolabel in monoterpenes but not alkanes. Furthermore, incubation of xylem sections with [14C]acetate resulted in incorporation of radiolabel into alkanes at rates up to 1.7 nmol h-1 g-1 fresh weight, a rate that exceeds most biosynthetic rates reported with other plant systems for the incorporation of this basic precursor into natural products. This suggests that P. jeffreyi may provide a suitable model for elucidating the enzymology and molecular biology of short-chain alkane biosynthesis.

  9. Identifying tissue-specific signal variation in MALDI mass spectrometric imaging by use of an internal standard

    NARCIS (Netherlands)

    Pirman, D.A.; Kiss, A.; Heeren, R.M.A.; Yost, R.A.

    2013-01-01

    Generating analyte-specific distribution maps of compounds in a tissue sample by matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging (MSI) has become a useful tool in numerous areas across the biological sciences. Direct analysis of the tissue sample provides MS images of

  10. Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis.

    Directory of Open Access Journals (Sweden)

    Omprakash Mittapalli

    Full Text Available 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 (248and 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.

  11. Molecular characterization of PRR13 and its tissue-specific expression in rainbow trout (Oncorhynchus mykiss).

    Science.gov (United States)

    Verleih, Marieke; Rebl, Alexander; Köllner, Bernd; Korytář, Tomáš; Kotterba, Günter; Anders, Eckhard; Wimmers, Klaus; Goldammer, Tom

    2010-12-01

    The proline-rich protein 13 (PRR13) is reported to be a key regulator of the resistance to cytostatica by decreasing the copy number of the proapoptotic gene thrombospondin-1. We isolated and characterized the complete PRR13 gene sequence of rainbow trout (Oncorhynchus mykiss). The gene comprises four exons and three introns, the latter of comparatively short lengths (100-811 bp). The full-length PRR13 cDNA consists of 1,101 nucleotides, including an open reading frame of 563 bp, which is predicted to encode a 187 amino acid protein with a molecular mass of 18.8 kDa. A continuous stretch of ten serine residues at the C-terminus is highly conserved and characteristic for vertebrate PRR13, but not for other known proline-rich proteins. Phylogenetic analyses suggest a clear separation of teleostean PRR13 proteins and those from mammalian and reptilian species. Comparison of the tissue-specific PRR13 mRNA abundance in two strains of the rainbow trout coastal form (TCO Steelhead II-WA vs. BORN Steelhead II-Germany) revealed an increased expression in the BORN trout in nearly all examined tissues. The major expression differences were detected in gill (2.29-fold) and in liver tissue (2.16-fold). Hence, the increased PRR13 expression in BORN trout might cause improved protection from natural cytostatica and therefore support our assumption that PRR13 is a candidate gene possibly involved in the varying ability of the two rainbow trout strains to handle environmental stress under local conditions of the Southern Baltic.

  12. 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.

  13. Cloning, expression and characterization of human tissue-specific DNA polymerase λ2

    Institute of Scientific and Technical Information of China (English)

    GU Fu; LI YuYang; L(U) Hong; YOU Chun; LIU JianPing; CHEN Ao; YU Yao; WANG Xiang; WAN DaFang; GU JianRen; YUAN HanYing

    2007-01-01

    DNA polymerase (POL) λ plays an important role during DNA repair and DNA nonhomologous recombination processes. A novel POL λ variant was cloned from a human liver cDNA library and named POL λ2 (GenBank Accession No. AY302442). POL λ2 has 2206 base pairs in length with an open reading frame of 1452 base pairs encoding a 482-amino-acids protein. Bioinformatics analysis reveals that POL λ2 spans 7.9 kb on human chromosome 10q24 and is composed of 8 exons and 7 introns. It has the specific domain of DNA polymerase X family-POL Xc at the C-terminus and BRCT domain at the N-terminus. POL λ2 was localized predominantly in nucleus in transfected L0-2 cells. It was expressed abundantly in liver and testis, weakly in ovary, and undetectably in other tested human tissues. In comparison with the expression ratio between POL λ and POL λ2 in normal liver tissues and hepatocellular carcinoma (HCC) adjacent tissues, the ratio was aberrant in 80% of those 15 HCC specimens examined due to the up-regulated expression of POL λ. This abnormality might be involved in hepatocarcinogenesis. The recombinant POL λ2 with His-tag was expressed as a soluble active protein in E.coli BL21 (DE3)CONDON Plus and purified by Ni-NTA resin and then desalted by Superdex-75 chromatography in an FPLC system. The analysis using isotope α-32p-dCTP incorporation in vitro showed that the purified recombinant POL λ2 exhibited DNA polymerase activity.

  14. 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

  15. Sex- and Tissue-Specific Methylome Changes in Brains of Mice Perinatally Exposed to Lead

    Science.gov (United States)

    Sánchez-Martín, Francisco Javier; Lindquist, Diana M.; Landero-Figueroa, Julio; Zhang, Xiang; Chen, Jing; Cecil, Kim M.; Medvedovic, Mario; Puga, Alvaro

    2014-01-01

    Changes in DNA methylation and subsequent changes in gene expression regulation are the hallmarks of age- and tissue-dependent epigenetic drift and plasticity resulting from the combinatorial integration of genetic determinants and environmental cues. To determine whether perinatal lead exposure caused persistent DNA methylation changes in target tissues, we exposed mouse dams to 0, 3 or 30 ppm of lead acetate in drinking water for a period extending from 2 months prior to mating, through gestation, until weaning of pups at postnatal day-21, and analyzed whole-genome DNA methylation in brain cortex and hippocampus of 2-month old exposed and unexposed progeny. Lead exposure resulted in hypermethylation of three differentially methylated regions in the hippocampus of females, but not males. These regions mapped to Rn4.5s, Sfi1, and Rn45s loci in mouse chromosomes 2, 11 and 17, respectively. At a conservative fdr<0.001, 1,623 additional CpG sites were differentially methylated in female hippocampus, corresponding to 117 unique genes. Sixty of these genes were tested for mRNA expression and showed a trend towards negative correlation between mRNA expression and methylation in exposed females but not males. No statistically significant methylome changes were detected in male hippocampus or in cortex of either sex. We conclude that exposure to lead during embryonic life, a time when the organism is most sensitive to environmental cues, appears to have a sex- and tissue-specific effect on DNA methylation that may produce pathological or physiological deviations from the epigenetic plasticity operative in unexposed mice. PMID:25530354

  16. Cloning, expression and characterization of human tissue-specific DNA polymerase λ2

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    DNA polymerase (POL) λ plays an important role during DNA repair and DNA nonhomologous recom-bination processes. A novel POL λ variant was cloned from a human liver cDNA library and named POL λ2 (GenBank Accession No. AY302442). POL λ2 has 2206 base pairs in length with an open reading frame of 1452 base pairs encoding a 482-amino-acids protein. Bioinformatics analysis reveals that POL λ2 spans 7.9 kb on human chromosome 10q24 and is composed of 8 exons and 7 introns. It has the specific domain of DNA polymerase X family-POL Xc at the C-terminus and BRCT domain at the N-terminus. POL λ2 was localized predominantly in nucleus in transfected L0-2 cells. It was expressed abundantly in liver and testis, weakly in ovary, and undetectably in other tested human tissues. In comparison with the expression ratio between POL λ and POL λ2 in normal liver tissues and hepato-cellular carcinoma (HCC) adjacent tissues, the ratio was aberrant in 80% of those 15 HCC specimens examined due to the up-regulated expression of POL λ. This abnormality might be involved in hepato-carcinogenesis. The recombinant POL λ2 with His-tag was expressed as a soluble active protein in E. coli BL21 (DE3)CONDON Plus and purified by Ni-NTA resin and then desalted by Superdex-75 chro-matography in an FPLC system. The analysis using isotope α-32P-dCTP incorporation in vitro showed that the purified recombinant POL λ2 exhibited DNA polymerase activity.

  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. Leptospira interrogans stably infects zebrafish embryos, altering phagocyte behavior and homing to specific tissues.

    Directory of Open Access Journals (Sweden)

    J Muse Davis

    Full Text Available Leptospirosis is an extremely widespread zoonotic infection with outcomes ranging from subclinical infection to fatal Weil's syndrome. Despite the global impact of the disease, key aspects of its pathogenesis remain unclear. To examine in detail the earliest steps in the host response to leptospires, we used fluorescently labelled Leptospira interrogans serovar Copenhageni to infect 30 hour post fertilization zebrafish embryos by either the caudal vein or hindbrain ventricle. These embryos have functional innate immunity but have not yet developed an adaptive immune system. Furthermore, they are optically transparent, allowing direct visualization of host-pathogen interactions from the moment of infection. We observed rapid uptake of leptospires by phagocytes, followed by persistent, intracellular infection over the first 48 hours. Phagocytosis of leptospires occasionally resulted in formation of large cellular vesicles consistent with apoptotic bodies. By 24 hours, clusters of infected phagocytes were accumulating lateral to the dorsal artery, presumably in early hematopoietic tissue. Our observations suggest that phagocytosis may be a key defense mechanism in the early stages of leptospirosis, and that phagocytic cells play roles in immunopathogenesis and likely in the dissemination of leptospires to specific target tissues.

  19. Therapeutic interventions of tissue specific autoimmune onset in systemic lupus erythematosus.

    Science.gov (United States)

    Dasgupta, Subhajit; Dasgupta, Shaoni

    2016-06-10

    Systemic lupus erythematosus (lupus) is a female predominant autoimmune disease. The auto reactive B cells and T helper cells together are known to develop self-reactive immune responses in different tissues like kidney, bone, cardiovascular and central nervous system. Progression of disease is associated with deposition of immune complex which initiates tissue damage. The therapy for lupus still includes corticosteroids to reduce allergic manifestations and inflammatory immune responses. Recent observations suggested that, mycophenolate mofetil and cyclophosphamide treatment in combination with corticosteroids have benefit in lupus therapy. The prospect of B cell depletion by CD20 targeted monoclonal antibody Rituximab has been demonstrated in lupus patients. The CD52 specific monoclonal antibody Alemtuzumab is another proposition for lupus therapy. The drug Belimumab inhibits B cell activation by altering BAFF/APRIL signal cascade. Recent discovery of the CD22 targeted Epratuzumab also shows therapeutic prospect. The researches on new generation drugs for autoimmune lupus include search for inhibitors of CD40-CD40Ligand interactions, CD86 activation, selective modulation of complement cascades. The choice of inhibitors of transcription factor NF-κBp65 and selective modulators for estrogen receptor alpha are proposed areas of lupus drug discovery research. Keeping a close eye on the mechanisms of disease onset, a comprehensive view is provided on recent therapy of systemic lupus erythematosus.

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Beachy, R N; Dai, Shunhong

    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.

  2. Inflammasome activation can mediate tissue-specific pathogenesis or protection in S. aureus infection

    Science.gov (United States)

    Melehani, Jason H.; Duncan, Joseph A.

    2016-01-01

    Staphylococcus aureus is a Gram-positive coccus that interacts with human hosts on a spectrum from quiet commensal to deadly pathogen. S. aureus is capable of infecting nearly every tissue in the body resulting in cellulitis, pneumonia, osteomyelitis, endocarditis, brain abscesses, bacteremia and more. S. aureus has a wide range factors that promote infection and each site of infection triggers a different response in the human host. In particular, the different patterns of inflammasome activation mediate tissue-specific pathogenesis in S. aureus infection. Although still a nascent field, understanding the unique host-pathogen interactions in each infection and the role of inflammasomes in mediating pathogenesis may lead to novel strategies for treating S. aureus infections. Reviews addressing S. aureus virulence and pathogenesis (Thammavongsa et al. 2015), as well as epidemiology and pathophysiology (Tong et al. 2015), have recently been published. This review will focus on S. aureus factors that activate inflammasomes and their impact on innate immune signaling and bacterial survival. PMID:27460814

  3. Tissue-specific defense and thermo-adaptive mechanisms of soybean seedlings under heat stress revealed by proteomic approach.

    Science.gov (United States)

    Ahsan, Nagib; Donnart, Tifenn; Nouri, Mohammad-Zaman; Komatsu, Setsuko

    2010-08-06

    A comparative proteomic approach was employed to explore tissue-specific protein expression patterns in soybean seedlings under heat stress. The changes in the protein expression profiles of soybean seedling leaves, stems, and roots were analyzed after exposure to high temperatures. A total of 54, 35, and 61 differentially expressed proteins were identified from heat-treated leaves, stems, and roots, respectively. Differentially expressed heat shock proteins (HSPs) and proteins involved in antioxidant defense were mostly up-regulated, whereas proteins associated with photosynthesis, secondary metabolism, and amino acid and protein biosynthesis were down-regulated in response to heat stress. A group of proteins, specifically low molecular weight HSPs and HSP70, were up-regulated and expressed in a similar manner in all tissues. Proteomic analysis indicated that the responses of HSP70, CPN-60 beta, and ChsHSP were tissue specific, and this observation was validated by immunoblot analysis. The heat-responsive sHSPs were not induced by other stresses such as cold and hydrogen peroxide. Taken together, these results suggest that to cope with heat stress soybean seedlings operate tissue-specific defenses and adaptive mechanisms, whereas a common defense mechanism associated with the induction of several HSPs was employed in all three tissues. In addition, tissue-specific proteins may play a crucial role in defending each type of tissues against thermal stress.

  4. Enhanced Soft Tissue Attachment and Fixation Using a Mechanically-Stimulated Cytoselective Tissue-Specific ECM Coating

    Science.gov (United States)

    2012-08-01

    use. This introduced bacteria into each new test and caused many bacterial infections. To fix this, the chamber design was altered and rebuilt...Tendons and Ligaments. In: Ma PX, Elisseeff J, editors. Scaffolding in Tissue Engineering. Boca Raton: CRC Press; 2005. p 385- 411. 2. Louie L

  5. Monitoring of interaction of low-frequency electric field with biological tissues upon optical clearing with optical coherence tomography

    Science.gov (United States)

    Peña, Adrián F.; Doronin, Alexander; Tuchin, Valery V.; Meglinski, Igor

    2014-08-01

    The influence of a low-frequency electric field applied to soft biological tissues ex vivo at normal conditions and upon the topical application of optical clearing agents has been studied by optical coherence tomography (OCT). The electro-kinetic response of tissues has been observed and quantitatively evaluated by the double correlation OCT approach, utilizing consistent application of an adaptive Wiener filtering and Fourier domain correlation algorithm. The results show that fluctuations, induced by the electric field within the biological tissues are exponentially increased in time. We demonstrate that in comparison to impedance measurements and the mapping of the temperature profile at the surface of the tissue samples, the double correlation OCT approach is much more sensitive to the changes associated with the tissues' electro-kinetic response. We also found that topical application of the optical clearing agent reduces the tissues' electro-kinetic response and is cooling the tissue, thus reducing the temperature induced by the electric current by a few degrees. We anticipate that dcOCT approach can find a new application in bioelectrical impedance analysis and monitoring of the electric properties of biological tissues, including the resistivity of high water content tissues and its variations.

  6. 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

    (dlc-1) in apoptosis are described. DLC-1 is a part of the motor complex dynein, which moves along microtubules inside the cell. DLC-1 has been demonstrated to have both dynein dependent and independent functions in mammalian cells, which is also apparent from the studies presented here. Specifically......, DLC-1 was found to play a cell-nonautonomous role in somatic tissue to negatively regulate the apoptotic response to ironizing radiation-induced apoptosis upstream of the KRIT1/CCM1 homolog KRI-1. Depletion of dlc-1 results in ectopic apoptosis in the germline, which is dependent on the BH3-only...... proteins EGL-1 and CED-13. These proteins are normally regulated by the p53 homolog CEP-1, however, DLC-1 regulates apoptosis independently of the function of CEP-1. Furthermore, the function of DLC-1 is independent of its association with dynein. The other apoptotic mechanism of DLC-1 regulates...

  7. The phenotype and tissue-specific nature of multipotent cells derived from human mature adipocytes.

    Science.gov (United States)

    Kou, Liang; Lu, Xiao-Wen; Wu, Min-Ke; Wang, Hang; Zhang, Yu-Jiao; Sato, Soh; Shen, Jie-Fei

    2014-02-21

    Dedifferentiated fat (DFAT) cells derived from mature adipocytes have been considered to be a homogeneous group of multipotent cells, which present to be an alternative source of adult stem cells for regenerative medicine. However, many aspects of the cellular nature about DFAT cells remained unclarified. This study aimed to elucidate the basic characteristics of DFAT cells underlying their functions and differentiation potentials. By modified ceiling culture technique, DFAT cells were converted from human mature adipocytes from the human buccal fat pads. Flow cytometry analysis revealed that those derived cells were a homogeneous population of CD13(+) CD29(+) CD105(+) CD44(+) CD31(-) CD34(-) CD309(-) α-SMA(-) cells. DFAT cells in this study demonstrated tissue-specific differentiation properties with strong adipogenic but much weaker osteogenic capacity. Neither did they express endothelial markers under angiogenic induction.

  8. Liver-targeting of interferon-alpha with tissue-specific domain antibodies.

    Directory of Open Access Journals (Sweden)

    Edward Coulstock

    Full Text Available Interferon alpha (IFNα is used for the treatment of hepatitis C infection and whilst efficacious it is associated with multiple adverse events including reduced leukocyte, erythrocyte, and platelet counts, fatigue, and depression. These events are most likely caused by systemic exposure to interferon. We therefore hypothesise that targeting the therapeutic directly to the intended site of action in the liver would reduce exposure in blood and peripheral tissue and hence improve the safety and tolerability of IFNα therapy. We genetically fused IFN to a domain antibody (dAb specific to a hepatocyte restricted antigen, asialoglycoprotein receptor (ASGPR. Our results show that the murine IFNα2 homolog (mIFNα2 fused to an ASGPR specific dAb, termed DOM26h-196-61, could be expressed in mammalian tissue culture systems and retains the desirable biophysical properties and activity of both fusion partners when measured in vitro. Furthermore a clear increase in in vivo targeting of the liver by mIFNα2-ASGPR dAb fusion protein, compared to that observed with either unfused mIFNα2 or mIFNα2 fused to an isotype control dAb VHD2 (which does not bind ASGPR was demonstrated using microSPECT imaging. We suggest that these findings may be applicable in the development of a liver-targeted human IFN molecule with improved safety and patient compliance in comparison to the current standard of care, which could ultimately be used as a treatment for human hepatitis virus infections.

  9. Tissue and time specific expression pattern of interferon regulated genes in the chicken.

    Science.gov (United States)

    Röll, Susanne; Härtle, Stefan; Lütteke, Thomas; Kaspers, Bernd; Härtle, Sonja

    2017-03-28

    Type I interferons are major players against viral infections and mediate their function by the induction of Interferon regulated genes (IRGs). Recently, it became obvious that these cytokines have a multitude of additional functions. Due to the unique features of the chickens' immune system, available data from mouse models are not easily transferable; hence we performed an extensive analysis of chicken IRGs. A broad database search for homologues to described mammalian IRGs (common IRGs, cIRGs) was combined with a transcriptome analysis of spleen and lung at different time points after application of IFNα. To apply physiological amounts of IFN, half-life of IFN in the chicken was determined. Interestingly, the calculated 36 min are considerably shorter than the ones obtained for human and mouse. Microarray analysis revealed many additional IRGs (newly identified IRGs; nIRGs) and network analysis for selected IRGs showed a broad interaction of nIRGs among each other and with cIRGs. We found that IRGs exhibit a highly tissue and time specific expression pattern as expression quality and quantity differed strongly between spleen and lung and over time. While in the spleen for many affected genes changes in RNA abundance peaked already after 3 h, an increasing or plateau-like regulation after 3, 6 and 9 h was observed in the lung. The induction or suppression of IRGs in chickens is both tissue and time specific and beside known antiviral mechanisms type I IFN induces many additional cellular functions. We confirmed many known IRGs and established a multitude of so far undescribed ones, thus providing a large database for future research on antiviral mechanisms and additional IFN functions in non-mammalian species.

  10. Microtubule-Actin Cross-Linking Factor 1: Domains, Interaction Partners, and Tissue-Specific Functions.

    Science.gov (United States)

    Goryunov, Dmitry; Liem, Ronald K H

    2016-01-01

    The cytoskeleton of most eukaryotic cells is composed of three principal filamentous components: actin filaments, microtubules (MTs), and intermediate filaments. It is a highly dynamic system that plays crucial roles in a wide range of cellular processes, including migration, adhesion, cytokinesis, morphogenesis, intracellular traffic and signaling, and structural flexibility. Among the large number of cytoskeleton-associated proteins characterized to date, microtubule-actin cross-linking factor 1 (MACF1) is arguably the most versatile integrator and modulator of cytoskeleton-related processes. MACF1 belongs to the plakin family of proteins, and within it, to the spectraplakin subfamily. These proteins are characterized by the ability to bridge MT and actin cytoskeletal networks in a dynamic fashion, which underlies their involvement in the regulation of cell migration, axonal extension, and vesicular traffic. Studying MACF1 functions has provided insights not only into the regulation of the cytoskeleton but also into molecular mechanisms of both normal cellular physiology and cellular pathology. Multiple MACF1 isoforms exist, composed of a large variety of alternatively spliced domains. Each of these domains mediates a specific set of interactions and functions. These functions are manifested in tissue and cell-specific phenotypes observed in conditional MACF1 knockout mice. The conditional models described to date reveal critical roles of MACF1 in mammalian skin, nervous system, heart muscle, and intestinal epithelia. Complete elimination of MACF1 is early embryonic lethal, indicating an essential role for MACF1 in early development. Further studies of MACF1 domains and their interactions will likely reveal multiple new roles of this protein in various tissues.

  11. 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

  12. Tissue-Specific Transcriptome Profiling of Plutella Xylostella Third Instar Larval Midgut

    Directory of Open Access Journals (Sweden)

    Wen Xie, Yanyuan Lei, Wei Fu, Zhongxia Yang, Xun Zhu, Zhaojiang Guo, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xuguo Zhou, Youjun Zhang

    2012-01-01

    Full Text Available The larval midgut of diamondback moth, Plutella xylostella, is a dynamic tissue that interfaces with a diverse array of physiological and toxicological processes, including nutrient digestion and allocation, xenobiotic detoxification, innate and adaptive immune response, and pathogen defense. Despite its enormous agricultural importance, the genomic resources for P. xylostella are surprisingly scarce. In this study, a Bt resistant P. xylostella strain was subjected to the in-depth transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes in the P. xylostella larval midgut.Using Illumina deep sequencing, we obtained roughly 40 million reads containing approximately 3.6 gigabases of sequence data. De novo assembly generated 63,312 ESTs with an average read length of 416bp, and approximately half of the P. xylostella sequences (45.4%, 28,768 showed similarity to the non-redundant database in GenBank with a cut-off E-value below 10-5. Among them, 11,092 unigenes were assigned to one or multiple GO terms and 16,732 unigenes were assigned to 226 specific pathways. In-depth analysis indentified genes putatively involved in insecticide resistance, nutrient digestion, and innate immune defense. Besides conventional detoxification enzymes and insecticide targets, novel genes, including 28 chymotrypsins and 53 ABC transporters, have been uncovered in the P. xylostella larval midgut transcriptome; which are potentially linked to the Bt toxicity and resistance. Furthermore, an unexpectedly high number of ESTs, including 46 serpins and 7 lysozymes, were predicted to be involved in the immune defense.As the first tissue-specific transcriptome analysis of P. xylostella, this study sheds light on the molecular understanding of insecticide resistance, especially Bt resistance in an agriculturally important insect pest, and lays the foundation for future functional genomics research. In

  13. In vivo noninvasive monitoring of dissolved oxygen concentration within an implanted tissue-engineered pancreatic construct.

    Science.gov (United States)

    Goh, Fernie; Sambanis, Athanassios

    2011-09-01

    The function of an implanted tissue-engineered pancreatic construct is influenced by many in vivo factors; however, assessing its function is based primarily on end physiologic effects. As oxygen significantly affects cell function, we established a dual perfluorocarbon method that utilizes (19)F nuclear magnetic resonance spectroscopy, with perfluorocarbons as oxygen concentration markers, to noninvasively monitor dissolved oxygen concentration (DO) in βTC-tet cell-containing alginate beads and at the implantation milieu. Beads were implanted in the peritoneal cavity of normal and streptozotocin-induced diabetic mice. Using this method, the feasibility of acquiring real-time in vivo DO measurements was demonstrated. Results showed that the mouse peritoneal environment is hypoxic and the DO is further reduced when βTC-tet cell constructs were implanted. The DO within cell-containing beads decreased considerably over time and could be correlated with the relative changes in the number of viable encapsulated cells. The reduction of construct DO due to the metabolic activity of the βTC-tet cells was also compatible with the implant therapeutic function, as observed in the reversal of hyperglycemia in diabetic mice. The importance of these findings in assessing implant functionality and host animal physiology is discussed. © Mary Ann Liebert, Inc.

  14. Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

    Directory of Open Access Journals (Sweden)

    Shamimuzzaman Md

    2012-07-01

    Full Text Available Abstract Background MicroRNAs (miRNAs regulate the expression of target genes by mediating gene silencing in both plants and animals. The miRNA targets have been extensively investigated in Arabidopsis and rice using computational prediction, experimental validation by overexpression in transgenic plants, and by degradome or PARE (parallel analysis of RNA ends sequencing. However, miRNA targets mostly remain unknown in soybean (Glycine max. More specifically miRNA mediated gene regulation at different seed developmental stages in soybean is largely unexplored. In order to dissect miRNA guided gene regulation in soybean developing seeds, we performed a transcriptome-wide experimental method using degradome sequencing to directly detect cleaved miRNA targets. Results In this study, degradome libraries were separately prepared from immature soybean cotyledons representing three stages of development and from seed coats of two stages. Sequencing and analysis of 10 to 40 million reads from each library resulted in identification of 183 different targets for 53 known soybean miRNAs. Among these, some were found only in the cotyledons representing cleavage by 25 miRNAs and others were found only in the seed coats reflecting cleavage by 12 miRNAs. A large number of targets for 16 miRNAs families were identified in both tissues irrespective of the stage. Interestingly, we identified more miRNA targets in the desiccating cotyledons of late seed maturation than in immature seed. We validated four different auxin response factor genes as targets for gma-miR160 via RNA ligase mediated 5’ rapid amplification of cDNA ends (RLM-5’RACE. Gene Ontology (GO analysis indicated the involvement of miRNA target genes in various cellular processes during seed development. Conclusions The miRNA targets in both the cotyledons and seed coats of several stages of soybean seed development have been elucidated by experimental evidence from comprehensive, high throughput

  15. In vivo monitoring of seeds and plant-tissue water absorption using optical coherence tomography and optical coherence microscopy

    Science.gov (United States)

    Sapozhnikova, Veronika V.; Kutis, Irina S.; Kutis, Sergey D.; Kuranov, Roman V.; Gelikonov, Grigory V.; Shabanov, Dmitry V.; Kamensky, Vladislav A.

    2004-07-01

    First experimental results on OCT imaging of internal structure of plant tissues and in situ OCT monitoring of plant tissue regeneration at different water supply are reported. Experiments for evaluating OCT capabilities were performed on Tradescantia. The investigation of seeds swelling was performed on wheat seeds (Triticum L.), barley seeds (Hordeum L.), long-fibred flax seeds (Linum usitatissimum L.) and cucumber seeds (Cucumis sativus L.). These OCT images correlate with standard microscopy data from the same tissue regions. Seeds were exposed to a low-intensity physical factor-the pulsed gradient magnetic field (GMF) with pulse duration 0.1 s and maximum amplitude 5 mT (4 successive pulses during 0.4 s). OCT and OCM enable effective monitoring of fast reactions in plants and seeds at different water supply.

  16. Generation and characterization of quinolone-specific DNA aptamers suitable for water monitoring.

    Science.gov (United States)

    Reinemann, C; Freiin von Fritsch, U; Rudolph, S; Strehlitz, B

    2016-03-15

    Quinolones are antibiotics that are accredited in human and veterinary medicine but are regularly used in high quantities also in industrial livestock farming. Since these compounds are often only incompletely metabolized, significant amounts contaminate the aquatic environment and negatively impact on a variety of different ecosystems. Although there is increasing awareness of problems caused by pharmaceutical pollution, available methods for the detection and elimination of numerous pharmaceutical residues are currently inefficient or expensive. While this also applies to antibiotics that may lead to multi-drug resistance in pathogenic bacteria, aptamer-based technologies potentially offer alternative approaches for sensitive and efficient monitoring of pharmaceutical micropollutants. Using the Capture-SELEX procedure, we here describe the selection of an aptamer pool with enhanced binding qualities for fluoroquinolones, a widely used group of antibiotics in both human and veterinary medicine. The selected aptamers were shown to detect various quinolones with high specificity, while specific binding activities to structurally unrelated drugs were not detectable. The quinolone-specific aptamers bound to ofloxacin, one of the most frequently prescribed fluoroquinolone, with high affinity (KD=0.1-56.9 nM). The functionality of quinolone-specific aptamers in real water samples was demonstrated in local tap water and in effluents of sewage plants. Together, our data suggest that these aptamers may be applicable as molecular receptors in biosensors or as catcher molecules in filter systems for improved monitoring and treatment of polluted water.

  17. Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes.

    Science.gov (United States)

    Nuss, Aaron M; Beckstette, Michael; Pimenova, Maria; Schmühl, Carina; Opitz, Wiebke; Pisano, Fabio; Heroven, Ann Kathrin; Dersch, Petra

    2017-01-31

    Pathogenic bacteria need to rapidly adjust their virulence and fitness program to prevent eradication by the host. So far, underlying adaptation processes that drive pathogenesis have mostly been studied in vitro, neglecting the true complexity of host-induced stimuli acting on the invading pathogen. In this study, we developed an unbiased experimental approach that allows simultaneous monitoring of genome-wide infection-linked transcriptional alterations of the host and colonizing extracellular pathogens. Using this tool for Yersinia pseudotuberculosis-infected lymphatic tissues, we revealed numerous alterations of host transcripts associated with inflammatory and acute-phase responses, coagulative activities, and transition metal ion sequestration, highlighting that the immune response is dominated by infiltrating neutrophils and elicits a mixed TH17/TH1 response. In consequence, the pathogen's response is mainly directed to prevent phagocytic attacks. Yersinia up-regulates the gene and expression dose of the antiphagocytic type III secretion system (T3SS) and induces functions counteracting neutrophil-induced ion deprivation, radical stress, and nutritional restraints. Several conserved bacterial riboregulators were identified that impacted this response. The strongest influence on virulence was found for the loss of the carbon storage regulator (Csr) system, which is shown to be essential for the up-regulation of the T3SS on host cell contact. In summary, our established approach provides a powerful tool for the discovery of infection-specific stimuli, induced host and pathogen responses, and underlying regulatory processes.

  18. Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules

    Science.gov (United States)

    Nassiri, Isar; Lombardo, Rosario; Lauria, Mario; Morine, Melissa J.; Moyseos, Petros; Varma, Vijayalakshmi; Nolen, Greg T.; Knox, Bridgett; Sloper, Daniel; Kaput, Jim; Priami, Corrado

    2016-07-01

    The investigation of the complex processes involved in cellular differentiation must be based on unbiased, high throughput data processing methods to identify relevant biological pathways. A number of bioinformatics tools are available that can generate lists of pathways ranked by statistical significance (i.e. by p-value), while ideally it would be desirable to functionally score the pathways relative to each other or to other interacting parts of the system or process. We describe a new computational method (Network Activity Score Finder - NASFinder) to identify tissue-specific, omics-determined sub-networks and the connections with their upstream regulator receptors to obtain a systems view of the differentiation of human adipocytes. Adipogenesis of human SBGS pre-adipocyte cells in vitro was monitored with a transcriptomic data set comprising six time points (0, 6, 48, 96, 192, 384 hours). To elucidate the mechanisms of adipogenesis, NASFinder was used to perform time-point analysis by comparing each time point against the control (0 h) and time-lapse analysis by comparing each time point with the previous one. NASFinder identified the coordinated activity of seemingly unrelated processes between each comparison, providing the first systems view of adipogenesis in culture. NASFinder has been implemented into a web-based, freely available resource associated with novel, easy to read visualization of omics data sets and network modules.

  19. The development of a computerized crop-specific drought monitoring system

    Energy Technology Data Exchange (ETDEWEB)

    Lourens, U.W.; Jager, J.M. de [Univ. of the Orange Free State, Bloemfontein (South Africa). Dept. of Agrometeorology

    1995-12-31

    A near real-time crop-specific drought monitoring system (DMS) that combines crop modeling and a Geographical Information System (GIS) has been developed in South Africa. The system is intended for use in decision support by resource managers concerned with drought aid. The condition of maize, wheat and rangeland can presently be monitored in the DMS. The system is a spatially distributed system with individual simulations being run for areas covering approximately 14 km{sup 2}. Values of the weather elements used to drive the models are obtained through interpolation of ground observations and processing of weather satellite imagery. Monitoring is undertaken throughout a production season, with updates provided on a fortnightly basis. Predictions of expected yield at the end of the season are made by using observed data up to the current date and completing the season with surrogate historical weather data. Appropriate surrogate scenarios are chosen based on the current season. After each monitoring run, simulated yield predictions for the season are compared with expected long-term yields of the crop produced in a particular region. A drought index class is assigned based on this comparison. Maps and tabulated information are produced in the GIS showing the spatial distribution of drought stricken areas and the intensity of drought in these areas. The maps and tables are distributed to government institutions and agricultural cooperatives.

  20. Comprehensive qualification and quantification of triacylglycerols with specific fatty acid chain composition in horse adipose tissue, human plasma and liver tissue.

    Science.gov (United States)

    Guan, Ming; Dai, Dongsheng; Li, Lin; Wei, Jinchao; Yang, Hui; Li, Shilei; Zhang, Yangyang; Lin, Yu; Xiong, Shaoxiang; Zhao, Zhenwen

    2017-09-01

    High levels of triacylglycerols (TGs) have been linked to cardiovascular disease and liver diseases. Comprehensively analyzing TGs is helpful to understand the TGs functions in these diseases. However, due to the existence of a large number of isomers TGs and the lack of commercial standards, precise analysis of individual triacylglycerol (TG) with specific fatty acid chain composition is full of challenge. In this work, ultra-performance liquid chromatography (UPLC) coupled with electrospray ionization (ESI) mass spectrometry (MS) were employed for comprehensive qualification and quantification of TGs with specific fatty acid chain composition in horse adipose tissue, human plasma and liver tissues including hepatocellular carcinoma (HCC) and para-carcinoma tissues. Multiple MS detection modes from QTRAP MS and FT-ICR MS were utilized, and hundreds of TG species (including many oxidized TG species) with their specific fatty acid chain compositions have been qualified and quantified. The isomer TGs interference, the isobaric interference, and oxidized TG species interference were firstly indicated. Several isomer TGs, for example, 18:1/20:1/18:2 TG and 20:3/18:1/18:0 TG, which were all 56:4 TG, demonstrated different trends in HCC tissue compared with para-carcinoma tissue, which showed the importance of analysis of TG with specific fatty acid chain composition. In addition, 10 TGs with the degree of unsaturation beyond three were significantly decreased, while 16:0/17:0/18:0 TG, no double bond, was significantly increased in the HCC tissue, which firstly revealed aberrant specific TG metabolism in HCC. This is a systematic report about comprehensive analysis of TGs by UPLC-ESI-MS, which is of significance for accurate analysis of these lipids. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Aldehyde dehydrogenase 3B1 (ALDH3B1): immunohistochemical tissue distribution and cellular-specific localization in normal and cancerous human tissues.

    Science.gov (United States)

    Marchitti, Satori A; Orlicky, David J; Brocker, Chad; Vasiliou, Vasilis

    2010-09-01

    Aldehyde dehydrogenase (ALDH) enzymes are critical in the detoxification of endogenous and exogenous aldehydes. Our previous findings indicate that the ALDH3B1 enzyme is expressed in several mouse tissues and is catalytically active toward aldehydes derived from lipid peroxidation, suggesting a potential role against oxidative stress. The aim of this study was to elucidate by immunohistochemistry the tissue, cellular, and subcellular distribution of ALDH3B1 in normal human tissues and in tumors of human lung, colon, breast, and ovary. Our results indicate that ALDH3B1 is expressed in a tissue-specific manner and in a limited number of cell types, including hepatocytes, proximal convoluted tubule cells, cerebellar astrocytes, bronchiole ciliated cells, testis efferent ductule ciliated cells, and histiocytes. ALDH3B1 expression was upregulated in a high percentage of human tumors (lung > breast = ovarian > colon). Increased ALDH3B1 expression in tumor cells may confer a growth advantage or be the result of an induction mechanism mediated by increased oxidative stress. Subcellular localization of ALDH3B1 was predominantly cytosolic in tissues, with the exception of normal human lung and testis, in which localization appeared membrane-bound or membrane-associated. The specificity of ALDH3B1 distribution may prove to be directly related to the functional role of this enzyme in human tissues.

  2. 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.

  3. A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish.

    Science.gov (United States)

    Ablain, Julien; Durand, Ellen M; Yang, Song; Zhou, Yi; Zon, Leonard I

    2015-03-23

    CRISPR/Cas9 technology of genome editing has greatly facilitated the targeted inactivation of genes in vitro and in vivo in a wide range of organisms. In zebrafish, it allows the rapid generation of knockout lines by simply injecting a guide RNA (gRNA) and Cas9 mRNA into one-cell stage embryos. Here, we report a simple and scalable CRISPR-based vector system for tissue-specific gene inactivation in zebrafish. As proof of principle, we used our vector with the gata1 promoter driving Cas9 expression to silence the urod gene, implicated in heme biosynthesis, specifically in the erythrocytic lineage. Urod targeting yielded red fluorescent erythrocytes in zebrafish embryos, recapitulating the phenotype observed in the yquem mutant. While F0 embryos displayed mosaic gene disruption, the phenotype appeared very penetrant in stable F1 fish. This vector system constitutes a unique tool to spatially control gene knockout and greatly broadens the scope of loss-of-function studies in zebrafish.

  4. Genetic regulation of tissue-specific expression of amylase structural genes in Drosophila melanogaster.

    Science.gov (United States)

    Abraham, I; Doane, W W

    1978-01-01

    Laboratory strains of Drosophila melanogaster were screened for spatial variations in adult midgut alpha-amylase (1,4-alpha-D-glucan glucanohydrolase, EC 3.2.1.1) expression. No strain-specific differences were found anteriorly, but three patterns of activity were discerned in the posterior midgut: A, activity throughout most of the region; B, activity in the anterior part of the region; and C, little or no activity. Alleles of a control gene, map, are responsible for this tissue-specific regulation of activity; e.g., mapA homozygotes produce the A pattern and mapC homozygotes the C pattern. The map locus was placed at 2--80 +/- on the genetic map of chromosome 2R, about two crossover units distal to the Amy structural gene region for alpha-amylase. Electrophoretic studies showed that mapA is trans acting in mapA/mapC flies, allowing expression of amylase isozymes coded for by genes on the opposite chromosome. The map gene behaves as a temporal gene that is clearly separable from the tightly linked, duplicated Amy structural genes. Images PMID:100784

  5. Tissue-Specific Apocarotenoid Glycosylation Contributes to Carotenoid Homeostasis in Arabidopsis Leaves.

    Science.gov (United States)

    Lätari, Kira; Wüst, Florian; Hübner, Michaela; Schaub, Patrick; Beisel, Kim Gabriele; Matsubara, Shizue; Beyer, Peter; Welsch, Ralf

    2015-08-01

    Attaining defined steady-state carotenoid levels requires balancing of the rates governing their synthesis and metabolism. Phytoene formation mediated by phytoene synthase (PSY) is rate limiting in the biosynthesis of carotenoids, whereas carotenoid catabolism involves a multitude of nonenzymatic and enzymatic processes. We investigated carotenoid and apocarotenoid formation in Arabidopsis (Arabidopsis thaliana) in response to enhanced pathway flux upon PSY overexpression. This resulted in a dramatic accumulation of mainly β-carotene in roots and nongreen calli, whereas carotenoids remained unchanged in leaves. We show that, in chloroplasts, surplus PSY was partially soluble, localized in the stroma and, therefore, inactive, whereas the membrane-bound portion mediated a doubling of phytoene synthesis rates. Increased pathway flux was not compensated by enhanced generation of long-chain apocarotenals but resulted in higher levels of C13 apocarotenoid glycosides (AGs). Using mutant lines deficient in carotenoid cleavage dioxygenases (CCDs), we identified CCD4 as being mainly responsible for the majority of AGs formed. Moreover, changed AG patterns in the carotene hydroxylase mutants lutein deficient1 (lut1) and lut5 exhibiting altered leaf carotenoids allowed us to define specific xanthophyll species as precursors for the apocarotenoid aglycons detected. In contrast to leaves, carotenoid hyperaccumulating roots contained higher levels of β-carotene-derived apocarotenals, whereas AGs were absent. These contrasting responses are associated with tissue-specific capacities to synthesize xanthophylls, which thus determine the modes of carotenoid accumulation and apocarotenoid formation. © 2015 American Society of Plant Biologists. All Rights Reserved.

  6. The SSC cycle: a PDCA approach to address site-specific characteristics in a continuous shallow water quality monitoring project.

    Science.gov (United States)

    Miles, Eduardo J

    2008-05-01

    In any water quality-monitoring project there are several critical success factors that must be adequately addressed in order to ensure the implementation and realization of the monitoring objectives. Site selection is one of these critical success factors. The monitoring sites must be selected to comply with the monitoring and data quality objectives. In the real world, ideal monitoring setting conditions are difficult to achieve, and compromises must be made in order to locate the monitoring stations that best represent the environment to be monitored. Site-specific characteristics are all the environmental, logistical and management factors particular to the monitoring site, that could influence the fulfilment of the monitoring and data quality objectives. Therefore, during the site selection process, it is essential to properly consider and evaluate these site-specific characteristics. The SSC cycle was developed with this goal in mind, to assist the monitoring team to systematically address site-specific characteristics. The cycle is a methodology to organize the site-specific characteristics in different categories, and to ensure a comprehensive overview of these characteristics throughout the project life cycle.

  7. Seasonal Liza aurata tissue-specific DNA integrity in a multi-contaminated coastal lagoon (Ria de Aveiro, Portugal).

    Science.gov (United States)

    Oliveira, M; Maria, V L; Ahmad, I; Pacheco, M; Santos, M A

    2010-10-01

    In this study, the DNA integrity of golden grey mullet (Liza aurata) collected in differently contaminated sites of a coastal lagoon, Ria de Aveiro (Portugal), was assessed, over the period of 1 year, using the DNA alkaline unwinding assay, in four different tissues (gill, kidney, liver and blood) and compared to a reference site. The four tissues displayed different DNA integrity basal levels, clearly affected by seasonal factors. Gill and kidney were, respectively, the most and least sensitive tissues. All sites demonstrated the capacity to interfere with DNA integrity. The sites displaying the highest and lowest DNA damage capability were, respectively, Barra (subject to naval traffic) and Vagos (contaminated with polycyclic aromatic hydrocarbons). In terms of seasonal variability, autumn seems to be the more critical season (more DNA damage) unlike summer when no DNA damage was found in any tissue. Data recommend the continued monitoring of this aquatic system.

  8. Tissue specific variation in biochemical compositions of Acorus calamus (L. leaves and rhizomes

    Directory of Open Access Journals (Sweden)

    Deepak Ganjewala

    2011-12-01

    Full Text Available Sweet Flag (Acorus calamus L. leaf and rhizome tissues were analyzed for biochemical compositions notably of carbohydrates and lipids. The glycolipid content measured in rhizome tissue was 62.3mg%/FW almost double the glycolipid content (28.8 mg%/FW in leaf tissues, whereas the sterol content in the leaf tissue (47.9 mg%/FW was three times of the sterol content in rhizome tissues (15.5 mg%/FW. Carbohydrates content such as total sugar, reducing sugar, sucrose and fructose measured in leaf and rhizome tissues were more or less similar, with slightly higher values of total sugar (18.2 mg%/FW in the leaf tissues. The study thus revealed variation in biochemical compositions in two different tissues leaf and rhizome of A. calamus.

  9. Tissue-specific alterations of PRL-1 and PRL-2 expression in cancer.

    Science.gov (United States)

    Dumaual, Carmen M; Sandusky, George E; Soo, Han Weng; Werner, Sean R; Crowell, Pamela L; Randall, Stephen K

    2012-01-01

    The PRL-1 and PRL-2 phosphatases have been implicated as oncogenic, however the involvement of these molecules in human neoplasms is not well understood. To increase understanding of the role PRL-1 and PRL-2 play in the neoplastic process, in situ hybridization was used to examine PRL-1 and PRL-2 mRNA expression in 285 normal, benign, and malignant human tissues of diverse origin. Immunohistochemical analysis was performed on a subset of these. PRL-1 and PRL-2 mRNA expression was also assessed in a small set of samples from a variety of diseases other than cancer. Where possible, associations with clinicopathological characteristics were evaluated. Alterations in PRL-1 or -2 expression were a frequent event, but the nature of those alterations was highly tumor type specific. PRL-1 was significantly overexpressed in 100% of hepatocellular and gastric carcinomas, but significantly under-expressed in 100% of ovarian, 80% of breast, and 75% of lung tumors. PRL-2 expression was significantly increased in 100% of hepatocellular carcinomas, yet significantly downregulated in 54% of kidney carcinomas. PRL-1 expression was correlated to patient gender in the bladder and to patient age in the brain and skeletal muscle. PRL-1 expression was also associated with tumor grade in the prostate, ovary, and uterus. These results suggest a pleiotropic role for PRL-1 and PRL-2 in the neoplastic process. These molecules may associate with tumor progression and serve as clinical markers of tumor aggressiveness in some tissues, but be involved in inhibition of tumor formation or growth in others.

  10. Tissue-Specific Distribution of Ginsenosides in Different Aged Ginseng and Antioxidant Activity of Ginseng Leaf

    Directory of Open Access Journals (Sweden)

    Ying-Chun Zhang

    2014-10-01

    Full Text Available The aim of this study was to systematically evaluate the effect of the cultivation year on the quality of different ginseng tissues. Qualitative and quantitative analyses of ginsenosides were conducted using a UPLC-UV-MS method. Eight main ginsenosides in three tissues (leaf, rhizome and main root and four parts (periderm, phloem, cambium and xylem of ginseng aged from 1 to 13 years were determined using a UPLC-PDA method. Additionally, the antioxidant capacities of ginseng leaves were analyzed by the DPPH, ABTS and HRSA methods. It was found that the contents of ginsenosides increased with cultivation years, causing a sequential content change of ginsenosides in an organ-specific manner: leaf > rhizome > main root. The ratio between protopanaxatriol (PPT, Rg1, Re and RF and protopanaxadiol (PPD, Rb1, Rb2, RC and Rd in the main root remained stable (about 1.0, while it increased in leaf from 1.37 to 3.14 and decreased in the rhizome from 0.99 to 0.72. The amount of ginsenosides accumulated in the periderm was 45.48 mg/g, which was more than twice as high compared with the other three parts. Furthermore, the antioxidant activities of ginseng leaves were measured as Trolox equivalents, showing that antioxidant activity increased along with time of cultivation. The results show that the best harvest time for shizhu ginseng is the fifth year of cultivation, and the root and rhizome could be used together within seven planting years for their similar PPT/PPD level. Besides, the quality of the ginseng products would be enhanced with the periderm. The ginseng leaf is rich in ginsenosides and has potential application for its antioxidant capacity.

  11. 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.

    Science.gov (United States)

    Morrison, Philippa K; Bing, Chen; Harris, Patricia A; Maltin, Charlotte A; Grove-White, Dai; Argo, Caroline McG

    2014-01-01

    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, adipose tissue

  12. Adipose tissue-specific dysregulation of angiotensinogen by oxidative stress in obesity

    OpenAIRE

    2010-01-01

    Adipose tissue expresses all components of the renin-angiotensin system including angiotensinogen (AGT). Recent studies have highlighted a potential role of AGT in adipose tissue function and homeostasis. However, some controversies surround the regulatory mechanisms of AGT in obese adipose tissue. In this context, we here demonstrated that the AGT messenger RNA (mRNA) level in human subcutaneous adipose tissue was significantly reduced in obese subjects as compared with nonobese subjects. Ad...

  13. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.

    Science.gov (United States)

    Argyridou, E; Huylmans, A K; Königer, A; Parsch, J

    2017-07-01

    As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.

  14. Monitoring cellular behaviour using Raman spectroscopy for tissue engineering and regenerative medicine applications.

    Science.gov (United States)

    Boyd, A R; Burke, G A; Meenan, B J

    2010-08-01

    Raman spectroscopy has been used to determine the chemical composition of materials for over 70 years. Recent spectacular advances in laser and CCD camera technology creating instruments with higher sensitivity and lower cost have initiated a strong resurgence in the technique, ranging from fundamental research to process control methodology. One such area of increased potential is in tissue engineering and regenerative medicine (TERM), where autologous cell culture, stem cell biology and growth of human cells on biomaterial scaffolds are of high importance. Traditional techniques for the in vitro analysis of biochemical cell processes involves cell techniques such as fixation, lysis or the use of radioactive or chemical labels which are time consuming and can involve the perpetuation of artefacts. Several studies have already shown the potential of Raman spectroscopy to provide useful information on key biochemical markers within cells, however, many of these studies have utilised micro- or confocal Raman to do this, which are not suited to the rapid and non-invasive monitoring of cells. For this study a versatile fit-for-purpose Raman spectrometer was used, employing a macro-sampling optical platform (laser spot size 100 mum at focus on the sample) to discriminate between different TERM relevant cell types and viable and non-viable cells. The results clearly show that the technique is capable of obtaining Raman spectra from live cells in a non-destructive, rapid and non-invasive manner, however, in these experiments it was not possible to discriminate between different cell lines. Despite this, notable differences were observed in the spectra obtained from viable and non-viable cells, showing significant changes in the spectral profiles of protein, DNA/RNA and lipid cell constituents after cell death. It is evident that the method employed here shows significant potential for further utilisation in TERM, providing data directly from live cells that fits within a

  15. Modulation sensing of fluorophores in tissue: a new approach to drug compliance monitoring

    Science.gov (United States)

    Abugo, Omoefe O.; Gryczynski, Zygmunt; Lakowicz, Joseph R.

    1999-10-01

    We describe a method to detect the presence of fluorophores in scattering media, including intralipid suspensions and chicken muscle covered with skin. The fluorophores were rhodamine 800 (Rb800) and indocyanine green (IcG), both of which can be excited at long wavelengths where there is minimal absorption by tissues. These fluorophores were dissolved in intralipid or in chicken muscle under skin. A method to approximate the fluorophore concentration in such samples was developed using a long lifetime reference fluorophores in a polymer film placed immediately on the illuminated surface of the sample. Because of the long lifetime of the reference film, the modulation of its emission at low frequencies near 2 MHz is near zero. Since the lifetime of Rh800 and IcG are below 2 ns the modulation of the combined emission is a measure of the intensity of the fluorophore (Rh800 or IcG) relative to the long lifetime reference. Using this method we were able to measure the concentration-dependent intensities of Rh800 and IcG in an intralipid suspension. Additionally, micromolar concentrations of these probes could be detected in chicken muscles, even when the muscle was covered with a layer of chicken skin. The presence of an India ink absorber in the intralipid had only a moderate effect on the modulation values. We suggest the use of this transdermal detection of long-wavelength fluorophores as a noninvasive method to monitor patient compliance when taking medicines used for treatment of chronic diseases such as AIDS or tuberculosis.

  16. Novel Insights into the Role of Caveolin-2 in Cell- and Tissue-Specific Signaling and Function

    Directory of Open Access Journals (Sweden)

    Grzegorz Sowa

    2011-01-01

    Full Text Available Caveolin-2 is one of the major protein components of cholesterol- and glycosphingolipid-rich flask-shaped invaginations of plasma membrane caveolae. A new body of evidence suggests that caveolin-2 plays an important, and often more direct, role than caveolin-1 in regulating signaling and function in a cell- and tissue type-specific manner. The purpose of this paper is to primarily focus on discussing how these recent discoveries may help better understand the specific contribution of caveolin-2 to lipid raft- and caveolae-regulated cell/tissue-specific signaling and functions.

  17. 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

  18. MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers.

    Science.gov (United States)

    Andzelm, Milena M; Cherry, Timothy J; Harmin, David A; Boeke, Annabel C; Lee, Charlotte; Hemberg, Martin; Pawlyk, Basil; Malik, Athar N; Flavell, Steven W; Sandberg, Michael A; Raviola, Elio; Greenberg, Michael E

    2015-04-08

    Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors (TFs) play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood. Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites and redirects it to retina-specific enhancers that lack the consensus MEF2-binding sequence. Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs and through selective activation of these enhancers to regulate tissue-specific genes.

  19. Field Assessment and Specification Review for Roller-Integrated Compaction Monitoring Technologies

    Directory of Open Access Journals (Sweden)

    David J. White

    2011-01-01

    Full Text Available Roller-integrated compaction monitoring (RICM technologies provide virtually 100-percent coverage of compacted areas with real-time display of the compaction measurement values. Although a few countries have developed quality control (QC and quality assurance (QA specifications, broader implementation of these technologies into earthwork construction operations still requires a thorough understanding of relationships between RICM values and traditional in situ point test measurements. The purpose of this paper is to provide: (a an overview of two technologies, namely, compaction meter value (CMV and machine drive power (MDP; (b a comprehensive review of field assessment studies, (c an overview of factors influencing statistical correlations, (d modeling for visualization and characterization of spatial nonuniformity; and (e a brief review of the current specifications.

  20. Infrared fiber optic temperature monitoring of biological tissues heated in a microwave oven

    Science.gov (United States)

    Belotserkovsky, Edward; Ashkenasy, Y.; Shenfeld, Ofer; Drizlikh, S.; Zur, Albert; Katzir, Abraham

    1993-05-01

    The heating of tissue by microwave radiation has attained a place of importance in various medical fields such as the treatment of malignancies, urinary retention and hypothermia. Accurate temperature measurements in these treated tissues is important for treatment planning and for the control of the heating process. It is also important to be able to measure spacial temperature distribution in the tissues because they are heated in a non uniform way by the microwave radiation. Fiber optic radiometry makes possible accurate temperature measurement in the presence of microwave radiation and does not require contact with the tissue. Using a IR silver halide fiber optic radiometric temperature sensor we obtained accurate temperature measurements of tissues heated by microwave, enabling us to control the heating process in all regions of the tissue. We also performed temperature mapping of the heated tissues and demonstrated the non-uniform temperature distributions in them.

  1. Serum biomarkers reflecting specific tumor tissue remodeling processes are valuable diagnostic tools for lung cancer.

    Science.gov (United States)

    Willumsen, Nicholas; Bager, Cecilie L; Leeming, Diana J; Smith, Victoria; Christiansen, Claus; Karsdal, Morten A; Dornan, David; Bay-Jensen, Anne-Christine

    2014-10-01

    Extracellular matrix (ECM) proteins, such as collagen type I and elastin, and intermediate filament (IMF) proteins, such as vimentin are modified and dysregulated as part of the malignant changes leading to disruption of tissue homeostasis. Noninvasive biomarkers that reflect such changes may have a great potential for cancer. Levels of matrix metalloproteinase (MMP) generated fragments of type I collagen (C1M), of elastin (ELM), and of citrullinated vimentin (VICM) were measured in serum from patients with lung cancer (n = 40), gastrointestinal cancer (n = 25), prostate cancer (n = 14), malignant melanoma (n = 7), chronic obstructive pulmonary disease (COPD) (n = 13), and idiopathic pulmonary fibrosis (IPF) (n = 10), as well as in age-matched controls (n = 33). The area under the receiver operating characteristics (AUROC) was calculated and a diagnostic decision tree generated from specific cutoff values. C1M and VICM were significantly elevated in lung cancer patients as compared with healthy controls (AUROC = 0.98, P < 0.0001) and other cancers (AUROC = 0.83 P < 0.0001). A trend was detected when comparing lung cancer with COPD+IPF. No difference could be seen for ELM. Interestingly, C1M and VICM were able to identify patients with lung cancer with a positive predictive value of 0.9 and an odds ratio of 40 (95% CI = 8.7-186, P < 0.0001). Biomarkers specifically reflecting degradation of collagen type I and citrullinated vimentin are applicable for lung cancer patients. Our data indicate that biomarkers reflecting ECM and IMF protein dysregulation are highly applicable in the lung cancer setting. We speculate that these markers may aid in diagnosing and characterizing patients with lung cancer.

  2. A real time dose monitoring and dose reconstruction tool for patient specific VMAT QA and delivery

    Energy Technology Data Exchange (ETDEWEB)

    Tyagi, Neelam; Yang Kai; Gersten, David; Yan Di [Department of Radiation Oncology, William Beaumont Hospital, 3601 West Thirteen Mile Road, Royal Oak, Michigan 48073 (United States)

    2012-12-15

    Purpose: To develop a real time dose monitoring and dose reconstruction tool to identify and quantify sources of errors during patient specific volumetric modulated arc therapy (VMAT) delivery and quality assurance. Methods: The authors develop a VMAT delivery monitor tool called linac data monitor that connects to the linac in clinical mode and records, displays, and compares real time machine parameters with the planned parameters. A new measure, called integral error, keeps a running total of leaf overshoot and undershoot errors in each leaf pair, multiplied by leaf width, and the amount of time during which the error exists in monitor unit delivery. Another tool reconstructs Pinnacle{sup 3} Trade-Mark-Sign format delivered plan based on the saved machine logfile and recalculates actual delivered dose in patient anatomy. Delivery characteristics of various standard fractionation and stereotactic body radiation therapy (SBRT) VMAT plans delivered on Elekta Axesse and Synergy linacs were quantified. Results: The MLC and gantry errors for all the treatment sites were 0.00 {+-} 0.59 mm and 0.05 {+-} 0.31 Degree-Sign , indicating a good MLC gain calibration. Standard fractionation plans had a larger gantry error than SBRT plans due to frequent dose rate changes. On average, the MLC errors were negligible but larger errors of up to 6 mm and 2.5 Degree-Sign were seen when dose rate varied frequently. Large gantry errors occurred during the acceleration and deceleration process, and correlated well with MLC errors (r= 0.858, p= 0.0004). PTV mean, minimum, and maximum dose discrepancies were 0.87 {+-} 0.21%, 0.99 {+-} 0.59%, and 1.18 {+-} 0.52%, respectively. The organs at risk (OAR) doses were within 2.5%, except some OARs that showed up to 5.6% discrepancy in maximum dose. Real time displayed normalized total positive integral error (normalized to the total monitor units) correlated linearly with MLC (r= 0.9279, p < 0.001) and gantry errors (r= 0.742, p= 0.005). There

  3. 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.

  4. 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.

  5. Induction of tissue- and stressor-specific kinomic responses in chickens exposed to hot and cold stresses.

    Science.gov (United States)

    Napper, Scott; Dadgar, Samira; Arsenault, Ryan J; Trost, Brett; Scruten, Erin; Kusalik, Anthony; Shand, Phyllis

    2015-06-01

    Defining cellular responses at the level of global cellular kinase (kinome) activity is a powerful approach to deciphering complex biology and identifying biomarkers. Here we report on the development of a chicken-specific peptide array and its application to characterizing kinome responses within the breast (pectoralis major) and thigh (iliotibialis) muscles of poultry subject to temperature stress to mimic conditions experienced by birds during commercial transport. Breast and thigh muscles exhibited unique kinome profiles, highlighting the distinct nature of these tissues. Against these distinct backgrounds, tissue- and temperature-specific kinome responses were observed. In breast, both cold and hot stresses activated calcium-dependent metabolic adaptations. Also within breast, but specific to cold stress, was the activation of ErbB signaling as well as dynamic patterns of phosphorylation of AMPK, a key regulatory enzyme of metabolism. In thigh, cold stress induced responses suggestive of the occurrence of tissue damage, including activation of innate immune signaling pathways and tissue repair pathways (TGF-β). In contrast, heat stress in thigh activated pathways associated with protein and fat metabolism through adipocytokine and mammalian target of rapamycin (mTOR) signaling. Defining the responses of these tissues to these stresses through conventional markers of pH, glycolytic potential, and meat quality offered a similar conclusion of the tissue- and stressor-specific responses, validating the kinome results. Collectively, the results of this study highlight the unique cellular responses of breast and thigh tissues to heat and cold stresses and may offer insight into the unique susceptibilities, as well as functional consequences, of these tissues to thermal stress. © 2015 Poultry Science Association Inc.

  6. Tissue specific haemoglobin gene expression suggests adaptation to local marine conditions in North Sea flounder (Platichthys flesus L.)

    DEFF Research Database (Denmark)

    Larsen, P.F.; Eg Nielsen, Einar; Hansen, M.M.

    2013-01-01

    of the haemoglobin alpha and beta subunit genes was studied in reciprocally transplanted European flounder Platichthys flesus from the highly saline North Sea and the brackish Baltic Sea. Clear differences in expression patterns of haemoglobin alpha and beta subunit genes were found among different types of tissue....... Finally, for kidney tissue a stress response was observed in one population, with gene up-regulation when North Sea flounders were transplanted to low salinity. This study underlines the importance of tissue specific gene expression and the significance of gene expression for evolution of local adaptation...... in high gene flow marine fishes. © 2013 The Genetics Society of Korea...

  7. Improved specificity for detection of Mycobacterium bovis in fresh tissues using IS6110 real-time PCR

    Directory of Open Access Journals (Sweden)

    Palmer Mitchell V

    2011-08-01

    Full Text Available Abstract Background Culture of M. bovis from diagnostic specimens is the gold standard for bovine tuberculosis diagnostics in the USA. Detection of M. bovis by PCR in tissue homogenates may provide a simple rapid method to complement bacterial culture. A significant impediment to PCR based assays on tissue homogenates is specificity since mycobacteria other than M. bovis may be associated with the tissues. Results Previously published IS6110 based PCR diagnostic assays, along with one developed in house, were tested against environmental mycobacteria commonly isolated from diagnostic tissues submitted to the National Veterinary Services Laboratory. A real-time PCR assay was developed (IS6110_T that had increased specificity over other IS6110 based assays. Of the 13 non-tuberculous mycobacteria tested with IS6110_T only M. wolinskyi was positive. Thirty M. bovis infected tissue homogenates and 18 control tissues were used to evaluate the potential for the assay as a diagnostic test. In this small sample, IS6110_T detected 20/30 samples from M. bovis infected animals and 0/18 control tissues. Conclusions The IS6110_T assay provides a PCR based assay system that is compatible with current diagnostic protocols for the detection of M. bovis in the USA and compliments current testing strategies.

  8. Primary structure and tissue-specific expression of blue crab (Callinectes sapidus) metallothionein isoforms.

    Science.gov (United States)

    Brouwer, M; Enghild, J; Hoexum-Brouwer, T; Thogersen, I; Truncali, A

    1995-01-01

    In aquatic animals, synthesis of the metal-binding protein metallothionein (MT) can be induced through exposure to elevated levels of metals in food or water. Whether the different routes of exposure lead to expression of different metallothionein isoforms in different tissues in unknown. In this study we examined the induction of metallothionein isoforms in the hepatopancreas and gills of the blue crab Callinectes sapidus. When blue crabs are exposed to cadmium in their diet, the metal accumulates in the hepatopancreas. Size-exclusion and anion-exchange chromatography show the presence of five low-molecular-mass cadmium-binding proteins. All of the observed cadmium-binding proteins belong to the class I MT family. They are designated as MT-Ia, MT-Ib, MT-Ic, MT-IIa and MT-IIb. All purified proteins run as single peaks upon rechromatography on anion-exchange HPLC, except for MT-Ic, which segregates into two peaks corresponding to MT-Ia and MT-Ic. The amino acid sequence of MT-Ia and MT-Ic is identical. MT-Ib differs from MT-Ia and MT-Ic only in having an extra N-terminal methionine. The 18 cysteine residues in MT-Ia and MT-IIa occur in identical positions; however, of the remaining 40 amino acids, 15 are found to be different. MT-IIb is identical with MT-IIa, except for an extra methionine residue at its N-terminal position. It appears therefore that, of the five observed CdMTs, only two are the products of distinct genes. CdMT-Ia and -IIa are posttranslationally modified forms of Ib and IIb, respectively, and CdMT-Ia and -Ic appear to be conformational isomers. Cadmium-induced expression of the two genes is tissue-specific. When crabs are exposed to cadmium in water, the metal accumulates in the gills, where it is bound to MT-II. MT-I is virtually absent. PMID:7487904

  9. Tuning of shortening speed in coleoid cephalopod muscle: no evidence for tissue-specific muscle myosin heavy chain isoforms.

    Science.gov (United States)

    Shaffer, Justin F; Kier, William M

    2016-03-01

    The contractile protein myosin II is ubiquitous in muscle. It is widely accepted that animals express tissue-specific myosin isoforms that differ in amino acid sequence and ATPase activity in order to tune muscle contractile velocities. Recent studies, however, suggested that the squid Doryteuthis pealeii might be an exception; members of this species do not express muscle-specific myosin isoforms, but instead alter sarcomeric ultrastructure to adjust contractile velocities. We investigated whether this alternative mechanism of tuning muscle contractile velocity is found in other coleoid cephalopods. We analyzed myosin heavy chain transcript sequences and expression profiles from muscular tissues of a cuttlefish, Sepia officinalis, and an octopus, Octopus bimaculoides, in order to determine if these cephalopods express tissue-specific myosin heavy chain isoforms. We identified transcripts of four and six different myosin heavy chain isoforms in S. officinalis and O. bimaculoides muscular tissues, respectively. Transcripts of all isoforms were expressed in all muscular tissues studied, and thus S. officinalis and O. bimaculoides do not appear to express tissue-specific muscle myosin isoforms. We also examined the sarcomeric ultrastructure in the transverse muscle fibers of the arms of O. bimaculoides and the arms and tentacles of S. officinalis using transmission electron microscopy and found that the fast contracting fibers of the prey capture tentacles of S. officinalis have shorter thick filaments than those found in the slower transverse muscle fibers of the arms of both species. It thus appears that coleoid cephalopods, including the cuttlefish and octopus, may use ultrastructural modifications rather than tissue-specific myosin isoforms to adjust contractile velocities.

  10. Patient-specific cardiovascular progenitor cells derived from integration-free induced pluripotent stem cells for vascular tissue regeneration.

    Science.gov (United States)

    Hu, Jiang; Wang, Yongyu; Jiao, Jiao; Liu, Zhongning; Zhao, Chao; Zhou, Zhou; Zhang, Zhanpeng; Forde, Kaitlynn; Wang, Lunchang; Wang, Jiangang; Baylink, David J; Zhang, Xiao-Bing; Gao, Shaorong; Yang, Bo; Chen, Y Eugene; Ma, Peter X

    2015-12-01

    Tissue-engineered blood vessels (TEBVs) are promising in regenerating a live vascular replacement. However, the vascular cell source is limited, and it is crucial to develop a scaffold that accommodates new type of vascular progenitor cells and facilitates in vivo lineage specification of the cells into functional vascular smooth muscle cells (VSMCs) to regenerate vascular tissue. In the present study, integration-free human induced pluripotent stem cells (hiPSCs) were established from patient peripheral blood mononuclear cells through episomal vector nucleofection of reprogramming factors. The established hiPSCs were then induced into mesoderm-originated cardiovascular progenitor cells (CVPCs) with a highly efficient directed lineage specification method. The derived CVPCs were demonstrated to be able to differentiate into functional VSMCs. Subcutaneous implantation of CVPCs seeded on macroporous nanofibrous poly(l-lactide) scaffolds led to in vivo VSMC lineage specification and matrix deposition inside the scaffolds. In summary, we established integration-free patient-specific hiPSCs from peripheral blood mononuclear cells, derived CVPCs through directed lineage specification, and developed an advanced scaffold for these progenitor cells to further differentiate in vivo into VSMCs and regenerate vascular tissue in a subcutaneous implantation model. This study has established an efficient patient-specific approach towards in vivo regeneration of vascular tissue.

  11. Development of a decision tree to classify the most accurate tissue-specific tissue to plasma partition coefficient algorithm for a given compound.

    Science.gov (United States)

    Yun, Yejin Esther; Cotton, Cecilia A; Edginton, Andrea N

    2014-02-01

    Physiologically based pharmacokinetic (PBPK) modeling is a tool used in drug discovery and human health risk assessment. PBPK models are mathematical representations of the anatomy, physiology and biochemistry of an organism and are used to predict a drug's pharmacokinetics in various situations. Tissue to plasma partition coefficients (Kp), key PBPK model parameters, define the steady-state concentration differential between tissue and plasma and are used to predict the volume of distribution. The experimental determination of these parameters once limited the development of PBPK models; however, in silico prediction methods were introduced to overcome this issue. The developed algorithms vary in input parameters and prediction accuracy, and none are considered standard, warranting further research. In this study, a novel decision-tree-based Kp prediction method was developed using six previously published algorithms. The aim of the developed classifier was to identify the most accurate tissue-specific Kp prediction algorithm for a new drug. A dataset consisting of 122 drugs was used to train the classifier and identify the most accurate Kp prediction algorithm for a certain physicochemical space. Three versions of tissue-specific classifiers were developed and were dependent on the necessary inputs. The use of the classifier resulted in a better prediction accuracy than that of any single Kp prediction algorithm for all tissues, the current mode of use in PBPK model building. Because built-in estimation equations for those input parameters are not necessarily available, this Kp prediction tool will provide Kp prediction when only limited input parameters are available. The presented innovative method will improve tissue distribution prediction accuracy, thus enhancing the confidence in PBPK modeling outputs.

  12. The Potential of Various Living Tissues for Monitoring Clenbuterol Abuse in Food-Producing Chinese Simmental Beef Cattle.

    Science.gov (United States)

    Li, Lijun; Tang, Chaohua; Zhang, Junmin; Zhao, Qingyu; Zhang, Kai

    2016-01-01

    We aimed to evaluate whether living tissues such as urine, plasma and hair were suitable for monitoring clenbuterol (CL) abuse after its subchronic administration of a growth-promoting dose to the Chinese Simmental beef cattle. Eight male, white and red pied Chinese Simmental beef cattle were involved in the experiment, and the CL dose was 16 µg/kg BW/day. Liquid chromatography tandem mass spectrometry (LC-MS-MS) was used to determine CL residues in different tissues, and the addition of D9-clenbuterol internal standard was applied to increase determination accuracy. The recovery of plasma, urine, hair and in vivo tissues was 88.5-114.2, 83.9-114.3, 88.6-116.9 and 85.3-121.7%, respectively. The results showed that CL residue concentrations in the plasma, on Days 14 after withdrawal and later, were lower than the limit of detection (LOD) (0.06 ng/mL) and CL residue in urine was lower than LOD (0.16 ng/mL) 42 days after treatment. CL significantly accumulated in the white and red hair and maintained more than 7.19 ± 2.19 pg/mg within the early withdrawal period of 70 days. A large number of CL were determined in all tested biological tissues, in which residues were higher than the maximum residue limits (MRLs) after dietary administration of CL for 21 days and pre-slaughter withdrawal period of ∼6 h. A particular concern is the slow depletion of residues of CL in some tissues like gluteus and liver still exceeding theirs MRLs, respectively, on Days 14 or 28 days after withdrawal. Our study indicated that plasma and urine could be available for monitoring CL abuse only within a short period of time. However, hair (including light-pigmented) as a target matrix can be selected to perform the long-period monitor of CL.

  13. Technical specifications for monitoring Community trends in zoonotic agents in foodstuffs and animal populations on request from EFSA

    DEFF Research Database (Denmark)

    Borck Høg, Birgitte; Chriél, Mariann; Korsgaard, Helle

    Technical specifications are proposed for the monitoring of temporal trends in zoonotic agents in animal and food populations at Community or Member State group level in the framework of Directive 2003/99/EC. Two types of trend monitoring are identified: trend watching, which covers general obser...

  14. Tissue-specific features of the X chromosome and nucleolus spatial dynamics in a malaria mosquito, Anopheles atroparvus

    Science.gov (United States)

    Bondarenko, Semen M.; Artemov, Gleb N.; Stegniy, Vladimir N.

    2017-01-01

    Spatial organization of chromosome territories is important for maintenance of genomic stability and regulation of gene expression. Recent studies have shown tissue-specific features of chromosome attachments to the nuclear envelope in various organisms including malaria mosquitoes. However, other spatial characteristics of nucleus organization, like volume and shape of chromosome territories, have not been studied in Anopheles. We conducted a thorough analysis of tissue-specific features of the X chromosome and nucleolus volume and shape in follicular epithelium and nurse cells of the Anopheles atroparvus ovaries using a modern open-source software. DNA of the polytene X chromosome from ovarian nurse cells was obtained by microdissection and was used as a template for amplification with degenerate oligo primers. A fluorescently labeled X chromosome painting probe was hybridized with formaldehyde-fixed ovaries of mosquitoes using a 3D-FISH method. The nucleolus was stained by immunostaining with an anti-fibrillarin antibody. The analysis was conducted with TANGO—a software for a chromosome spatial organization analysis. We show that the volume and position of the X chromosome have tissue-specific characteristics. Unlike nurse cell nuclei, the growth of follicular epithelium nuclei is not accompanied with the proportional growth of the X chromosome. However, the shape of the X chromosome does not differ between the tissues. The dynamics of the X chromosome attachment regions location is tissue-specific and it is correlated with the process of nucleus growth in follicular epithelium and nurse cells. PMID:28158219

  15. Tissue oxygen monitoring by photoacoustic lifetime imaging (PALI) and its application to image-guided photodynamic therapy (PDT)

    Science.gov (United States)

    Shao, Qi; Morgounova, Ekaterina; Ashkenazi, Shai

    2015-03-01

    The oxygen partial pressure (pO2), which results from the balance between oxygen delivery and its consumption, is a key component of the physiological state of a tissue. Images of oxygen distribution can provide essential information for identifying hypoxic tissue and optimizing cancer treatment. Previously, we have reported a noninvasive in vivo imaging modality based on photoacoustic lifetime. The technique maps the excited triplet state of oxygen-sensitive dye, thus reflects the spatial and temporal distribution of tissue oxygen. We have applied PALI on tumor on small animals to identify hypoxia area. We also showed that PALI is able monitor changes of tissue oxygen, in an acute ischemia and breathing modulation model. Here we present our work on developing a treatment/imaging modality (PDT-PALI) that integrates PDT and a combined ultrasound/photoacoustic imaging system. The system provides real-time feedback of three essential parameters namely: tissue oxygen, light penetration in tumor location, and distribution of photosensitizer. Tissue oxygen imaging is performed by applying PALI, which relies on photoacoustic probing of oxygen-dependent, excitation lifetime of Methylene Blue (MB) photosensitizer. Lifetime information can also be used to generate image showing the distribution of photosensitizer. The level and penetration depth of PDT illumination can be deduced from photoacoustic imaging at the same wavelength. All images will be combined with ultrasound B-mode images for anatomical reference.

  16. Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues.

    Science.gov (United States)

    Kennedy, Jacob J; Whiteaker, Jeffrey R; Schoenherr, Regine M; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N; Baird, Geoffrey Stuart; Paulovich, Amanda G

    2016-08-01

    Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues. Although the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope-labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e., nine processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R(2) = 0.94) and immuno-MRM (R(2) = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens.

  17. Adipocyte-specific deletion of mTOR inhibits adipose tissue development and causes insulin resistance in mice.

    Science.gov (United States)

    Shan, Tizhong; Zhang, Pengpeng; Jiang, Qinyang; Xiong, Yan; Wang, Yizhen; Kuang, Shihuan

    2016-09-01

    The in vivo role of mechanistic target of rapamycin (mTOR) in the development and function of adipose tissue, especially brown adipose tissue (BAT), is not well understood. Here, we aimed to assess the effect of mTOR (also known as Mtor) knockout on adipose tissues and systemic energy metabolism. We generated adipocyte-specific mTOR-knockout mice (Adipoq-mTOR) by crossing adiponectin-Cre (Adipoq-Cre) mice with mTOR (flox/flox) mice. The mice were then subjected to morphological, physiological (indirect calorimetry, glucose and insulin tolerance tests) and gene expression analyses to determine the role of mTOR in adipose tissues. We provide in vivo evidence that mTOR is essential for adipose tissue development and growth. Deletion of mTOR decreased the mass of both BAT and white adipose tissues (WAT) and induced browning of WAT. In addition, ablation of mTOR in adipose tissues caused insulin resistance and fatty liver in the Adipoq-mTOR mice. Furthermore, mTOR was required for adipocyte differentiation in vivo and activation of PPARγ ameliorated the differentiation deficiency of the mTOR-null adipocytes. Our findings demonstrate that mTOR is a critical regulator of adipogenesis and systemic energy metabolism. Our study provides key insights into the role of mTOR in adipose tissues; such knowledge may facilitate the development of novel strategies with which to treat obesity and related metabolic diseases.

  18. Site-specific Protocol for Monitoring Marsh Birds : Don Edwards San Francisco Bay and San Pablo Bay National Wildlife Refuges

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This site-specific survey protocol provides standardized methods for monitoring marsh birds and was designed for use by the U.S. Fish and Wildlife Service (USFWS) on...

  19. A thermal monitoring sheet with low influence from adjacent waterbolus for tissue surface thermometry during clinical hyperthermia.

    Science.gov (United States)

    Arunachalam, Kavitha; Maccarini, Paolo F; Stauffer, Paul R

    2008-10-01

    This paper presents a complete thermal analysis of a novel conformal surface thermometer design with directional sensitivity for real-time temperature monitoring during hyperthermia treatments of large superficial cancer. The thermal monitoring sheet (TMS) discussed in this paper consists of a 2-D array of fiberoptic sensors embedded between two layers of flexible, low-loss, and thermally conductive printed circuit board (PCB) film. Heat transfer across all interfaces from the tissue surface through multiple layers of insulating dielectrics surrounding the small buried temperature sensor and into an adjacent temperature-regulated water coupling bolus was studied using 3-D thermal simulation software. Theoretical analyses were carried out to identify the most effective differential TMS probe configuration possible with commercially available flexible PCB materials and to compare their thermal responses with omnidirectional probes commonly used in clinical hyperthermia. A TMS sensor design that employs 0.0508-mm Kapton MTB and 0.2032-mm Kapton HN flexible polyimide films is proposed for tissue surface thermometry with low influence from the adjacent waterbolus. Comparison of the thermal simulations with clinical probes indicates the new differential TMS probe design to outperform in terms of both transient response and steady-state accuracy in selectively reading the tissue surface temperature, while decreasing the overall thermal barrier of the probe between the coupling waterbolus and tissue surface.

  20. Extending the tissue microarray data exchange specification for inclusion of data analysis results

    Directory of Open Access Journals (Sweden)

    Oliver Lyttleton

    2011-01-01

    Full Text Available Background: The Tissue Microarray Data Exchange Specification (TMA DES is an eXtensible Markup Language (XML specification for encoding TMA experiment data in a machine-readable format that is also human readable. TMA DES defines Common Data Elements (CDEs that form a basic vocabulary for describing TMA data. TMA data are routinely subjected to univariate and multivariate statistical analysis to determine differences or similarities between pathologically distinct groups of tumors for one or more markers or between markers for different groups. Such statistical analysis tests include the t-test, ANOVA, Chi-square, Mann-Whitney U, and Kruskal-Wallis tests. All these generate output that needs to be recorded and stored with TMA data. Materials and Methods: We propose extending the TMA DES to include syntactic and semantic definitions of CDEs for describing the results of statistical analyses performed upon TMA DES data. These CDEs are described in this paper and it is illustrated how they can be added to the TMA DES. We created a Document Type Definition (DTD file defining the syntax for these CDEs, and a set of ISO 11179 entries providing semantic definitions for them. We describe how we wrote a program in R that read TMA DES data from an XML file, performed statistical analyses on that data, and created a new XML file containing both the original XML data and CDEs representing the results of our analyses. This XML file was submitted to XML parsers in order to confirm that they conformed to the syntax defined in our extended DTD file. TMA DES XML files with deliberately introduced errors were also parsed in order to verify that our new DTD file could perform error checking. Finally, we also validated an existing TMA DES XML file against our DTD file in order to demonstrate the backward compatibility of our DTD. Results: Our experiments demonstrated the encoding of analysis results using our proposed CDEs. We used XML parsers to confirm that these

  1. MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data.

    Science.gov (United States)

    El Amrani, Khadija; Stachelscheid, Harald; Lekschas, Fritz; Kurtz, Andreas; Andrade-Navarro, Miguel A

    2015-08-28

    Identification of marker genes associated with a specific tissue/cell type is a fundamental challenge in genetic and cell research. Marker genes are of great importance for determining cell identity, and for understanding tissue specific gene function and the molecular mechanisms underlying complex diseases. We have developed a new bioinformatics tool called MGFM (Marker Gene Finder in Microarray data) to predict marker genes from microarray gene expression data. Marker genes are identified through the grouping of samples of the same type with similar marker gene expression levels. We verified our approach using two microarray data sets from the NCBI's Gene Expression Omnibus public repository encompassing samples for similar sets of five human tissues (brain, heart, kidney, liver, and lung). Comparison with another tool for tissue-specific gene identification and validation with literature-derived established tissue markers established functionality, accuracy and simplicity of our tool. Furthermore, top ranked marker genes were experimentally validated by reverse transcriptase-polymerase chain reaction (RT-PCR). The sets of predicted marker genes associated with the five selected tissues comprised well-known genes of particular importance in these tissues. The tool is freely available from the Bioconductor web site, and it is also provided as an online application integrated into the CellFinder platform ( http://cellfinder.org/analysis/marker ). MGFM is a useful tool to predict tissue/cell type marker genes using microarray gene expression data. The implementation of the tool as an R-package as well as an application within CellFinder facilitates its use.

  2. Structural basis of specific inhibition of tissue-type plasminogen activator by plasminogen activators inhibitor-1

    Directory of Open Access Journals (Sweden)

    Lihu Gong

    2016-03-01

    Full Text Available Thrombosis is a leading cause of death worldwide [1]. Recombinant tissue-type plasminogen activator (tPA is the FDA-approved thrombolytic drug for ischemic strokes, myocardial infarction and pulmonary embolism. tPA is a multi-domain serine protease of the trypsin-family [2] and catalyses the critical step in fibrinolysis [3], converting the zymogen plasminogen to the active serine protease plasmin, which degrades the fibrin network of thrombi and blood clots. tPA is rapidly inactivated by endogenous plasminogen activators inhibitor-1 (PAI-1 [4] (Fig. 1. Engineering on tPA to reduce its inhibition by PAI-1 without compromising its thrombolytic effect is a continuous effort [5]. Tenecteplase (TNK-tPA is a newer generation of tPA variant showing slower inhibition by PAI-1 [6]. Extensive studies to understand the molecular interactions between tPA and PAI-1 have been carried out [7–18], however, the precise details at atomic resolution remain unknown. We report the crystal structure of tPA·PAI-1 complex here. The methods required to achieve these data include: (1 recombinant expression and purification of a PAI-1 variant (14-1B containing four mutations (N150H, K154T, Q319L, and M354I, and a tPA serine protease domain (tPA-SPD variant with three mutations (C122A, N173Q, and S195A, in the chymotrypsin numbering [19]; (2 formation of a tPA-SPD·PAI-1 Michaëlis complex in vitro [19]; and (3 solving the three-dimensional structure for this complex by X-ray crystallography [deposited in the PDB database as 5BRR]. The data explain the specificity of PAI-1 for tPA and uPA [19,20], and provide structural basis to design newer generation of PAI-1-resistant tPA variants as thrombolytic agents [19].

  3. Effect of exercise on burn-induced changes in tissue-specific glucose metabolism.

    Science.gov (United States)

    Carter, Edward A; Paul, Kasie; Bonab, Ali A; Tompkins, Ronald G; Fischman, Alan J

    2014-01-01

    Exercise is a component of the clinical management for burn patients, to help reduce muscle wasting associated with prolonged hospitalization. In the present study the authors examined 2-deoxy-2-[18F] fluoro-D-glucose (18FDG) uptake in mice subjected to burn injury with and without exercise. Mice had their the dorsums shaven, were placed in molds, and the exposed area was immersed in 90°C water for 9 seconds followed by resuscitation with saline (2 ml) to produce a 30% full-thickness burn injury. Twenty-four hours later, the mice were subjected to treadmill exercise for 1 hour. Before exercise, mice were injected with ~50 μCi 18FDG. Mice were killed after running and a complete biodistribution was performed. Exercise produced a stimulation of 18FDG update by skeletal muscle and heart, while reducing 18FDG accumulation in brain. Burn injury had no significant effect on 18FDG update by skeletal muscle, but did increase 18FDG accumulation in heart, while reducing 18FDG accumulation in brain. However, exercise combined with a burn injury produced a significant increase in 18FDG uptake in the skeletal muscle compared with the burned mice, as great as that produced in the sham animals subjected to exercise. The combination of burn plus exercise appeared to prevent the stimulation of 18FDG uptake by the heart produced by burn injury alone. Exercise treatment did not correct the changes in 18FDG uptake in the brain produced by burn injury. Separately, exercise and burn injury significantly increased serum interleukin-6 levels, increases that were higher when exercise was combined with the burn injury. These findings suggest that exercise may exert some therapeutic effects in burn patients by tissue-specific modulation of glucose metabolism, and these changes may be related to interleukin-6.

  4. Monitoring programmed cell death of living plant tissues in microfluidics using electrochemical and optical techniques

    DEFF Research Database (Denmark)

    Mark, Christina; Zor, Kinga; Heiskanen, Arto

    This project focuses on developing and applying a tissue culture system with electrochemical and optical detection techniques for tissue culture of barley aleurone layer to increase understanding of the underlying mechanisms of programmed cell death (PCD) in plants. The major advantage of electro...

  5. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation.

    Science.gov (United States)

    Mendizabal, Isabel; Yi, Soojin V

    2016-01-01

    CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation. © The Author 2015. Published by Oxford University Press.

  6. Psychosocial trajectories of men monitoring prostate-specific antigen levels following surgery for prostate cancer.

    Science.gov (United States)

    Bailey, Donald E; Wallace Kazer, Meredith; Polascik, Thomas J; Robertson, Cary

    2014-07-01

    To describe the psychosocial trajectories of men treated surgically for prostate cancer after monitoring their prostate-specific antigen (PSA) levels until 24 months post-treatment. Descriptive longitudinal study. Urology clinic at Duke University Health System. 12 men diagnosed and treated for prostate cancer. Men were interviewed in their homes at baseline and at 24 months and via telephone at 6, 12, and 18 months. Scores from the Profile of Mood States, Mishel Uncertainty in Illness Scale, Self-Control Schedule, and Cantril's Ladder were entered into a database for analysis. Graphs of individual participants' scores were plotted. PSA values, mood state, cognitive reframing, impact of event, quality of life, illness uncertainty, and growth through uncertainty were measured. Three trajectories were identified (i.e., stable, unstable, and mixed) and graphed using a typological or health pattern approach. Monitoring PSA levels is critical for men treated for prostate cancer. This study provides preliminary data on the psychological trajectories of men during the first 24 months postprostatectomy. Rising PSA levels that are associated with the recurrence of disease can cause psychosocial distress among men with prostate cancer.

  7. Monitoring of Pathogen-Specific T-Cell Immune Reconstitution after Allogeneic Hematopoietic Stem Cell Transplantation

    Science.gov (United States)

    Fuji, Shigeo; Kapp, Markus; Einsele, Hermann

    2013-01-01

    The clinical outcome after allogeneic hematopoietic stem cell transplantation (HSCT) has been significantly improved during the last decades with regard to the reduction in organ failure, infection, and severe acute graft-versus-host disease. However, severe complications due to infectious diseases are still one of the major causes of morbidity and mortality after allogeneic HSCT, in particular in patients receiving haploidentical HSCT or cord blood transplant due to a slow and often incomplete immune reconstitution. In order to improve the immune control of pathogens without an increased risk of alloreactivity, adoptive immunotherapy using highly enriched pathogen-specific T cells offers a promising approach. In order to identify patients who are at high risk for infectious diseases, several monitoring assays have been developed with potential for the guidance of immunosuppressive drugs and adoptive immunotherapy in clinical practice. In this article, we aim to give a comprehensive overview regarding current developments of T-cell monitoring techniques focusing on T cells against viruses and fungi. In particular, we will focus on rather simple, fast, non-labor-intensive, cellular assays which could be integrated in routine clinical screening approaches. PMID:24062744

  8. Pre-transplantation specification of stem cells to cardiac lineage for regeneration of cardiac tissue.

    Science.gov (United States)

    Mayorga, Maritza; Finan, Amanda; Penn, Marc

    2009-03-01

    Myocardial infarction (MI) is a lead cause of mortality in the Western world. Treatment of acute MI is focused on restoration of antegrade flow which inhibits further tissue loss, but does not restore function to damaged tissue. Chronic therapy for injured myocardial tissue involves medical therapy that attempts to minimize pathologic remodeling of the heart. End stage therapy for chronic heart failure (CHF) involves inotropic therapy to increase surviving cardiac myocyte function or mechanical augmentation of cardiac performance. Not until the point of heart transplantation, a limited resource at best, does therapy focus on the fundamental problem of needing to replace injured tissue with new contractile tissue. In this setting, the potential for stem cell therapy has garnered significant interest for its potential to regenerate or create new contractile cardiac tissue. While to date adult stem cell therapy in clinical trials has suggested potential benefit, there is waning belief that the approaches used to date lead to regeneration of cardiac tissue. As the literature has better defined the pathways involved in cardiac differentiation, preclinical studies have suggested that stem cell pretreatment to direct stem cell differentiation prior to stem cell transplantation may be a more efficacious strategy for inducing cardiac regeneration. Here we review the available literature on pre-transplantation conditioning of stem cells in an attempt to better understand stem cell behavior and their readiness in cell-based therapy for myocardial regeneration.

  9. A selective historical review of congener-specific human tissue measurements as sensitive and specific biomarkers of exposure to dioxins and related compounds.

    Science.gov (United States)

    Schecter, A

    1998-04-01

    Estimating internal exposure or dose of dioxins and related chemicals such as dibenzofurans and dioxinlike polychlorinated biphenyls is relatively straightforward in laboratory animals because a known dose is given and the amount absorbed can be measured. In wildlife, direct tissue measurement and measurement of environmental samples have both recently been used to estimate exposure. Until recently, human studies used only indirect indicators such as skin lesions to qualitatively estimate exposure to these chlorinated organic compounds. Environmental measurements have also sometimes been used to estimate human exposure. Dioxins in human tissue were not measured until the 1970s, when 2,3,7,8-tetrachlorodibenzo-p-dioxin was measured in mothers' milk; congener-specific measurement of dioxins and dibenzofurans in tissues (blood, milk, and adipose tissue) of the general population and exposed workers was first performed in the United States in the 1980s. Measurement in a sensitive and specific fashion of the 17 toxic dioxin and dibenzofuran congeners currently found in human tissue from industrial countries began in the 1980s. The use of known chemical standards, capillary columns, high resolution gas chromatography and mass spectrometry (GC-MS) has now become relatively common. GC-MS analysis of blood is currently accepted as the gold standard for estimating human exposure to dioxins. However, analyses are still costly and time consuming, and worldwide there are few qualified laboratories. There is currently a lack of knowledge concerning kinetics at higher and lower exposure levels for most of the toxic dioxin congeners and of levels in target tissues of concern.

  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