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Sample records for alternative differentiation reveals

  1. Characterization of the interferon genes in homozygous rainbow trout reveals two novel genes, alternate splicing and differential regulation of duplicated genes

    Science.gov (United States)

    Purcell, M.K.; Laing, K.J.; Woodson, J.C.; Thorgaard, G.H.; Hansen, J.D.

    2009-01-01

    The genes encoding the type I and type II interferons (IFNs) have previously been identified in rainbow trout and their proteins partially characterized. These previous studies reported a single type II IFN (rtIFN-??) and three rainbow trout type I IFN genes that are classified into either group I (rtIFN1, rtIFN2) or group II (rtIFN3). In this present study, we report the identification of a novel IFN-?? gene (rtIFN-??2) and a novel type I group II IFN (rtIFN4) in homozygous rainbow trout and predict that additional IFN genes or pseudogenes exist in the rainbow trout genome. Additionally, we provide evidence that short and long forms of rtIFN1 are actively and differentially transcribed in homozygous trout, and likely arose due to alternate splicing of the first exon. Quantitative reverse transcriptase PCR (qRT-PCR) assays were developed to systematically profile all of the rainbow trout IFN transcripts, with high specificity at an individual gene level, in na??ve fish and after stimulation with virus or viral-related molecules. Cloned PCR products were used to ensure the specificity of the qRT-PCR assays and as absolute standards to assess transcript abundance of each gene. All IFN genes were modulated in response to Infectious hematopoietic necrosis virus (IHNV), a DNA vaccine based on the IHNV glycoprotein, and poly I:C. The most inducible of the type I IFN genes, by all stimuli tested, were rtIFN3 and the short transcript form of rtIFN1. Gene expression of rtIFN-??1 and rtIFN-??2 was highly up-regulated by IHNV infection and DNA vaccination but rtIFN-??2 was induced to a greater magnitude. The specificity of the qRT-PCR assays reported here will be useful for future studies aimed at identifying which cells produce IFNs at early time points after infection. ?? 2008 Elsevier Ltd.

  2. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation.

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    Salomonis, Nathan; Schlieve, Christopher R; Pereira, Laura; Wahlquist, Christine; Colas, Alexandre; Zambon, Alexander C; Vranizan, Karen; Spindler, Matthew J; Pico, Alexander R; Cline, Melissa S; Clark, Tyson A; Williams, Alan; Blume, John E; Samal, Eva; Mercola, Mark; Merrill, Bradley J; Conklin, Bruce R

    2010-06-01

    Two major goals of regenerative medicine are to reproducibly transform adult somatic cells into a pluripotent state and to control their differentiation into specific cell fates. Progress toward these goals would be greatly helped by obtaining a complete picture of the RNA isoforms produced by these cells due to alternative splicing (AS) and alternative promoter selection (APS). To investigate the roles of AS and APS, reciprocal exon-exon junctions were interrogated on a genome-wide scale in differentiating mouse embryonic stem (ES) cells with a prototype Affymetrix microarray. Using a recently released open-source software package named AltAnalyze, we identified 144 genes for 170 putative isoform variants, the majority (67%) of which were predicted to alter protein sequence and domain composition. Verified alternative exons were largely associated with pathways of Wnt signaling and cell-cycle control, and most were conserved between mouse and human. To examine the functional impact of AS, we characterized isoforms for two genes. As predicted by AltAnalyze, we found that alternative isoforms of the gene Serca2 were targeted by distinct microRNAs (miRNA-200b, miRNA-214), suggesting a critical role for AS in cardiac development. Analysis of the Wnt transcription factor Tcf3, using selective knockdown of an ES cell-enriched and characterized isoform, revealed several distinct targets for transcriptional repression (Stmn2, Ccnd2, Atf3, Klf4, Nodal, and Jun) as well as distinct differentiation outcomes in ES cells. The findings herein illustrate a critical role for AS in the specification of ES cells with differentiation, and highlight the utility of global functional analyses of AS. PMID:20498046

  3. Alternative Splicing of G9a Regulates Neuronal Differentiation

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    Ana Fiszbein

    2016-03-01

    Full Text Available Chromatin modifications are critical for the establishment and maintenance of differentiation programs. G9a, the enzyme responsible for histone H3 lysine 9 dimethylation in mammalian euchromatin, exists as two isoforms with differential inclusion of exon 10 (E10 through alternative splicing. We find that the G9a methyltransferase is required for differentiation of the mouse neuronal cell line N2a and that E10 inclusion increases during neuronal differentiation of cultured cells, as well as in the developing mouse brain. Although E10 inclusion greatly stimulates overall H3K9me2 levels, it does not affect G9a catalytic activity. Instead, E10 increases G9a nuclear localization. We show that the G9a E10+ isoform is necessary for neuron differentiation and regulates the alternative splicing pattern of its own pre-mRNA, enhancing E10 inclusion. Overall, our findings indicate that by regulating its own alternative splicing, G9a promotes neuron differentiation and creates a positive feedback loop that reinforces cellular commitment to differentiation.

  4. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation

    OpenAIRE

    Salomonis, Nathan; Schlieve, Christopher R.; Pereira, Laura; Wahlquist, Christine; Colas, Alexandre; Zambon, Alexander C.; Vranizan, Karen; Spindler, Matthew J.; Alexander R Pico; Cline, Melissa S; Tyson A Clark; Williams, Alan; John E Blume; Samal, Eva; Mercola, Mark

    2010-01-01

    Two major goals of regenerative medicine are to reproducibly transform adult somatic cells into a pluripotent state and to control their differentiation into specific cell fates. Progress toward these goals would be greatly helped by obtaining a complete picture of the RNA isoforms produced by these cells due to alternative splicing (AS) and alternative promoter selection (APS). To investigate the roles of AS and APS, reciprocal exon–exon junctions were interrogated on a genome-wide scale in ...

  5. When Unified Teacher Pay Scales Meet Differential Alternative Returns

    Science.gov (United States)

    Walsh, Patrick

    2014-01-01

    This paper quantifies the extent to which unified teacher pay scales and differential alternatives produce opportunity costs that are asymmetric in math and verbal skills. Data from the Baccalaureate and Beyond 1997 and 2003 follow-ups are used to estimate a fully parametric, selection-corrected wage equation for nonteachers, which is then used to…

  6. AN INVESTIGATION OF DIFFERENTIAL REINFORCEMENT OF ALTERNATIVE BEHAVIOR WITHOUT EXTINCTION

    OpenAIRE

    Athens, Elizabeth S; Vollmer, Timothy R

    2010-01-01

    We manipulated relative reinforcement for problem behavior and appropriate behavior using differential reinforcement of alternative behavior (DRA) without an extinction component. Seven children with developmental disabilities participated. We manipulated duration (Experiment 1), quality (Experiment 2), delay (Experiment 3), or a combination of each (Experiment 4), such that reinforcement favored appropriate behavior rather than problem behavior even though problem behavior still produced rei...

  7. An Investigation of Differential Reinforcement of Alternative Behavior without Extinction

    Science.gov (United States)

    Athens, Elizabeth S.; Vollmer, Timothy R.

    2010-01-01

    We manipulated relative reinforcement for problem behavior and appropriate behavior using differential reinforcement of alternative behavior (DRA) without an extinction component. Seven children with developmental disabilities participated. We manipulated duration (Experiment 1), quality (Experiment 2), delay (Experiment 3), or a combination of…

  8. An alternative RNA polymerase I structure reveals a dimer hinge.

    Science.gov (United States)

    Kostrewa, Dirk; Kuhn, Claus-D; Engel, Christoph; Cramer, Patrick

    2015-09-01

    RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-centre cleft and the `connector' that mediates Pol I dimerization [Engel et al. (2013), Nature (London), 502, 650-655]. Here, a Pol I structure in an alternative crystal form that was solved by molecular replacement using the original atomic Pol I structure is reported. The resulting alternative structure lacks the expander but still shows an expanded active-centre cleft. The neighbouring Pol I monomers form a homodimer with a relative orientation distinct from that observed previously, establishing the connector as a hinge between Pol I monomers.

  9. Transcriptome analysis reveals differential splicing events in IPF lung tissue.

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    Tracy Nance

    Full Text Available Idiopathic pulmonary fibrosis (IPF is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%, and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%. We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10 and POSTN (RNA-Seq adjusted pval = 2.06e-09, which encode the extracellular matrix proteins collagen alpha-3(VI and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF.

  10. Transcriptome analysis reveals differential splicing events in IPF lung tissue.

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    Tracy Nance

    Full Text Available Idiopathic pulmonary fibrosis (IPF is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%, and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%. We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10 and POSTN (RNA-Seq adjusted pval = 2.06e-09, which encode the extracellular matrix proteins collagen alpha-3(VI and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF.

  11. Transcriptome Reveals Cathepsin K in Periodontal Ligament Differentiation.

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    Yamada, S; Ozaki, N; Tsushima, K; Yamaba, S; Fujihara, C; Awata, T; Sakashita, H; Kajikawa, T; Kitagaki, J; Yamashita, M; Yanagita, M; Murakami, S

    2016-08-01

    Periodontal ligaments (PDLs) play an important role in remodeling the alveolar bond and cementum. Characterization of the periodontal tissue transcriptome remains incomplete, and an improved understanding of PDL features could aid in developing new regenerative therapies. Here, we aimed to generate and analyze a large human PDL transcriptome. We obtained PDLs from orthodontic treatment patients, isolated the RNA, and used a vector-capping method to make a complementary DNA library from >20,000 clones. Our results revealed that 58% of the sequences were full length. Furthermore, our analysis showed that genes expressed at the highest frequencies included those for collagen type I, collagen type III, and proteases. We also found 5 genes whose expressions have not been previously reported in human PDL. To access which of the highly expressed genes might be important for PDL cell differentiation, we used real-time polymerase chain reaction to measure their expression in differentiating cells. Among the genes tested, the cysteine protease cathepsin K had the highest upregulation, so we measured its relative expression in several tissues, as well as in osteoclasts, which are known to express high levels of cathepsin K. Our results revealed that PDL cells express cathepsin K at similar levels as osteoclasts, which are both expressed at higher levels than those of the other tissues tested. We also measured cathepsin K protein expression and enzyme activity during cell differentiation and found that both increased during this process. Immunocytochemistry experiments revealed that cathepsin K localizes to the interior of lysosomes. Last, we examined the effect of inhibiting cathepsin K during cell differentiation and found that cathepsin K inhibition stimulated calcified nodule formation and increased the levels of collagen type I and osteocalcin gene expression. Based on these results, cathepsin K seems to regulate collagen fiber accumulation during human PDL cell

  12. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

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    Alicia R Martin

    2014-08-01

    Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

  13. Differential metabolism of Mycoplasma species as revealed by their genomes

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    Fabricio B.M. Arraes

    2007-01-01

    Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

  14. Global Gene Expression Profiling and Alternative Splicing Events during the Chondrogenic Differentiation of Human Cartilage Endplate-Derived Stem Cells

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    Jin Shang

    2015-01-01

    Full Text Available Low back pain (LBP is a very prevalent disease and degenerative disc diseases (DDDs usually account for the LBP. However, the pathogenesis of DDDs is complicated and difficult to elucidate. Alternative splicing is a sophisticated regulatory process which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. In addition, the cartilage endplate-derived stem cells have been discovered and identified by our research group. In this paper, we continue to investigate gene expression profiling and alternative splicing events during chondrogenic differentiation of cartilage endplate-derived stem cells. We adopted Affymetrix Human Transcriptome Array 2.0 (HTA 2.0 to compare the transcriptional and splicing changes between the control and differentiated samples. RT-PCR and quantitative PCR are used to validate the microarray results. The GO and KEGG pathway analysis was also performed. After bioinformatics analysis of the data, we detected 1953 differentially expressed genes. In terms of alternative splicing, the Splicing Index algorithm was used to select alternatively spliced genes. We detected 4411 alternatively spliced genes. GO and KEGG pathway analysis also revealed several functionally involved biological processes and signaling pathways. To our knowledge, this is the first study to investigate the alternative splicing mechanisms in chondrogenic differentiation of stem cells on a genome-wide scale.

  15. Small molecules reveal an alternative mechanism of Bax activation.

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    Brahmbhatt, Hetal; Uehling, David; Al-Awar, Rima; Leber, Brian; Andrews, David

    2016-04-15

    The pro-apoptotic protein Bax commits a cell to death by permeabilizing the mitochondrial outer membrane (MOM). To obtain small-molecule probes for elucidating the molecular mechanism(s) of Bax activation, we screened for compounds that induced Bax-mediated liposome permeabilization. We identified five structurally different small molecules that promoted both Bax targeting to and oligomerization at membranes. All five compounds initiated Bax oligomerization in the absence of membranes by a mechanism unlike Bax activation by Bcl-2 homology 3 domain (BH3) proteins. Some of the compounds induced Bax/Bak-dependent apoptosis in cells. Activation of Bax by the most active compound was poorly inhibited by the anti-apoptotic protein Bcl-XL and requires a cysteine residue at position 126 of Bax that is not required for activation by BH3 proteins. Our results reveal a novel pathway for Bax activation independent of pro-apoptotic BH3 proteins that may have important implications for the regulation of Bax activity in cells. PMID:26916338

  16. Eye movement monitoring reveals differential influences of emotion on memory

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    Lily Riggs

    2010-11-01

    Full Text Available Research shows that memory for emotional aspects of an event may be enhanced at the cost of impaired memory for surrounding peripheral details. However, this has only been assessed directly via verbal reports which reveal the outcome of a long stream of processing but cannot shed light on how/when emotion may affect the retrieval process. In the present experiment, eye movement monitoring was used as an indirect measure of memory as it can reveal aspects of online memory processing. For example, do emotions modulate the nature of memory representations or the speed with which such memories can be accessed? Participants viewed central negative and neutral scenes surrounded by three neutral objects and after a brief delay, memory was assessed indirectly via eye movement monitoring and then directly via verbal reports. Consistent with the previous literature, emotion enhanced central and impaired peripheral memory as indexed by eye movement scanning and verbal reports. This suggests that eye movement scanning may contribute and/or is related to conscious access of memory. However, the central/peripheral tradeoff effect was not observed in an early measure of eye movement behavior, i.e. participants were faster to orient to a critical region of change in the periphery irrespective of whether it was previously studied in a negative or neutral context. These findings demonstrate emotion’s differential influences on different aspects of retrieval. In particular, emotion appears to affect the detail within, and/or the evaluation of, stored memory representations, but it may not affect the initial access to those representations.

  17. Differential Reinforcement of Alternative Behavior in Center-Based Classrooms: Evaluation of Pre-Teaching the Alternative Behavior

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    LeGray, Matthew W.; Dufrene, Brad A.; Mercer, Sterett; Olmi, D. Joe; Sterling, Heather

    2013-01-01

    This study investigated the effectiveness of a differential reinforcement of alternative behavior procedure in decreasing disruptive behavior while simultaneously increasing the appropriate behavior of four children of typical development between the ages of 4 and 6 in center-based classrooms. We began with brief functional analyses for each…

  18. Differential Shannon entropy and differential coefficient of variation: alternatives and augmentations to differential expression in the search for disease-related genes.

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    Wang, Kai; Phillips, Charles A; Rogers, Gary L; Barrenas, Fredrik; Benson, Mikael; Langston, Michael A

    2014-01-01

    Differential expression has been a standard tool for analysing case-control transcriptomic data since the advent of microarray technology. It has proved invaluable in characterising the molecular mechanisms of disease. Nevertheless, the expression profile of a gene across samples can be perturbed in ways that leave the expression level unaltered, while a biological effect is nonetheless present. This paper describes and analyses differential Shannon entropy and differential coefficient of variation, two alternate techniques for identifying genes of interest. Ontological analysis across 16 human disease datasets demonstrates that these alternatives are effective at identifying disease-related genes not found by mere differential expression alone. Because the two alternate techniques are based on somewhat different mathematical formulations, they tend to produce somewhat different gene lists. Moreover, each may pinpoint genes completely overlooked by the other. Thus, measures of entropy and variation can be used to replace or better yet augment standard differential expression computations.

  19. Expression of Two Novel Alternatively Spliced COL2A1 Isoforms During Chondrocyte Differentiation

    OpenAIRE

    McAlinden, Audrey; Johnstone, Brian; Kollar, John; Kazmi, Najam; Hering, Thomas M.

    2007-01-01

    Alternative splicing of the type II procollagen gene (COL2A1) is developmentally-regulated during chondrogenesis. Type IIA procollagen (+ exon 2) is synthesized by chondroprogenitor cells while type IIB procollagen (- exon 2) is synthesized by differentiated chondrocytes. Here, we report expression of two additional alternatively spliced COL2A1 isoforms during chondrocyte differentiation of bone marrow derived mesenchymal stem cells (MSCs). One isoform, named IIC, contains only the first 34 n...

  20. Spinal cord injury reveals multilineage differentiation of ependymal cells.

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    Konstantinos Meletis

    2008-07-01

    Full Text Available Spinal cord injury often results in permanent functional impairment. Neural stem cells present in the adult spinal cord can be expanded in vitro and improve recovery when transplanted to the injured spinal cord, demonstrating the presence of cells that can promote regeneration but that normally fail to do so efficiently. Using genetic fate mapping, we show that close to all in vitro neural stem cell potential in the adult spinal cord resides within the population of ependymal cells lining the central canal. These cells are recruited by spinal cord injury and produce not only scar-forming glial cells, but also, to a lesser degree, oligodendrocytes. Modulating the fate of ependymal progeny after spinal cord injury may offer an alternative to cell transplantation for cell replacement therapies in spinal cord injury.

  1. A genome wide analysis of alternative splicing events during the osteogenic differentiation of human cartilage endplate-derived stem cells.

    Science.gov (United States)

    Shang, Jin; Wang, Honggang; Fan, Xin; Shangguan, Lei; Liu, Huan

    2016-08-01

    Low back pain is a prevalent disease, which leads to suffering and disabilities in a vast number of individuals. Degenerative disc diseases are usually the underlying causes of low back pain. However, the pathogenesis of degenerative disc diseases is highly complex and difficult to determine. Current therapies for degenerative disc diseases are various. In particular, cell-based therapies have proven to be effective and promising. Our research group has previously isolated and identified the cartilage endplate‑derived stem cells. In addition, alternative splicing is a sophisticated regulatory mechanism, which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. The present study continued to investigate alternative splicing events in osteogenic differentiation of cartilage endplate‑derived stem cells. An Affymetrix Human Transcriptome Array 2.0 was used to detect splicing changes between the control and differentiated samples. Additionally, molecular function and pathway analysis were also performed. Following rigorous bioinformatics analysis of the data, 3,802 alternatively spliced genes were identified, and 10 of these were selected for validation by reverse transcription‑polymerase chain reaction. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis also revealed numerous enriched GO terms and signaling pathways. To the best of our knowledge, the present study is the first to investigate alternative splicing mechanisms in osteogenic differentiation of stem cells on a genome‑wide scale. The illumination of molecular mechanisms of stem cell osteogenic differentiation may assist the development novel bioengineered methods to treat degenerative disc diseases.

  2. A genome wide analysis of alternative splicing events during the osteogenic differentiation of human cartilage endplate-derived stem cells.

    Science.gov (United States)

    Shang, Jin; Wang, Honggang; Fan, Xin; Shangguan, Lei; Liu, Huan

    2016-08-01

    Low back pain is a prevalent disease, which leads to suffering and disabilities in a vast number of individuals. Degenerative disc diseases are usually the underlying causes of low back pain. However, the pathogenesis of degenerative disc diseases is highly complex and difficult to determine. Current therapies for degenerative disc diseases are various. In particular, cell-based therapies have proven to be effective and promising. Our research group has previously isolated and identified the cartilage endplate‑derived stem cells. In addition, alternative splicing is a sophisticated regulatory mechanism, which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. The present study continued to investigate alternative splicing events in osteogenic differentiation of cartilage endplate‑derived stem cells. An Affymetrix Human Transcriptome Array 2.0 was used to detect splicing changes between the control and differentiated samples. Additionally, molecular function and pathway analysis were also performed. Following rigorous bioinformatics analysis of the data, 3,802 alternatively spliced genes were identified, and 10 of these were selected for validation by reverse transcription‑polymerase chain reaction. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis also revealed numerous enriched GO terms and signaling pathways. To the best of our knowledge, the present study is the first to investigate alternative splicing mechanisms in osteogenic differentiation of stem cells on a genome‑wide scale. The illumination of molecular mechanisms of stem cell osteogenic differentiation may assist the development novel bioengineered methods to treat degenerative disc diseases. PMID:27278552

  3. Introducing Differential Equations Students to the Fredholm Alternative--In Staggered Doses

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    Savoye, Philippe

    2011-01-01

    The development, in an introductory differential equations course, of boundary value problems in parallel with initial value problems and the Fredholm Alternative. Examples are provided of pairs of homogeneous and nonhomogeneous boundary value problems for which existence and uniqueness issues are considered jointly. How this heightens students'…

  4. Comparing Main and Collateral Effects of Extinction and Differential Reinforcement of Alternative Behavior

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    Petscher, Erin Seligson; Bailey, Jon S.

    2008-01-01

    This study evaluated the effects and collateral effects of extinction (EXT) and differential reinforcement of alternative behavior (DRA) interventions with inappropriate vocalizations and work refusal. Both interventions have been used frequently to reduce problem behaviors. The benefits of these interventions have been established yet may be…

  5. The Role of Alternative Splicing in the Control of Immune Homeostasis and Cellular Differentiation.

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    Yabas, Mehmet; Elliott, Hannah; Hoyne, Gerard F

    2016-01-01

    Alternative splicing of pre-mRNA helps to enhance the genetic diversity within mammalian cells by increasing the number of protein isoforms that can be generated from one gene product. This provides a great deal of flexibility to the host cell to alter protein function, but when dysregulation in splicing occurs this can have important impact on health and disease. Alternative splicing is widely used in the mammalian immune system to control the development and function of antigen specific lymphocytes. In this review we will examine the splicing of pre-mRNAs yielding key proteins in the immune system that regulate apoptosis, lymphocyte differentiation, activation and homeostasis, and discuss how defects in splicing can contribute to diseases. We will describe how disruption to trans-acting factors, such as heterogeneous nuclear ribonucleoproteins (hnRNPs), can impact on cell survival and differentiation in the immune system. PMID:26703587

  6. Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei.

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    Daniel Nilsson

    Full Text Available Trans-splicing of leader sequences onto the 5'ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 5'splice sites and analyze the corresponding gene expression profile, that we term spliced leader trapping (SLT. The method can be applied to any organism with a sequenced genome and trans-splicing of a conserved leader sequence. We analyzed the expression profiles and splicing patterns of bloodstream and insect forms of the parasite Trypanosoma brucei. We detected the 5' splice sites of 85% of the annotated protein-coding genes and, contrary to previous reports, found up to 40% of transcripts to be differentially expressed. Furthermore, we discovered more than 2500 alternative splicing events, many of which appear to be stage-regulated. Based on our findings we hypothesize that alternatively spliced transcripts present a new means of regulating gene expression and could potentially contribute to protein diversity in the parasite. The entire dataset can be accessed online at TriTrypDB or through: http://splicer.unibe.ch/.

  7. Alternative Splicing of Neuronal Differentiation Factor TRF2 Regulated by HNRNPH1/H2

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    Ioannis Grammatikakis

    2016-05-01

    Full Text Available During neuronal differentiation, use of an alternative splice site on the rat telomere repeat-binding factor 2 (TRF2 mRNA generates a short TRF2 protein isoform (TRF2-S capable of derepressing neuronal genes. However, the RNA-binding proteins (RBPs controlling this splicing event are unknown. Here, using affinity pull-down analysis, we identified heterogeneous nuclear ribonucleoproteins H1 and H2(HNRNPH as RBPs specifically capable of interacting with the spliced RNA segment (exon 7 of Trf2 pre-mRNA. HNRNPH proteins prevent the production of the short isoform of Trf2 mRNA, as HNRNPH silencing selectively elevates TRF2-S levels. Accordingly, HNRNPH levels decline while TRF2-S levels increase during neuronal differentiation. In addition, CRISPR/Cas9-mediated deletion of hnRNPH2 selectively accelerates the NGF-triggered differentiation of rat pheochromocytoma cells into neurons. In sum, HNRNPH is a splicing regulator of Trf2 pre-mRNA that prevents the expression of TRF2-S, a factor implicated in neuronal differentiation.

  8. Genetic differentiation of watermelon landrace types in Mali revealed by microsatellite (SSR) markers

    DEFF Research Database (Denmark)

    Nantoume, Aminata Dolo; Andersen, Sven Bode; Jensen, Brita Dahl

    2013-01-01

    This study describes the genetic differentiation of a collection of 134 watermelon landrace accessions from Mali, representing red fleshed dessert and white fleshed seed and cooking type watermelons from five regions, plus three commercial dessert type cultivars with red flesh. The material...... the accessions into use groups (dessert, cooking, seed processing) explained 25 % of the variation. When categorising the accessions further into 10 landrace types, differentiated on the basis of use groups, local accession name, flesh colour and seed phenotype, these landrace types explained 26...... % of the variation. Analysis with the software Structure revealed that the accessions with confidence could be separated into two major genetic groups, related to flesh colour (red and white) of the watermelon fruits. The same analysis further indicated that the material may be differentiated into eight genetic sub...

  9. Functional Features of Trans-differentiated Hair Cells Mediated by Atoh1 Reveals a Primordial Mechanism

    OpenAIRE

    Yang, Juanmei; Bouvron, Sonia; Lv, Ping; Chi, Fanglu; Yamoah, Ebenezer N.

    2012-01-01

    Evolution has transformed a simple ear with few vestibular maculae into a complex 3-dimensional structure consisting of nine distinct endorgans. It is debatable whether the sensory epithelia underwent progressive segregation or emerged from distinct sensory patches. To address these uncertainties we examined the morphological and functional phenotype of trans-differentiated rat hair cells to reveal their primitive or endorgan-specific origins. Additionally, it is uncertain how Atoh1-mediated ...

  10. Two isoforms of TALDO1 generated by alternative translational initiation show differential nucleocytoplasmic distribution to regulate the global metabolic network

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    Moriyama, Tetsuji; Tanaka, Shu; Nakayama, Yasumune; Fukumoto, Masahiro; Tsujimura, Kenji; Yamada, Kohji; Bamba, Takeshi; Yoneda, Yoshihiro; Fukusaki, Eiichiro; Oka, Masahiro

    2016-01-01

    Transaldolase 1 (TALDO1) is a rate-limiting enzyme involved in the pentose phosphate pathway, which is traditionally thought to occur in the cytoplasm. In this study, we found that the gene TALDO1 has two translational initiation sites, generating two isoforms that differ by the presence of the first 10 N-terminal amino acids. Notably, the long and short isoforms were differentially localised to the cell nucleus and cytoplasm, respectively. Pull-down and in vitro transport assays showed that the long isoform, unlike the short one, binds to importin α and is actively transported into the nucleus in an importin α/β-dependent manner, demonstrating that the 10 N-terminal amino acids are essential for its nuclear localisation. Additionally, we found that these two isoforms can form homo- and/or hetero-dimers with different localisation dynamics. A metabolite analysis revealed that the subcellular localisation of TALDO1 is not crucial for its activity in the pentose phosphate pathway. However, the expression of these two isoforms differentially affected the levels of various metabolites, including components of the tricarboxylic acid cycle, nucleotides, and sugars. These results demonstrate that the nucleocytoplasmic distribution of TALDO1, modulated via alternative translational initiation and dimer formation, plays an important role in a wide range of metabolic networks. PMID:27703206

  11. Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining

    Science.gov (United States)

    van Schendel, Robin; van Heteren, Jane; Welten, Richard; Tijsterman, Marcel

    2016-01-01

    For more than half a century, genotoxic agents have been used to induce mutations in the genome of model organisms to establish genotype-phenotype relationships. While inaccurate replication across damaged bases can explain the formation of single nucleotide variants, it remained unknown how DNA damage induces more severe genomic alterations. Here, we demonstrate for two of the most widely used mutagens, i.e. ethyl methanesulfonate (EMS) and photo-activated trimethylpsoralen (UV/TMP), that deletion mutagenesis is the result of polymerase Theta (POLQ)-mediated end joining (TMEJ) of double strand breaks (DSBs). This discovery allowed us to survey many thousands of available C. elegans deletion alleles to address the biology of this alternative end-joining repair mechanism. Analysis of ~7,000 deletion breakpoints and their cognate junctions reveals a distinct order of events. We found that nascent strands blocked at sites of DNA damage can engage in one or more cycles of primer extension using a more downstream located break end as a template. Resolution is accomplished when 3’ overhangs have matching ends. Our study provides a step-wise and versatile model for the in vivo mechanism of POLQ action, which explains the molecular nature of mutagen-induced deletion alleles. PMID:27755535

  12. Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins

    Directory of Open Access Journals (Sweden)

    Stephanie C. Huelga

    2012-02-01

    Full Text Available Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS in human cells. Using splicing-sensitive microarrays, crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and autoregulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.

  13. Differential effects of uninostril and alternate nostril pranayamas on cardiovascular parameters and reaction time

    Directory of Open Access Journals (Sweden)

    Ananda Balayogi Bhavanani

    2014-01-01

    Full Text Available Background: Recent studies have reported the differential physiological and psychological effects of yogic uninostril breathing (UNB and alternate nostril breathing (ANB techniques. This study aims to determine differential effects of these techniques on reaction time (RT, heart rate (HR, and blood pressure (BP. Materials and Methods: Twenty yoga-trained subjects came to the lab on six different days and RT, HR, and BP were recorded randomly before and after nine rounds of right UNB (surya nadi [SN], left UNB (chandra nadi [CN], right initiated ANB (surya bhedana [SB], left initiated ANB (chandra bhedana [CB], nadi shuddhi (NS, and normal breathing (NB. Results: Overall comparison of ∆ % changes showed statistically significant differences between groups for all parameters. There was an overall reduction in HR- and BP-based parameters following CB, CN, and NS with concurrent increases following SB and SN. The differential effects of right nostril initiated (SB and SN and left nostril initiated (CB, CN, and NS UNB and ANB techniques were clearly evidenced. Changes following NB were insignificant in all respects. The overall comparison of ∆ % changes for RT showed statistically significant differences between groups that were significantly lowered following both SB and SN. Discussion and Conclusion: Our study provides evidence of sympathomimetic effects of right nostril initiated pranayamas with sympatholytic/parasympathomimetic effect following left nostril initiated pranayamas. We suggest that the main effect of UNB and ANB techniques is determined by the nostril used for inspiration rather than that used for expiration. We conclude that right and left yogic UNB and ANB techniques have differential physiological effects that are in tune with the traditional swara yoga concept that air flow through right nostril (SN and pingala swara is activatory in nature, whereas the flow through left nostril (CN and ida swara is relaxatory.

  14. An Oncogenic Role for Alternative NF-κB Signaling in DLBCL Revealed upon Deregulated BCL6 Expression

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    Baochun Zhang

    2015-05-01

    Full Text Available Diffuse large B cell lymphoma (DLBCL is a complex disease comprising diverse subtypes and genetic profiles. Possibly because of the prevalence of genetic alterations activating canonical NF-κB activity, a role for oncogenic lesions that activate the alternative NF-κB pathway in DLBCL has remained elusive. Here, we show that deletion/mutation of TRAF3, a negative regulator of the alternative NF-κB pathway, occurs in ∼15% of DLBCLs and that it often coexists with BCL6 translocation, which prevents terminal B cell differentiation. Accordingly, in a mouse model constitutive activation of the alternative NF-κB pathway cooperates with BCL6 deregulation in DLBCL development. This work demonstrates a key oncogenic role for the alternative NF-κB pathway in DLBCL development.

  15. Immunoproteomics of Brucella abortus reveals differential antibody profiles between S19-vaccinated and naturally infected cattle.

    Science.gov (United States)

    Pajuaba, Ana C A M; Silva, Deise A O; Almeida, Karine C; Cunha-Junior, Jair P; Pirovani, Carlos P; Camillo, Luciana R; Mineo, José R

    2012-03-01

    Brucella abortus is a Gram-negative intracellular bacterium that causes infectious abortion in food-producing animals and chronic infection in humans. This study aimed to characterize a B. abortus S19 antigen preparation obtained by Triton X-114 (TX-114) extraction through immunoproteomics to differentiate infected from vaccinated cattle. Three groups of bovine sera were studied: GI, 30 naturally infected cows; GII, 30 S19-vaccinated heifers; and GIII, 30 nonvaccinated seronegative cows. One-dimensional (1D) and two-dimensional electrophoretic profiles of TX-114 hydrophilic phase antigen revealed a broad spectrum of polypeptides (10-79 kDa). 1D immunoblot showed widespread seroreactivity profile in GI compared with restricted profile in GII. Three antigenic components (10, 12, 17 kDa) were recognized exclusively by GI sera, representing potential markers of infection and excluding vaccinal response. The proteomic characterization revealed 56 protein spots, 27 of which were antigenic spots showing differential seroreactivity profile between GI and GII, especially polypeptides abortus S19 proteins (Invasion protein B, Sod, Dps, Ndk, and Bfr), which were related with antigenicity in naturally infected cattle. In conclusion, immunoproteomics of this new antigen preparation enabled the characterization of proteins that could be used as tools to develop sensitive and specific immunoassays for serodiagnosis of bovine brucellosis, with emphasis on differentiation between S19 vaccinated and infected cattle. PMID:22539433

  16. Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

    OpenAIRE

    Shao, Wei; Zhao, Qiong-Yi; Wang, Xiu-Ye; Xu, Xin-Yan; Tang, Qing; Li, Muwang; Li, Xuan; Xu, Yong-Zhen

    2012-01-01

    Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. The authors identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is ...

  17. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Institute of Scientific and Technical Information of China (English)

    Yonglong Yu; Dong Zhu; Chaoying Ma; Hui Cao; Yaping Wang; Yanhao Xu; Wenying Zhang; Yueming Yan

    2016-01-01

    Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20) during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA) was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further informa-tion about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  18. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Directory of Open Access Journals (Sweden)

    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  19. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors.

    Directory of Open Access Journals (Sweden)

    Nathan Salomonis

    2009-11-01

    Full Text Available The role of alternative splicing in self-renewal, pluripotency and tissue lineage specification of human embryonic stem cells (hESCs is largely unknown. To better define these regulatory cues, we modified the H9 hESC line to allow selection of pluripotent hESCs by neomycin resistance and cardiac progenitors by puromycin resistance. Exon-level microarray expression data from undifferentiated hESCs and cardiac and neural precursors were used to identify splice isoforms with cardiac-restricted or common cardiac/neural differentiation expression patterns. Splice events for these groups corresponded to the pathways of cytoskeletal remodeling, RNA splicing, muscle specification, and cell cycle checkpoint control as well as genes with serine/threonine kinase and helicase activity. Using a new program named AltAnalyze (http://www.AltAnalyze.org, we identified novel changes in protein domain and microRNA binding site architecture that were predicted to affect protein function and expression. These included an enrichment of splice isoforms that oppose cell-cycle arrest in hESCs and that promote calcium signaling and cardiac development in cardiac precursors. By combining genome-wide predictions of alternative splicing with new functional annotations, our data suggest potential mechanisms that may influence lineage commitment and hESC maintenance at the level of specific splice isoforms and microRNA regulation.

  20. Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

    OpenAIRE

    Gan, Qiang; Chepelev, Iouri; Wei, Gang; Tarayrah, Lama; Cui, Kairong; Zhao, Keji; Chen, Xin

    2010-01-01

    Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understandings of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously.

  1. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine

    OpenAIRE

    Zhen Sheng; Yi Sun; Ruixin Zhu; Na Jiao; Kailin Tang; Zhiwei Cao; Chao Ma

    2015-01-01

    Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, R...

  2. Transcriptome Bioinformatical Analysis of Vertebrate Stages of Schistosoma japonicum Reveals Alternative Splicing Events

    OpenAIRE

    Xinye Wang; Xindong Xu; Xingyu Lu; Yuanbin Zhang; Weiqing Pan

    2015-01-01

    Alternative splicing is a molecular process that contributes greatly to the diversification of proteome and to gene functions. Understanding the mechanisms of stage-specific alternative splicing can provide a better understanding of the development of eukaryotes and the functions of different genes. Schistosoma japonicum is an infectious blood-dwelling trematode with a complex lifecycle that causes the tropical disease schistosomiasis. In this study, we analyzed the transcriptome of Schistoso...

  3. Novel Molecular Insights into Classical and Alternative Activation States of Microglia as Revealed by Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Proteomics.

    Science.gov (United States)

    Bell-Temin, Harris; Culver-Cochran, Ashley E; Chaput, Dale; Carlson, Christina M; Kuehl, Melanie; Burkhardt, Brant R; Bickford, Paula C; Liu, Bin; Stevens, Stanley M

    2015-12-01

    Microglia, the resident immune cells of the brain, have been shown to display a complex spectrum of roles that span from neurotrophic to neurotoxic depending on their activation status. Microglia can be classified into four stages of activation, M1, which most closely matches the classical (pro-inflammatory) activation stage, and the alternative activation stages M2a, M2b, and M2c. The alternative activation stages have not yet been comprehensively analyzed through unbiased, global-scale protein expression profiling. In this study, BV2 mouse immortalized microglial cells were stimulated with agonists specific for each of the four stages and total protein expression for 4644 protein groups was quantified using SILAC-based proteomic analysis. After validating induction of the various stages through a targeted cytokine assay and Western blotting of activation states, the data revealed novel insights into the similarities and differences between the various states. The data identify several protein groups whose expression in the anti-inflammatory, pro-healing activation states are altered presumably to curtail inflammatory activation through differential protein expression, in the M2a state including CD74, LYN, SQST1, TLR2, and CD14. The differential expression of these proteins promotes healing, limits phagocytosis, and limits activation of reactive nitrogen species through toll-like receptor cascades. The M2c state appears to center around the down-regulation of a key member in the formation of actin-rich phagosomes, SLP-76. In addition, the proteomic data identified a novel activation marker, DAB2, which is involved in clathrin-mediated endocytosis and is significantly different between M2a and either M1 or M2b states. Western blot analysis of mouse primary microglia stimulated with the various agonists of the classical and alternative activation states revealed a similar trend of DAB2 expression compared with BV2 cells.

  4. Effect of alternation of agar and agarose on the green plant differentiation frequency of calli from wild rice

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ In vitro culture of wild rice was difficult. Recently, we found that high agarose concentration of different media could improve the green plant differentiation frequency of calli from wild rice. We tested the effectiveness of alternation of agar and agarose in different media.

  5. Fair Pairs and Three Part Praise--Developing the Sustained Use of Differential Reinforcement of Alternative Behaviour

    Science.gov (United States)

    Williams, Hugh

    2012-01-01

    A training course of two after-school sessions was run for teaching assistants (TAs) in a UK inner city primary school. The subject of the training was classroom use of a version of differential reinforcement of alternative behaviours (DRAs) known as Fair Pairs. The training introduced the concept of "Three Part Praise" within Fair Pairs. The…

  6. Teacher Implementation of Trial-Based Functional Analysis and Differential Reinforcement of Alternative Behavior for Students with Challenging Behavior

    Science.gov (United States)

    Flynn, Susan D.; Lo, Ya-yu

    2016-01-01

    The purpose of this study was to examine the effects of a training package on three middle school special education teachers' accurate implementation of trial-based functional analysis (TBFA) and differential reinforcement of alternative behavior (DRA) with their students with autism spectrum disorders or emotional and behavioral disorders in the…

  7. Differential Reinforcement of Alternative Behavior Increases Resistance to Extinction: Clinical Demonstration, Animal Modeling, and Clinical Test of One Solution

    Science.gov (United States)

    Mace, F. Charles; McComas, Jennifer J.; Mauro, Benjamin C.; Progar, Patrick R.; Taylor, Bridget; Ervin, Ruth; Zangrillo, Amanda N.

    2010-01-01

    Basic research with pigeons on behavioral momentum suggests that differential reinforcement of alternative behavior (DRA) can increase the resistance of target behavior to change. This finding suggests that clinical applications of DRA may inadvertently increase the persistence of target behavior even as it decreases its frequency. We conducted…

  8. Multivoxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

    DEFF Research Database (Denmark)

    Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.;

    2013-01-01

    human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during...... vocalization, compared with during passive listening. One network of regions appears to encode an “error signal” regardless of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across...... presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple...

  9. Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

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    Iain C. Macaulay

    2016-02-01

    Full Text Available The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment.

  10. Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes.

    Directory of Open Access Journals (Sweden)

    I-Hsuan Lin

    Full Text Available Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs and the hypomethylation of the megabase-sized partially methylated domains (PMDs are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.

  11. Structures of HSF2 Reveal Mechanisms for Differential Regulation of Human Heat Shock Factors

    Science.gov (United States)

    Jaeger, Alex M.; Pemble, Charles W.; Sistonen, Lea; Thiele, Dennis J.

    2016-01-01

    Heat Shock Transcription Factor (HSF) family members function in stress protection and in human disease including proteopathies, neurodegeneration and cancer. The mechanisms that drive distinct post-translational modifications, co-factor recruitment and target gene activation for specific HSF paralogs are unknown. We present high-resolution crystal structures of the human HSF2 DNA-binding domain (DBD) bound to DNA, revealing an unprecedented view of HSFs that provides insights into their unique biology. The HSF2 DBD structures resolve a novel carboxyl-terminal helix that directs the coiled-coil domain to wrap around DNA, exposing paralog-specific sequences of the DBD surface, for differential post-translational modifications and co-factor interactions. We further demonstrate a direct interaction between HSF1 and HSF2 through their coiled-coil domains. Together, these features provide a new model for HSF structure as the basis for differential and combinatorial regulation to influence the transcriptional response to cellular stress. PMID:26727490

  12. Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics.

    Science.gov (United States)

    Wu, Xia; Vellaichamy, Adaikkalam; Wang, Dongping; Zamdborg, Leonid; Kelleher, Neil L; Huber, Steven C; Zhao, Youfu

    2013-02-21

    Protein lysine acetylation (LysAc) has recently been demonstrated to be widespread in E. coli and Salmonella, and to broadly regulate bacterial physiology and metabolism. However, LysAc in plant pathogenic bacteria is largely unknown. Here we first report the lysine acetylome of Erwinia amylovora, an enterobacterium causing serious fire blight disease of apples and pears. Immunoblots using generic anti-lysine acetylation antibodies demonstrated that growth conditions strongly affected the LysAc profiles in E. amylovora. Differential LysAc profiles were also observed for two E. amylovora strains, known to have differential virulence in plants, indicating translational modification of proteins may be important in determining virulence of bacterial strains. Proteomic analysis of LysAc in two E. amylovora strains identified 141 LysAc sites in 96 proteins that function in a wide range of biological pathways. Consistent with previous reports, 44% of the proteins are involved in metabolic processes, including central metabolism, lipopolysaccharide, nucleotide and amino acid metabolism. Interestingly, for the first time, several proteins involved in E. amylovora virulence, including exopolysaccharide amylovoran biosynthesis- and type III secretion-associated proteins, were found to be lysine acetylated, suggesting that LysAc may play a major role in bacterial virulence. Comparative analysis of LysAc sites in E. amylovora and E. coli further revealed the sequence and structural commonality for LysAc in the two organisms. Collectively, these results reinforce the notion that LysAc of proteins is widespread in bacterial metabolism and virulence. PMID:23234799

  13. Splicing reporter mice revealed the evolutionally conserved switching mechanism of tissue-specific alternative exon selection.

    Directory of Open Access Journals (Sweden)

    Akihide Takeuchi

    Full Text Available Since alternative splicing of pre-mRNAs is essential for generating tissue-specific diversity in proteome, elucidating its regulatory mechanism is indispensable to understand developmental process or tissue-specific functions. We have been focusing on tissue-specific regulation of mutually exclusive selection of alternative exons because this implies the typical molecular mechanism of alternative splicing regulation and also can be good examples to elicit general rule of "splice code". So far, mutually exclusive splicing regulation has been explained by the outcome from the balance of multiple regulators that enhance or repress either of alternative exons discretely. However, this "balance" model is open to questions of how to ensure the selection of only one appropriate exon out of several candidates and how to switch them. To answer these questions, we generated an original bichromatic fluorescent splicing reporter system for mammals using fibroblast growth factor-receptor 2 (FGFR2 gene as model. By using this splicing reporter, we demonstrated that FGFR2 gene is regulated by the "switch-like" mechanism, in which key regulators modify the ordered splice-site recognition of two mutually exclusive exons, eventually ensure single exon selection and their distinct switching. Also this finding elucidated the evolutionally conserved "splice code," in which combination of tissue-specific and broadly expressed RNA binding proteins regulate alternative splicing of specific gene in a tissue-specific manner. These findings provide the significant cue to understand how a number of spliced genes are regulated in various tissue-specific manners by a limited number of regulators, eventually to understand developmental process or tissue-specific functions.

  14. Differential spectral power alteration following acupuncture at different designated places revealed by magnetoencephalography

    Science.gov (United States)

    You, Youbo; Bai, Lijun; Dai, Ruwei; Xue, Ting; Zhong, Chongguang; Liu, Zhenyu; Wang, Hu; Feng, Yuanyuan; Wei, Wenjuan; Tian, Jie

    2012-03-01

    As an ancient therapeutic technique in Traditional Chinese Medicine, acupuncture has been used increasingly in modern society to treat a range of clinical conditions as an alternative and complementary therapy. However, acupoint specificity, lying at the core of acupuncture, still faces many controversies. Considering previous neuroimaging studies on acupuncture have mainly employed functional magnetic resonance imaging, which only measures the secondary effect of neural activity on cerebral metabolism and hemodynamics, in the current study, we adopted an electrophysiological measurement technique named magnetoencephalography (MEG) to measure the direct neural activity. 28 healthy college students were recruited in this study. We filtered MEG data into 5 consecutive frequency bands (delta, theta, alpha, beta and gamma band) and grouped 140 sensors into 10 main brain regions (left/right frontal, central, temporal, parietal and occipital regions). Fast Fourier Transformation (FFT) based spectral analysis approach was further performed to explore the differential band-limited power change patterns of acupuncture at Stomach Meridian 36 (ST36) using a nearby nonacupoint (NAP) as control condition. Significantly increased delta power and decreased alpha as well as beta power in bilateral frontal ROIs were observed following stimulation at ST36. Compared with ST36, decreased alpha power in left and right central, right parietal as well as right temporal ROIs were detected in NAP group. Our research results may provide additional evidence for acupoint specificity.

  15. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

    Directory of Open Access Journals (Sweden)

    Shuiquan eTang

    2016-02-01

    Full Text Available The genomes of two closely related Dehalobacter strains (strain CF and strain DCA were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF, 1,1,1-trichloroethane (1,1,1-TCA and 1,1-dichloroethane (1,1-DCA. The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA and strain DCA (that dechlorinates 1,1-DCA each contain 17 putative reductive dehalogenase homologous (rdh genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB, and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and greater than 99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1 and corrinoid biosynthesis pathways (strains E1 and PER-K23. The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to Dehalococcoides mccartyi

  16. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates.

    Science.gov (United States)

    Tang, Shuiquan; Wang, Po Hsiang; Higgins, Steven A; Löffler, Frank E; Edwards, Elizabeth A

    2016-01-01

    The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis

  17. Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri.

    Science.gov (United States)

    Arnoux, E; Eraud, C; Navarro, N; Tougard, C; Thomas, A; Cavallo, F; Vetter, N; Faivre, B; Garnier, S

    2014-12-01

    Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40-50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was associated with a very strong genetic differentiation (Fst from 0.073-0.153), making this pattern a remarkable case in birds given the very small spatial scale considered. Molecular data (mitochondrial control region sequences and microsatellite genotypes) suggest that this strong differentiation could have occurred in situ, although alternative hypotheses cannot be fully discarded. This study suggests that the ongoing habitat fragmentation, especially in tropical forests, may have a deeper impact than previously thought on avian populations.

  18. Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing.

    Science.gov (United States)

    Pancsa, Rita; Macossay-Castillo, Mauricio; Kosol, Simone; Tompa, Peter

    2016-01-01

    In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computational methods, we describe the structural and functional properties of previously proposed D. melanogaster and S. cerevisiae TR proteins and extensions. We found that in D. melanogaster TR affects long proteins in mainly regulatory roles. Their TR-extensions are structurally disordered and rich in binding motifs, which, together with their cell-type- and developmental stage-dependent inclusion, suggest that similarly to alternatively spliced exons they rewire cellular interaction networks in a temporally and spatially controlled manner. In contrast, yeast TR proteins are rather short and fulfil mainly housekeeping functions, like translation. Yeast extensions usually lack disorder and linear motifs, which precludes elucidating their functional relevance with sufficient confidence. Therefore we propose that by being much more restricted and by lacking clear functional hallmarks in yeast as opposed to fruit fly, TR shows remarkable parallels with alternative splicing. Additionally, the lack of conservation of TR extensions among orthologous TR proteins suggests that TR-mediated functions may be generally specific to lower taxonomic levels. PMID:27561673

  19. ROS play a critical role in the differentiation of alternatively activated macrophages and the occurrence of tumor-associated macrophages

    Institute of Scientific and Technical Information of China (English)

    Yan Zhang; Swati Choksi; Kun Chen; Yelena Pobezinskaya; Ilona Linnoila; Zheng-Gang Liu

    2013-01-01

    Differentiation to different types of macrophages determines their distinct functions.Tumor-associated macrophages (TAMs) promote tumorigenesis owing to their proangiogenic and immune-suppressive functions similar to those of alternatively activated (M2) macrophages.We report that reactive oxygen species (ROS) production is critical for macrophage differentiation and that inhibition of superoxide (O2-) production specifically blocks the differentiation of M2 macrophages.We found that when monocytes are triggered to differentiate,O2-is generated and is needed for the biphasic ERK activation,which is critical for macrophage differentiation.We demonstrated that ROS elimination by butylated hydroxyanisole (BHA) and other ROS inhibitors blocks macrophage differentiation.However,the inhibitory effect of ROS elimination on macrophage differentiation is overcome when cells are polarized to classically activated (M1),but not M2,macrophages.More importantly,the continuous administration of the ROS inhibitor BHA efficiently blocked the occurrence of TAMs and markedly suppressed tumorigenesis in mouse cancer models.Targeting TAMs by blocking ROS can be a potentially effective method for cancer treatment.

  20. Revealed Comparative Advantage and the Alternatives as Measures of International Specialization

    DEFF Research Database (Denmark)

    Laursen, Keld

    2015-01-01

    This paper provides an analysis of Balassa's 'revealed comparative advantage' (RCA). It shows that when using RCA, it should be adjusted such that it becomes symmetric around its neutral value. The proposed adjusted index is called 'revealed symmetric comparative advantage' (RSCA). The theoretical...... Balance, Chi Square, and Bowen's Net Trade Index. The result of the analysis is that RSCA-on balance-is the best measure of comparative advantage....... discussion focuses on the properties of RSCA and empirical evidence, based on the Jarque-Bera test for normality of the regression error terms, using both the RCA and RSCA indices. We compare RSCA to other measures of international trade specialization including the Michaely index, the Contribution to Trade...

  1. Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

    Science.gov (United States)

    Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

    2016-09-01

    There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.

  2. Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina

    DEFF Research Database (Denmark)

    Gallo, G.; Renzone, G.; Alduina, R.;

    2010-01-01

    A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...

  3. Functional characterisation of an intron retaining K+ transporter of barley reveals intron-mediated alternate splicing

    KAUST Repository

    Shahzad, K.

    2015-01-01

    Intron retention in transcripts and the presence of 5 and 3 splice sites within these introns mediate alternate splicing, which is widely observed in animals and plants. Here, functional characterisation of the K+ transporter, HvHKT2;1, with stably retained introns from barley (Hordeum vulgare) in yeast (Saccharomyces cerevisiae), and transcript profiling in yeast and transgenic tobacco (Nicotiana tabacum) is presented. Expression of intron-retaining HvHKT2;1 cDNA (HvHKT2;1-i) in trk1, trk2 yeast strain defective in K+ uptake restored growth in medium containing hygromycin in the presence of different concentrations of K+ and mediated hypersensitivity to Na+. HvHKT2;1-i produces multiple transcripts via alternate splicing of two regular introns and three exons in different compositions. HKT isoforms with retained introns and exon skipping variants were detected in relative expression analysis of (i) HvHKT2;1-i in barley under native conditions, (ii) in transgenic tobacco plants constitutively expressing HvHKT2;1-i, and (iii) in trk1, trk2 yeast expressing HvHKT2;1-i under control of an inducible promoter. Mixed proportions of three HKT transcripts: HvHKT2;1-e (first exon region), HvHKT2;1-i1 (first intron) and HvHKT2;1-i2 (second intron) were observed. The variation in transcript accumulation in response to changing K+ and Na+ concentrations was observed in both heterologous and plant systems. These findings suggest a link between intron-retaining transcripts and different splice variants to ion homeostasis, and their possible role in salt stress.

  4. Characterization of an electrochemical mercury sensor using alternating current, cyclic, square wave and differential pulse voltammetry

    Energy Technology Data Exchange (ETDEWEB)

    Guerreiro, Gabriela V.; Zaitouna, Anita J.; Lai, Rebecca Y., E-mail: rlai2@unl.edu

    2014-01-31

    Graphical abstract: -- Highlights: •An electrochemical Hg(II) sensor based on T–Hg(II)–T sensing motif was fabricated. •A methylene blue-modified DNA probe was used to fabricate the sensor. •Sensor performance was evaluated using ACV, CV, SWV, and DPV. •The sensor behaves as a “signal-off” sensor in ACV and CV. •The sensor behaves as either a “signal-on” or “signal-off” sensor in SWV and DPV. -- Abstract: Here we report the characterization of an electrochemical mercury (Hg{sup 2+}) sensor constructed with a methylene blue (MB)-modified and thymine-containing linear DNA probe. Similar to the linear probe electrochemical DNA sensor, the resultant sensor behaved as a “signal-off” sensor in alternating current voltammetry and cyclic voltammetry. However, depending on the applied frequency or pulse width, the sensor can behave as either a “signal-off” or “signal-on” sensor in square wave voltammetry (SWV) and differential pulse voltammetry (DPV). In SWV, the sensor showed “signal-on” behavior at low frequencies and “signal-off” behavior at high frequencies. In DPV, the sensor showed “signal-off” behavior at short pulse widths and “signal-on” behavior at long pulse widths. Independent of the sensor interrogation technique, the limit of detection was found to be 10 nM, with a linear dynamic range between 10 nM and 500 nM. In addition, the sensor responded to Hg{sup 2+} rather rapidly; majority of the signal change occurred in <20 min. Overall, the sensor retains all the characteristics of this class of sensors; it is reagentless, reusable, sensitive, specific and selective. This study also highlights the feasibility of using a MB-modified probe for real-time sensing of Hg{sup 2+}, which has not been previously reported. More importantly, the observed “switching” behavior in SWV and DPV is potentially generalizable and should be applicable to most sensors in this class of dynamics-based electrochemical biosensors.

  5. Structure of Est3 reveals a bimodal surface with differential roles in telomere replication.

    Science.gov (United States)

    Rao, Timsi; Lubin, Johnathan W; Armstrong, Geoffrey S; Tucey, Timothy M; Lundblad, Victoria; Wuttke, Deborah S

    2014-01-01

    Telomerase is essential for continuous cellular proliferation. Substantial insights have come from studies of budding yeast telomerase, which consists of a catalytic core in association with two regulatory proteins, ever shorter telomeres 1 and 3 (Est1 and Est3). We report here a high-resolution structure of the Est3 telomerase subunit determined using a recently developed strategy that combines minimal NMR experimental data with Rosetta de novo structure prediction algorithms. Est3 adopts an overall protein fold which is structurally similar to that adopted by the shelterin component TPP1. However, the characteristics of the surface of the experimentally determined Est3 structure are substantially different from those predicted by prior homology-based models of Est3. Structure-guided mutagenesis of the complete surface of the Est3 protein reveals two adjacent patches on a noncanonical face of the protein that differentially mediate telomere function. Mapping these two patches on the Est3 structure defines a set of shared features between Est3 and HsTPP1, suggesting an analogous multifunctional surface on TPP1.

  6. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  7. Species versus guild level differentiation revealed across the annual cycle by isotopic niche examination.

    Science.gov (United States)

    Bodey, Thomas W; Ward, Eric J; Phillips, Richard A; McGill, Rona A R; Bearhop, Stuart

    2014-03-01

    Interspecific competitive interactions typically result in niche differentiation to alleviate competition through mechanisms including character displacement. However, competition is not the sole constraint on resource partitioning, and its effects are mediated by factors including the environmental context in which species coexist. Colonial seabirds provide an excellent opportunity to investigate the importance of competition in shaping realized niche widths because their life histories lead to variation in intra- and interspecific competition across the annual cycle. Dense breeding aggregations result in intense competition for prey in surrounding waters, whereas non-breeding dispersal to larger geographical areas produces lower densities of competitors. Bayesian hierarchical models of the isotopic niche, closely aligned to the trophic niche, reveal the degree of segregation between species and functional groups during both time periods. Surprisingly, species explained far more of the variance in the isotopic niche during the non-breeding than the breeding period. Our results underline the key role of non-breeding dynamics in alleviating competition and promoting distinctions between species through the facilitation of resource partitioning. Such situations may be common in a diverse range of communities sustained by ephemeral but abundant food items. This highlights how consideration of the hierarchical grouping of competitive interactions alongside consideration of abiotic constraints across the complete annual cycle allows a full understanding of the role of competition in driving patterns of character displacement. PMID:24215391

  8. Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation.

    Directory of Open Access Journals (Sweden)

    Masato S Ota

    2009-04-01

    Full Text Available The sense of taste is of critical importance to animal survival. Although studies of taste signal transduction mechanisms have provided detailed information regarding taste receptor calcium signaling molecules (TRCSMs, required for sweet/bitter/umami taste signal transduction, the ontogeny of taste cells is still largely unknown. We used a novel approach to investigate the molecular regulation of taste system development in mice by combining in silico and in vivo analyses. After discovering that TRCSMs colocalized within developing circumvallate papillae (CVP, we used computational analysis of the upstream regulatory regions of TRCSMs to investigate the possibility of a common regulatory network for TRCSM transcription. Based on this analysis, we identified Hes1 as a likely common regulatory factor, and examined its function in vivo. Expression profile analyses revealed that decreased expression of nuclear HES1 correlated with expression of type II taste cell markers. After stage E18, the CVP of Hes1(-/ (- mutants displayed over 5-fold more TRCSM-immunoreactive cells than did the CVP of their wild-type littermates. Thus, according to our composite analyses, Hes1 is likely to play a role in orchestrating taste cell differentiation in developing taste buds.

  9. Differential Reinforcement of Alternative Behavior Increases Resistance to Extinction: Clinical Demonstration, Animal Modeling, and Clinical Test of One Solution

    OpenAIRE

    Mace, F. Charles; McComas, Jennifer J; Mauro, Benjamin C.; Progar, Patrick R; Taylor, Bridget; Ervin, Ruth; Zangrillo, Amanda N

    2010-01-01

    Basic research with pigeons on behavioral momentum suggests that differential reinforcement of alternative behavior (DRA) can increase the resistance of target behavior to change. This finding suggests that clinical applications of DRA may inadvertently increase the persistence of target behavior even as it decreases its frequency. We conducted three coordinated experiments to test whether DRA has persistence-strengthening effects on clinically significant target behavior and then tested the ...

  10. Molecular cloning and functional characterization of a mouse gene upregulated by lipopolysaccharide treatment reveals alternative splicing

    International Nuclear Information System (INIS)

    Treatment of mouse cells with lipopolysaccharide (LPS) potently initiates an inflammatory response, but the underlying mechanisms are unclear. We therefore sought to characterize cDNA sequences of a new mouse LPS-responsive gene, and to evaluate the effects of MLrg. Full-length cDNAs were obtained from LPS-treated NIH3T3 cells. We report that the MLrg gene produces two alternative splice products (GenBank Accession Nos. (DQ316984) and (DQ320011)), respectively, encoding MLrgW and MLrgS polypeptides. Both proteins contain zinc finger and leucine zipper domains and are thus potential regulators of transcription. Expression of MLrgW and MLrgS were robustly upregulated following LPS treatment, and the proteins were localized predominantly in the nuclear membrane and cytoplasm. In stable transfectants over-expressing MLrgW the proportion of cells in G1 phase was significantly reduced, while in cells over-expressing MLrgS the proportion of cells in G2 was significantly increased; both proteins are thus potential regulators of cell cycle progression. Upregulation of MLrgW and MLrgS may be an important component of the LPS inflammatory pathway and of the host response to infection with GNB.

  11. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.

    Directory of Open Access Journals (Sweden)

    Zhen Sheng

    Full Text Available Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.

  12. Alternative to the Kohn-Sham equations: The Pauli potential differential equation

    Science.gov (United States)

    Levämäki, H.; Nagy, Á.; Kokko, K.; Vitos, L.

    2015-12-01

    A recently developed theoretical framework of performing self-consistent orbital-free (OF) density functional theory (DFT) calculations at Kohn-Sham DFT level accuracy is tested in practice. The framework is valid for spherically symmetric systems. Numerical results for the Beryllium atom are presented and compared to accurate Kohn-Sham data. These calculations make use of a differential equation that we have developed for the so called Pauli potential, a key quantity in OF-DFT. The Pauli potential differential equation and the OF Euler equation form a system of two coupled differential equations, which have to be solved simultaneously within the DFT self-consistent loop.

  13. A microfluidic platform reveals differential response of regulatory T cells to micropatterned costimulation arrays.

    Science.gov (United States)

    Lee, Joung-Hyun; Dustin, Michael L; Kam, Lance C

    2015-11-01

    T cells are key mediators of adaptive immunity. However, the overall immune response is often directed by minor subpopulations of this heterogeneous family of cells, owing to specificity of activation and amplification of functional response. Knowledge of differences in signaling and function between T cell subtypes is far from complete, but is clearly needed for understanding and ultimately leveraging this branch of the adaptive immune response. This report investigates differences in cell response to micropatterned surfaces by conventional and regulatory T cells. Specifically, the ability of cells to respond to the microscale geometry of TCR/CD3 and CD28 engagement is made possible using a magnetic-microfluidic device that overcomes limitations in imaging efficiency associated with conventional microscopy equipment. This device can be readily assembled onto micropatterned surfaces while maintaining the activity of proteins and other biomolecules necessary for such studies. In operation, a target population of cells is tagged using paramagnetic beads, and then trapped in a divergent magnetic field within the chamber. Following washing, the target cells are released to interact with a designated surface. Characterization of this system with mouse CD4(+) T cells demonstrated a 50-fold increase in target-to-background cell purity, with an 80% collection efficiency. Applying this approach to CD4(+)CD25(+) regulatory T cells, it is then demonstrated that these rare cells respond less selectively to micro-scale features of anti-CD3 antibodies than CD4(+)CD25(-) conventional T cells, revealing a difference in balance between TCR/CD3 and LFA-1-based adhesion. PKC-θ localized to the distal pole of regulatory T cells, away from the cell-substrate interface, suggests a mechanism for differential regulation of TCR/LFA-1-based adhesion. Moreover, specificity of cell adhesion to anti-CD3 features was dependent on the relative position of anti-CD28 signaling within the cell

  14. Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

    Directory of Open Access Journals (Sweden)

    Ferrari Francesco

    2009-06-01

    Full Text Available Abstract Background Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS, a Chinese Spring terminal deletion line (CS_5AL-10 and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions. Results The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed in Creso (which lacks the D genome or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region. Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10. Conclusion Bread and durum wheat genotypes were characterized by a different physiological reaction to water

  15. Comorbid Analysis of Genes Associated with Autism Spectrum Disorders Reveals Differential Evolutionary Constraints

    Science.gov (United States)

    David, Maude M.; Enard, David; Ozturk, Alp; Daniels, Jena; Jung, Jae-Yoon; Diaz-Beltran, Leticia; Wall, Dennis. P.

    2016-01-01

    The burden of comorbidity in Autism Spectrum Disorder (ASD) is substantial. The symptoms of autism overlap with many other human conditions, reflecting common molecular pathologies suggesting that cross-disorder analysis will help prioritize autism gene candidates. Genes in the intersection between autism and related conditions may represent nonspecific indicators of dysregulation while genes unique to autism may play a more causal role. Thorough literature review allowed us to extract 125 ICD-9 codes comorbid to ASD that we mapped to 30 specific human disorders. In the present work, we performed an automated extraction of genes associated with ASD and its comorbid disorders, and found 1031 genes involved in ASD, among which 262 are involved in ASD only, with the remaining 779 involved in ASD and at least one comorbid disorder. A pathway analysis revealed 13 pathways not involved in any other comorbid disorders and therefore unique to ASD, all associated with basal cellular functions. These pathways differ from the pathways associated with both ASD and its comorbid conditions, with the latter being more specific to neural function. To determine whether the sequence of these genes have been subjected to differential evolutionary constraints, we studied long term constraints by looking into Genomic Evolutionary Rate Profiling, and showed that genes involved in several comorbid disorders seem to have undergone more purifying selection than the genes involved in ASD only. This result was corroborated by a higher dN/dS ratio for genes unique to ASD as compare to those that are shared between ASD and its comorbid disorders. Short-term evolutionary constraints showed the same trend as the pN/pS ratio indicates that genes unique to ASD were under significantly less evolutionary constraint than the genes associated with all other disorders. PMID:27414027

  16. Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

    International Nuclear Information System (INIS)

    Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma

  17. A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus

    Directory of Open Access Journals (Sweden)

    Quintela Maria

    2008-12-01

    Full Text Available Abstract Background There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10-3 and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (πt was between 1.30 × 10-4 and 7.66 × 10-3 (average πt = 2.72 × 10-3 ± 2.06 × 10-3 and silent nucleotide diversity varied between 4.20 × 10-4and 2.76 × 10-2 (average πS = 9.22 × 10-3 ± 7.43 × 10-4. The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10-3 (average πa = 5.08 × 10-4 ± 7.43 × 103, which suggest that purifying selection is strong in these genes. FST values based on synonymous SNP's varied between -5.60 × 10-4 and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of FST = 0.03 (95% CI: 0.006 – 0.057 over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low

  18. The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion.

    Science.gov (United States)

    Hollerer, Ina; Curk, Tomaz; Haase, Bettina; Benes, Vladimir; Hauer, Christian; Neu-Yilik, Gabriele; Bhuvanagiri, Madhuri; Hentze, Matthias W; Kulozik, Andreas E

    2016-09-01

    Stress adaptation plays a pivotal role in biological processes and requires tight regulation of gene expression. In this study, we explored the effect of cellular stress on mRNA polyadenylation and investigated the implications of regulated polyadenylation site usage on mammalian gene expression. High-confidence polyadenylation site mapping combined with global pre-mRNA and mRNA expression profiling revealed that stress induces an accumulation of genes with differentially expressed polyadenylated mRNA isoforms in human cells. Specifically, stress provokes a global trend in polyadenylation site usage toward decreased utilization of promoter-proximal poly(A) sites in introns or ORFs and increased utilization of promoter-distal polyadenylation sites in intergenic regions. This extensively affects gene expression beyond regulating mRNA abundance by changing mRNA length and by altering the configuration of open reading frames. Our study highlights the impact of post-transcriptional mechanisms on stress-dependent gene regulation and reveals the differential expression of alternatively polyadenylated transcripts as a common stress-induced mechanism in mammalian cells. PMID:27407180

  19. Immortalized mesenchymal stem cells: an alternative to primary mesenchymal stem cells in neuronal differentiation and neuroregeneration associated studies

    Directory of Open Access Journals (Sweden)

    Gong Min

    2011-11-01

    Full Text Available Abstract Background Mesenchymal stem cells (MSCs can be induced to differentiate into neuronal cells under appropriate cellular conditions and transplanted in brain injury and neurodegenerative diseases animal models for neuroregeneration studies. In contrast to the embryonic stem cells (ESCs, MSCs are easily subject to aging and senescence because of their finite ability of self-renewal. MSCs senescence seriously affected theirs application prospects as a promising tool for cell-based regenerative medicine and tissue engineering. In the present study, we established a reversible immortalized mesenchymal stem cells (IMSCs line by using SSR#69 retrovirus expressing simian virus 40 large T (SV40T antigen as an alternative to primary MSCs. Methods The retroviral vector SSR#69 expressing simian virus 40 large T (SV40T antigen was used to construct IMSCs. IMSCs were identified by flow cytometry to detect cell surface makers. To investigate proliferation and differentiation potential of IMSCs, cell growth curve determination and mesodermal trilineage differentiation tests were performed. Neuronal differentiation characteristics of IMSCs were detected in vitro. Before IMSCs transplantation, we excluded its tumorigenicity in nude mice firstly. The Morris water maze tests and shuttle box tests were performed five weeks after HIBD models received cells transplantation therapy. Results In this study, reversible IMSCs were constructed successfully and had the similar morphology and cell surface makers as primary MSCs. IMSCs possessed better ability of proliferation and anti-senescence compared with primary MSCs, while maintained multilineage differentiation capacity. Neural-like cells derived from IMSCs had similar expressions of neural-specific genes, protein expression patterns and resting membrane potential (RMP compared with their counterparts derived from primary MSCs. There was no bump formation in nude mice subcutaneously injected with IMSCs. IMSCs

  20. Implications to Postsecondary Faculty of Alternative Calculation Methods of Gender-Based Wage Differentials.

    Science.gov (United States)

    Hagedorn, Linda Serra

    1998-01-01

    A study explored two distinct methods of calculating a precise measure of gender-based wage differentials among college faculty. The first estimation considered wage differences using a formula based on human capital; the second included compensation for past discriminatory practices. Both measures were used to predict three specific aspects of…

  1. Direct differentiation of atrial and ventricular myocytes from human embryonic stem cells by alternating retinoid signals

    Institute of Scientific and Technical Information of China (English)

    Qiangzhe Zhang; Li Chen; Tian Tian; Xin Wang; Pu Li; Jurgen Hescheler; Guangju Ji; Yue Ma; Junjie Jiang; Pengcheng Han; Qi Yuan; Jing Zhang; Xiaoqian Zhang; Yanyan Xu; Henghua Cao; Qingzhang Meng

    2011-01-01

    Although myocyte cell transplantation studies have suggested a promising therapeutic potential for myocardial infarction, a major obstacle to the development of clinical therapies for myocardial repair is the difficulties associated with obtaining relatively homogeneous ventricular myocytes for transplantation. Human embryonic stem cells (hESCs)are a promising source of cardiomyocytes. Here we report that retinoid signaling regulates the fate specification of atrial versus ventricular myocytes during cardiac differentiation of hESCs. We found that both Noggin and the panretinoic acid receptor antagonist BMS-189453 (RAi) significantly increased the cardiac differentiation efficiency of hESCs. To investigate retinoid functions, we compared Noggin+RAi-treated cultures with Noggin+RA-treated cultures. Our results showed that the expression levels of the ventricular-specific gene IRX-4 were radically elevated in Noggin+RAi-treated cultures. MLC-2V, another ventricular-specific marker, was expressed in the majority of the cardiomyocytes in Noggin+RAi-treated cultures, hut not in the cardiomyocytes of Noggin+RA-treated cultures. Flow cytometry analysis and electrophysiologicai studies indicated that with 64.7 ± 0.88% (mean ± s.e.m) cardiac differentiation efficiency, 83% of the cardiomyocytes in Noggin+RAi-treated cultures had embryonic ventricular-like action potentials (APs). With 50.7 ± 1.76% cardiac differentiation efficiency, 94% of the cardiomyocytes in Noggin+RA-treated cultures had embryonic atrial-like APs. These results were further confirmed by imaging studies that assessed the patterns and properties of the Ca2+ sparks of the cardiomyocytes from the two cultures. These findings demonstrate that retinoid signaling specifies the atrial versus ventricular differentiation of hESCs. This study also shows that relatively homogeneous embryonic atrial- and ventricular-like myocyte populations can be efficiently derived from hESCs by specifically regulating Noggin

  2. Boolean Modeling Reveals the Necessity of Transcriptional Regulation for Bistability in PC12 Cell Differentiation.

    Science.gov (United States)

    Offermann, Barbara; Knauer, Steffen; Singh, Amit; Fernández-Cachón, María L; Klose, Martin; Kowar, Silke; Busch, Hauke; Boerries, Melanie

    2016-01-01

    The nerve growth factor NGF has been shown to cause cell fate decisions toward either differentiation or proliferation depending on the relative activity of downstream pERK, pAKT, or pJNK signaling. However, how these protein signals are translated into and fed back from transcriptional activity to complete cellular differentiation over a time span of hours to days is still an open question. Comparing the time-resolved transcriptome response of NGF- or EGF-stimulated PC12 cells over 24 h in combination with protein and phenotype data we inferred a dynamic Boolean model capturing the temporal sequence of protein signaling, transcriptional response and subsequent autocrine feedback. Network topology was optimized by fitting the model to time-resolved transcriptome data under MEK, PI3K, or JNK inhibition. The integrated model confirmed the parallel use of MAPK/ERK, PI3K/AKT, and JNK/JUN for PC12 cell differentiation. Redundancy of cell signaling is demonstrated from the inhibition of the different MAPK pathways. As suggested in silico and confirmed in vitro, differentiation was substantially suppressed under JNK inhibition, yet delayed only under MEK/ERK inhibition. Most importantly, we found that positive transcriptional feedback induces bistability in the cell fate switch. De novo gene expression was necessary to activate autocrine feedback that caused Urokinase-Type Plasminogen Activator (uPA) Receptor signaling to perpetuate the MAPK activity, finally resulting in the expression of late, differentiation related genes. Thus, the cellular decision toward differentiation depends on the establishment of a transcriptome-induced positive feedback between protein signaling and gene expression thereby constituting a robust control between proliferation and differentiation.

  3. Structure of the voltage-gated K⁺ channel Eag1 reveals an alternative voltage sensing mechanism.

    Science.gov (United States)

    Whicher, Jonathan R; MacKinnon, Roderick

    2016-08-12

    Voltage-gated potassium (K(v)) channels are gated by the movement of the transmembrane voltage sensor, which is coupled, through the helical S4-S5 linker, to the potassium pore. We determined the single-particle cryo-electron microscopy structure of mammalian K(v)10.1, or Eag1, bound to the channel inhibitor calmodulin, at 3.78 angstrom resolution. Unlike previous K(v) structures, the S4-S5 linker of Eag1 is a five-residue loop and the transmembrane segments are not domain swapped, which suggest an alternative mechanism of voltage-dependent gating. Additionally, the structure and position of the S4-S5 linker allow calmodulin to bind to the intracellular domains and to close the potassium pore, independent of voltage-sensor position. The structure reveals an alternative gating mechanism for K(v) channels and provides a template to further understand the gating properties of Eag1 and related channels. PMID:27516594

  4. Dental pulp stem cells differentiation reveals new insights in Oct4A dynamics.

    Directory of Open Access Journals (Sweden)

    Federico Ferro

    Full Text Available Although the role played by the core transcription factor network, which includes c-Myc, Klf4, Nanog, and Oct4, in the maintenance of embryonic stem cell (ES pluripotency and in the reprogramming of adult cells is well established, its persistence and function in adult stem cells are still debated. To verify its persistence and clarify the role played by these molecules in adult stem cell function, we investigated the expression pattern of embryonic and adult stem cell markers in undifferentiated and fully differentiated dental pulp stem cells (DPSC. A particular attention was devoted to the expression pattern and intracellular localization of the stemness-associated isoform A of Oct4 (Oct4A. Our data demonstrate that: Oct4, Nanog, Klf4 and c-Myc are expressed in adult stem cells and, with the exception of c-Myc, they are significantly down-regulated following differentiation. Cell differentiation was also associated with a significant reduction in the fraction of DPSC expressing the stem cell markers CD10, CD29 and CD117. Moreover, a nuclear to cytoplasm shuttling of Oct4A was identified in differentiated cells, which was associated with Oct4A phosphorylation. The present study would highlight the importance of the post-translational modifications in DPSC stemness maintenance, by which stem cells balance self-renewal versus differentiation. Understanding and controlling these mechanisms may be of great importance for stemness maintenance and stem cells clinical use, as well as for cancer research.

  5. By Ounce or By Calorie: The Differential Effects of Alternative Sugar-Sweetened Beverage Tax Strategies

    OpenAIRE

    Zhen, Chen; Brissette, Ian F.; Ryan R. Ruff

    2014-01-01

    The obesity epidemic and excessive consumption of sugar-sweetened beverages have led to proposals of economics-based interventions to promote healthy eating in the United States. Targeted food and beverage taxes and subsidies are prominent examples of such potential intervention strategies. This paper examines the differential effects of taxing sugar-sweetened beverages by calories and by ounces on beverage demand. To properly measure the extent of substitution and complementarity between bev...

  6. Computational modeling reveals that a combination of chemotaxis and differential adhesion leads to robust cell sorting during tissue patterning.

    Directory of Open Access Journals (Sweden)

    Rui Zhen Tan

    Full Text Available Robust tissue patterning is crucial to many processes during development. The "French Flag" model of patterning, whereby naïve cells in a gradient of diffusible morphogen signal adopt different fates due to exposure to different amounts of morphogen concentration, has been the most widely proposed model for tissue patterning. However, recently, using time-lapse experiments, cell sorting has been found to be an alternative model for tissue patterning in the zebrafish neural tube. But it remains unclear what the sorting mechanism is. In this article, we used computational modeling to show that two mechanisms, chemotaxis and differential adhesion, are needed for robust cell sorting. We assessed the performance of each of the two mechanisms by quantifying the fraction of correct sorting, the fraction of stable clusters formed after correct sorting, the time needed to achieve correct sorting, and the size variations of the cells having different fates. We found that chemotaxis and differential adhesion confer different advantages to the sorting process. Chemotaxis leads to high fraction of correct sorting as individual cells will either migrate towards or away from the source depending on its cell type. However after the cells have sorted correctly, there is no interaction among cells of the same type to stabilize the sorted boundaries, leading to cell clusters that are unstable. On the other hand, differential adhesion results in low fraction of correct clusters that are more stable. In the absence of morphogen gradient noise, a combination of both chemotaxis and differential adhesion yields cell sorting that is both accurate and robust. However, in the presence of gradient noise, the simple combination of chemotaxis and differential adhesion is insufficient for cell sorting; instead, chemotaxis coupled with delayed differential adhesion is required to yield optimal sorting.

  7. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

    Directory of Open Access Journals (Sweden)

    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  8. Microarray analysis reveals expression regulation of Wnt antagonists in differentiating osteoblasts

    NARCIS (Netherlands)

    Vaes, B.L.T.; Dechering, K.J.; Someren, van P.; Hendriks, J.M.A.; Ven, van de C.J.J.M.; Feijen, A.; Mummery, C.L.; Reinders, M.J.T.; Olijve, W.; Zoelen, van E.J.J.; Steegenga, W.T.

    2005-01-01

    Wnt signaling has been implicated in regulating bone formation by controlling osteoblast proliferation and function. Although stabilization of ß-catenin by Wnt has been shown to increase alkaline phosphatase expression and osteoblast differentiation, the precise role of Wnt signaling during the proc

  9. Microarray analysis reveals expression regulation of Wnt antagonists in differentiating osteoblasts

    NARCIS (Netherlands)

    Vaes, B.L.T.; Dechering, K.J.; Someren, E.P. van; Hendriks, J.M.; Ven, C.J. van de; Feijen, A.; Mummery, C.L.; Reinders, M.J.; Olijve, W.; Zoelen, E.J.J. van; Steegenga, W.T.

    2005-01-01

    Wnt signaling has been implicated in regulating bone formation by controlling osteoblast proliferation and function. Although stabilization of beta-catenin by Wnt has been shown to increase alkaline phosphatase expression and osteoblast differentiation, the precise role of Wnt signaling during the p

  10. Species versus guild level differentiation revealed across the annual cycle by isotopic niche examination

    OpenAIRE

    Bodey, Thomas W.; Ward, Eric J.; Phillips, Richard A.; McGill, Rona A.R.; Bearhop, Stuart

    2014-01-01

    Summary 1.Interspecific competitive interactions typically result in niche differentiation to alleviate competition through mechanisms including character displacement. However, competition is not the sole constraint on resource partitioning, and its effects are mediated by factors including the environmental context in which species coexist. 2.Colonial seabirds provide an excellent opportunity to investigate the importance of competition in shaping realized niche widths because their ...

  11. The differential effects of switching costs and attractiveness of alternatives on customer loyalty

    OpenAIRE

    Magalhães, Sara Henriques de Jesus Paninho

    2009-01-01

    Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação. There is an increasing recognition among marketing scholars and practitioners of the importance of the influence of switching costs and attractiveness of alternatives in the relationship between customer satisfaction and customer loyalty. To date, however, there is a lack of research about the process through which these variables influence the satisfaction-loyalty...

  12. Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism

    Science.gov (United States)

    Xiong, Jie; Tao, Tao; Zheng, Xiaoguo; Wei, Haibin; Yue, Yunxia; Chen, Liang; Luo, Lijun

    2016-01-01

    The stress-induced epimutations could be inherited over generations and play important roles in plant adaption to stressful environments. Upland rice has been domesticated in water-limited environments for thousands of years and accumulated drought-induced epimutations of DNA methylation, making it epigenetically differentiated from lowland rice. To study the epigenetic differentiation between upland and lowland rice ecotypes on their drought-resistances, the epigenetic variation was investigated in 180 rice landraces under both normal and osmotic conditions via methylation-sensitive amplified polymorphism (MSAP) technique. Great alterations (52.9~54.3% of total individual-locus combinations) of DNA methylation are recorded when rice encountering the osmotic stress. Although the general level of epigenetic differentiation was very low, considerable level of ΦST (0.134~0.187) was detected on the highly divergent epiloci (HDE). The HDE detected in normal condition tended to stay at low levels in upland rice, particularly the ones de-methylated in responses to osmotic stress. Three out of four selected HDE genes differentially expressed between upland and lowland rice under normal or stressed conditions. Moreover, once a gene at HDE was up-/down-regulated in responses to the osmotic stress, its expression under the normal condition was higher/lower in upland rice. This result suggested expressions of genes at the HDE in upland rice might be more adaptive to the osmotic stress. The epigenetic divergence and its influence on the gene expression should contribute to the higher drought-resistance in upland rice as it is domesticated in the water-limited environment. PMID:27380174

  13. Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.

    Directory of Open Access Journals (Sweden)

    Yuichi Nakajima

    Full Text Available The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts. We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L and 44 were mt-Short (mt-S. Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs among the 53 mt-L colonies (NMLL/N = 0.189, and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159. Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001. Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

  14. Quantitative proteomics reveals differential biological processes in healthy neonatal cord neutrophils and adult neutrophils

    KAUST Repository

    Zhu, Jiang

    2014-06-11

    Neonatal neutrophils are characterized by the immaturity of bactericidal mechanisms that contributes largely to neonatal mortality. However, underlying molecular mechanism associated with the immaturity remains incompletely understood. In this study, we performed comparative proteomic analysis on neonatal neutrophils derived from human cord blood and adult peripheral neutrophils. A total of 1332 proteins were identified and quantified, and 127 proteins were characterized as differentially expressed between adult and cord neutrophils. The differentially expressed proteins are mapped in KEGG pathways into five clusters and indicated impaired functions of neonatal neutrophils in proteasome, lysosome, phagosome, and leukocyte transendothelial migration. In particular, many proteins associated with NETosis, a critical mechanism for antimicrobial process and auto-clearance, were also found to be downregulated in cord neutrophils. This study represents a first comparative proteome profiling of neonatal and adult neutrophils, and provides a global view of differentially expressed proteome for enhancing our understanding of their various functional difference. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. By Ounce or By Calorie: The Differential Effects of Alternative Sugar-Sweetened Beverage Tax Strategies.

    Science.gov (United States)

    Zhen, Chen; Brissette, Ian F; Ruff, Ryan R

    2014-07-01

    The obesity epidemic and excessive consumption of sugar-sweetened beverages have led to proposals of economics-based interventions to promote healthy eating in the United States. Targeted food and beverage taxes and subsidies are prominent examples of such potential intervention strategies. This paper examines the differential effects of taxing sugar-sweetened beverages by calories and by ounces on beverage demand. To properly measure the extent of substitution and complementarity between beverage products, we developed a fully modified distance metric model of differentiated product demand that endogenizes the cross-price effects. We illustrated the proposed methodology in a linear approximate almost ideal demand system, although other flexible demand systems can also be used. In the empirical application using supermarket scanner data, the product-level demand model consists of 178 beverage products with combined market share of over 90%. The novel demand model outperformed the conventional distance metric model in non-nested model comparison tests and in terms of the economic significance of model predictions. In the fully modified model, a calorie-based beverage tax was estimated to cost $1.40 less in compensating variation than an ounce-based tax per 3,500 beverage calories reduced. This difference in welfare cost estimates between two tax strategies is more than three times as much as the difference estimated by the conventional distance metric model. If applied to products purchased from all sources, a 0.04-cent per kcal tax on sugar-sweetened beverages is predicted to reduce annual per capita beverage intake by 5,800 kcal. PMID:25414517

  16. Targeted deletion of Atg5 reveals differential roles of autophagy in keratin K5-expressing epithelia

    Energy Technology Data Exchange (ETDEWEB)

    Sukseree, Supawadee [Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna (Austria); Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Bangkok (Thailand); Rossiter, Heidemarie; Mildner, Michael [Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna (Austria); Pammer, Johannes [Institute of Clinical Pathology, Medical University of Vienna, Vienna (Austria); Buchberger, Maria; Gruber, Florian [Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna (Austria); Watanapokasin, Ramida [Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Bangkok (Thailand); Tschachler, Erwin [Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna (Austria); Eckhart, Leopold, E-mail: leopold.eckhart@meduniwien.ac.at [Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna (Austria)

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer We generated mice lacking Atg5 and autophagy in keratin K5-positive epithelia. Black-Right-Pointing-Pointer Suppression of autophagy in thymic epithelium was not associated with signs of autoimmunity. Black-Right-Pointing-Pointer Autophagy was required for normal terminal differentiation of preputial gland cells. Black-Right-Pointing-Pointer Autophagy-deficient cells of the preputial glands degraded nuclear DNA prematurely. -- Abstract: Autophagy contributes to the homeostasis of many tissues, yet its role in epithelia is incompletely understood. A recent report proposed that Atg5-dependent autophagy in thymic epithelial cells is essential for their function in the negative selection of self-reactive T-cells and, thus, for the suppression of tissue inflammation. Here we crossed mice carrying floxed alleles of the Atg5 gene with mice expressing the Cre recombinase under the control of the keratin K5 promoter to suppress autophagy in all K5-positive epithelia. The efficiency of autophagy abrogation was confirmed by immunoanalyses of LC3, which was converted to the autophagy-associated LC3-II form in normal but not Atg5-deficient cells, and of p62, which accumulated in Atg5-deficient cells. Mice carrying the epithelium-specific deletion of Atg5 showed normal weight gain, absence of tissue inflammation, and a normal morphology of the thymic epithelium. By contrast, autophagy-deficient epithelial cells of the preputial gland showed aberrant eosinophilic staining in histology and premature degradation of nuclear DNA during terminal differentiation. Taken together, the results of this study suggest that autophagy is dispensable for the suppression of autoimmunity by thymic epithelial cells but essential for normal differentiation of the preputial gland in mice.

  17. Targeted deletion of Atg5 reveals differential roles of autophagy in keratin K5-expressing epithelia

    International Nuclear Information System (INIS)

    Highlights: ► We generated mice lacking Atg5 and autophagy in keratin K5-positive epithelia. ► Suppression of autophagy in thymic epithelium was not associated with signs of autoimmunity. ► Autophagy was required for normal terminal differentiation of preputial gland cells. ► Autophagy-deficient cells of the preputial glands degraded nuclear DNA prematurely. -- Abstract: Autophagy contributes to the homeostasis of many tissues, yet its role in epithelia is incompletely understood. A recent report proposed that Atg5-dependent autophagy in thymic epithelial cells is essential for their function in the negative selection of self-reactive T-cells and, thus, for the suppression of tissue inflammation. Here we crossed mice carrying floxed alleles of the Atg5 gene with mice expressing the Cre recombinase under the control of the keratin K5 promoter to suppress autophagy in all K5-positive epithelia. The efficiency of autophagy abrogation was confirmed by immunoanalyses of LC3, which was converted to the autophagy-associated LC3-II form in normal but not Atg5-deficient cells, and of p62, which accumulated in Atg5-deficient cells. Mice carrying the epithelium-specific deletion of Atg5 showed normal weight gain, absence of tissue inflammation, and a normal morphology of the thymic epithelium. By contrast, autophagy-deficient epithelial cells of the preputial gland showed aberrant eosinophilic staining in histology and premature degradation of nuclear DNA during terminal differentiation. Taken together, the results of this study suggest that autophagy is dispensable for the suppression of autoimmunity by thymic epithelial cells but essential for normal differentiation of the preputial gland in mice.

  18. Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics.

    Directory of Open Access Journals (Sweden)

    Xiangdong Chen

    Full Text Available Cotton fiber qualities including length, strength and fineness are known to be controlled by genes affecting cell elongation and secondary cell wall (SCW biosynthesis, but the molecular mechanisms that govern development of fiber traits are largely unknown. Here, we evaluated an interspecific backcrossed population from G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 for fiber characteristics in four-year environments under field conditions, and detected 12 quantitative trait loci (QTL and QTL-by-environment interactions by multi-QTL joint analysis. Further analysis of fiber growth and gene expression between TM-1 and Hai7124 showed greater differences at 10 and 25 days post-anthesis (DPA. In this two period important for fiber performances, we integrated genome-wide expression profiling with linkage analysis using the same genetic materials and identified in total 916 expression QTL (eQTL significantly (P<0.05 affecting the expression of 394 differential genes. Many positional cis-/trans-acting eQTL and eQTL hotspots were detected across the genome. By comparative mapping of eQTL and fiber QTL, a dataset of candidate genes affecting fiber qualities was generated. Real-time quantitative RT-PCR (qRT-PCR analysis confirmed the major differential genes regulating fiber cell elongation or SCW synthesis. These data collectively support molecular mechanism for G. hirsutum and G. barbadense through differential gene regulation causing difference of fiber qualities. The down-regulated expression of abscisic acid (ABA and ethylene signaling pathway genes and high-level and long-term expression of positive regulators including auxin and cell wall enzyme genes for fiber cell elongation at the fiber developmental transition stage may account for superior fiber qualities.

  19. Molecular Mechanisms of Fiber Differential Development between G. barbadense and G. hirsutum Revealed by Genetical Genomics

    Science.gov (United States)

    Chen, Xiangdong; Guo, Wangzhen; Liu, Bingliang; Zhang, Yuanming; Song, Xianliang; Cheng, Yu; Zhang, Lili; Zhang, Tianzhen

    2012-01-01

    Cotton fiber qualities including length, strength and fineness are known to be controlled by genes affecting cell elongation and secondary cell wall (SCW) biosynthesis, but the molecular mechanisms that govern development of fiber traits are largely unknown. Here, we evaluated an interspecific backcrossed population from G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 for fiber characteristics in four-year environments under field conditions, and detected 12 quantitative trait loci (QTL) and QTL-by-environment interactions by multi-QTL joint analysis. Further analysis of fiber growth and gene expression between TM-1 and Hai7124 showed greater differences at 10 and 25 days post-anthesis (DPA). In this two period important for fiber performances, we integrated genome-wide expression profiling with linkage analysis using the same genetic materials and identified in total 916 expression QTL (eQTL) significantly (P<0.05) affecting the expression of 394 differential genes. Many positional cis-/trans-acting eQTL and eQTL hotspots were detected across the genome. By comparative mapping of eQTL and fiber QTL, a dataset of candidate genes affecting fiber qualities was generated. Real-time quantitative RT-PCR (qRT-PCR) analysis confirmed the major differential genes regulating fiber cell elongation or SCW synthesis. These data collectively support molecular mechanism for G. hirsutum and G. barbadense through differential gene regulation causing difference of fiber qualities. The down-regulated expression of abscisic acid (ABA) and ethylene signaling pathway genes and high-level and long-term expression of positive regulators including auxin and cell wall enzyme genes for fiber cell elongation at the fiber developmental transition stage may account for superior fiber qualities. PMID:22253876

  20. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.

    Science.gov (United States)

    Akagi, Takashi; Hanada, Toshio; Yaegaki, Hideaki; Gradziel, Thomas M; Tao, Ryutaro

    2016-06-01

    Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops. PMID:27085183

  1. Differential gene expression and alternative splicing between diploid and tetraploid watermelon.

    Science.gov (United States)

    Saminathan, Thangasamy; Nimmakayala, Padma; Manohar, Sumanth; Malkaram, Sridhar; Almeida, Aldo; Cantrell, Robert; Tomason, Yan; Abburi, Lavanya; Rahman, Mohammad A; Vajja, Venkata G; Khachane, Amit; Kumar, Brajendra; Rajasimha, Harsha K; Levi, Amnon; Wehner, Todd; Reddy, Umesh K

    2015-03-01

    The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits. PMID:25520388

  2. Differential proteins of the optic ganglion in octopus vulgaris under methanol stress revealed using proteomics.

    Science.gov (United States)

    Huang, Lin; Huang, Qing-Yu; Chen, Hai-Bin; Huang, Fu-Sheng; Huang, He-Qing

    2011-10-01

    An analytical approach using the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) technique separated the proteome from the optic ganglia of Octopus vulgaris (OVOG). Approximately 600 protein spots were detected from the extraction when applying 150 μg protein to a 2D-PAGE gel in the pH range 5.0-8.0. Compared to the control, significant changes of 18 protein spots were observed in OVOG under the stress of native seawater containing 2% methanol for 72 h. Among these spots, we found that eight were down-regulated and ten were up-regulated in the gels, which were further identified using both peptide mass fingerprinting and database searches. Significant proteins such as glyceraldehyde-3-phosphate dehydrogenase, alpha subunit of succinyl-CoA synthetase, alcohol dehydrogenase, and long-chain specific acyl-CoA dehydrogenase were up-regulated proteins, whereas putative ABC transporter was a down -regulated protein. These differential proteins at the level of subcellular localization were further classified using LOCtree software with a hierarchical system of support vector machines. We found that most of the differential proteins in the gel could be identified as mitochondrial proteins, suggesting that these protective or marker proteins might help to prevent methanol poisoning via the mitochondria in the optical ganglia. The results indicated that both beta-tubulin and beta-actin were potential biomarkers as up-regulated proteins for monitoring methanol toxicosis associated with fish foods such as octopus and shark.

  3. Regionally-specified second trimester fetal neural stem cells reveals differential neurogenic programming.

    Directory of Open Access Journals (Sweden)

    Yiping Fan

    Full Text Available Neural stem/progenitor cells (NSC have the potential for treatment of a wide range of neurological diseases such as Parkinson Disease and multiple sclerosis. Currently, NSC have been isolated only from hippocampus and subventricular zone (SVZ of the adult brain. It is not known whether NSC can be found in all parts of the developing mid-trimester central nervous system (CNS when the brain undergoes massive transformation and growth. Multipotent NSC from the mid-trimester cerebra, thalamus, SVZ, hippocampus, thalamus, cerebellum, brain stem and spinal cord can be derived and propagated as clonal neurospheres with increasing frequencies with increasing gestations. These NSC can undergo multi-lineage differentiation both in vitro and in vivo, and engraft in a developmental murine model. Regionally-derived NSC are phenotypically distinct, with hippocampal NSC having a significantly higher neurogenic potential (53.6% over other sources (range of 0%-27.5%, p<0.004. Whole genome expression analysis showed differential gene expression between these regionally-derived NSC, which involved the Notch, epidermal growth factor as well as interleukin pathways. We have shown the presence of phenotypically-distinct regionally-derived NSC from the mid-trimester CNS, which may reflect the ontological differences occurring within the CNS. Aside from informing on the role of such cells during fetal growth, they may be useful for different cellular therapy applications.

  4. Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.

    Science.gov (United States)

    Thomason, Maureen K; Bischler, Thorsten; Eisenbart, Sara K; Förstner, Konrad U; Zhang, Aixia; Herbig, Alexander; Nieselt, Kay; Sharma, Cynthia M; Storz, Gisela

    2015-01-01

    While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type E. coli and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the rnc and rne mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in E. coli and is easily accessible, together with the cDNA coverage plots, in an online genome browser.

  5. Differential proteomics reveals multiple components in retrogradely transported axoplasm after nerve injury.

    Science.gov (United States)

    Perlson, Eran; Medzihradszky, Katalin F; Darula, Zsuzsanna; Munno, David W; Syed, Naweed I; Burlingame, Alma L; Fainzilber, Mike

    2004-05-01

    Information on axonal damage is conveyed to neuronal cell bodies by a number of signaling modalities, including the post-translational modification of axoplasmic proteins. Retrograde transport of a subset of such proteins is thought to induce or enhance a regenerative response in the cell body. Here we report the use of a differential 2D-PAGE approach to identify injury-correlated retrogradely transported proteins in nerves of the mollusk Lymnaea. A comprehensive series of gels at different pI ranges allowed resolution of approximately 4000 spots by silver staining, and 172 of these were found to differ between lesioned versus control nerves. Mass spectrometric sequencing of 134 differential spots allowed their assignment to over 40 different proteins, some belonging to a vesicular ensemble blocked by the lesion and others comprising an up-regulated ensemble highly enriched in calpain cleavage products of an intermediate filament termed RGP51 (retrograde protein of 51 kDa). Inhibition of RGP51 expression by RNA interference inhibits regenerative outgrowth of adult Lymnaea neurons in culture. These results implicate regulated proteolysis in the formation of retrograde injury signaling complexes after nerve lesion and suggest that this signaling modality utilizes a wide range of protein components.

  6. Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

    Energy Technology Data Exchange (ETDEWEB)

    Hawley, Alyse K.; Brewer, Heather M.; Norbeck, Angela D.; Pasa-Tolic, Ljiljana; Hallam, Steven J.

    2014-08-05

    Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified marine waters. Currently OMZs are expanding due to global climate change. This expansion alters marine ecosystem function and the productivity of fisheries due to habitat compression and changes in biogeochemical cycling leading to fixed nitrogen loss and greenhouse gas production. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally anoxic fjord, Saanich Inlet to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification and inorganic carbon fixation predominantly co-varied with abundance and distribution patterns of Thaumarchaeota, Nitrospira, Planctomycetes and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Within these groups, pathways mediating inorganic carbon fixation and nitrogen and sulfur transformations were differentially expressed across the redoxcline. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters and denitrification, sulfur-oxidation and inorganic carbon fixation pathways affiliated with SUP05 dominated suboxic and anoxic waters. Nitrite-oxidation and anammox pathways affiliated with Nitrospina and Planctomycetes respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The differential expression of these pathways under changing water column redox conditions has quantitative implications for coupled biogeochemical cycling linking different modes of inorganic carbon fixation with distributed nitrogen and sulfur-based energy metabolism extensible to coastal and open ocean OMZs.

  7. Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    Full Text Available Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low CaratioMg ratio in A. lyrata.

  8. Mature adipocyte proteome reveals differentially altered protein abundances between lean, overweight and morbidly obese human subjects.

    Science.gov (United States)

    Benabdelkamel, Hicham; Masood, Afshan; Almidani, Ghaith M; Alsadhan, Abdulmajeed A; Bassas, Abdulelah F; Duncan, Mark W; Alfadda, Assim A

    2015-02-01

    Overweight (OW) and obese individuals are considered to be graded parts of the scale having increasing weight as a common feature. They may not, however, be part of the same continuum and may differ metabolically. In this study we applied an untargeted proteomic approach to compare protein abundances in mature adipocytes derived from the subcutaneous adipose tissue of overweight and morbidly obese female subjects to those of lean age matched controls. Mature adipocytes were isolated from liposuction samples of abdominal subcutaneous adipose tissue collected from both lean (L; n = 7, 23.3 ± 0.4 kg/m(2); mean BMI ± SD), overweight (OW; n = 8, 27.9 ± 0.6 kg/m(2); mean BMI ± SD) and morbidly obese (MOB; n = 7, 44.8 ± 3.8 kg/m(2); mean BMI ± SD) individuals. Total protein extracts were then compared by two-dimensional difference in gel electrophoresis (2D DIGE). One hundred and ten differentially expressed protein spots (i.e., fitting the statistical criteria ANOVA test, p interaction; in contrast, in the MOB group the major interacting pathways are associated with lipid metabolism, small molecule biochemistry and cancer. The differences in abundance of the differentially regulated proteins were validated by immunoblotting. These findings provide insights into metabolic differences in OW and MOB individuals. PMID:25498962

  9. Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system.

    Science.gov (United States)

    Hu, Qi; Guo, Xue; Liang, Yili; Hao, Xiaodong; Ma, Liyuan; Yin, Huaqun; Liu, Xueduan

    2015-01-01

    The microbial community in a biological heap leaching (BHL) system is crucial for the decomposition of ores. However, the microbial community structure and functional differentiation in different parts of a biological heap leaching system are still unknown. In this study, metagenomic sequencing was used to fully illuminate the microbial community differentiation in the pregnant leach solution (PLS) and leaching heap (LH) of a BHL system. Long-read sequences (1.3 million) were obtained for the two samples, and the MG_RAST server was used to perform further analysis. The taxa analysis results indicated that the dominant genera of PLS is autotrophic bacterium Acidithiobacillus, but heterotrophic bacterium Acidiphilium is predominant in LH. Furthermore, functional annotation and hierarchical comparison with different reference samples showed that the abundant presence of genes was involved in transposition, DNA repair and heavy metal transport. The sequences related to transposase, which is important for the survival of the organism in the hostile environment, were both mainly classified into Acidiphilium for PLS and LH. These results indicated that not only autotrophic bacteria such as Acidithiobacillus, but also heterotrophic bacteria such as Acidiphilium, were essential participants in the bioleaching process. This new meta-view research will further facilitate the effective application of bioleaching.

  10. Genome-wide functional analysis of plasmodium protein phosphatases reveals key regulators of parasite development and differentiation

    KAUST Repository

    Guttery, David S.

    2014-07-09

    Reversible protein phosphorylation regulated by kinases and phosphatases controls many cellular processes. Although essential functions for the malaria parasite kinome have been reported, the roles of most protein phosphatases (PPs) during Plasmodium development are unknown. We report a functional analysis of the Plasmodium berghei protein phosphatome, which exhibits high conservation with the P. falciparum phosphatome and comprises 30 predicted PPs with differential and distinct expression patterns during various stages of the life cycle. Gene disruption analysis of P. berghei PPs reveals that half of the genes are likely essential for asexual blood stage development, whereas six are required for sexual development/sporogony in mosquitoes. Phenotypic screening coupled with transcriptome sequencing unveiled morphological changes and altered gene expression in deletion mutants of two N-myristoylated PPs. These findings provide systematic functional analyses of PPs in Plasmodium, identify how phosphatases regulate parasite development and differentiation, and can inform the identification of drug targets for malaria. © 2014 The Authors.

  11. Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

    DEFF Research Database (Denmark)

    Hattori, Naoko; Niwa, Tohru; Kimura, Kana;

    2013-01-01

    . Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell......Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which...... population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination...

  12. Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae)

    OpenAIRE

    David Behringer; Heike Zimmermann; Birgit Ziegenhagen; Sascha Liepelt

    2015-01-01

    Increasing drought periods as a result of global climate change pose a threat to many tree species by possibly outpacing their adaptive capabilities. Revealing the genetic basis of drought stress response is therefore implemental for future conservation strategies and risk assessment. Access to informative genomic regions is however challenging, especially for conifers, partially due to their large genomes, which puts constraints on the feasibility of whole genome scans. Candidate genes offer...

  13. Genome differentiation in Magonoliaceae as revealed from meiotic pairing in interspecific and intergeneric hybrids

    Institute of Scientific and Technical Information of China (English)

    Shou-Zhou ZHANG; Ya-Ling WANG; Zi-Can HE; Erland EJDER

    2011-01-01

    The cross compatibility within and between Yulania Spach and Michelia L.(Magnoliaceae) is relatively good and various such hybrids,obtained by conventional artificial hybridization,are available.The aim of the present study was to determine the extent of genome differentiation between the species involved in these crosses through the observation of chromosome pairing during meiosis in pollen mother cells (PMCs) of the hybrids.Chromosome pairing behavior was studied in five species (2n =38) and two interspecific hybrids of Michelia,eight species (2n =38,76 and 114) and 10 interspecific hybrids of Yulania,and three intergeneric hybrids between Michelia and Yulania.The results showed that chromosome pairing was normal with bivalent formation in diploid parental species and in interspecific hybrids.In addition to bivalents,multivalents were encountered in polyploid parental species and polyploid interspecific hybrids.In the intergeneric hybrids between a tetraploid Yulania and two diploid Michelia,19 chromosomes,most likely originating from Michelia,were unable to synapse from zygotene to metaphase I.Meiotic chromosome pairing indicated a high degree of homology between species within Michelia and Yulania and less homology between the genomes of these two genera.The differentiation of morphological characters and the distinctness of natural distribution also support the conclusion that these two genera are likely independent monophyletic groups.This suggests that the two genera were split at early evolution of Magnoliaceae and the overlapping characteristics in external morphology and internal structures of the two genera may be the result of parallel evolution or ancient common ancestry.

  14. Transcriptome Display During Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis.

    Science.gov (United States)

    Zeng, Qifan; Liu, Shikai; Yao, Jun; Zhang, Yu; Yuan, Zihao; Jiang, Chen; Chen, Ailu; Fu, Qiang; Su, Baofeng; Dunham, Rex; Liu, Zhanjiang

    2016-07-01

    Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture species in the United States. It is also a suitable model for studying the mechanisms of sex determination and differentiation because of its sexual plasticity and exhibition of both genetic and environmental sex determination. The testicular differentiation in male channel catfish normally starts between 90 and 102 days postfertilization (dpf), while the ovarian differentiation starts early from 19 dpf. As such, efforts to better understand the postponed testicular development at the molecular level are needed. Toward that end, we conducted transcriptomic comparison of gene expression of male and female gonads at 90, 100, and 110 dpf using high-throughput RNA-Seq. Transcriptomic profiles of male gonads on 90 and 100 dpf exhibited high similarities except for a small number of significantly up-regulated genes that were involved in development of germ cell-supporting somatic cells, while drastic changes were observed during 100-110 dpf, with a group of highly up-regulated genes that were involved in germ cells development, including nanog and pou5f1 Transcriptomic comparison between testes and ovaries identified male-preferential genes, such as gsdf, cxcl12, as well as other cytokines mediated the development of the gonad into a testis. Co-expression analysis revealed highly correlated genes and potential pathways underlying germ cell differentiation and spermatogonia stem cell development. The candidate genes and pathways identified in this study set the foundation for further studies on sex determination and differentiation in catfish as well as other teleosts. PMID:27307075

  15. Cerebral hemovelocity reveals differential resource allocation strategies for extraverts and introverts during vigilance.

    Science.gov (United States)

    Shaw, Tyler H; Nguyen, Cynthia; Satterfield, Kelly; Ramirez, Raul; McKnight, Patrick E

    2016-02-01

    Extraversion--one of the Big 5 personality factors--correlates negatively with vigilance, but most studies focus on performance outcomes and not the performance process. Previous research has shown that transcranial Doppler sonography (TCD), which measures cerebral blood flow velocity (CBFV), can be used to examine resource allocation strategies during vigilance performance. Hence, this study was designed to assess the attentional resource allocation strategies of introverts and extraverts using the CBFV measure. Twelve extroverts and 13 introverts monitored a 60-min vigilance task for a critical signal--the absence of a line on a five-circle array. The results revealed an overall performance decrement that was not modulated by extraversion. We observed an interaction between extraversion and time; CBFV declined in the introversion group, but not in the extraversion group. Additionally, an interaction between cerebral hemisphere and personality revealed that extraverts were recruiting resources from both the left and right cerebral hemispheres, while introverts only recruited resources from the right hemisphere. The results suggest that extraverts can allocate compensatory effort to mask performance differences. We discuss the theoretical and practical implications of these findings and offer future research directions that may help us understand these effects. PMID:26563163

  16. Regionally-specified second trimester fetal neural stem cells reveals differential neurogenic programming.

    Science.gov (United States)

    Fan, Yiping; Marcy, Guillaume; Lee, Eddy S M; Rozen, Steve; Mattar, Citra N Z; Waddington, Simon N; Goh, Eyleen L K; Choolani, Mahesh; Chan, Jerry K Y

    2014-01-01

    Neural stem/progenitor cells (NSC) have the potential for treatment of a wide range of neurological diseases such as Parkinson Disease and multiple sclerosis. Currently, NSC have been isolated only from hippocampus and subventricular zone (SVZ) of the adult brain. It is not known whether NSC can be found in all parts of the developing mid-trimester central nervous system (CNS) when the brain undergoes massive transformation and growth. Multipotent NSC from the mid-trimester cerebra, thalamus, SVZ, hippocampus, thalamus, cerebellum, brain stem and spinal cord can be derived and propagated as clonal neurospheres with increasing frequencies with increasing gestations. These NSC can undergo multi-lineage differentiation both in vitro and in vivo, and engraft in a developmental murine model. Regionally-derived NSC are phenotypically distinct, with hippocampal NSC having a significantly higher neurogenic potential (53.6%) over other sources (range of 0%-27.5%, pcells during fetal growth, they may be useful for different cellular therapy applications.

  17. Differential Proteomics of Urinary Exovesicles from Classical Galactosemic Patients Reveals Subclinical Kidney Insufficiency.

    Science.gov (United States)

    Staubach, Simon; Pekmez, Murat; Hanisch, Franz-Georg

    2016-06-01

    Classical galactosemia is caused by a nearly complete deficiency of galactose-1-phosphate uridyltransferase (GALT; EC 2.7.712), resulting in a severely impaired galactose metabolism with galactose-1-phosphate and galactitol accumulation. Even on a galactose-restricted diet, patients develop serious long-term complications of the central nervous system and ovaries that may result from chronic cell-toxic effects exerted by endogenous galactose. To address the question of whether disease-associated cellular perturbations could affect the kidney function of the patients, we performed differential proteomics of detergent-resistant membranes from urinary exovesicles. Galactosemic samples (showing drastic shifts from high-mannose to complex-type N-glycosylation on exosomal N-glycoproteins) and healthy, sex-matched controls were analyzed in quadruplex iTRAQ experiments performed in biological and technical replicates. Particularly in the female patient group, the most striking finding was a drastic increase of abundant serum (glyco)proteins, like albumin, leucine-rich α-2-glycoprotein, fetuin, immunoglobulins, prostaglandin H2 d-isomerase, and α-1-microglobulin protein (AMBP), pointing to a subclinical failure of kidney filter function in galactosemic patients and resulting in a heavy overload of exosomal membranes with adsorbed serum (glyco)proteins. Several of these proteins are connected to TBMN and IgAN, proteinuria, and renal damage. The impairment of renal protein filtration was also indicated by increased protein contents derived from extracellular matrices and lysosomes. PMID:27103203

  18. Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies.

    Science.gov (United States)

    Indoliya, Yuvraj; Tiwari, Poonam; Chauhan, Abhisekh Singh; Goel, Ridhi; Shri, Manju; Bag, Sumit Kumar; Chakrabarty, Debasis

    2016-01-01

    Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells. PMID:26973288

  19. Nylon Filter Arrays Reveal Differential Expression of Expressed Sequence Tags in Wheat Roots Under Aluminum Stress

    Institute of Scientific and Technical Information of China (English)

    Kai XIAO; Gui-Hua BAI; Brett F CARVER

    2005-01-01

    To enrich differentially expressed sequence tags (ESTs) for aluminum (Al) tolerance, cDNA subtraction libraries were generated from Al-stressed roots of two wheat (Triticum aestivum L.) nearisogenic lines (NILs) contrasting in Al-tolerance gene(s) from the Al-tolerant cultivar Atlas 66, using suppression subtractive hybridization (SSH). Expression patterns of the ESTs were investigated with nylon filter arrays containing 614 cDNA clones from the subtraction library. Gene expression profiles from macroarray analysis indicated that 25 ESTs were upregulated in the tolerant NIL in response to Al stress. The result from Northern analysis of selected upregulated ESTs was similar to that from macroarray analysis. These highly expressed ESTs showed high homology with genes involved in signal transduction, oxidative stress alleviation, membrane structure, Mg2+ transportation, and other functions. Under Al stress, the Al-tolerant NIL may possess altered structure or function of the cell wall, plasma membrane, and mitochondrion. The wheat response to Al stress may involve complicated defense-related signaling and metabolic pathways.The present experiment did not detect any induced or activated genes involved in the synthesis of malate and other organic acids in wheat under Al-stress.

  20. A Quantitative Proteomic Analysis of Hemogenic Endothelium Reveals Differential Regulation of Hematopoiesis by SOX17

    Directory of Open Access Journals (Sweden)

    Raedun L. Clarke

    2015-08-01

    Full Text Available The in vitro derivation of hematopoietic stem cells (HSCs from pluripotent stem cells (PSCs is complicated by the existence of multiple overlapping embryonic blood cell programs called primitive, erythromyeloid progenitor (EMP, and definitive. As HSCs are only generated during the definitive stage of hematopoiesis, deciphering the regulatory pathways that control the emergence of this program and identifying markers that distinguish it from the other programs are essential. To identify definitive specific pathways and marker sets, we used label-free proteomics to determine the proteome of embryo-derived and mouse embryonic stem cell-derived VE-CADHERIN+CD45− definitive hematopoietic progenitors. With this approach, we identified Stat1 as a marker that distinguishes the definitive erythroid lineage from the primitive- and EMP-derived lineages. Additionally, we provide evidence that the generation of the Stat1+ definitive lineage is dependent on Sox17. These findings establish an approach for monitoring the emergence of definitive hematopoiesis in the PSC differentiation cultures.

  1. Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation.

    Science.gov (United States)

    Tsai, Chen-Hsun; Liao, Rick; Chou, Brendan; Contreras, Lydia M

    2015-03-01

    Small noncoding RNAs (sRNAs) are posttranscriptional regulators that have been identified in multiple species and shown to play essential roles in responsive mechanisms to environmental stresses. The natural ability of specific bacteria to resist high levels of radiation has been of high interest to mechanistic studies of DNA repair and biomolecular protection. Deinococcus radiodurans is a model extremophile for radiation studies that can survive doses of ionizing radiation of >12,000 Gy, 3,000 times higher than for most vertebrates. Few studies have investigated posttranscriptional regulatory mechanisms of this organism that could be relevant in its general gene regulatory patterns. In this study, we identified 199 potential sRNA candidates in D. radiodurans by whole-transcriptome deep sequencing analysis and confirmed the expression of 41 sRNAs by Northern blotting and reverse transcriptase PCR (RT-PCR). A total of 8 confirmed sRNAs showed differential expression during recovery after acute ionizing radiation (15 kGy). We have also found and confirmed 7 sRNAs in Deinococcus geothermalis, a closely related radioresistant species. The identification of several novel sRNAs in Deinococcus bacteria raises important questions about the evolution and nature of global gene regulation in radioresistance.

  2. Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies.

    Science.gov (United States)

    Indoliya, Yuvraj; Tiwari, Poonam; Chauhan, Abhisekh Singh; Goel, Ridhi; Shri, Manju; Bag, Sumit Kumar; Chakrabarty, Debasis

    2016-01-01

    Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells.

  3. Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes.

    Science.gov (United States)

    Dean, Samuel; Moreira-Leite, Flavia; Varga, Vladimir; Gull, Keith

    2016-08-30

    The transition zone (TZ) of eukaryotic cilia and flagella is a structural intermediate between the basal body and the axoneme that regulates ciliary traffic. Mutations in genes encoding TZ proteins (TZPs) cause human inherited diseases (ciliopathies). Here, we use the trypanosome to identify TZ components and localize them to TZ subdomains, showing that the Bardet-Biedl syndrome complex (BBSome) is more distal in the TZ than the Meckel syndrome (MKS) complex. Several of the TZPs identified here have human orthologs. Functional analysis shows essential roles for TZPs in motility, in building the axoneme central pair apparatus and in flagellum biogenesis. Analysis using RNAi and HaloTag fusion protein approaches reveals that most TZPs (including the MKS ciliopathy complex) show long-term stable association with the TZ, whereas the BBSome is dynamic. We propose that some Bardet-Biedl syndrome and MKS pleiotropy may be caused by mutations that impact TZP complex dynamics. PMID:27519801

  4. Large-scale computations on histology images reveal grade-differentiating parameters for breast cancer

    Directory of Open Access Journals (Sweden)

    Katsinis Constantine

    2006-10-01

    Full Text Available Abstract Background Tumor classification is inexact and largely dependent on the qualitative pathological examination of the images of the tumor tissue slides. In this study, our aim was to develop an automated computational method to classify Hematoxylin and Eosin (H&E stained tissue sections based on cancer tissue texture features. Methods Image processing of histology slide images was used to detect and identify adipose tissue, extracellular matrix, morphologically distinct cell nuclei types, and the tubular architecture. The texture parameters derived from image analysis were then applied to classify images in a supervised classification scheme using histologic grade of a testing set as guidance. Results The histologic grade assigned by pathologists to invasive breast carcinoma images strongly correlated with both the presence and extent of cell nuclei with dispersed chromatin and the architecture, specifically the extent of presence of tubular cross sections. The two parameters that differentiated tumor grade found in this study were (1 the number density of cell nuclei with dispersed chromatin and (2 the number density of tubular cross sections identified through image processing as white blobs that were surrounded by a continuous string of cell nuclei. Classification based on subdivisions of a whole slide image containing a high concentration of cancer cell nuclei consistently agreed with the grade classification of the entire slide. Conclusion The automated image analysis and classification presented in this study demonstrate the feasibility of developing clinically relevant classification of histology images based on micro- texture. This method provides pathologists an invaluable quantitative tool for evaluation of the components of the Nottingham system for breast tumor grading and avoid intra-observer variability thus increasing the consistency of the decision-making process.

  5. Differentiation of four Indian aboriginal cattle populations revealed by STR markers.

    Science.gov (United States)

    Sharma, R; Maitra, A; Pandey, A K; Mishra, B P

    2012-06-01

    Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 +/- 0.04 in Binjharpuri to 0.664 +/- 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 +/- 0.02 and 0.720 +/- 0.01, respectively. In the overall population, the homozygote excess (F(IT)) of 0.132 +/- 0.03, was partly due to the genetic differentiation among breeds (F(ST) = 0.044 +/- 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F(IS) = 0.094 +/- 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei's Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership. PMID:22946330

  6. Differential proteomic analysis of STAT6 knockout mice reveals new regulatory function in liver lipid homeostasis.

    Science.gov (United States)

    Iff, Joël; Wang, Wei; Sajic, Tatjana; Oudry, Nathalie; Gueneau, Estelle; Hopfgartner, Gérard; Varesio, Emmanuel; Szanto, Ildiko

    2009-10-01

    Increased inflammatory signaling is a key feature of metabolic disorders. In this context, the role of increased pro-inflammatory signals has been extensively studied. By contrast, no efforts have been dedicated to study the contrasting scenario: the attenuation of anti-inflammatory signals and their role in metabolic homeostasis. IL-4 and IL-13 are anti-inflammatory cytokines signaling through the Signal Transducer and Activator of Transcription 6 (STAT6). Our study was aimed at evaluating the lack of STAT6 signaling on liver homeostasis. To this end we analyzed the liver proteome of wild type and STAT6 knock-out mice using 2D nanoscale LC-MS/MS with iTRAQ labeling technique. The coordinated changes in proteins identified by this quantitative proteome analysis indicated disturbed lipid homeostasis and a state of hepatocellular stress. Most significantly, the expression of the liver fatty acid binding protein (FABP1) was increased in the knock-out mice. In line with the elevated FABP1 expression we found latent liver lipid accumulation in the STAT6-deficient mice which was further aggravated when mice were challenged by a high fat diet. In conclusion, our study revealed a so far uncharacterized role for STAT6 in regulating liver lipid homeostasis and demonstrates the importance of anti-inflammatory signaling in the defense against the development of liver steatosis. PMID:19663508

  7. Feather isotope analysis reveals differential patterns of habitat and resource use in populations of white-winged doves

    Science.gov (United States)

    Carleton, Scott A.; Martinez Del Rio, Carlos; Robinson, Timothy J.

    2015-01-01

    The white-winged dove (Zenaida asiatica) serves an important ecological role as a diurnal pollinator of the saguaro cactus in the Sonoran desert and an economic role as a highly sought after game bird in North America. White-winged doves are intimately linked to anthropogenic changes on the landscape and because of this, have experienced dramatic population fluctuations over the last 75 years in response, both positively and negatively, to anthropogenic changes on the landscape. To understand the factors driving population growth and decline of migratory species like the white-winged dove, it is imperative we study resource use on both their breeding and wintering grounds. To understand how populations are distributed on the wintering grounds, we tested an alternative to band recovery approaches by using stable isotope analysis. Before we could use isotope analysis to link breeding and wintering locations for this species, we first needed to determine if hydrogen (δ2H) and carbon (δ13C) stable isotopes in feather tissue (δ2Hf and δ13Cf, respectively) could differentiate among populations of white-winged doves across their breeding range in Texas, New Mexico, and Arizona. δ2Hf and δ13Cf not only differentiated between populations of white-winged doves that breed in the United States, but δ2Hf also provided further differentiation in white-winged doves that breed in native Sonoran Desert and agricultural habitats in the western portion of their range. Ecological processes associated with desert resources and anthropogenic influences, specifically saguaro cacti and irrigated crops, largely determined δ2Hf in some white-winged doves in Arizona whereas δ2H of precipitation (δ2Hp) largely determined δ2Hfof doves in New Mexico and Texas. This study highlights the usefulness of stable isotope analysis to differentiate populations of animals across the landscape and the insight isotopes can provide into habitat and resource use. Published 2015. This article

  8. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

    Directory of Open Access Journals (Sweden)

    Adam C. Wilkinson

    2013-10-01

    Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

  9. Alternative Splicing and Differential Expression of Two Transcripts of Nicotine Adenine Dinucleotide Phosphate Oxidase B Gene from Zea mays

    Institute of Scientific and Technical Information of China (English)

    Fan Lin; Yun Zhang; Ming-Yi Jiang

    2009-01-01

    With the exception of rice, little is known about the existence of respiratory burst oxidase homolog (rboh) gene in cereals. The present study reports the cloning and analysis of a novel rboh gene, termed ZmrbohB, from maize (Zea mays L.). The full-length cDNA of ZmrbohB encodes a 942 amino acid protein containing all of the respiratory burst oxidase homolog catalytically critical motifs.Altemative splicing of ZmrbohB has generated two transcript isoforms, ZmrbohB-α and -β. Spliced transcript ZmrbohB-β retains an unspliced intron 11 that carries a premature termination codon and probably leads to nonsense-mediated mRNA decay. Expression analysis showed that two splice isoforms were differentially expressed in various tissues and at different developmental stages, and the major product was ZmrbohB-α. The transcripts of ZmrbohB-α accumulated markedly when the maize seedlings were subjected to various abiotic stimuli, such as wounding, cold (4℃), heat (40℃), UV and salinity stress. In addition, several abiotic stimuli also affected the alternative splicing pattern of ZmrbohB except wounding. These results provide new insight into roles in the expression regulation of plant rboh genes and suggest that ZmrbohB gene may play a role in response to environmental stresses.

  10. Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Ryan Li

    Full Text Available Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma (HNSCC is unclear. Our study queried exon-level expression to implicate splice variants in HNSCC tumors.We performed a comparative genome-wide analysis of 44 HNSCC tumors and 25 uvulopalatopharyngoplasty (UPPP tissue samples at an exon expression level. In our comparison we ranked genes based upon a novel score-the Maximum-Minimum Exon Score (MMES--designed to predict the likelihood of an alternative splicing event occurring. We validated predicted alternative splicing events using quantitative RT-PCR on an independent cohort.After MMES scoring of 17,422 genes, the top 900 genes with the highest scores underwent additional manual inspection of expression patterns in a graphical analysis. The genes LAMA3, DST, VEGFC, SDHA, RASIP1, and TP63 were selected for further validation studies because of a high frequency of alternative splicing suggested in our graphical analysis, and literature review showing their biological relevance and known splicing patterns. We confirmed TP63 as having dominant expression of the short DeltaNp63 isoform in HNSCC tumor samples, consistent with prior reports. Two of the six genes (LAMA3 and DST validated by quantitative RT-PCR for tumor-specific alternative splicing events (Student's t test, P<0.001.Alternative splicing events of oncologically relevant proteins occur in HNSCC. The number of genes expressing tumor-specific splice variants needs further elucidation, as does the functional significance of selective isoform expression.

  11. Differential appearance of isoforms and cultivar variation in protein temporal profiles revealed in the maturing barley grain proteome

    DEFF Research Database (Denmark)

    Finnie, Christine; Bak-Jensen, K.S.; Laugesen, Sabrina;

    2006-01-01

    Proteome analysis of mature barley (Hordeum vulgare subsp. vulgare) seeds has led to the identification of proteins in about 450 spots on 2D-gels. To shed light on the role of some of these proteins, their temporal appearance was monitored over 5 weeks during grain-filling and maturation of field......-grown barley. Appearance profiles are described for 105 proteins identified in 185 2D-gel spots in the overlapping pI ranges 4-7 and 6-11. Grouping of proteins according to appearance across functional categories revealed instances of differential regulation of protein forms. Thus, a single 1-cys......-peroxiredoxin isoform was identified in three spots, one present throughout grain filling, one appearing during desiccation and one observed only in mature seeds. This suggested post-translational modification of the protein to different degrees during seed maturation. Distinct isoforms of several proteins were...

  12. Transcriptional profiling of cortical versus cancellous bone from mechanically-loaded murine tibiae reveals differential gene expression.

    Science.gov (United States)

    Kelly, Natalie H; Schimenti, John C; Ross, F Patrick; van der Meulen, Marjolein C H

    2016-05-01

    Mechanical loading is an anabolic stimulus that increases bone mass, and thus a promising method to counteract osteoporosis-related bone loss. The mechanism of this anabolism remains unclear, and needs to be established for both cortical and cancellous envelopes individually. We hypothesized that cortical and cancellous bone display different gene expression profiles at baseline and in response to mechanical loading. To test this hypothesis, the left tibiae of 10-week-old female C57Bl/6 mice were subjected to one session of axial tibial compression (9N, 1200cycles, 4Hz triangle waveform) and euthanized 3 and 24h following loading. The right limb served as the contralateral control. We performed RNA-seq on marrow-free metaphyseal samples from the cortical shell and the cancellous core to determine differential gene expression at baseline (control limb) and in response to load. Differential expression was verified with qPCR. Cortical and cancellous bone exhibited distinctly different transcriptional profiles basally and in response to mechanical loading. More genes were differentially expressed with loading at 24h with more genes downregulated at 24h than at 3h in both tissues. Enhanced Wnt signaling dominated the response in cortical bone at 3 and 24h, but in cancellous bone only at 3h. In cancellous bone at 24h many muscle-related genes were downregulated. These findings reveal key differences between cortical and cancellous genetic regulation in response to mechanical loading. Future studies at different time points and multiple loading sessions will add to our knowledge of cortical and cancellous mechanotransduction with the potential to identify new targets for mouse genetic knockout studies and drugs to treat osteoporosis. PMID:26876048

  13. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases.

    Directory of Open Access Journals (Sweden)

    Steven J Bark

    Full Text Available Secretory vesicles are required for release of chemical messengers to mediate intercellular signaling among human biological systems. It is necessary to define the organization of the protein architecture of the 'human' dense core secretory vesicles (DCSV to understand mechanisms for secretion of signaling molecules essential for cellular regulatory processes. This study, therefore, conducted extensive quantitative proteomics and systems biology analyses of human DCSV purified from human pheochromocytoma. Over 600 human DCSV proteins were identified with quantitative evaluation of over 300 proteins, revealing that most proteins participate in producing peptide hormones and neurotransmitters, enzymes, and the secretory machinery. Systems biology analyses provided a model of interacting DCSV proteins, generating hypotheses for differential intracellular protein kinases A and C signaling pathways. Activation of cellular PKA and PKC pathways resulted in differential secretion of neuropeptides, catecholamines, and β-amyloid of Alzheimer's disease for mediating cell-cell communication. This is the first study to define a model of the protein architecture of human DCSV for human disease and health.

  14. Negative differential mobility for negative carriers as revealed by space charge measurements on crosslinked polyethylene insulated model cables

    Science.gov (United States)

    Teyssedre, G.; Vu, T. T. N.; Laurent, C.

    2015-12-01

    Among features observed in polyethylene materials under relatively high field, space charge packets, consisting in a pulse of net charge that remains in the form of a pulse as it crosses the insulation, are repeatedly observed but without complete theory explaining their formation and propagation. Positive charge packets are more often reported, and the models based on negative differential mobility(NDM) for the transport of holes could account for some charge packets phenomenology. Conversely, NDM for electrons transport has never been reported so far. The present contribution reports space charge measurements by pulsed electroacoustic method on miniature cables that are model of HVDC cables. The measurements were realized at room temperature or with a temperature gradient of 10 °C through the insulation under DC fields on the order 30-60 kV/mm. Space charge results reveal systematic occurrence of a negative front of charges generated at the inner electrode that moves toward the outer electrode at the beginning of the polarization step. It is observed that the transit time of the front of negative charge increases, and therefore the mobility decreases, with the applied voltage. Further, the estimated mobility, in the range 10-14-10-13 m2 V-1 s-1 for the present results, increases when the temperature increases for the same condition of applied voltage. The features substantiate the hypothesis of negative differential mobility used for modelling space charge packets.

  15. Targeted disruption of the LAMA3 gene in mice reveals abnormalities in survival and late stage differentiation of epithelial cells.

    Science.gov (United States)

    Ryan, M C; Lee, K; Miyashita, Y; Carter, W G

    1999-06-14

    Laminin 5 regulates anchorage and motility of epithelial cells through integrins alpha6beta4 and alpha3beta1, respectively. We used targeted disruption of the LAMA3 gene, which encodes the alpha3 subunit of laminin 5 and other isoforms, to examine developmental functions that are regulated by adhesion to the basement membrane (BM). In homozygous null animals, profound epithelial abnormalities were detected that resulted in neonatal lethality, consistent with removal of all alpha3-laminin isoforms from epithelial BMs. Alterations in three different cellular functions were identified. First, using a novel tissue adhesion assay, we found that the mutant BM could not induce stable adhesion by integrin alpha6beta4, consistent with the presence of junctional blisters and abnormal hemidesmosomes. In the absence of laminin 5 function, we were able to detect a new ligand for integrin alpha3beta1 in the epidermal BM, suggesting that basal keratinocytes can utilize integrin alpha3beta1 to interact with an alternative ligand. Second, we identified a survival defect in mutant epithelial cells that could be rescued by exogenous laminin 5, collagen, or an antibody against integrin alpha6beta4, suggesting that signaling through beta1 or beta4 integrins is sufficient for survival. Third, we detected abnormalities in ameloblast differentiation in developing mutant incisors indicating that events downstream of adhesion are affected in mutant animals. These results indicate that laminin 5 has an important role in regulating tissue organization, gene expression, and survival of epithelium. PMID:10366601

  16. Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-Like Cells.

    Science.gov (United States)

    Kondo, Yuki; Nurani, Alif Meem; Saito, Chieko; Ichihashi, Yasunori; Saito, Masato; Yamazaki, Kyoko; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Fukuda, Hiroo

    2016-06-01

    Cell differentiation is a complex process involving multiple steps, from initial cell fate specification to final differentiation. Procambial/cambial cells, which act as vascular stem cells, differentiate into both xylem and phloem cells during vascular development. Recent studies have identified regulatory cascades for xylem differentiation. However, the molecular mechanism underlying phloem differentiation is largely unexplored due to technical challenges. Here, we established an ectopic induction system for phloem differentiation named Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL). Our results verified similarities between VISUAL-induced Arabidopsis thaliana phloem cells and in vivo sieve elements. We performed network analysis using transcriptome data with VISUAL to dissect the processes underlying phloem differentiation, eventually identifying a factor involved in the regulation of the master transcription factor gene APL Thus, our culture system opens up new avenues not only for genetic studies of phloem differentiation, but also for future investigations of multidirectional differentiation from vascular stem cells. PMID:27194709

  17. Latitudinal gradients in tree ring stable carbon and oxygen isotopes reveal differential climate influences of the North American Monsoon System

    Science.gov (United States)

    Szejner, Paul; Wright, William E.; Babst, Flurin; Belmecheri, Soumaya; Trouet, Valerie; Leavitt, Steven W.; Ehleringer, James R.; Monson, Russell K.

    2016-07-01

    The arrival of the North American Monsoon System (NAMS) terminates a presummer hyperarid period in the southwestern United States (U.S.), providing summer moisture that is favorable for forest growth. Montane forests in this region rely on winter snowpack to drive much of their growth; the extent to which they use NAMS moisture is uncertain. We addressed this by studying stable carbon and oxygen isotopes in earlywood and latewood from 11 sites along a latitudinal gradient extending from Arizona and New Mexico to Utah. This study provides the first regional perspective on the relative roles of winter versus summer precipitation as an ecophysiological resource. Here we present evidence that Ponderosa pine uses NAMS moisture differentially across this gradient. 13C/12C ratios suggest that photosynthetic water use efficiency during latewood formation is more sensitive to summer precipitation at the northern than at the southern sites. This is likely due to the fact that NAMS moisture provides sufficiently favorable conditions for tree photosynthesis and growth during most years in the southern sites, whereas the northern sites experience larger summer moisture variability, which in some years is limiting growth. Cellulose δ18O and δ13C values revealed that photoassimilates in the southern sites were produced under higher vapor pressure deficit conditions during spring compared to summer, demonstrating a previously underappreciated effect of seasonal differences in atmospheric humidity on tree ring isotope ratios. Our findings suggest that future changes in NAMS will potentially alter productivity and photosynthetic water use dynamics differentially along latitudinal gradients in southwestern U.S. montane forests.

  18. Extracellular matrix of adipogenically differentiated mesenchymal stem cells reveals a network of collagen filaments, mostly interwoven by hexagonal structural units.

    Science.gov (United States)

    Ullah, Mujib; Sittinger, Michael; Ringe, Jochen

    2013-01-01

    Extracellular matrix (ECM) is the non-cellular component of tissues, which not only provides biological shelter but also takes part in the cellular decisions for diverse functions. Every tissue has an ECM with unique composition and topology that governs the process of determination, differentiation, proliferation, migration and regeneration of cells. Little is known about the structural organization of matrix especially of MSC-derived adipogenic ECM. Here, we particularly focus on the composition and architecture of the fat ECM to understand the cellular behavior on functional bases. Thus, mesenchymal stem cells (MSC) were adipogenically differentiated, then, were transferred to adipogenic propagation medium, whereas they started the release of lipid droplets leaving bare network of ECM. Microarray analysis was performed, to indentify the molecular machinery of matrix. Adipogenesis was verified by Oil Red O staining of lipid droplets and by qPCR of adipogenic marker genes PPARG and FABP4. Antibody staining demonstrated the presence of collagen type I, II and IV filaments, while alkaline phosphatase activity verified the ossified nature of these filaments. In the adipogenic matrix, the hexagonal structures were abundant followed by octagonal structures, whereas they interwoven in a crisscross manner. Regarding molecular machinery of adipogenic ECM, the bioinformatics analysis revealed the upregulated expression of COL4A1, ITGA7, ITGA7, SDC2, ICAM3, ADAMTS9, TIMP4, GPC1, GPC4 and downregulated expression of COL14A1, ADAMTS5, TIMP2, TIMP3, BGN, LAMA3, ITGA2, ITGA4, ITGB1, ITGB8, CLDN11. Moreover, genes associated with integrins, glycoproteins, laminins, fibronectins, cadherins, selectins and linked signaling pathways were found. Knowledge of the interactive-language between cells and matrix could be beneficial for the artificial designing of biomaterials and bioscaffolds. PMID:23851162

  19. Negative differential mobility for negative carriers as revealed by space charge measurements on crosslinked polyethylene insulated model cables

    Energy Technology Data Exchange (ETDEWEB)

    Teyssedre, G., E-mail: gilbert.teyssedre@laplace.univ-tlse.fr; Laurent, C. [Université de Toulouse, UPS, INPT, LAPLACE (Laboratoire Plasma et Conversion d' Energie), 118 route de Narbonne, F-31062 Toulouse cedex 9 (France); CNRS, LAPLACE, F-31062 Toulouse (France); Vu, T. T. N. [Université de Toulouse, UPS, INPT, LAPLACE (Laboratoire Plasma et Conversion d' Energie), 118 route de Narbonne, F-31062 Toulouse cedex 9 (France); Electric Power University, 235 Hoang Quoc Viet, 10000 Hanoi (Viet Nam)

    2015-12-21

    Among features observed in polyethylene materials under relatively high field, space charge packets, consisting in a pulse of net charge that remains in the form of a pulse as it crosses the insulation, are repeatedly observed but without complete theory explaining their formation and propagation. Positive charge packets are more often reported, and the models based on negative differential mobility(NDM) for the transport of holes could account for some charge packets phenomenology. Conversely, NDM for electrons transport has never been reported so far. The present contribution reports space charge measurements by pulsed electroacoustic method on miniature cables that are model of HVDC cables. The measurements were realized at room temperature or with a temperature gradient of 10 °C through the insulation under DC fields on the order 30–60 kV/mm. Space charge results reveal systematic occurrence of a negative front of charges generated at the inner electrode that moves toward the outer electrode at the beginning of the polarization step. It is observed that the transit time of the front of negative charge increases, and therefore the mobility decreases, with the applied voltage. Further, the estimated mobility, in the range 10{sup −14}–10{sup −13} m{sup 2} V{sup −1} s{sup −1} for the present results, increases when the temperature increases for the same condition of applied voltage. The features substantiate the hypothesis of negative differential mobility used for modelling space charge packets.

  20. Transcriptome profiling of the eyestalk of precocious juvenile Chinese mitten crab reveals putative neuropeptides and differentially expressed genes.

    Science.gov (United States)

    Xu, Zhiqiang; Zhao, Muzi; Li, Xuguang; Lu, Quanping; Li, Yuehua; Ge, Jiachun; Pan, Jianlin

    2015-09-15

    Chinese mitten crabs that reach maturity 1 year earlier than normal crabs are known as precocious juvenile crabs. The molecular mechanisms underlying the precocity of the Chinese mitten crab are poorly understood. To identify the genes that may be involved in the control of precocity in Chinese mitten crab, we measured the expression profile of eyestalk genes in precocious and normally developed juvenile crabs using high-throughput sequencing on an Illumina HiSeq 2500 platform. We obtained 56,446,284 raw reads from the precocious crabs and 58,029,476 raw reads from the normally developed juvenile crabs. Reads from the two libraries were combined into a single data set. De novo assembly of the combined read set yielded 78,777 unigenes with an average length of 1563 bp. A total of 41,405 unigenes with predicted ORFs were selected for functional annotation. Among these genes, we identified three neuropeptide genes belonging to the crustacean hyperglycemic hormone family and two neuropeptide genes encoding the chromatophorotropic hormones. Transcriptome comparison between the two libraries revealed 42 genes that exhibited significant differential expression, of which 29 genes were up-regulated and 13 genes were down-regulated in the precocious crabs. To confirm the sequencing data, six differentially expressed genes with functional annotations were selected and validated by qRT-PCR. In conclusion, we obtained the comprehensive transcriptome of the eyestalk tissues of precocious juvenile crabs. The sequencing results may provide new insights into the biomolecular basis of precocity in the Chinese mitten crab.

  1. Analysis of the Isoprenoid Biosynthesis Pathways in Listeria monocytogenes Reveals a Role for the Alternative 2-C-Methyl-d-Erythritol 4-Phosphate Pathway in Murine Infection▿

    OpenAIRE

    Begley, Máire; Bron, Peter A; Heuston, Sinead; Casey, Pat G.; Englert, Nadine; Wiesner, Jochen; Jomaa, Hassan; Gahan, Cormac G. M.; Hill, Colin

    2008-01-01

    Most bacteria synthesize isoprenoids through one of two essential pathways which provide the basic building block, isopentyl diphosphate (IPP): either the classical mevalonate pathway or the alternative non-mevalonate 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. However, postgenomic analyses of the Listeria monocytogenes genome revealed that this pathogen possesses the genetic capacity to produce the complete set of enzymes involved in both pathways. The nonpathogenic species Listeria i...

  2. Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.

    Directory of Open Access Journals (Sweden)

    Andrea eVega

    2015-11-01

    Full Text Available Nitrogen (N is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.

  3. Differential Features between Chronic Skin Inflammatory Diseases Revealed in Skin-Humanized Psoriasis and Atopic Dermatitis Mouse Models.

    Science.gov (United States)

    Carretero, Marta; Guerrero-Aspizua, Sara; Illera, Nuria; Galvez, Victoria; Navarro, Manuel; García-García, Francisco; Dopazo, Joaquin; Jorcano, Jose Luis; Larcher, Fernando; del Rio, Marcela

    2016-01-01

    Psoriasis and atopic dermatitis are chronic and relapsing inflammatory diseases of the skin affecting a large number of patients worldwide. Psoriasis is characterized by a T helper type 1 and/or T helper type 17 immunological response, whereas acute atopic dermatitis lesions exhibit T helper type 2-dominant inflammation. Current single gene and signaling pathways-based models of inflammatory skin diseases are incomplete. Previous work allowed us to model psoriasis in skin-humanized mice through proper combinations of inflammatory cell components and disruption of barrier function. Herein, we describe and characterize an animal model for atopic dermatitis using similar bioengineered-based approaches, by intradermal injection of human T helper type 2 lymphocytes in regenerated human skin after partial removal of stratum corneum. In this work, we have extensively compared this model with the previous and an improved version of the psoriasis model, in which T helper type 1 and/or T helper type 17 lymphocytes replace exogenous cytokines. Comparative expression analyses revealed marked differences in specific epidermal proliferation and differentiation markers and immune-related molecules, including antimicrobial peptides. Likewise, the composition of the dermal inflammatory infiltrate presented important differences. The availability of accurate and reliable animal models for these diseases will contribute to the understanding of the pathogenesis and provide valuable tools for drug development and testing. PMID:26763433

  4. Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses

    Science.gov (United States)

    Li, Jianfang; Yang, Yuchen; Chen, Qipian; Fang, Lu; He, Ziwen; Guo, Wuxia; Qiao, Sitan; Wang, Zhengzhen; Guo, Miaomiao; Zhong, Cairong; Zhou, Renchao; Shi, Suhua

    2016-01-01

    Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia. PMID:27380895

  5. Proteome profiling of the growth phases of Leishmania pifanoi promastigotes in axenic culture reveals differential abundance of immunostimulatory proteins.

    Science.gov (United States)

    Alcolea, Pedro J; Alonso, Ana; García-Tabares, Francisco; Mena, María del Carmen; Ciordia, Sergio; Larraga, Vicente

    2016-06-01

    Leishmaniasis is a term that encompasses a compendium of neglected tropical diseases caused by dimorphic and digenetic protozoan parasites from the genus Leishmania (Kinetoplastida: Trypanosomatidae). The clinical manifestations of neotropical cutaneous leishmaniasis (NCL) caused by Leishmania pifanoi and other species of the "Leishmania mexicana complex" mainly correspond to anergic diffuse cutaneous leishmaniasis (ADCL), which is the origin of considerable morbidity. Despite the outstanding advances in the characterization of the trypanosomatid genomes and proteomes, the biology of this species has been scarcely explored. However, the close relation of L. pifanoi to the sequenced species L. mexicana and others included in the "L. mexicana complex" allowed us to perform a two-dimension electrophoresis (2DE) approach to the promastigote proteome at the differential expression level. Protein identifications were performed by matrix-assisted laser desorption-ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF). This insight has revealed similarities and differences between L. pifanoi and other species responsible for cutaneous and visceral leishmaniasis. Interestingly, certain proteins that were previously described as immunostimulatory (elongation factor 1β, trypanothione peroxidase, heat shock protein 70, enolase, GDP-forming succinyl-CoA and aldehyde dehydrogenase) are more abundant in the final growth stages of promastigotes (late-logarithmic and/or stationary phase) in the case of L. pifanoi. PMID:26992294

  6. Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation.

    Science.gov (United States)

    Weng, Lingjie; Li, Yi; Xie, Xiaohui; Shi, Yongsheng

    2016-06-01

    mRNA alternative polyadenylation (APA) is a critical mechanism for post-transcriptional gene regulation and is often regulated in a tissue- and/or developmental stage-specific manner. An ultimate goal for the APA field has been to be able to computationally predict APA profiles under different physiological or pathological conditions. As a first step toward this goal, we have assembled a poly(A) code for predicting tissue-specific poly(A) sites (PASs). Based on a compendium of over 600 features that have known or potential roles in PAS selection, we have generated and refined a machine-learning algorithm using multiple high-throughput sequencing-based data sets of tissue-specific and constitutive PASs. This code can predict tissue-specific PASs with >85% accuracy. Importantly, by analyzing the prediction performance based on different RNA features, we found that PAS context, including the distance between alternative PASs and the relative position of a PAS within the gene, is a key feature for determining the susceptibility of a PAS to tissue-specific regulation. Our poly(A) code provides a useful tool for not only predicting tissue-specific APA regulation, but also for studying its underlying molecular mechanisms. PMID:27095026

  7. RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells.

    Directory of Open Access Journals (Sweden)

    Kersti Jääger

    Full Text Available BACKGROUND: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation of stem and progenitor cells. Mesenchymal stem cells (MSCs that have the ability to differentiate into various cell types, have been isolated from the stromal fraction of virtually all tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell composition. METHODOLOGY/PRINCIPAL FINDINGS: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types, adipose tissue-derived MSCs (AdMSCs and dermal fibroblasts (FBs along adipogenic, osteogenic and chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated donor-matched AdMSCs and FBs are distinct populations that stay different upon differentiation into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression occur early in differentiation and persist over time in both AdMSCs and FBs. Further, AdMSCs and FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics of chondrogenic differentiation. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that stromal stem cells including AdMSCs and dermal FBs exploit different molecular mechanisms of differentiation to reach a common cell fate. The early mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic differentiation but are distinct for chondrogenic differentiation between AdMSCs and FBs.

  8. Masked priming of conceptual features reveals differential brain activation during unconscious access to conceptual action and sound information.

    Directory of Open Access Journals (Sweden)

    Natalie M Trumpp

    Full Text Available Previous neuroimaging studies suggested an involvement of sensory-motor brain systems during conceptual processing in support of grounded cognition theories of conceptual memory. However, in these studies with visible stimuli, contributions of strategic imagery or semantic elaboration processes to observed sensory-motor activity cannot be entirely excluded. In the present study, we therefore investigated the electrophysiological correlates of unconscious feature-specific priming of action- and sound-related concepts within a novel feature-priming paradigm to specifically probe automatic processing of conceptual features without the contribution of possibly confounding factors such as orthographic similarity or response congruency. Participants were presented with a masked subliminal prime word and a subsequent visible target word. In the feature-priming conditions primes as well as targets belonged to the same conceptual feature dimension (action or sound, e.g., typewriter or radio whereas in the two non-priming conditions, either the primes or the targets consisted of matched control words with low feature relevance (e.g., butterfly or candle. Event-related potential analyses revealed unconscious feature-specific priming effects at fronto-central electrodes within 100 to 180 ms after target stimulus onset that differed with regard to topography and underlying neural generators. In congruency with previous findings under visible stimulation conditions, these differential subliminal ERP feature-priming effects demonstrate an unconscious automatic access to action versus sound features of concepts. The present results therefore support grounded cognition theory suggesting that activity in sensory and motor areas during conceptual processing can also occur unconsciously and is not mandatorily accompanied by a vivid conscious experience of the conceptual content such as in imagery.

  9. Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird.

    Science.gov (United States)

    Ornelas, Juan Francisco; González, Clementina; Hernández-Baños, Blanca E; García-Moreno, Jaime

    2016-02-01

    The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue-throated populations (Sierra Madre del Sur); two groups of amethyst-throated populations (Trans-Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39-0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue- and amethyst-throated populations does not correspond to the 2-MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species' suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest-interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic

  10. Systems biology of tissue-specific response to Anaplasma phagocytophilum reveals differentiated apoptosis in the tick vector Ixodes scapularis.

    Directory of Open Access Journals (Sweden)

    Nieves Ayllón

    2015-03-01

    Full Text Available Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector, Ixodes scapularis. Global tissue-specific response and apoptosis signaling pathways were characterized in I. scapularis nymphs and adult female midguts and salivary glands infected with A. phagocytophilum using a systems biology approach combining transcriptomics and proteomics. Apoptosis was selected for pathway-focused analysis due to its role in bacterial infection of tick cells. The results showed tissue-specific differences in tick response to infection and revealed differentiated regulation of apoptosis pathways. The impact of bacterial infection was more pronounced in tick nymphs and midguts than in salivary glands, probably reflecting bacterial developmental cycle. All apoptosis pathways described in other organisms were identified in I. scapularis, except for the absence of the Perforin ortholog. Functional characterization using RNA interference showed that Porin knockdown significantly increases tick colonization by A. phagocytophilum. Infection with A. phagocytophilum produced complex tissue-specific alterations in transcript and protein levels. In tick nymphs, the results suggested a possible effect of bacterial infection on the inhibition of tick immune response. In tick midguts, the results suggested that A. phagocytophilum infection inhibited cell apoptosis to facilitate and establish infection through up-regulation of the JAK/STAT pathway. Bacterial infection inhibited the intrinsic apoptosis pathway in tick salivary glands by down-regulating Porin expression that resulted in the inhibition of Cytochrome c release as the anti-apoptotic mechanism to facilitate bacterial infection. However, tick salivary glands may promote apoptosis to limit bacterial infection through induction of the extrinsic apoptosis pathway. These dynamic

  11. Feedback-Controlled Transcranial Alternating Current Stimulation Reveals a Functional Role of Sleep Spindles in Motor Memory Consolidation.

    Science.gov (United States)

    Lustenberger, Caroline; Boyle, Michael R; Alagapan, Sankaraleengam; Mellin, Juliann M; Vaughn, Bradley V; Fröhlich, Flavio

    2016-08-22

    Transient episodes of brain oscillations are a common feature of both the waking and the sleeping brain. Sleep spindles represent a prominent example of a poorly understood transient brain oscillation that is impaired in disorders such as Alzheimer's disease and schizophrenia. However, the causal role of these bouts of thalamo-cortical oscillations remains unknown. Demonstrating a functional role of sleep spindles in cognitive processes has, so far, been hindered by the lack of a tool to target transient brain oscillations in real time. Here, we show, for the first time, selective enhancement of sleep spindles with non-invasive brain stimulation in humans. We developed a system that detects sleep spindles in real time and applies oscillatory stimulation. Our stimulation selectively enhanced spindle activity as determined by increased sigma activity after transcranial alternating current stimulation (tACS) application. This targeted modulation caused significant enhancement of motor memory consolidation that correlated with the stimulation-induced change in fast spindle activity. Strikingly, we found a similar correlation between motor memory and spindle characteristics during the sham night for the same spindle frequencies and electrode locations. Therefore, our results directly demonstrate a functional relationship between oscillatory spindle activity and cognition. PMID:27476602

  12. Spike-interval triggered averaging reveals a quasi-periodic spiking alternative for stochastic resonance in catfish electroreceptors.

    Directory of Open Access Journals (Sweden)

    Martin J M Lankheet

    Full Text Available Catfish detect and identify invisible prey by sensing their ultra-weak electric fields with electroreceptors. Any neuron that deals with small-amplitude input has to overcome sensitivity limitations arising from inherent threshold non-linearities in spike-generation mechanisms. Many sensory cells solve this issue with stochastic resonance, in which a moderate amount of intrinsic noise causes irregular spontaneous spiking activity with a probability that is modulated by the input signal. Here we show that catfish electroreceptors have adopted a fundamentally different strategy. Using a reverse correlation technique in which we take spike interval durations into account, we show that the electroreceptors generate a supra-threshold bias current that results in quasi-periodically produced spikes. In this regime stimuli modulate the interval between successive spikes rather than the instantaneous probability for a spike. This alternative for stochastic resonance combines threshold-free sensitivity for weak stimuli with similar sensitivity for excitations and inhibitions based on single interspike intervals.

  13. A co-culture model of the hippocampal neurogenic niche reveals differential effects of astrocytes, endothelial cells and pericytes on proliferation and differentiation of adult murine precursor cells

    Directory of Open Access Journals (Sweden)

    Fanny Ehret

    2015-11-01

    Full Text Available The niche concept of stem cell biology proposes a functional unit between the precursor cells and their local microenvironment, to which several cell types might contribute by cell–cell contacts, extracellular matrix, and humoral factors. We here established three co-culture models (with cell types separated by membrane for both adherent monolayers and neurospheres to address the potential influence of different niche cell types in the neurogenic zone of the adult hippocampus of mice. Astrocytes and endothelial cells enhanced precursor cell proliferation and neurosphere formation. Endothelial factors also led to a prolonged increase in proliferation after growth factor withdrawal, which otherwise induces differentiation. All niche cell types enhanced cell survival in monolayer cultures, endothelial cells also stimulated neuronal differentiation. A parallel trend elicited by astrocytes did not reach conventional statistical significance. Pericytes had variable effects here. We did not observe changes in differentiation in neurosphere co-cultures. In summary, our data indicate that in precursor cell culture protocols survival could be improved by adding as yet unknown factors physiologically contributed by astrocytes and endothelial cells. Our findings also underscore the complexity of the niche and the differential impact of factors from the different sources on distinct aspects of neuronal development. With the help of the models presented here, identification of these factors and their specific biological activity can now be initiated.

  14. Unlike PPAR{gamma}, PPAR{alpha} or PPAR{beta}/{delta} activation does not promote human monocyte differentiation toward alternative macrophages

    Energy Technology Data Exchange (ETDEWEB)

    Bouhlel, Mohamed Amine [Univ Lille Nord de France, F-59000 Lille (France); Inserm U545, F-59000 Lille (France); UDSL, F-59000 Lille (France); Institut Pasteur de Lille, F-59019 Lille (France); Brozek, John [Genfit, Loos (France); Derudas, Bruno [Univ Lille Nord de France, F-59000 Lille (France); Inserm U545, F-59000 Lille (France); UDSL, F-59000 Lille (France); Institut Pasteur de Lille, F-59019 Lille (France); Zawadzki, Christophe; Jude, Brigitte [Inserm ERI-9 and Equipe d' Accueil 2693, IFR114, Universite de Lille, Lille (France); Staels, Bart, E-mail: bart.staels@pasteur-lille.fr [Univ Lille Nord de France, F-59000 Lille (France); Inserm U545, F-59000 Lille (France); UDSL, F-59000 Lille (France); Institut Pasteur de Lille, F-59019 Lille (France); Chinetti-Gbaguidi, Giulia [Univ Lille Nord de France, F-59000 Lille (France); Inserm U545, F-59000 Lille (France); UDSL, F-59000 Lille (France); Institut Pasteur de Lille, F-59019 Lille (France)

    2009-08-28

    Macrophages adapt their response to micro-environmental signals. While Th1 cytokines promote pro-inflammatory M1 macrophages, Th2 cytokines promote an 'alternative' anti-inflammatory M2 macrophage phenotype. Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors expressed in macrophages where they control the inflammatory response. It has been shown that PPAR{gamma} promotes the differentiation of monocytes into anti-inflammatory M2 macrophages in humans and mice, while a role for PPAR{beta}/{delta} in this process has been reported only in mice and no data are available for PPAR{alpha}. Here, we show that in contrast to PPAR{gamma}, expression of PPAR{alpha} and PPAR{beta}/{delta} overall does not correlate with the expression of M2 markers in human atherosclerotic lesions, whereas a positive correlation with genes of lipid metabolism exists. Moreover, unlike PPAR{gamma}, PPAR{alpha} or PPAR{beta}/{delta} activation does not influence human monocyte differentiation into M2 macrophages in vitro. Thus, PPAR{alpha} and PPAR{beta}/{delta} do not appear to modulate the alternative differentiation of human macrophages.

  15. Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue

    Institute of Scientific and Technical Information of China (English)

    LI Mei; ZHAO ChunJiang

    2009-01-01

    Oxygen concentration is essential for appropriate metabolism. Hypoxia can exert a significant impact on physiological alteration of the cell and organism. Tibetan Chicken (Gallus gallus) is a Chinese in-digenous breed inhabiting in Tibetan areas, which is also a chicken breed living at high altitude for the longest time in the world. It has developed an adaptive mechanism to hypoxia, which is demonstrated by that Tibetan Chicken has much higher hatchability than low-land chicken breeds in high-altitude areas of Tibet. In the present study, Tibetan Chicken fertilized full sib eggs were incubated up to Ham-burger-Hamilton stage 43 under 13% and 21% oxygen concentration, respectively. Shouguang Chicken and Dwarf Recessive White Chicken were used as control groups. The hearts in all of the 3 chicken breeds under hypoxic and normoxic conditions were isolated and hybridized to GeneChip Chicken Genome Array to study molecular mechanisms underlying the adaptation to high altitude of Tibetan Chicken. As a result, 50 transcripts highly expressed in hypoxia are screened out. Among up-regulated genes, some are involved in the gone ontology (GO) such as cell growth, cell difference, muscle con-traction and signal transduction. However, the expression levels of 21 transcripts are lower in hypoxia than those in normoxia. Some down-regulated genes take part in cell communication, ion transport, protein amino acid phosphorylation and signal transduction. Interestingly, gene enrichment analyses of these differential gone expressions are mainly associated with immune system response and ion channel activity in response to stimulus. Moreover, the transcriptional expression profiles analyzed by hierarchical clustering and CPP-SOM software in all of the 3 different chicken breeds revealed that TI-betan Chicken is much closely related to Shouguang Chicken rather than Dwarf Recessive White Chicken. In addition, 12 transcripts of Tibetan Chicken breed-specific expressed genes were

  16. Study on Tibetan Chicken embryonic adaptability to chronic hypoxia by revealing differential gene expression in heart tissue

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Oxygen concentration is essential for appropriate metabolism.Hypoxia can exert a significant impact on physiological alteration of the cell and organism.Tibetan Chicken(Gallus gallus) is a Chinese indigenous breed inhabiting in Tibetan areas,which is also a chicken breed living at high altitude for the longest time in the world.It has developed an adaptive mechanism to hypoxia,which is demonstrated by that Tibetan Chicken has much higher hatchability than low-land chicken breeds in high-altitude areas of Tibet.In the present study,Tibetan Chicken fertilized full sib eggs were incubated up to Hamburger-Hamilton stage 43 under 13% and 21% oxygen concentration,respectively.Shouguang Chicken and Dwarf Recessive White Chicken were used as control groups.The hearts in all of the 3 chicken breeds under hypoxic and normoxic conditions were isolated and hybridized to Genechip Chicken Genome Array to study molecular mechanisms underlying the adaptation to high altitude of Tibetan Chicken.As a result,50 transcripts highly expressed in hypoxia are screened out.Among up-regulated genes,some are involved in the gene ontology(GO) such as cell growth,cell difference,muscle contraction and signal transduction.However,the expression levels of 21 transcripts are lower in hypoxia than those in normoxia.Some down-regulated genes take part in cell communication,ion transport,protein amino acid phosphorylation and signal transduction.Interestingly,gene enrichment analyses of these differential gene expressions are mainly associated with immune system response and ion channel activity in response to stimulus.Moreover,the transcriptional expression profiles analyzed by hierarchical clustering and CPP-SOM software in all of the 3 different chicken breeds revealed that Tibetan Chicken is much closely related to Shouguang Chicken rather than Dwarf Recessive White Chicken.In addition,12 transcripts of Tibetan Chicken breed-specific expressed genes were identified,which seem to result in a

  17. Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators

    DEFF Research Database (Denmark)

    Rabiee, Atefeh; Schwämmle, Veit; Sidoli, Simone;

    2016-01-01

    . New insights into phosphorylation-dependent signaling networks that impact on nuclear proteins and controls adipocyte differentiation and cell fate. Adipocytes (fat cells) are important endocrine and metabolic cells critical for systemic insulin sensitivity. Both adipose excess and insufficiency...

  18. Mapping enteroendocrine cell populations in transgenic mice reveals an unexpected degree of complexity in cellular differentiation within the gastrointestinal tract

    OpenAIRE

    1990-01-01

    The gastrointestinal tract is lined with a monolayer of cells that undergo perpetual and rapid renewal. Four principal, terminally differentiated cell types populate the monolayer, enterocytes, goblet cells, Paneth cells, and enteroendocrine cells. This epithelium exhibits complex patterns of regional differentiation, both from crypt- to-villus and from duodenum-to-colon. The "liver" fatty acid binding protein (L-FABP) gene represents a useful model for analyzing the molecular basis for intes...

  19. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders

    DEFF Research Database (Denmark)

    Keers, Robert; Coleman, Jonathan R I; Lester, Kathryn J;

    2016-01-01

    BACKGROUND: The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such...... variants has so far been limited to preselected candidate genes. In this study we extended the differential susceptibility hypothesis from a candidate gene to a genome-wide approach to test whether a polygenic score of environmental sensitivity predicted response to cognitive behavioural therapy (CBT) in...... children with anxiety disorders. METHODS: We identified variants associated with environmental sensitivity using a novel method in which within-pair variability in emotional problems in 1,026 monozygotic twin pairs was examined as a function of the pairs' genotype. We created a polygenic score of...

  20. Differential reinforcement of alternative behavior and demand fading in the treatment of escape-maintained destructive behavior.

    OpenAIRE

    Piazza, C C; Moes, D R; Fisher, W W

    1996-01-01

    The escape-maintained destructive behavior of a boy with autism was reduced during instructional sequences with differential reinforcement of compliance (DRA), escape extinction without physical guidance, and demand fading. The procedure decreased destructive behaviors to near-zero levels and greatly increased compliance.

  1. Differential Reinforcement of Alternative Behavior and Demand Fading in the Treatment of Escape-Maintained Destructive Behavior.

    Science.gov (United States)

    Piazza, Cathleen C.; And Others

    1996-01-01

    A study of an 11-year-old boy with autism and mild mental retardation found that his escape-maintained destructive behavior was reduced during instructional sequences with differential reinforcement of compliance, escape extinction without physical guidance, and demand fading. The procedure decreased destructive behaviors to near-zero levels and…

  2. Energy dispersive x-ray diffractometry as a tool alternative to differential scanning calorimetry for investigating polymer phase transitions

    International Nuclear Information System (INIS)

    Recently, a technique based on energy dispersive x-ray diffraction has been proposed to follow the polymer phase transitions. However, the potentialities of this method were not clear, as well as the experimental conditions in which it is more convenient than differential scanning calorimetry, generally used for the same purpose. In the present letter, the answer to this question is provided. It is shown that the two methods are complementary, rather than equivalent, the heating rate being the relevant parameter to establish which is preferable. The demonstration of this statement is given through the observation of the complex thermal properties of a reference sample studied in both ways at progressively lower heating rates. The connection between such unusual application of x-ray diffraction and the differential scanning calorimetry is discussed in terms of the two possible definitions of entropy

  3. Synchrotron radiation X-ray microfluorescence reveals polarized distribution of atomic elements during differentiation of pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Simone C Cardoso

    Full Text Available The mechanisms underlying pluripotency and differentiation in embryonic and reprogrammed stem cells are unclear. In this work, we characterized the pluripotent state towards neural differentiated state through analysis of trace elements distribution using the Synchrotron Radiation X-ray Fluorescence Spectroscopy. Naive and neural-stimulated embryoid bodies (EB derived from embryonic and induced pluripotent stem (ES and iPS cells were irradiated with a spatial resolution of 20 µm to make elemental maps and qualitative chemical analyses. Results show that these embryo-like aggregates exhibit self-organization at the atomic level. Metallic elements content rises and consistent elemental polarization pattern of P and S in both mouse and human pluripotent stem cells were observed, indicating that neural differentiation and elemental polarization are strongly correlated.

  4. Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation

    Directory of Open Access Journals (Sweden)

    Holger A. Russ

    2016-01-01

    Full Text Available Current approaches in human embryonic stem cell (hESC to pancreatic beta cell differentiation have largely been based on knowledge gained from developmental studies of the epithelial pancreas, while the potential roles of other supporting tissue compartments have not been fully explored. One such tissue is the pancreatic mesenchyme that supports epithelial organogenesis throughout embryogenesis. We hypothesized that detailed characterization of the pancreatic mesenchyme might result in the identification of novel factors not used in current differentiation protocols. Supplementing existing hESC differentiation conditions with such factors might create a more comprehensive simulation of normal development in cell culture. To validate our hypothesis, we took advantage of a novel transgenic mouse model to isolate the pancreatic mesenchyme at distinct embryonic and postnatal stages for subsequent proteomic analysis. Refined sample preparation and analysis conditions across four embryonic and prenatal time points resulted in the identification of 21,498 peptides with high-confidence mapping to 1,502 proteins. Expression analysis of pancreata confirmed the presence of three potentially important factors in cell differentiation: Galectin-1 (LGALS1, Neuroplastin (NPTN, and the Laminin α-2 subunit (LAMA2. Two of the three factors (LGALS1 and LAMA2 increased expression of pancreatic progenitor transcript levels in a published hESC to beta cell differentiation protocol. In addition, LAMA2 partially blocks cell culture induced beta cell dedifferentiation. Summarily, we provide evidence that proteomic analysis of supporting tissues such as the pancreatic mesenchyme allows for the identification of potentially important factors guiding hESC to pancreas differentiation.

  5. Genetic variability, differentiation, and founder effect in golden jackals (Canis aureus) from Serbia as revealed by mitochondrial DNA and nuclear microsatellite loci.

    Science.gov (United States)

    Zachos, Frank E; Cirovic, Dusko; Kirschning, Julia; Otto, Marthe; Hartl, Günther B; Petersen, Britt; Honnen, Ann-Christin

    2009-04-01

    We analyzed 121 golden jackals (Canis aureus) from six sample sites in Serbia with regard to genetic variability and differentiation as revealed by mitochondrial control region sequences and eight nuclear microsatellite loci. There was no variation at all in the mtDNA sequences, and nuclear variability was very low (average observed and expected heterozygosity of 0.29 and 0.34, respectively). This is in line with the considerable recent range expansion of this species in the Balkans and indicates a strong founder effect in the recently established Serbian population. We did not find evidence of differentiation between the northeastern jackals and those from the plain of Srem or those in between. F-statistics and Bayesian Structure analyses, however, were indicative of a low degree of overall differentiation in the Serbian population. A vagrant Austrian jackal that was also analyzed was genetically indistinguishable from its Serbian conspecifics. PMID:19169806

  6. Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells.

    Science.gov (United States)

    Metzakopian, Emmanouil; Bouhali, Kamal; Alvarez-Saavedra, Matías; Whitsett, Jeffrey A; Picketts, David J; Ang, Siew-Lan

    2015-04-01

    Midbrain dopamine neuronal progenitors develop into heterogeneous subgroups of neurons, such as substantia nigra pars compacta, ventral tegmental area and retrorubal field, that regulate motor control, motivated and addictive behaviours. The development of midbrain dopamine neurons has been extensively studied, and these studies indicate that complex cross-regulatory interactions between extrinsic and intrinsic molecules regulate a precise temporal and spatial programme of neurogenesis in midbrain dopamine progenitors. To elucidate direct molecular interactions between multiple regulatory factors during neuronal differentiation in mice, we characterised genome-wide binding sites of the forkhead/winged helix transcription factor Foxa1, which functions redundantly with Foxa2 to regulate the differentiation of mDA neurons. Interestingly, our studies identified a rostral brain floor plate Neurog2 enhancer that requires direct input from Otx2, Foxa1, Foxa2 and an E-box transcription factor for its transcriptional activity. Furthermore, the chromatin remodelling factor Smarca1 was shown to function downstream of Foxa1 and Foxa2 to regulate differentiation from immature to mature midbrain dopaminergic neurons. Our genome-wide Foxa1-bound cis-regulatory sequences from ChIP-Seq and Foxa1/2 candidate target genes from RNA-Seq analyses of embryonic midbrain dopamine cells also provide an excellent resource for probing mechanistic insights into gene regulatory networks involved in the differentiation of midbrain dopamine neurons.

  7. Differential Protein Expression in Sugarcane during Sugarcane-Sporisorium scitamineum Interaction Revealed by 2-DE and MALDI-TOF-TOF/MS

    OpenAIRE

    Youxiong Que; Liping Xu; Jianwei Lin; Miaohong Ruan; Muqing Zhang; Rukai Chen

    2011-01-01

    To understand the molecular basis of a specific plant-pathogen interaction, it is important to identify plant proteins that respond to the pathogen attack. Two sugarcane varieties, NCo376 and Ya71-374, were used in this study. By applying 2-dimensional electrophoresis (2-DE), the protein expression profile of sugarcane after inoculating with Sporisorium scitamineum was analyzed. In total, 23 differentially expressed proteins were identified by MALDI-TOF-TOF/MS. Bioinformatics analysis reveale...

  8. Fibrillin binds calcium and is coded by cDNAs that reveal a multidomain structure and alternatively spliced exons at the 5[prime] end

    Energy Technology Data Exchange (ETDEWEB)

    Corson, G.M.; Chalberg, S.C.; Charbonneau, N.L.; Sakai, L.Y. (Oregon Health Sciences Univ., Portland (United States)); Dietz, H.C. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))

    1993-08-01

    Fibrillin is an important structural protein of the extracellular matrix. It is a large cysteine-rich glycoprotein with extensive intrachain disulfide bonds, likely contributed by multiple EGF-like repeats. The authors have previously published 6.9 kb of FBN1 cDNA sequence. FBN1 cDNA clones that extend the sequence 3089 bp in the 5[prime] direction are described in this report. The deduced primary structure suggests that fibrillin in composed of multiple domains. The most predominant features the presence of 43 calcium binding EGF-like repeats. They demonstrate here that fibrillin molecules bind calcium. In addition, three alternatively spliced exons at the 5[prime] end are described. Analysis of 5.8 kb of surrounding genomic sequence revealed a 1.8-kb CpG island spanning the alternatively spliced exons and the next downstream exon. Since FBN1 is the gene responsible for Marfan syndrome, the information presented here will be useful in identifying new mutations and in understanding the function of fibrillin in the pathogenesis of the disease. 42 refs., 7 figs.

  9. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders

    Science.gov (United States)

    Keers, Robert; Coleman, Jonathan R.I.; Lester, Kathryn J.; Roberts, Susanna; Breen, Gerome; Thastum, Mikael; Bögels, Susan; Schneider, Silvia; Heiervang, Einar; Meiser-Stedman, Richard; Nauta, Maaike; Creswell, Cathy; Thirlwall, Kerstin; Rapee, Ronald M.; Hudson, Jennifer L.; Lewis, Cathryn; Plomin, Robert; Eley, Thalia C.

    2016-01-01

    Background The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such variants has so far been limited to preselected candidate genes. In this study we extended the differential susceptibility hypothesis from a candidate gene to a genome-wide approach to test whether a polygenic score of environmental sensitivity predicted response to cognitive behavioural therapy (CBT) in children with anxiety disorders. Methods We identified variants associated with environmental sensitivity using a novel method in which within-pair variability in emotional problems in 1,026 monozygotic twin pairs was examined as a function of the pairs' genotype. We created a polygenic score of environmental sensitivity based on the whole-genome findings and tested the score as a moderator of parenting on emotional problems in 1,406 children and response to individual, group and brief parent-led CBT in 973 children with anxiety disorders. Results The polygenic score significantly moderated the effects of parenting on emotional problems and the effects of treatment. Individuals with a high score responded significantly better to individual CBT than group CBT or brief parent-led CBT (remission rates: 70.9, 55.5 and 41.6%, respectively). Conclusions Pending successful replication, our results should be considered exploratory. Nevertheless, if replicated, they suggest that individuals with the greatest environmental sensitivity may be more likely to develop emotional problems in adverse environments but also benefit more from the most intensive types of treatment. PMID:27043157

  10. Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation

    OpenAIRE

    Mansfield, Kyle D.; Keene, Jack D.

    2011-01-01

    The ubiquitously expressed RNA-binding protein HuR increases the stability and translation of mRNAs encoding growth regulatory proteins that promote proliferation in a variety of cell types. However, the three neuron-specific ELAV/Hu proteins, HuB, HuC and HuD, while binding to the same types of mRNAs, are required instead for neuronal differentiation, and it becomes difficult to reconcile these contrary functions when all four Hu proteins are expressed in the same neuron. HuR mRNA exists as ...

  11. Gender-Differentiated Parenting Revisited: Meta-Analysis Reveals Very Few Differences in Parental Control of Boys and Girls

    Science.gov (United States)

    Endendijk, Joyce J.; Groeneveld, Marleen G.; Bakermans-Kranenburg, Marian J.; Mesman, Judi

    2016-01-01

    Although various theories describe mechanisms leading to differential parenting of boys and girls, there is no consensus about the extent to which parents do treat their sons and daughters differently. The last meta-analyses on the subject were conducted more than fifteen years ago, and changes in gender-specific child rearing in the past decade are quite plausible. In the current set of meta-analyses, based on 126 observational studies (15,034 families), we examined mothers’ and fathers’ differential use of autonomy-supportive and controlling strategies with boys and girls, and the role of moderators related to the decade in which the study was conducted, the observational context, and sample characteristics. Databases of Web of Science, ERIC, PsychInfo, Online Contents, Picarta, and Proquest were searched for studies examining differences in observed parental control of boys and girls between the ages of 0 and 18 years. Few differences were found in parents’ use of control with boys and girls. Parents were slightly more controlling with boys than with girls, but the effect size was negligible (d = 0.08). The effect was larger, but still small, in normative groups and in samples with younger children. No overall effect for gender-differentiated autonomy-supportive strategies was found (d = 0.03). A significant effect of time emerged: studies published in the 1970s and 1980s reported more autonomy-supportive strategies with boys than toward girls, but from 1990 onwards parents showed somewhat more autonomy-supportive strategies with girls than toward boys. Taking into account parents’ gender stereotypes might uncover subgroups of families where gender-differentiated control is salient, but based on our systematic review of the currently available large data base we conclude that in general the differences between parenting of boys versus girls are minimal. PMID:27416099

  12. Gender-Differentiated Parenting Revisited: Meta-Analysis Reveals Very Few Differences in Parental Control of Boys and Girls.

    Science.gov (United States)

    Endendijk, Joyce J; Groeneveld, Marleen G; Bakermans-Kranenburg, Marian J; Mesman, Judi

    2016-01-01

    Although various theories describe mechanisms leading to differential parenting of boys and girls, there is no consensus about the extent to which parents do treat their sons and daughters differently. The last meta-analyses on the subject were conducted more than fifteen years ago, and changes in gender-specific child rearing in the past decade are quite plausible. In the current set of meta-analyses, based on 126 observational studies (15,034 families), we examined mothers' and fathers' differential use of autonomy-supportive and controlling strategies with boys and girls, and the role of moderators related to the decade in which the study was conducted, the observational context, and sample characteristics. Databases of Web of Science, ERIC, PsychInfo, Online Contents, Picarta, and Proquest were searched for studies examining differences in observed parental control of boys and girls between the ages of 0 and 18 years. Few differences were found in parents' use of control with boys and girls. Parents were slightly more controlling with boys than with girls, but the effect size was negligible (d = 0.08). The effect was larger, but still small, in normative groups and in samples with younger children. No overall effect for gender-differentiated autonomy-supportive strategies was found (d = 0.03). A significant effect of time emerged: studies published in the 1970s and 1980s reported more autonomy-supportive strategies with boys than toward girls, but from 1990 onwards parents showed somewhat more autonomy-supportive strategies with girls than toward boys. Taking into account parents' gender stereotypes might uncover subgroups of families where gender-differentiated control is salient, but based on our systematic review of the currently available large data base we conclude that in general the differences between parenting of boys versus girls are minimal. PMID:27416099

  13. Gender-Differentiated Parenting Revisited: Meta-Analysis Reveals Very Few Differences in Parental Control of Boys and Girls.

    Directory of Open Access Journals (Sweden)

    Joyce J Endendijk

    Full Text Available Although various theories describe mechanisms leading to differential parenting of boys and girls, there is no consensus about the extent to which parents do treat their sons and daughters differently. The last meta-analyses on the subject were conducted more than fifteen years ago, and changes in gender-specific child rearing in the past decade are quite plausible. In the current set of meta-analyses, based on 126 observational studies (15,034 families, we examined mothers' and fathers' differential use of autonomy-supportive and controlling strategies with boys and girls, and the role of moderators related to the decade in which the study was conducted, the observational context, and sample characteristics. Databases of Web of Science, ERIC, PsychInfo, Online Contents, Picarta, and Proquest were searched for studies examining differences in observed parental control of boys and girls between the ages of 0 and 18 years. Few differences were found in parents' use of control with boys and girls. Parents were slightly more controlling with boys than with girls, but the effect size was negligible (d = 0.08. The effect was larger, but still small, in normative groups and in samples with younger children. No overall effect for gender-differentiated autonomy-supportive strategies was found (d = 0.03. A significant effect of time emerged: studies published in the 1970s and 1980s reported more autonomy-supportive strategies with boys than toward girls, but from 1990 onwards parents showed somewhat more autonomy-supportive strategies with girls than toward boys. Taking into account parents' gender stereotypes might uncover subgroups of families where gender-differentiated control is salient, but based on our systematic review of the currently available large data base we conclude that in general the differences between parenting of boys versus girls are minimal.

  14. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation.

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    Shen-Hsi Yang

    Full Text Available Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of pluripotency or differentiation. In this study we have focused on how mouse embryonic stem cells begin to differentiate and lose pluripotency and, in particular, the role that the ERK MAP kinase and GSK3 signaling pathways play in this process. Through a genome-wide siRNA screen we have identified more than 400 genes involved in loss of pluripotency and promoting the onset of differentiation. These genes were functionally associated with the ERK and/or GSK3 pathways, providing an important resource for studying the roles of these pathways in controlling escape from the pluripotent ground state. More detailed analysis identified MAP kinase phosphatases as a focal point of regulation and demonstrated an important role for these enzymes in controlling ERK activation kinetics and subsequently determining early embryonic stem cell fate decisions.

  15. Comparative genomic analysis of transgenic poplar dwarf mutant reveals numerous differentially expressed genes involved in energy flow.

    Science.gov (United States)

    Chen, Su; Bai, Shuang; Liu, Guifeng; Li, Huiyu; Jiang, Jing

    2014-01-01

    In our previous research, the Tamarix androssowii LEA gene (Tamarix androssowii late embryogenesis abundant protein Mrna, GenBank ID: DQ663481) was transferred into Populus simonii × Populus nigra. Among the eleven transgenic lines, one exhibited a dwarf phenotype compared to the wild type and other transgenic lines, named dwf1. To uncover the mechanisms underlying this phenotype, digital gene expression libraries were produced from dwf1, wild-type, and other normal transgenic lines, XL-5 and XL-6. Gene expression profile analysis indicated that dwf1 had a unique gene expression pattern in comparison to the other two transgenic lines. Finally, a total of 1246 dwf1-unique differentially expressed genes were identified. These genes were further subjected to gene ontology and pathway analysis. Results indicated that photosynthesis and carbohydrate metabolism related genes were significantly affected. In addition, many transcription factors genes were also differentially expressed in dwf1. These various differentially expressed genes may be critical for dwarf mutant formation; thus, the findings presented here might provide insight for our understanding of the mechanisms of tree growth and development. PMID:25192286

  16. Genetic Differentiation of Japanese Sardinella (Sardinella zunasi)Populations in the Northwest Pacific Revealed by ISSR Analysis

    Institute of Scientific and Technical Information of China (English)

    YING Yiping; GAO Tianxiang; MIAO Zhenqing

    2011-01-01

    Knowledge of population genetic structure plays an important role in fisheries management.In this research,Inter-Simple-Sequence-Repeat (ISSR) markers were employed to evaluate the genetic structure of Japanese sardinella (Sardinella zunasi) populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic primers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was detected between the Chinese and Japanese populations by both AMOVA and pairwise Fsr analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.

  17. High genetic differentiation of Aegla longirostri (Crustacea, Decapoda, Anomura) populations in southern Brazil revealed by multi-loci microsatellite analysis.

    Science.gov (United States)

    Bartholomei-Santos, M L; Roratto, P A; Santos, S

    2011-01-01

    Species with a broad distribution rarely have the same genetic make-up throughout their entire range. In some cases, they may constitute a cryptic complex consisting of a few species, each with a narrow distribution, instead of a single-, widely distributed species. These differences can have profound impacts for biodiversity conservation planning. The genetic differentiation of four populations of Aegla longirostri, a freshwater crab found in two geographically isolated basins in Rio Grande do Sul State, Brazil, was investigated by analyzing pentanucleotide multi-loci microsatellites in a heteroduplex assay. Although no morphological differences were evident, we found significant genetic differentiation among the four populations, based on F(ST) values and clustering analysis. This high level of differentiation may be indicative of cryptic species in these populations. If this hypothesis is correct, then the species occurring in the Ibicuí-Mirim River, at the southern limit of the Atlantic Rain Forest, would be under threat, considering its very restricted distribution. PMID:22179994

  18. Genetic differentiation revealed by selective loci of drought-responding EST-SSRs between upland and lowland rice in China.

    Directory of Open Access Journals (Sweden)

    Hui Xia

    Full Text Available Upland and lowland rice (Oryza sativa L. represent two of the most important rice ecotypes adapted to ago-ecosystems with contrasting soil-water conditions. Upland rice, domesticated in the water-limited environment, contains valuable drought-resistant characters that can be used in water-saving breeding. Knowledge about the divergence between upland and lowland rice will provide valuable cues for the evolution of drought-resistance in rice. Genetic differentiation between upland and lowland rice was explored by 47 Simple Sequence Repeats (SSRs located in drought responding expressed sequence tags (ESTs among 377 rice landraces. The morphological traits of drought-resistance were evaluated in the field experiments. Different outlier loci were detected in the japonica and indica subspecies, respectively. Considerable genetic differentiation between upland and lowland rice on these outlier loci was estimated in japonica (Fst = 0.258 and indica (Fst = 0.127. Furthermore, populations of the upland and lowland ecotypes were clustered separately on these outlier loci. A significant correlation between genetic distance matrices and the dissimilarity matrices of drought-resistant traits was determined, indicating a certain relationship between the upland-lowland rice differentiation and the drought-resistance. Divergent selections occur between upland and lowland rice on the drought-resistance as the Qsts of some drought-resistant traits are significantly higher than the neutral Fst. In addition, the upland- and lowland-preferable alleles responded differently among ecotypes or allelic types under osmotic stress. This shows the evolutionary signature of drought resistance at the gene expression level. The findings of this study can strengthen our understanding of the evolution of drought-resistance in rice with significant implications in the improvement of rice drought-resistance.

  19. Differential gene expression profile reveals deregulation of pregnancy specific β1 glycoprotein 9 early during colorectal carcinogenesis

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    Gallinger Steven

    2005-06-01

    Full Text Available Abstract Background APC (Adenomatous polyposis coli plays an important role in the pathogenesis of both familial and sporadic colorectal cancer. Patients carrying germline APC mutations develop multiple colonic adenomas at younger age and higher frequency than non-carrier cases which indicates that silencing of one APC allele may be sufficient to initiate the transformation process. Methods To elucidate the biological dysregulation underlying adenoma formation we examined global gene expression profiles of adenomas and corresponding normal mucosa from an FAP patient. Differential expression of the most significant gene identified in this study was further validated by mRNA in situ hybridization, reverse transcriptase PCR and Northern blotting in different sets of adenomas, tumours and cancer cell lines. Results Eighty four genes were differentially expressed between all adenomas and corresponding normal mucosa, while only seven genes showed differential expression within the adenomas. The first group included pregnancy specific β-1 glycoprotein 9 (PSG9 (p PSG9 is a member of the carcinoembryonic antigen (CEA/PSG family and is produced at high levels during pregnancy, mainly by syncytiotrophoblasts. Further analysis of sporadic and familial colorectal cancer confirmed that PSG9 is ectopically upregulated in vivo by cancer cells. In total, deregulation of PSG9 mRNA was detected in 78% (14/18 of FAP adenomas and 75% (45/60 of sporadic colorectal cancer cases tested. Conclusion Detection of PSG9 expression in adenomas, and at higher levels in FAP cases, indicates that germline APC mutations and defects in Wnt signalling modulate PSG9 expression. Since PSG9 is not found in the non-pregnant adult except in association with cancer, and it appears to be an early molecular event associated with colorectal cancer monitoring of its expression may be useful as a biomarker for the early detection of this disease.

  20. Modelling the spatio-temporal cell dynamics reveals novel insights on cell differentiation and proliferation in the small intestinal crypt.

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    Carmen Pin

    Full Text Available We developed a slow structural relaxation model to describe cellular dynamics in the crypt of the mouse small intestine. Cells are arranged in a three dimensional spiral the size of which dynamically changes according to cell production demands of adjacent villi. Cell differentiation and proliferation is regulated through Wnt and Notch signals, the strength of which depends on the local cell composition. The highest level of Wnt activity is associated with maintaining equipotent stem cells (SC, Paneth cells and common goblet-Paneth cell progenitors (CGPCPs intermingling at the crypt bottom. Low levels of Wnt signalling area are associated with stem cells giving rise to secretory cells (CGPCPs, enteroendocrine or Tuft cells and proliferative absorptive progenitors. Deciding between these two fates, secretory and stem/absorptive cells, depends on Notch signalling. Our model predicts that Notch signalling inhibits secretory fate if more than 50% of cells they are in contact with belong to the secretory lineage. CGPCPs under high Wnt signalling will differentiate into Paneth cells while those migrating out from the crypt bottom differentiate into goblet cells. We have assumed that mature Paneth cells migrating upwards undergo anoikis. Structural relaxation explains the localisation of Paneth cells to the crypt bottom in the absence of active forces. The predicted crypt generation time from one SC is 4-5 days with 10-12 days needed to reach a structural steady state. Our predictions are consistent with experimental observations made under altered Wnt and Notch signalling. Mutations affecting stem cells located at the crypt floor have a 50% chance of being propagated throughout the crypt while mutations in cells above are rarely propagated. The predicted recovery time of an injured crypt losing half of its cells is approximately 2 days.

  1. Genetic differentiation of strongyloides stercoralis from two different climate zones revealed by 18S ribosomal DNA sequence comparison.

    Science.gov (United States)

    Pakdee, Wallop; Thaenkham, Urusa; Dekumyoy, Paron; Sa-Nguankiat, Surapol; Maipanich, Wanna; Pubampen, Somchit

    2012-11-01

    Over 70 countries in tropical and subtropical zones are endemic areas for Strongyloides stercoralis, with a higher prevalence of the parasite often occurring in tropical regions compared to subtropical ones. In order to explore genetic variations of S. stercoralis form different climate zones, 18S ribosomal DNA of parasite specimens obtained from Thailand were sequenced and compared with those from Japan. The maximum likelihood indicates that S. stercoralis populations from these two different climate zones have genetically diverged. The genetic relationship between S. stercoralis populations is not related to the host species, but rather to moisture and temperature. These factors may directly drive genetic differentiation among isolated populations of S. stercoralis.

  2. Trend of telomerase activity change during human iPSC self-renewal and differentiation revealed by a quartz crystal microbalance based assay

    Science.gov (United States)

    Zhou, Yitian; Zhou, Ping; Xin, Yinqiang; Wang, Jie; Zhu, Zhiqiang; Hu, Ji; Wei, Shicheng; Ma, Hongwei

    2014-11-01

    Telomerase plays an important role in governing the life span of cells for its capacity to extend telomeres. As high activity of telomerase has been found in stem cells and cancer cells specifically, various methods have been developed for the evaluation of telomerase activity. To overcome the time-consuming procedures and complicated manipulations of existing methods, we developed a novel method named Telomeric Repeat Elongation Assay based on Quartz crystal microbalance (TREAQ) to monitor telomerase activity during the self-renewal and differentiation of human induced pluripotent stem cells (hiPSCs). TREAQ results indicated hiPSCs possess invariable telomerase activity for 11 passages on Matrigel and a steady decline of telomerase activity when differentiated for different periods, which is confirmed with existing golden standard method. The pluripotency of hiPSCs during differentiation could be estimated through monitoring telomerase activity and compared with the expression levels of markers of pluripotency gene via quantitative real time PCR. Regular assessment for factors associated with pluripotency or stemness was expensive and requires excessive sample consuming, thus TREAQ could be a promising alternative technology for routine monitoring of telomerase activity and estimate the pluripotency of stem cells.

  3. Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways.

    Science.gov (United States)

    Erdem, Cemal; Nagle, Alison M; Casa, Angelo J; Litzenburger, Beate C; Wang, Yu-Fen; Taylor, D Lansing; Lee, Adrian V; Lezon, Timothy R

    2016-09-01

    Insulin and insulin-like growth factor I (IGF1) influence cancer risk and progression through poorly understood mechanisms. To better understand the roles of insulin and IGF1 signaling in breast cancer, we combined proteomic screening with computational network inference to uncover differences in IGF1 and insulin induced signaling. Using reverse phase protein array, we measured the levels of 134 proteins in 21 breast cancer cell lines stimulated with IGF1 or insulin for up to 48 h. We then constructed directed protein expression networks using three separate methods: (i) lasso regression, (ii) conventional matrix inversion, and (iii) entropy maximization. These networks, named here as the time translation models, were analyzed and the inferred interactions were ranked by differential magnitude to identify pathway differences. The two top candidates, chosen for experimental validation, were shown to regulate IGF1/insulin induced phosphorylation events. First, acetyl-CoA carboxylase (ACC) knock-down was shown to increase the level of mitogen-activated protein kinase (MAPK) phosphorylation. Second, stable knock-down of E-Cadherin increased the phospho-Akt protein levels. Both of the knock-down perturbations incurred phosphorylation responses stronger in IGF1 stimulated cells compared with insulin. Overall, the time-translation modeling coupled to wet-lab experiments has proven to be powerful in inferring differential interactions downstream of IGF1 and insulin signaling, in vitro.

  4. Proteomic analysis of hyperadhesive Candida glabrata clinical isolates reveals a core wall proteome and differential incorporation of adhesins.

    Science.gov (United States)

    Gómez-Molero, Emilia; de Boer, Albert D; Dekker, Henk L; Moreno-Martínez, Ana; Kraneveld, Eef A; Ichsan; Chauhan, Neeraj; Weig, Michael; de Soet, Johannes J; de Koster, Chris G; Bader, Oliver; de Groot, Piet W J

    2015-12-01

    Attachment to human host tissues or abiotic medical devices is a key step in the development of infections by Candida glabrata. The genome of this pathogenic yeast codes for a large number of adhesins, but proteomic work using reference strains has shown incorporation of only few adhesins in the cell wall. By making inventories of the wall proteomes of hyperadhesive clinical isolates and reference strain CBS138 using mass spectrometry, we describe the cell wall proteome of C. glabrata and tested the hypothesis that hyperadhesive isolates display differential incorporation of adhesins. Two clinical strains (PEU382 and PEU427) were selected, which both were hyperadhesive to polystyrene and showed high surface hydrophobicity. Cell wall proteome analysis under biofilm-forming conditions identified a core proteome of about 20 proteins present in all C. glabrata strains. In addition, 12 adhesin-like wall proteins were identified in the hyperadherent strains, including six novel adhesins (Awp8-13) of which only Awp12 was also present in CBS138. We conclude that the hyperadhesive capacity of these two clinical C. glabrata isolates is correlated with increased and differential incorporation of cell wall adhesins. Future studies should elucidate the role of the identified proteins in the establishment of C. glabrata infections. PMID:26546455

  5. Differentiation between vergence and saccadic functional activity within the human frontal eye fields and midbrain revealed through fMRI.

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    Yelda Alkan

    Full Text Available PURPOSE: Eye movement research has traditionally studied solely saccade and/or vergence eye movements by isolating these systems within a laboratory setting. While the neural correlates of saccadic eye movements are established, few studies have quantified the functional activity of vergence eye movements using fMRI. This study mapped the neural substrates of vergence eye movements and compared them to saccades to elucidate the spatial commonality and differentiation between these systems. METHODOLOGY: The stimulus was presented in a block design where the 'off' stimulus was a sustained fixation and the 'on' stimulus was random vergence or saccadic eye movements. Data were collected with a 3T scanner. A general linear model (GLM was used in conjunction with cluster size to determine significantly active regions. A paired t-test of the GLM beta weight coefficients was computed between the saccade and vergence functional activities to test the hypothesis that vergence and saccadic stimulation would have spatial differentiation in addition to shared neural substrates. RESULTS: Segregated functional activation was observed within the frontal eye fields where a portion of the functional activity from the vergence task was located anterior to the saccadic functional activity (z>2.3; p0.2. CONCLUSION: Functional MRI can elucidate the differences between the vergence and saccade neural substrates within the frontal eye fields and midbrain.

  6. Proteomic Analysis of Human Brain Microvascular Endothelial Cells Reveals Differential Protein Expression in Response to Enterovirus 71 Infection

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    Wenying Luo

    2015-01-01

    Full Text Available 2D DIGE technology was employed on proteins prepared from human brain microvascular endothelial cells (HBMEC, to study the differentially expressed proteins in cells at 0 h, 1 h, 16 h, and 24 h after infection. Proteins found to be differentially expressed were identified with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDITOF/TOF MS analysis. We identified 43 spots showing changes of at least 2.5 fold up- or downregulated expressions in EV71-infected cells at different time when comparing to control, and 28 proteins could be successfully identified by MALDI TOF/TOF mass spectrometry analysis. 4 proteins were significantly upregulated, and 6 proteins were downregulated, another 18 proteins were different expression at different incubation time. We identified changes in the expression of 12 cellular metabolism-related proteins, 5 molecules involved in cytoskeleton, 3 molecules involved in energy metabolism, 2 molecules involved in signal transduction, 1 molecule involved in the ubiquitin-proteasome pathway, 1 molecule involved in cell cycle, 1 molecule involved in apoptosis-related protein, 1 molecular chaperone, and 2 unknown proteins. These findings build up a comprehensive profile of the HBMEC proteome and provide a useful basis for further analysis of the pathogenic mechanism that underlies EV71 infections to induce severe neural complications.

  7. Human 45,X Fibroblast Transcriptome Reveals Distinct Differentially Expressed Genes Including Long Noncoding RNAs Potentially Associated with the Pathophysiology of Turner Syndrome

    Science.gov (United States)

    Patowary, Ashok; Scaria, Vinod; Sivasubbu, Sridhar; Deobagkar, Deepti D.

    2014-01-01

    Turner syndrome is a chromosomal abnormality characterized by the absence of whole or part of the X chromosome in females. This X aneuploidy condition is associated with a diverse set of clinical phenotypes such as gonadal dysfunction, short stature, osteoporosis and Type II diabetes mellitus, among others. These phenotypes differ in their severity and penetrance among the affected individuals. Haploinsufficiency for a few X linked genes has been associated with some of these disease phenotypes. RNA sequencing can provide valuable insights to understand molecular mechanism of disease process. In the current study, we have analysed the transcriptome profiles of human untransformed 45,X and 46,XX fibroblast cells and identified differential expression of genes in these two karyotypes. Functional analysis revealed that these differentially expressing genes are associated with bone differentiation, glucose metabolism and gonadal development pathways. We also report differential expression of lincRNAs in X monosomic cells. Our observations provide a basis for evaluation of cellular and molecular mechanism(s) in the establishment of Turner syndrome phenotypes. PMID:24932682

  8. Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome.

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    Shriram N Rajpathak

    Full Text Available Turner syndrome is a chromosomal abnormality characterized by the absence of whole or part of the X chromosome in females. This X aneuploidy condition is associated with a diverse set of clinical phenotypes such as gonadal dysfunction, short stature, osteoporosis and Type II diabetes mellitus, among others. These phenotypes differ in their severity and penetrance among the affected individuals. Haploinsufficiency for a few X linked genes has been associated with some of these disease phenotypes. RNA sequencing can provide valuable insights to understand molecular mechanism of disease process. In the current study, we have analysed the transcriptome profiles of human untransformed 45,X and 46,XX fibroblast cells and identified differential expression of genes in these two karyotypes. Functional analysis revealed that these differentially expressing genes are associated with bone differentiation, glucose metabolism and gonadal development pathways. We also report differential expression of lincRNAs in X monosomic cells. Our observations provide a basis for evaluation of cellular and molecular mechanism(s in the establishment of Turner syndrome phenotypes.

  9. Alternate Immersion in an External Glucose Solution Differentially Affects Blood Sugar Values in Older Versus Younger Zebrafish Adults.

    Science.gov (United States)

    Connaughton, Victoria P; Baker, Cassandra; Fonde, Lauren; Gerardi, Emily; Slack, Carly

    2016-04-01

    Recently, zebrafish have been used to examine hyperglycemia-induced complications (retinopathy and neuropathy), as would occur in individuals with diabetes. Current models to induce hyperglycemia in zebrafish include glucose immersion and streptozotocin injections. Both are effective, although neither is reported to elevate blood sugar values for more than 1 month. In this article, we report differences in hyperglycemia induction and maintenance in young (4-11 months) versus old (1-3 years) zebrafish adults. In particular, older fish immersed in an alternating constant external glucose solution (2%) for 2 months displayed elevated blood glucose levels for the entire experimental duration. In contrast, younger adults displayed only transient hyperglycemia, suggesting the fish were acclimating to the glucose exposure protocol. However, modifying the immersion protocol to include a stepwise increasing glucose concentration (from 1% → 2%→3%) resulted in maintained hyperglycemia in younger zebrafish adults for up to 2 months. Glucose-exposed younger fish collected after 8 weeks of exposure also displayed a significant decrease in wet weight. Taken together, these data suggest different susceptibilities to hyperglycemia in older and younger fish and that stepwise increasing glucose concentrations of 1% are required for maintenance of hyperglycemia in younger adults, with higher concentrations of glucose resulting in greater increases in blood sugar values. PMID:26771444

  10. Denaturing gradient gel electrophoresis (DGGE as a powerful novel alternative for differentiation of epizootic ISA virus variants.

    Directory of Open Access Journals (Sweden)

    Marisela Carmona

    Full Text Available Infectious Salmon Anemia is a devastating disease critically affecting world-wide salmon production. Chile has been particularly stricken by this disease which in all cases has been directly related with its causative agent, a novel orthomyxovirus which presents specific and distinctive infective features. Among these, two molecular markers have been directly associated with pathogenicity in two of the eight RNA sub genomic coding units of the virus: an insertion hot spot region present in viral segment 5 and a Highly Polymorphic Region (HPR located in viral segment 6. Here we report the successful adaptation of a PCR-dependent denaturing gel electrophoresis technique (DGGE, which enables differentiation of selected reported HPR epizootic variants detected in Chile. At the same time, the technique allows us to distinguish one nucleotide differences in sequences associated with the intriguing, and still not well-understood, insertion events which tend to occur on RNA Segment 5. Thus, the versatility of the technique opens new opportunities for improved understanding of the complex biology of all ISA variants as well as possible applications to other highly variable pathogens.

  11. Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation.

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    Hironori Waki

    2011-10-01

    Full Text Available Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type-specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq. FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA-mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our

  12. Salient features in locomotor evolutionary adaptations of proboscideans revealed via the differential scaling of limb long bones

    CERN Document Server

    Kokshenev, Valery B

    2009-01-01

    The standard differential scaling of proportions in limb long bones (length against circumference) is applied to a phylogenetically wide sample of the Proboscidea, Elephantidae and the Asian (Elephas maximus) and African elephant (Loxodonta africana). In order to investigate allometric patterns in proboscideans and terrestrial mammals with parasagittal limb kinematics, the computed slopes (slenderness exponents) are compared with published values for mammals and studied within a framework of theoretical models of long bone scaling under gravity and muscle forces. Limb bone allometry in E. maximus and the Elephantidae are congruent with adaptation to bending and/or torsion induced by muscular forces during fast locomotion, as in other mammals, whereas limb bones in L. africana appear adapted for coping with the compressive forces of gravity. Consequently, hindlimb bones are expected to be more compliant than forelimb bones in accordance with in vivo studies on elephant locomotory kinetics and kinematics, and t...

  13. Differentially expressed genes in autosomal dominant osteopetrosis type II osteoclasts reveal known and novel pathways for osteoclast biology.

    Science.gov (United States)

    Coudert, Amélie E; Del Fattore, Andrea; Baulard, Céline; Olaso, Robert; Schiltz, Corinne; Collet, Corinne; Teti, Anna; de Vernejoul, Marie-Christine

    2014-03-01

    Autosomal dominant osteopetrosis type II (ADO II) is a rare, heritable bone disorder characterized by a high bone mass and insufficient osteoclast activity. Mutations in the CLCN7 gene have been reported to cause ADO II. To gain novel insights into the pathways dysregulated in ADOII osteoclasts, we identified changes in gene expression in osteoclasts from patients with a heterozygous mutation of CLCN7. To do this, we carried out a transcriptomic study comparing gene expression in the osteoclasts of patients with ADO II and healthy donors. Our data show that, according to our selection criteria, 182 genes were differentially expressed in osteoclasts from patients and controls. From the 18 displaying the highest change in microarray, we confirmed differential expression for seven by qPCR. Although two of them have previously been found to be expressed in osteoclasts (ITGB5 and SERPINE2), the other five (CES1 (carboxyl esterase 1), UCHL1 (ubiquitin carboxy-terminal esterase L1, also known as ubiquitin thiolesterase), WARS (tryptophanyl-tRNA synthetase), GBP4 (guanylate-binding protein 4), and PRF1) are not yet known to have a role in this cell type. At the protein level, we confirmed elevated expression of ITGB5 and reduced expression of WARS, PRF1, and SERPINE2. Transfection of ClC-7 harboring the G215R mutation into osteoclasts resulted in an increased ITGB5 and reduced PRF1 expression of borderline significance. Finally, we observed that the ADO II patients presented a normal or increased serum level of bone formation markers, demonstrating a coupling between dysfunctional osteoclasts and osteoblasts. Sphingosine kinase 1 mRNA was expressed at the same level in ADO II and control osteoclasts. In conclusion, these data suggest that in addition to an acidification dysfunction caused by the CLCN7 mutation, a change in ITGB5, PRF1, WARS, and SERPINE2 expression could be part of the osteoclastic phenotype of ADO II.

  14. High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.

    Directory of Open Access Journals (Sweden)

    Muyan Chen

    Full Text Available The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of the sea cucumber (Apostichopus japonicus, using Solexa deep sequencing technology. We identified 308 sea cucumber miRNAs, including 18 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA state (animals that had passed through aestivation and returned to the active state. We identified 42 differentially expressed miRNAs [RPM (reads per million >10, |FC| (|fold change| ≥ 1, FDR (false discovery rate <0.01] during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes and GO analysis suggest that these miRNAs could play important roles in global transcriptional depression and cell differentiation during aestivation. High-throughput sequencing data and microarray data have been submitted to GEO database.

  15. Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants

    OpenAIRE

    Silas P. Rodrigues; José A. Ventura; Aguilar, Clemente; Nakayasu, Ernesto S; Choi, Hyungwon; Sobreira, Tiago J. P.; Nohara, Lilian L.; Wermelinger, Luciana S.; Almeida, Igor C.; Zingali, Russolina B.; Fernandes, Patricia M. B.

    2012-01-01

    Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers’ regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulate...

  16. High-throughput sequencing reveals differential expression of miRNAs in prehierarchal follicles of laying and brooding geese.

    Science.gov (United States)

    Yu, Jing; He, Ke; Ren, Ting; Lou, Yaping; Zhao, Ayong

    2016-07-01

    Broodiness is the primary factor influencing egg production in geese, in which several genes and miRNAs participate. Detailed spatiotemporal profiles of miRNAs encompassing follicle development levels, however, are lacking. In this study, we collected preovulatory follicles (classified as small white follicles, large white follicles, and small yellow follicles) from brooding and laying geese and aimed to analyze microRNA (miRNA or miR) during folliculogenesis. High-throughput sequencing and bioinformatics analysis were used to identify the miRNAs involved in follicle development. The let7 family, miR-10 family, and miR-143 family were abundant in these libraries, and they have been suggested to play a housekeeping role during folliculogenesis. Joint comparisons revealed 23 upregulated and 21 downregulated miRNAs (in at least two comparisons of follicles during brooding and laying, P < 0.1) in the laying stage. Unlike reproduction pathways reported for ovaries, GO and KEGG analysis suggested pathways for cell apoptosis and proliferation, such as the regulation of actin cytoskeleton, endocytosis, axon guidance, pathways in cancer, tight junctions, focal adhesion, the MAPK signaling pathway, cytokine-cytokine receptor interactions, and the Wnt signaling pathway in folliculogenesis. This study revealed the miRNAs that were directly involved in follicular atresia, and our results added to the understanding of the functional involvement of miRNAs during specific stages of follicle development. PMID:27199452

  17. Nanoscale analysis of pyritized microfossils reveals differential heterotrophic consumption in the ~1.9-Ga Gunflint chert.

    Science.gov (United States)

    Wacey, David; McLoughlin, Nicola; Kilburn, Matt R; Saunders, Martin; Cliff, John B; Kong, Charlie; Barley, Mark E; Brasier, Martin D

    2013-05-14

    The 1.88-Ga Gunflint biota is one of the most famous Precambrian microfossil lagerstätten and provides a key record of the biosphere at a time of changing oceanic redox structure and chemistry. Here, we report on pyritized replicas of the iconic autotrophic Gunflintia-Huroniospora microfossil assemblage from the Schreiber Locality, Canada, that help capture a view through multiple trophic levels in a Paleoproterozoic ecosystem. Nanoscale analysis of pyritic Gunflintia (sheaths) and Huroniospora (cysts) reveals differing relic carbon and nitrogen distributions caused by contrasting spectra of decay and pyritization between taxa, reflecting in part their primary organic compositions. In situ sulfur isotope measurements from individual microfossils (δ(34)S(V-CDT) +6.7‰ to +21.5‰) show that pyritization was mediated by sulfate-reducing microbes within sediment pore waters whose sulfate ion concentrations rapidly became depleted, owing to occlusion of pore space by coeval silicification. Three-dimensional nanotomography reveals additional pyritized biomaterial, including hollow, cellular epibionts and extracellular polymeric substances, showing a preference for attachment to Gunflintia over Huroniospora and interpreted as components of a saprophytic heterotrophic, decomposing community. This work also extends the record of remarkable biological preservation in pyrite back to the Paleoproterozoic and provides criteria to assess the authenticity of even older pyritized microstructures that may represent some of the earliest evidence for life on our planet.

  18. Genetic differentiation of Octopus minor (Mollusca, Cephalopoda) off the northern coast of China as revealed by amplified fragment length polymorphisms.

    Science.gov (United States)

    Yang, J M; Sun, G H; Zheng, X D; Ren, L H; Wang, W J; Li, G R; Sun, B C

    2015-12-02

    Octopus minor (Sasaki, 1920) is an economically important cephalopod that is found in the northern coastal waters of China. In this study, we investigated genetic differentiation in fishery populations using amplified fragment length polymorphisms (AFLPs). A total of 150 individuals were collected from five locations: Dalian (DL), Yan-tai (YT), Qingdao (QD), Lianyungang (LY), and Zhoushan (ZS), and 243 reproducible bands were amplified using five AFLP primer combinations. The percentage of polymorphic bands ranged from 53.33 to 76.08%. Nei's genetic identity ranged from 0.9139 to 0.9713, and the genetic distance ranged from 0.0291 to 0.0900. A phylogenetic tree was constructed using the unweighted pair group method with arithmetic mean, based on the genetic distance. The DL and YT populations originated from one clade, while the QD, LY, and ZS populations originated from another. The results indicate that the O. minor stock consisted of two genetic populations with an overall significantly analogous FST value (0.1088, P octopus fisheries, so that this marine resource can be conserved for its long-term utilization.

  19. Proteomic responses reveal the differential effects induced by cadmium in mussels Mytilus galloprovincialis at early life stages.

    Science.gov (United States)

    Xu, Lanlan; Peng, Xiao; Yu, Deliang; Ji, Chenglong; Zhao, Jianmin; Wu, Huifeng

    2016-08-01

    Cadmium (Cd) has become an important metal contaminant and posed severe risk on the organisms in the coastal environments of the Bohai Sea. Marine mussel Mytilus galloprovincialis is widely distributed along the Bohai coast and consumed as seafood by local residents. Evidences indicate that the early stages of marine organisms are more sensitive to metal contaminants. In this study, we applied two-dimensional electrophoresis-based proteomics to characterize the biological effects of Cd (50 μg L(-1)) in the early life stages (D-shape larval and juvenile) of mussels. The different proteomic responses demonstrated the differential responsive mechanisms to Cd exposure in these two early life stages of mussels. In details, results indicated that Cd mainly induced immune and oxidative stresses in both D-shape larval and juvenile mussels via different pathways. In addition, the significant up-regulation of triosephosphate isomerase and metallothionein confirmed the enhanced energy demand and mobilized detoxification mechanism in D-shape larval mussels exposed to Cd. In juvenile mussels, Cd exposure also induced clear apoptosis. Overall, this work suggests that Cd is a potential immune toxicant to mussel M. galloprovincialis at early life stages.

  20. EPG Recordings Reveal Differential Feeding Behaviors in Sogatella furcifera in Response to Plant Virus Infection and Transmission Success.

    Science.gov (United States)

    Lei, Wenbin; Li, Pei; Han, Yongqiang; Gong, Shaolong; Yang, Lang; Hou, Maolin

    2016-01-01

    Plant viruses are primarily transmitted by insect vectors and virus infection may influence on the vectors' feeding behaviors. Using an electrical penetration graph, we detected that infection with the Southern rice black-streaked dwarf virus (SRBSDV) in the white-backed planthopper (WBPH) and in rice plants both altered the vector's feeding behavior. When viruliferous WBPH (carrying SRBSDV) were fed on uninfected plants, they spent more time in salivation and phloem sap ingestion than non-viruliferous insects. In comparison with uninfected plants, infected plants showed an arrestant effect on non-viruliferous WBPH for phloem sap ingestion. Differential feeding behaviors were also detected between the WBPH that inoculated or acquired SRBSDV and those that failed to. The WBPH that inoculated SRBSDV exhibited more probing bouts, salivation events and phloem sap ingestion events and longer salivation than those that failed to. The WBPH that acquired SRBSDV were quicker to reach phloem and spent more time in phloem sap ingestion than those that failed to. These behavior alterations in the vector may have adaptive advantages for SRBSDV transmission and spread success because greater salivation by viruliferous vectors on uninfected hosts will promote virus inoculation, whereas more sap ingestion by non-viruliferous vectors on infected hosts will promote virus acquisition. PMID:27492995

  1. Proteomic responses reveal the differential effects induced by cadmium in mussels Mytilus galloprovincialis at early life stages.

    Science.gov (United States)

    Xu, Lanlan; Peng, Xiao; Yu, Deliang; Ji, Chenglong; Zhao, Jianmin; Wu, Huifeng

    2016-08-01

    Cadmium (Cd) has become an important metal contaminant and posed severe risk on the organisms in the coastal environments of the Bohai Sea. Marine mussel Mytilus galloprovincialis is widely distributed along the Bohai coast and consumed as seafood by local residents. Evidences indicate that the early stages of marine organisms are more sensitive to metal contaminants. In this study, we applied two-dimensional electrophoresis-based proteomics to characterize the biological effects of Cd (50 μg L(-1)) in the early life stages (D-shape larval and juvenile) of mussels. The different proteomic responses demonstrated the differential responsive mechanisms to Cd exposure in these two early life stages of mussels. In details, results indicated that Cd mainly induced immune and oxidative stresses in both D-shape larval and juvenile mussels via different pathways. In addition, the significant up-regulation of triosephosphate isomerase and metallothionein confirmed the enhanced energy demand and mobilized detoxification mechanism in D-shape larval mussels exposed to Cd. In juvenile mussels, Cd exposure also induced clear apoptosis. Overall, this work suggests that Cd is a potential immune toxicant to mussel M. galloprovincialis at early life stages. PMID:27302865

  2. High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne

    Science.gov (United States)

    Pan, Lang; Wang, Zhaoyun; Cai, Jia; Gao, Haitao; Zhao, Hongwei; Dong, Liyao

    2016-01-01

    Non-target site resistance (NTSR) to herbicides is an increasing concern for weed control. The majority of previous studies have focused on metabolic resistance mechanisms of NTSR, but no research exists on gene regulation mechanisms behind herbicide resistance, such as microRNA (miRNA). Here, we identified 3 American sloughgrass (Beckmannia syzigachne Steud.) populations containing fenoxaprop-P-ethyl-resistant plants. We then constructed small RNA libraries and subjected them to deep sequencing and bioinformatics analyses. Forty known and 36 potentially novel, predicted miRNAs were successfully identified. Of these, we identified 3 conserved, predicted candidate NTSR-determinant miRNAs and their potential corresponding target genes, as well as 4 novel potential miRNAs with high count. Target gene prediction and annotation indicated that these 7 differentially expressed miRNAs potentially play a role in regulating specific stress-responsive genes, very likely related to herbicide resistance. Expression profiles were determined with quantitative real-time PCR. The present study is a novel, large-scale characterization of weed miRNAs. The results should further our understanding of miRNA expression profiles associated with herbicide resistance, allowing for the development of more effective weed management strategies. PMID:27353151

  3. High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne.

    Science.gov (United States)

    Pan, Lang; Wang, Zhaoyun; Cai, Jia; Gao, Haitao; Zhao, Hongwei; Dong, Liyao

    2016-01-01

    Non-target site resistance (NTSR) to herbicides is an increasing concern for weed control. The majority of previous studies have focused on metabolic resistance mechanisms of NTSR, but no research exists on gene regulation mechanisms behind herbicide resistance, such as microRNA (miRNA). Here, we identified 3 American sloughgrass (Beckmannia syzigachne Steud.) populations containing fenoxaprop-P-ethyl-resistant plants. We then constructed small RNA libraries and subjected them to deep sequencing and bioinformatics analyses. Forty known and 36 potentially novel, predicted miRNAs were successfully identified. Of these, we identified 3 conserved, predicted candidate NTSR-determinant miRNAs and their potential corresponding target genes, as well as 4 novel potential miRNAs with high count. Target gene prediction and annotation indicated that these 7 differentially expressed miRNAs potentially play a role in regulating specific stress-responsive genes, very likely related to herbicide resistance. Expression profiles were determined with quantitative real-time PCR. The present study is a novel, large-scale characterization of weed miRNAs. The results should further our understanding of miRNA expression profiles associated with herbicide resistance, allowing for the development of more effective weed management strategies. PMID:27353151

  4. Analysis of Drosophila p8 and p52 mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation

    Science.gov (United States)

    Cruz-Becerra, Grisel; Juárez, Mandy; Valadez-Graham, Viviana

    2016-01-01

    Eukaryotic gene expression is activated by factors that interact within complex machinery to initiate transcription. An important component of this machinery is the DNA repair/transcription factor TFIIH. Mutations in TFIIH result in three human syndromes: xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Transcription and DNA repair defects have been linked to some clinical features of these syndromes. However, how mutations in TFIIH affect specific developmental programmes, allowing organisms to develop with particular phenotypes, is not well understood. Here, we show that mutations in the p52 and p8 subunits of TFIIH have a moderate effect on the gene expression programme in the Drosophila testis, causing germ cell differentiation arrest in meiosis, but no Polycomb enrichment at the promoter of the affected differentiation genes, supporting recent data that disagree with the current Polycomb-mediated repression model for regulating gene expression in the testis. Moreover, we found that TFIIH stability is not compromised in p8 subunit-depleted testes that show transcriptional defects, highlighting the role of p8 in transcription. Therefore, this study reveals how defects in TFIIH affect a specific cell differentiation programme and contributes to understanding the specific syndrome manifestations in TFIIH-afflicted patients.

  5. Population differentiation and phylogeographic pattern of a relict species, Conandron ramondioides (Gesneriaceae), revealed from sequence polymorphism and haplotypes of the CYCLOIDEA gene

    Institute of Scientific and Technical Information of China (English)

    Li-Hong XIAO; Zhi LI; Rui WANG; yin-Zheng WANG

    2012-01-01

    Historical events are expected to affect population genetic differentiation and DNA molecular evolution,but the impact of these effects remains a matter of debate.Here,for Conandron ramondioides (Gesneriaceae),we analyzed the genetic structure and phylogeographical pattern of 248 individuals from 13 populations,distributed in mainland China and Taiwan Island,based on the nucleotide sequence and haplotype of the coding sequence of CYCLOIDEA1 (GCYC1).Among the populations,we found a high level of haplotype diversity (h =0.831) and a relatively low level of nucleotide diversity (Dij =0.004).Both the haplotype network and the neighbor-joining tree constructed from GCYC1 haplotypes suggest two major geographical groupings,one on the mainland and the other on Taiwan.Consistently,AMOVA analysis revealed high genetic differentiation between these groupings,with 84.65% variation partitioning the two regions,and the two groupings shared no haplotype.On the mainland,population genetic differentiation was correlated with more recent events,presumably Pleistocene glaciations and human activities since the Neolithic.In addition,C.ramondioides GCYC1 rapidly accumulated neutral mutations,consistent with this gene being silenced or down-regulated in actinomorphic lineages of the Lamiales,such as Conandron.

  6. Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.

    Science.gov (United States)

    Zhang, Yuchao; Li, Weijia; Dou, Yujuan; Zhang, Junxiang; Jiang, Guihua; Miao, Lixiang; Han, Guofen; Liu, Yuexue; Li, He; Zhang, Zhihong

    2015-01-01

    Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca.

  7. Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.

    Directory of Open Access Journals (Sweden)

    Yuchao Zhang

    Full Text Available Fragaria vesca (2n = 2x = 14, the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb. It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW and red (Ruegen, RG fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2% had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs, including MYB (putative MYB86 and MYB39, WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca.

  8. Differential phosphorylation of perilipin 1A at the initiation of lipolysis revealed by novel monoclonal antibodies and high content analysis.

    Directory of Open Access Journals (Sweden)

    Patrick M McDonough

    Full Text Available Lipolysis in adipocytes is regulated by phosphorylation of lipid droplet-associated proteins, including perilipin 1A and hormone-sensitive lipase (HSL. Perilipin 1A is potentially phosphorylated by cAMP(adenosine 3',5'-cyclic monophosphate-dependent protein kinase (PKA on several sites, including conserved C-terminal residues, serine 497 (PKA-site 5 and serine 522 (PKA-site 6. To characterize perilipin 1A phosphorylation, novel monoclonal antibodies were developed, which selectively recognize perilipin 1A phosphorylation at PKA-site 5 and PKA-site 6. Utilizing these novel antibodies, as well as antibodies selectively recognizing HSL phosphorylation at serine 563 or serine 660, we used high content analysis to examine the phosphorylation of perilipin 1A and HSL in adipocytes exposed to lipolytic agents. We found that perilipin PKA-site 5 and HSL-serine 660 were phosphorylated to a similar extent in response to forskolin (FSK and L-γ-melanocyte stimulating hormone (L-γ-MSH. In contrast, perilipin PKA-site 6 and HSL-serine 563 were phosphorylated more slowly and L-γ-MSH was a stronger agonist for these sites compared to FSK. When a panel of lipolytic agents was tested, including multiple concentrations of isoproterenol, FSK, and L-γ-MSH, the pattern of results was virtually identical for perilipin PKA-site 5 and HSL-serine 660, whereas a distinct pattern was observed for perilipin PKA-site 6 and HSL-serine 563. Notably, perilipin PKA-site 5 and HSL-serine 660 feature two arginine residues upstream from the phospho-acceptor site, which confers high affinity for PKA, whereas perilipin PKA-site 6 and HSL-serine 563 feature only a single arginine. Thus, we suggest perilipin 1A and HSL are differentially phosphorylated in a similar manner at the initiation of lipolysis and arginine residues near the target serines may influence this process.

  9. Differential phosphorylation of perilipin 1A at the initiation of lipolysis revealed by novel monoclonal antibodies and high content analysis.

    Science.gov (United States)

    McDonough, Patrick M; Maciejewski-Lenoir, Dominique; Hartig, Sean M; Hanna, Rita A; Whittaker, Ross; Heisel, Andrew; Nicoll, James B; Buehrer, Benjamin M; Christensen, Kurt; Mancini, Maureen G; Mancini, Michael A; Edwards, Dean P; Price, Jeffrey H

    2013-01-01

    Lipolysis in adipocytes is regulated by phosphorylation of lipid droplet-associated proteins, including perilipin 1A and hormone-sensitive lipase (HSL). Perilipin 1A is potentially phosphorylated by cAMP(adenosine 3',5'-cyclic monophosphate)-dependent protein kinase (PKA) on several sites, including conserved C-terminal residues, serine 497 (PKA-site 5) and serine 522 (PKA-site 6). To characterize perilipin 1A phosphorylation, novel monoclonal antibodies were developed, which selectively recognize perilipin 1A phosphorylation at PKA-site 5 and PKA-site 6. Utilizing these novel antibodies, as well as antibodies selectively recognizing HSL phosphorylation at serine 563 or serine 660, we used high content analysis to examine the phosphorylation of perilipin 1A and HSL in adipocytes exposed to lipolytic agents. We found that perilipin PKA-site 5 and HSL-serine 660 were phosphorylated to a similar extent in response to forskolin (FSK) and L-γ-melanocyte stimulating hormone (L-γ-MSH). In contrast, perilipin PKA-site 6 and HSL-serine 563 were phosphorylated more slowly and L-γ-MSH was a stronger agonist for these sites compared to FSK. When a panel of lipolytic agents was tested, including multiple concentrations of isoproterenol, FSK, and L-γ-MSH, the pattern of results was virtually identical for perilipin PKA-site 5 and HSL-serine 660, whereas a distinct pattern was observed for perilipin PKA-site 6 and HSL-serine 563. Notably, perilipin PKA-site 5 and HSL-serine 660 feature two arginine residues upstream from the phospho-acceptor site, which confers high affinity for PKA, whereas perilipin PKA-site 6 and HSL-serine 563 feature only a single arginine. Thus, we suggest perilipin 1A and HSL are differentially phosphorylated in a similar manner at the initiation of lipolysis and arginine residues near the target serines may influence this process.

  10. Quantitative Western ligand blotting reveals common patterns and differential features of IGFBP-fingerprints in domestic ruminant breeds and species.

    Science.gov (United States)

    Wirthgen, Elisa; Höflich, Christine; Spitschak, Marion; Helmer, Carina; Brand, Bodo; Langbein, Jan; Metzger, Friedrich; Hoeflich, Andreas

    2016-02-01

    The insulin-like growth factor binding proteins (IGFBPs) are determinants of local IGF-effects and thus have an impact on growth and metabolism in vertebrate species. In farm animals, IGFBPs are associated with traits such as growth rate, body composition, milk production, or fertility. It may be assumed, that selective breeding and characteristic phenotypes of breeds are related to differential expression of IGFBPs. Therefore, the aim of the present study was to investigate the effects of selective breeding on blood IGFBP concentrations of farm animals. Breeds of the sheep, goat, and cattle species were investigated. IGFBP-3, -2, and -4 were analyzed with quantitative Western ligand blotting (qWLB), enabling comprehensive monitoring of intact IGFBPs with IGF-binding capacity. We show that in sera of all species and breeds investigated, IGFBP-3, -2, and -4 were simultaneously detectable by qWLB analysis. IGFBP-3 and the total amount of IGFBPs were significantly increased (Pcows had higher levels of IGFBP-4 (P<0.05), if compared to conventional crossbreeds of beef cattle. In Dwarf goats the ratio of IGFBP-3/IGFBP-2 was about 3-fold higher than in other goat breeds (P<0.001). The total IGFBP amount of Toggenburg goats was reduced (P<0.05), compared to the other goat breeds. In conclusion, our data indicate that common and specific features of IGFBP fingerprints are found in different ruminant species and breeds. Our findings may introduce quantitative Western ligand blotting as an attractive tool for biomarker development and molecular phenotyping in farm animal breeds. PMID:26597140

  11. Genome‐wide analysis reveals conserved transcriptional responses downstream of resting potential change in Xenopus embryos, axolotl regeneration, and human mesenchymal cell differentiation

    Science.gov (United States)

    Pai, Vaibhav P.; Martyniuk, Christopher J.; Echeverri, Karen; Sundelacruz, Sarah; Kaplan, David L.

    2015-01-01

    Abstract Endogenous bioelectric signaling via changes in cellular resting potential (V mem) is a key regulator of patterning during regeneration and embryogenesis in numerous model systems. Depolarization of V mem has been functionally implicated in dedifferentiation, tumorigenesis, anatomical re‐specification, and appendage regeneration. However, no unbiased analyses have been performed to understand genome‐wide transcriptional responses to V mem change in vivo. Moreover, it is unknown which genes or gene networks represent conserved targets of bioelectrical signaling across different patterning contexts and species. Here, we use microarray analysis to comparatively analyze transcriptional responses to V mem depolarization. We compare the response of the transcriptome during embryogenesis (Xenopus development), regeneration (axolotl regeneration), and stem cell differentiation (human mesenchymal stem cells in culture) to identify common networks across model species that are associated with depolarization. Both subnetwork enrichment and PANTHER analyses identified a number of key genetic modules as targets of V mem change, and also revealed important (well‐conserved) commonalities in bioelectric signal transduction, despite highly diverse experimental contexts and species. Depolarization regulates specific transcriptional networks across all three germ layers (ectoderm, mesoderm, and endoderm) such as cell differentiation and apoptosis, and this information will be used for developing mechanistic models of bioelectric regulation of patterning. Moreover, our analysis reveals that V mem change regulates transcripts related to important disease pathways such as cancer and neurodegeneration, which may represent novel targets for emerging electroceutical therapies. PMID:27499876

  12. Differential Dopamine Release Dynamics in the Nucleus Accumbens Core and Shell Reveal Complementary Signals for Error Prediction and Incentive Motivation

    Science.gov (United States)

    Cacciapaglia, Fabio; Wightman, R. Mark; Carelli, Regina M.

    2015-01-01

    Mesolimbic dopamine (DA) is phasically released during appetitive behaviors, though there is substantive disagreement about the specific purpose of these DA signals. For example, prediction error (PE) models suggest a role of learning, while incentive salience (IS) models argue that the DA signal imbues stimuli with value and thereby stimulates motivated behavior. However, within the nucleus accumbens (NAc) patterns of DA release can strikingly differ between subregions, and as such, it is possible that these patterns differentially contribute to aspects of PE and IS. To assess this, we measured DA release in subregions of the NAc during a behavioral task that spatiotemporally separated sequential goal-directed stimuli. Electrochemical methods were used to measure subsecond NAc dopamine release in the core and shell during a well learned instrumental chain schedule in which rats were trained to press one lever (seeking; SL) to gain access to a second lever (taking; TL) linked with food delivery, and again during extinction. In the core, phasic DA release was greatest following initial SL presentation, but minimal for the subsequent TL and reward events. In contrast, phasic shell DA showed robust release at all task events. Signaling decreased between the beginning and end of sessions in the shell, but not core. During extinction, peak DA release in the core showed a graded decrease for the SL and pauses in release during omitted expected rewards, whereas shell DA release decreased predominantly during the TL. These release dynamics suggest parallel DA signals capable of supporting distinct theories of appetitive behavior. SIGNIFICANCE STATEMENT Dopamine signaling in the brain is important for a variety of cognitive functions, such as learning and motivation. Typically, it is assumed that a single dopamine signal is sufficient to support these cognitive functions, though competing theories disagree on how dopamine contributes to reward-based behaviors. Here, we have

  13. A novel Atoh1 "self-terminating" mouse model reveals the necessity of proper Atoh1 level and duration for hair cell differentiation and viability.

    Directory of Open Access Journals (Sweden)

    Ning Pan

    Full Text Available Atonal homolog1 (Atoh1 is a bHLH transcription factor essential for inner ear hair cell differentiation. Targeted expression of Atoh1 at various stages in development can result in hair cell differentiation in the ear. However, the level and duration of Atoh1 expression required for proper hair cell differentiation and maintenance remain unknown. We generated an Atoh1 conditional knockout (CKO mouse line using Tg(Atoh1-cre, in which the cre expression is driven by an Atoh1 enhancer element that is regulated by Atoh1 protein to "self-terminate" its expression. The mutant mice show transient, limited expression of Atoh1 in all hair cells in the ear. In the organ of Corti, reduction and delayed deletion of Atoh1 result in progressive loss of almost all the inner hair cells and the majority of the outer hair cells within three weeks after birth. The remaining cells express hair cell marker Myo7a and attract nerve fibers, but do not differentiate normal stereocilia bundles. Some Myo7a-positive cells persist in the cochlea into adult stages in the position of outer hair cells, flanked by a single row of pillar cells and two to three rows of disorganized Deiters cells. Gene expression analyses of Atoh1, Barhl1 and Pou4f3, genes required for survival and maturation of hair cells, reveal earlier and higher expression levels in the inner compared to the outer hair cells. Our data show that Atoh1 is crucial for hair cell mechanotransduction development, viability, and maintenance and also suggest that Atoh1 expression level and duration may play a role in inner vs. outer hair cell development. These genetically engineered Atoh1 CKO mice provide a novel model for establishing critical conditions needed to regenerate viable and functional hair cells with Atoh1 therapy.

  14. Label-free quantitative phosphoproteomic analysis reveals differentially regulated proteins and pathway in PRRSV-infected pulmonary alveolar macrophages.

    Science.gov (United States)

    Luo, Rui; Fang, Liurong; Jin, Hui; Wang, Dang; An, Kang; Xu, Ningzhi; Chen, Huanchun; Xiao, Shaobo

    2014-03-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen of swine worldwide and causes significant economic losses. Through regulating the host proteins phosphorylation, PRRSV was found to manipulate the activities of several signaling molecules to regulate innate immune responses. However, the role of protein phosphorylation during PRRSV infection and the signal pathways responsible for it are relatively unknown. Here liquid chromatography-tandem mass spectrometry for label-free quantitative phosphoproteomics was applied to systematically investigate the global phosphorylation events in PRRSV-infected pulmonary alveolar macrophages. In total, we identified 2125 unique phosphosites, of which the phosphorylation level of 292 phosphosites on 242 proteins and 373 phosphosites on 249 proteins was significantly altered at 12 and 36 h pi, respectively. The phosphoproteomics data were analyzed using ingenuity pathways analysis to identify defined canonical pathways and functional networks. Pathway analysis revealed that PRRSV-induced inflammatory cytokines production was probably due to the activation of mitogen-activated protein kinase and NF-κB signal pathway, which were regulated by several protein kinases during virus infection. Interacting network analysis indicated that altered phosphoproteins were involved in cellular assembly and organization, protein synthesis, molecular transport, and signal transduction in PRRSV infected cells. These pathways and functional networks analysis could provide direct insights into the biological significance of phosphorylation events modulated by PRRSV and may help us elucidate the pathogenic mechanisms of PRRSV infection. PMID:24533505

  15. Differential dynamic engagement within 24 SH3 domain: peptide complexes revealed by co-linear chemical shift perturbation analysis.

    Directory of Open Access Journals (Sweden)

    Elliott J Stollar

    Full Text Available There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences.

  16. Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene.

    Science.gov (United States)

    Crees, Jennifer J; Carbone, Chris; Sommer, Robert S; Benecke, Norbert; Turvey, Samuel T

    2016-03-30

    The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18,700 mammalian zooarchaeological records for the last 11,700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of 'static' past baselines to inform current-day environmental management and restoration. PMID:27009229

  17. Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene

    Science.gov (United States)

    Crees, Jennifer J.; Carbone, Chris; Sommer, Robert S.; Benecke, Norbert; Turvey, Samuel T.

    2016-01-01

    The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18 700 mammalian zooarchaeological records for the last 11 700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of ‘static’ past baselines to inform current-day environmental management and restoration. PMID:27009229

  18. Genome sequence comparison reveals a candidate gene involved in male-hermaphrodite differentiation in papaya (Carica papaya) trees.

    Science.gov (United States)

    Ueno, Hiroki; Urasaki, Naoya; Natsume, Satoshi; Yoshida, Kentaro; Tarora, Kazuhiko; Shudo, Ayano; Terauchi, Ryohei; Matsumura, Hideo

    2015-04-01

    The sex type of papaya (Carica papaya) is determined by the pair of sex chromosomes (XX, female; XY, male; and XY(h), hermaphrodite), in which there is a non-recombining genomic region in the Y and Y(h) chromosomes. This region is presumed to be involved in determination of males and hermaphrodites; it is designated as the male-specific region in the Y chromosome (MSY) and the hermaphrodite-specific region in the Y(h) chromosome (HSY). Here, we identified the genes determining male and hermaphrodite sex types by comparing MSY and HSY genomic sequences. In the MSY and HSY genomic regions, we identified 14,528 nucleotide substitutions and 965 short indels with a large gap and two highly diverged regions. In the predicted genes expressed in flower buds, we found no nucleotide differences leading to amino acid changes between the MSY and HSY. However, we found an HSY-specific transposon insertion in a gene (SVP like) showing a similarity to the Short Vegetative Phase (SVP) gene. Study of SVP-like transcripts revealed that the MSY allele encoded an intact protein, while the HSY allele encoded a truncated protein. Our findings demonstrated that the SVP-like gene is a candidate gene for male-hermaphrodite determination in papaya.

  19. Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants.

    Science.gov (United States)

    Rodrigues, Silas P; Ventura, José A; Aguilar, Clemente; Nakayasu, Ernesto S; Choi, HyungWon; Sobreira, Tiago J P; Nohara, Lilian L; Wermelinger, Luciana S; Almeida, Igor C; Zingali, Russolina B; Fernandes, Patricia M B

    2012-06-18

    Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers' regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses.

  20. Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants.

    Science.gov (United States)

    Rodrigues, Silas P; Ventura, José A; Aguilar, Clemente; Nakayasu, Ernesto S; Choi, HyungWon; Sobreira, Tiago J P; Nohara, Lilian L; Wermelinger, Luciana S; Almeida, Igor C; Zingali, Russolina B; Fernandes, Patricia M B

    2012-06-18

    Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers' regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses. PMID:22465191

  1. Crystal Structures of Wild-type and Mutant Methicillin-resistant Staphylococcus aureus Dihydrofolate Reductase Reveal an Alternative Conformation of NADPH that may be Linked to Trimethoprim Resistance

    Energy Technology Data Exchange (ETDEWEB)

    Frey, K.; Liu, J; Lombardo, M; Bolstad, D; Wright, D; Anderson, A

    2009-01-01

    Both hospital- and community-acquired Staphylococcus aureus infections have become major health concerns in terms of morbidity, suffering and cost. Trimethoprim-sulfamethoxazole (TMP-SMZ) is an alternative treatment for methicillin-resistant S. aureus (MRSA) infections. However, TMP-resistant strains have arisen with point mutations in dihydrofolate reductase (DHFR), the target for TMP. A single point mutation, F98Y, has been shown biochemically to confer the majority of this resistance to TMP. Using a structure-based approach, we have designed a series of novel propargyl-linked DHFR inhibitors that are active against several trimethoprim-resistant enzymes. We screened this series against wild-type and mutant (F98Y) S. aureus DHFR and found that several are active against both enzymes and specifically that the meta-biphenyl class of these inhibitors is the most potent. In order to understand the structural basis of this potency, we determined eight high-resolution crystal structures: four each of the wild-type and mutant DHFR enzymes bound to various propargyl-linked DHFR inhibitors. In addition to explaining the structure-activity relationships, several of the structures reveal a novel conformation for the cofactor, NADPH. In this new conformation that is predominantly associated with the mutant enzyme, the nicotinamide ring is displaced from its conserved location and three water molecules complete a network of hydrogen bonds between the nicotinamide ring and the protein. In this new position, NADPH has reduced interactions with the inhibitor. An equilibrium between the two conformations of NADPH, implied by their occupancies in the eight crystal structures, is influenced both by the ligand and the F98Y mutation. The mutation induced equilibrium between two NADPH-binding conformations may contribute to decrease TMP binding and thus may be responsible for TMP resistance.

  2. Molecular diagnostic tools for detection and differentiation of phytoplasmas based on chaperonin-60 reveal differences in host plant infection patterns.

    Directory of Open Access Journals (Sweden)

    Tim J Dumonceaux

    Full Text Available Phytoplasmas ('Candidatus Phytoplasma' spp. are insect-vectored bacteria that infect a wide variety of plants, including many agriculturally important species. The infections can cause devastating yield losses by inducing morphological changes that dramatically alter inflorescence development. Detection of phytoplasma infection typically utilizes sequences located within the 16S-23S rRNA-encoding locus, and these sequences are necessary for strain identification by currently accepted standards for phytoplasma classification. However, these methods can generate PCR products >1400 bp that are less divergent in sequence than protein-encoding genes, limiting strain resolution in certain cases. We describe a method for accessing the chaperonin-60 (cpn60 gene sequence from a diverse array of 'Ca.Phytoplasma' spp. Two degenerate primer sets were designed based on the known sequence diversity of cpn60 from 'Ca.Phytoplasma' spp. and used to amplify cpn60 gene fragments from various reference samples and infected plant tissues. Forty three cpn60 sequences were thereby determined. The cpn60 PCR-gel electrophoresis method was highly sensitive compared to 16S-23S-targeted PCR-gel electrophoresis. The topology of a phylogenetic tree generated using cpn60 sequences was congruent with that reported for 16S rRNA-encoding genes. The cpn60 sequences were used to design a hybridization array using oligonucleotide-coupled fluorescent microspheres, providing rapid diagnosis and typing of phytoplasma infections. The oligonucleotide-coupled fluorescent microsphere assay revealed samples that were infected simultaneously with two subtypes of phytoplasma. These tools were applied to show that two host plants, Brassica napus and Camelina sativa, displayed different phytoplasma infection patterns.

  3. Integrating nap and night-time sleep into sleep patterns reveals differential links to health-relevant outcomes.

    Science.gov (United States)

    Devine, Jaime K; Wolf, Jutta M

    2016-04-01

    Both night-time sleep and nap behaviour have been linked consistently to health outcomes. Although reasons for napping are usually tied to night-time sleep, the majority of studies assess their effects independently. The current study thus aimed to examine the health relevance of patterns of sleep behaviour that take into account both night-time and daytime sleep habits. Night-time sleep, recorded during 7 days via actigraphy from 313 participants (aged 34-82 years) of the Midlife in the United States II Biomarker study, was assessed. Blood and urine specimens were assayed for noradrenaline, interleukin-6 and C-reactive protein. Participants self-reported nap behaviour, depressive symptoms, perceived chronic stress and the presence of medical symptoms and conditions. Overall, nappers (n = 208) showed elevated waist-hip ratios, C-reactive protein and interleukin-6 levels compared to non-nappers and reported more physiological symptoms and conditions (all P ≤ 0.019). Within nappers, cluster analysis revealed three patterns of sleep behaviour-infrequent nappers with good night-time sleep, frequent nappers with good night-time sleep and nappers with poor night-time sleep. Nappers with poor night-time sleep thereby exhibited elevated noradrenaline levels, depressive symptoms and perceived stress scores compared to other groups (all P ≤ 0.041). These findings support the idea that nap-health relationships are complex, in that frequency of napping and accumulation of nap sleep is not related linearly to health consequences. Assessing nap behaviour in conjunction with night-time sleep behaviour appeared crucial to elucidate further the health relevance of napping, particularly in terms of psychological health outcomes, including chronic stress and depressive symptoms. PMID:26718988

  4. Distinct motifs in the intracellular domain of human CD30 differentially activate canonical and alternative transcription factor NF-κB signaling.

    Directory of Open Access Journals (Sweden)

    Sarah L Buchan

    Full Text Available The TNF-receptor superfamily member CD30 is expressed on normal and malignant lymphocytes, including anaplastic large cell lymphoma (ALCL cells. CD30 transmits multiple effects, including activation of NF-κB signaling, cell proliferation, growth arrest and apoptosis. How CD30 generates these pleiotropic effects is currently unknown. Herein we describe ALCL cells expressing truncated forms of the CD30 intracellular domain that allowed us to identify the key regions responsible for transmitting its biological effects in lymphocytes. The first region (CD30(519-537 activated both the alternative and canonical NF-κB pathways as detected by p100 and IκBα degradation, IKKβ-dependent transcription of both IκBα and the cyclin-dependent kinase inhibitor p21(WAF1/CIP1 and induction of cell cycle arrest. In contrast, the second region of CD30 (CD30(538-595 induced some aspects of canonical NF-κB activation, including transcription of IκBα, but failed to activate the alternative NF-κB pathway or drive p21(WAF1/CIP1-mediated cell-cycle arrest. Direct comparison of canonical NF-κB activation by the two motifs revealed 4-fold greater p65 nuclear translocation following CD30(519-537 engagement. These data reveal that independent regions of the CD30 cytoplasmic tail regulate the magnitude and type of NF-κB activation and additionally identify a short motif necessary for CD30-driven growth arrest signals in ALCL cells.

  5. Revealed Attention

    OpenAIRE

    Masatlioglu, Yusufcan; NAKAJIMA, Daisuke; Ozbay, Erkut Y

    2012-01-01

    The standard revealed preference argument relies on an implicit assumption that a decision maker considers all feasible alternatives. The marketing and psychology literatures, however, provide wellestablished evidence that consumers do not consider all brands in a given market before making a purchase (Limited Attention). In this paper, we illustrate how one can deduce both the decision maker's preference and the alternatives to which she pays attention and inattention from the observed behav...

  6. Revealed Attention

    OpenAIRE

    Yusufcan Masatlioglu; Daisuke Nakajima; Ozbay, Erkut Y

    2012-01-01

    The standard revealed preference argument relies on an implicit assumption that a decision maker considers all feasible alternatives. The marketing and psychology literatures, however, provide well-established evidence that consumers do not consider all brands in a given market before making a purchase (Limited Attention). In this paper, we illustrate how one can deduce both the decision maker's preference and the alternatives to which she pays attention and inattention from the observed beha...

  7. Integrative genomic analysis in K562 chronic myelogenous leukemia cells reveals that proximal NCOR1 binding positively regulates genes that govern erythroid differentiation and Imatinib sensitivity.

    Science.gov (United States)

    Long, Mark D; van den Berg, Patrick R; Russell, James L; Singh, Prashant K; Battaglia, Sebastiano; Campbell, Moray J

    2015-09-01

    To define the functions of NCOR1 we developed an integrative analysis that combined ENCODE and NCI-60 data, followed by in vitro validation. NCOR1 and H3K9me3 ChIP-Seq, FAIRE-seq and DNA CpG methylation interactions were related to gene expression using bootstrapping approaches. Most NCOR1 combinations (24/44) were associated with significantly elevated level expression of protein coding genes and only very few combinations related to gene repression. DAVID's biological process annotation revealed that elevated gene expression was uniquely associated with acetylation and ETS binding. A matrix of gene and drug interactions built on NCI-60 data identified that Imatinib significantly targeted the NCOR1 governed transcriptome. Stable knockdown of NCOR1 in K562 cells slowed growth and significantly repressed genes associated with NCOR1 cistrome, again, with the GO terms acetylation and ETS binding, and significantly dampened sensitivity to Imatinib-induced erythroid differentiation. Mining public microarray data revealed that NCOR1-targeted genes were significantly enriched in Imatinib response gene signatures in cell lines and chronic myelogenous leukemia (CML) patients. These approaches integrated cistrome, transcriptome and drug sensitivity relationships to reveal that NCOR1 function is surprisingly most associated with elevated gene expression, and that these targets, both in CML cell lines and patients, associate with sensitivity to Imatinib.

  8. Alternate cadmium exposure differentially affects the content of gamma-aminobutyric acid (GABA) and taurine within the hypothalamus, median eminence, striatum and prefrontal cortex of male rats

    Energy Technology Data Exchange (ETDEWEB)

    Esquifino, A.I. [Dept. de Bioquimica y Biologia Molecular III, Universidad Complutense, Madrid (Spain); Seara, R.; Fernandez-Rey, E.; Lafuente, A. [Lab. de Toxicologia, Universidad de Vigo, Orense (Spain)

    2001-05-01

    This work examines changes of gamma aminobutyric acid (GABA) and taurine contents in the hypothalamus, striatum and prefrontal cortex of the rat after an alternate schedule of cadmium administration. Age-associated changes were also evaluated, of those before puberty and after adult age. In control rats GABA content decreased with age in the median eminence and in anterior, mediobasal and posterior hypothalamus, prefrontal cortex and the striatum. Taurine content showed similar results with the exception of mediobasal hypothalamus and striatum, where no changes were detected. In pubertal rats treated with cadmium from 30 to 60 days of life, GABA content significantly decreased in all brain regions except in the striatum. When cadmium was administered from day 60 to 90 of life, GABA content was significantly changed in prefrontal cortex only compared with the age matched controls. Taurine content showed similar results in pubertal rats, with the exception of the median eminence and the mediobasal hypothalamus, neither of which showed a change. However, when cadmium was administered to rats from day 60 to 90 of life, taurine content only changed in prefrontal cortex compared with the age matched controls. These results suggest that cadmium differentially affects GABA and taurine contents within the hypothalamus, median eminence, striatum and prefrontal cortex as a function of age. (orig.)

  9. Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray

    International Nuclear Information System (INIS)

    Ciz1 promotes initiation of mammalian DNA replication and is present within nuclear matrix associated DNA replication factories. Depletion of Ciz1 from normal and cancer cells restrains entry to S phase and inhibits cell proliferation. Several alternative splicing events with putative functional consequences have been identified and reported, but many more variants are predicted to exist based on publicly available mRNAs and expressed sequence tags. Here we report the development and validation of a custom exon and exon-junction microarray focused on the human CIZ1 gene, capable of reproducible detection of differential splice-variant expression. Using a pair of paediatric cancer cell lines and a pool of eight normal lines as reference, the array identified expected and novel CIZ1 splicing events. One novel variant (delta 8-12) that encodes a predicted protein lacking key functional sites, was validated by quantitative RT-PCR and found to be over-represented in a range of other cancer cell lines, and over half of a panel of primary lung tumours. Expression of CIZ1 delta 8-12 appears to be restricted to cancer cells, and may therefore be a useful novel biomarker

  10. Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations.

    Science.gov (United States)

    Zhou, Yang; Utsunomiya, Yuri T; Xu, Lingyang; Hay, El Hamidi Abdel; Bickhart, Derek M; Sonstegard, Tad S; Van Tassell, Curtis P; Garcia, Jose Fernando; Liu, George E

    2016-01-01

    We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle. PMID:27381368

  11. Genetic differentiation and genetic diversity of Castanopsis (Fagaceae, the dominant tree species in Japanese broadleaved evergreen forests, revealed by analysis of EST-associated microsatellites.

    Directory of Open Access Journals (Sweden)

    Kyoko Aoki

    Full Text Available The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata. Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species and the Ryukyu Islands (for C. sieboldii is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may

  12. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  13. Holistic microstructural techniques reveal synchronous and alternating andalusite and staurolite growth during three tectonic events resulted from shifting partitioning of growth vs deformation

    Science.gov (United States)

    Bell, T. H.; Fay, C.

    2016-10-01

    Excellent inclusion trails in a sample containing both staurolite and andalusite porphyroblasts are used to demonstrate techniques that allow the intimate relationships between deformation and porphyroblast growth to be recognized, described in detail and understood. This approach reveals three main phases of growth of both mineral phases, some of which was demonstrably synchronous, during three tectonic events. Each main period of growth occurred during the early stages of three deformations that were successively near orthogonal. However, extra periods are distinguishable in andalusite in some of these events because this phase occurs as clusters of large crystals that vary in orientation by 2° to > 10°. All foliations defined by all inclusion trails within every porphyroblast inflect/intersect about an axis trending at 025° (called a FIA). This indicates that the direction of the horizontal component of bulk shortening was identical for the first and third of the three deformations recorded by porphyroblast growth. Portions of sigmoidal to slightly spiral-shaped inclusion trails in most porphyroblast clusters locally diverge in opposite directions due to overprinting orthogonal bulk shortening typical of that which forms millipede geometries. These microstructures confirm the role of coaxial bulk shortening in initiating porphyroblast growth in an environment that locally becomes strongly non-coaxial as the deformation intensifies in the same event. In this sample, increasing non-coaxiality as the deformation intensified resulted in the same asymmetry for each of the three events and thus an overall spiral-like shape. Differing stages in the development of these bulk-shortening geometries preserved in adjacent or touching phases negate any role for porphyroblast rotation during ductile deformation. Andalusite and staurolite grew without any inter-reaction in locations where they lie in contact. This multiply repeated growth behaviour initiated within zones of

  14. Variation of pathways and network profiles reveals the differential pharmacological mechanisms of each effective component to treat middle cerebral artery ischemia-reperfusion mice.

    Science.gov (United States)

    Dang, HaiXia; Li, KangNing; Yu, YaNan; Zhang, YingYing; Liu, Jun; Wang, PengQian; Li, Bing; Wang, HaiNan; Li, Haixia; Wang, Zhong; Wang, YongYan

    2016-01-01

    Using a system pharmacology strategy, this study evaluated the unique pharmacological characteristics of three different neuroprotective compounds for the treatment of cerebral ischemia-reperfusion. A microarray including 374 brain ischemia-related genes was used to identify the differentially expressed genes among five treatment groups: baicalin, jasminoidin, ursodeoxycholic acid, sham, and vehicle, and MetaCore analysis software was applied to identify the significantly altered pathways, processes and interaction network parameters. At pathway level, 46, 25, and 31 pathways were activated in the baicalin, jasminoidin, and ursodeoxycholic acid groups, respectively. Thirteen pathways mainly related with apoptosis and development were commonly altered in the three groups. Additionally, baicalin also targeted pathways related with development, neurophysiologic process and cytoskeleton remodeling, while jasminoidin targeted pathways related with cell cycle and ursodeoxycholic acid targeted those related with apoptosis and development. At process level, three processes were commonly regulated by the three groups in the top 10 processes. Further interaction network analysis revealed that baicalin, jasminoidin, and ursodeoxycholic acid displayed unique features either on network topological parameters or network structure. Additional overlapping analysis demonstrated that compared with ursodeoxycholic acid, the pharmacological mechanism of baicalin was more similar with that of jasminoidin in treating brain ischemia. The data presented in this study may contribute toward the understanding of the common and differential pharmacological mechanisms of these three compounds. PMID:26168995

  15. MALDI Mass Spectrometry Imaging Reveals Decreased CK5 Levels in Vulvar Squamous Cell Carcinomas Compared to the Precursor Lesion Differentiated Vulvar Intraepithelial Neoplasia

    Directory of Open Access Journals (Sweden)

    Chao Zhang

    2016-07-01

    Full Text Available Vulvar cancer is the fourth most common gynecological cancer worldwide. However, limited studies have been completed on the molecular characterization of vulvar squamous cell carcinoma resulting in a poor understanding of the disease initiation and progression. Analysis and early detection of the precursor lesion of HPV-independent vulvar squamous cell carcinoma (VSCC, differentiated vulvar intraepithelial neoplasia (dVIN, is of great importance given dVIN lesions have a high level of malignant potential. Here we present an examination of adjacent normal vulvar epithelium, dVIN, and VSCC from six patients by peptide Matrix-assisted laser desorption/ionization Mass Spectrometry Imaging (MALDI-MSI. The results reveal the differential expression of multiple peptides from the protein cytokeratin 5 (CK5 across the three vulvar tissue types. The difference observed in the relative abundance of CK5 by MALDI-MSI between the healthy epithelium, dVIN, and VSCC was further analyzed by immunohistochemistry (IHC in tissue from eight VSCC patients. A decrease in CK5 immunostaining was observed in the VSCC compared to the healthy epithelium and dVIN. These results provide an insight into the molecular fingerprint of the vulvar intraepithelial neoplasia that appears to be more closely related to the healthy epithelium than the VSCC.

  16. De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure.

    Science.gov (United States)

    Hill, Camilla Beate; Cassin, Andrew; Keeble-Gagnère, Gabriel; Doblin, Monika S; Bacic, Antony; Roessner, Ute

    2016-01-01

    Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes. PMID:27527578

  17. MALDI Mass Spectrometry Imaging Reveals Decreased CK5 Levels in Vulvar Squamous Cell Carcinomas Compared to the Precursor Lesion Differentiated Vulvar Intraepithelial Neoplasia.

    Science.gov (United States)

    Zhang, Chao; Arentz, Georgia; Winderbaum, Lyron; Lokman, Noor A; Klingler-Hoffmann, Manuela; Mittal, Parul; Carter, Christopher; Oehler, Martin K; Hoffmann, Peter

    2016-01-01

    Vulvar cancer is the fourth most common gynecological cancer worldwide. However, limited studies have been completed on the molecular characterization of vulvar squamous cell carcinoma resulting in a poor understanding of the disease initiation and progression. Analysis and early detection of the precursor lesion of HPV-independent vulvar squamous cell carcinoma (VSCC), differentiated vulvar intraepithelial neoplasia (dVIN), is of great importance given dVIN lesions have a high level of malignant potential. Here we present an examination of adjacent normal vulvar epithelium, dVIN, and VSCC from six patients by peptide Matrix-assisted laser desorption/ionization Mass Spectrometry Imaging (MALDI-MSI). The results reveal the differential expression of multiple peptides from the protein cytokeratin 5 (CK5) across the three vulvar tissue types. The difference observed in the relative abundance of CK5 by MALDI-MSI between the healthy epithelium, dVIN, and VSCC was further analyzed by immunohistochemistry (IHC) in tissue from eight VSCC patients. A decrease in CK5 immunostaining was observed in the VSCC compared to the healthy epithelium and dVIN. These results provide an insight into the molecular fingerprint of the vulvar intraepithelial neoplasia that appears to be more closely related to the healthy epithelium than the VSCC. PMID:27399691

  18. Ancient DNA of the extinct lava shearwater (Puffinus olsoni from the Canary Islands reveals incipient differentiation within the P. puffinus complex.

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    Oscar Ramirez

    Full Text Available BACKGROUND: The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands. METHODOLOGY/PRINCIPAL FINDINGS: We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni from Fuerteventura (Canary Islands, the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species. CONCLUSIONS: The phylogenetic analyses based on the DNA data reveal that: (i the "Puffinus puffinus complex", an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae, shows unresolved phylogenetic relationships; (ii despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus.

  19. Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6

    Directory of Open Access Journals (Sweden)

    An Chung-Il

    2011-10-01

    Full Text Available Abstract Background Sox6 is a multi-faceted transcription factor involved in the terminal differentiation of many different cell types in vertebrates. It has been suggested that in mice as well as in zebrafish Sox6 plays a role in the terminal differentiation of skeletal muscle by suppressing transcription of slow fiber specific genes. In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-seq analyses to identify Sox6 target genes in mouse fetal myotubes and generated muscle-specific Sox6 knockout (KO mice to determine the Sox6 null muscle phenotype in adult mice. Results We have identified 1,066 Sox6 binding sites using mouse fetal myotubes. The Sox6 binding sites were found to be associated with slow fiber-specific, cardiac, and embryonic isoform genes that are expressed in the sarcomere as well as transcription factor genes known to play roles in muscle development. The concurrently performed RNA polymerase II (Pol II ChIP-seq analysis revealed that 84% of the Sox6 peak-associated genes exhibited little to no binding of Pol II, suggesting that the majority of the Sox6 target genes are transcriptionally inactive. These results indicate that Sox6 directly regulates terminal differentiation of muscle by affecting the expression of sarcomere protein genes as well as indirectly through influencing the expression of transcription factors relevant to muscle development. Gene expression profiling of Sox6 KO skeletal and cardiac muscle revealed a significant increase in the expression of the genes associated with Sox6 binding. In the absence of the Sox6 gene, there was dramatic upregulation of slow fiber-specific, cardiac, and embryonic isoform gene expression in Sox6 KO skeletal muscle and fetal isoform gene expression in Sox6 KO cardiac muscle, thus confirming the role Sox6 plays as a transcriptional suppressor in muscle development

  20. Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

    Directory of Open Access Journals (Sweden)

    Ahn Jong Hwa

    2011-01-01

    Full Text Available Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

  1. Stem cell-like differentiation potentials of endometrial side population cells as revealed by a newly developed in vivo endometrial stem cell assay.

    Directory of Open Access Journals (Sweden)

    Kaoru Miyazaki

    Full Text Available BACKGROUND: Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP, but not endometrial main population cells (EMP, exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay. METHODOLOGY/PRINCIPAL FINDINGS: ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom, a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells. CONCLUSIONS/SIGNIFICANCE: We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo

  2. HPV-16 E7 reveals a link between DNA replication stress, FANCD2 and alternative lengthening of telomeres (ALT)-associated PML bodies (APBs)

    OpenAIRE

    Spardy, Nicole; Duensing, Anette; Hoskins, Elizabeth E.; Wells, Susanne I.; Duensing, Stefan

    2008-01-01

    Expression of the high-risk human papillomavirus (HPV-16) E7 oncoprotein extends the life span of primary human keratinocytes and partially restores telomere length in the absence of telomerase. The molecular basis of this activity is incompletely understood. Here, we show that HPV-16 E7 induces an increased formation of alternative lengthening of telomeres (ALT)-associated PML bodies (APBs) in early passage primary human keratinocytes as well as HPV-negative tumor cells. This activity was fo...

  3. Conditional Expression of Oncogenic C-RAF in Mouse Pulmonary Epithelial Cells Reveals Differential Tumorigenesis and Induction of Autophagy Leading to Tumor Regression

    Directory of Open Access Journals (Sweden)

    Fatih Ceteci

    2011-11-01

    Full Text Available Here we describe a novel conditional mouse lung tumor model for investigation of the pathogenesis of human lung cancer. On the basis of the frequent involvement of the Ras-RAF-MEK-ERK signaling pathway in human non–small cell lung carcinoma (NSCLC, we have explored the target cell availability, reversibility, and cell type specificity of transformation by oncogenic C-RAF. Targeting expression to alveolar type II cells or to Clara cells, the two likely precursors of human NSCLC, revealed differential tumorigenicity between these cells. Whereas expression of oncogenic C-RAF in alveolar type II cells readily induced multifocal macroscopic lung tumors independent of the developmental state, few tumors with type II pneumocytes features and incomplete penetrance were found when targeted to Clara cells. Induced tumors did not progress and were strictly dependent on the initiating oncogene. Deinduction of mice resulted in tumor regression due to autophagy rather than apoptosis. Induction of autophagic cell death in regressing lung tumors suggests the use of autophagy enhancers as a treatment choice for patients with NSCLC.

  4. Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5 and altered Axin-1 expression during tumour progression

    Directory of Open Access Journals (Sweden)

    Reich Jens G

    2006-06-01

    Full Text Available Abstract Background Splicing processes might play a major role in carcinogenesis and tumour progression. The Wnt pathway is of crucial relevance for cancer progression. Therefore we focussed on the Wnt/β-catenin signalling pathway in order to validate the expression of sequences predicted as alternatively spliced by bioinformatic methods. Splice variants of its key molecules were selected, which may be critical components for the understanding of colorectal tumour progression and may have the potential to act as biological markers. For some of the Wnt pathway genes the existence of splice variants was either proposed (e.g. β-Catenin and CTNNB1 or described only in non-colon tissues (e.g. GSK3β or hitherto not published (e.g. LRP5. Results Both splice variants – normal and alternative form – of all selected Wnt pathway components were found to be expressed in cell lines as well as in samples derived from tumour, normal and healthy tissues. All splice positions corresponded totally with the bioinformatical prediction as shown by sequencing. Two hitherto not described alternative splice forms (CTNNB1 and LRP5 were detected. Although the underlying EST data used for the bioinformatic analysis suggested a tumour-specific expression neither a qualitative nor a significant quantitative difference between the expression in tumour and healthy tissues was detected. Axin-1 expression was reduced in later stages and in samples from carcinomas forming distant metastases. Conclusion We were first to describe that splice forms of crucial genes of the Wnt-pathway are expressed in human colorectal tissue. Newly described splicefoms were found for β-Catenin, LRP5, GSK3β, Axin-1 and CtBP1. However, the predicted cancer specificity suggested by the origin of the underlying ESTs was neither qualitatively nor significant quantitatively confirmed. That let us to conclude that EST sequence data can give adequate hints for the existence of alternative splicing

  5. SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

    Directory of Open Access Journals (Sweden)

    Jun Dong

    Full Text Available Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS, North Yellow Sea (NYS, and Bohai Sea (BS in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8 were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO, determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the

  6. Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.

    Science.gov (United States)

    Chen, Wei; Yao, Qiuming; Patil, Gunvant B; Agarwal, Gaurav; Deshmukh, Rupesh K; Lin, Li; Wang, Biao; Wang, Yongqin; Prince, Silvas J; Song, Li; Xu, Dong; An, Yongqiang C; Valliyodan, Babu; Varshney, Rajeev K; Nguyen, Henry T

    2016-01-01

    Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2724 and 3498 DEGs were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement. PMID:27486466

  7. cDNA-AFLP analysis reveals differential gene expression in incompatible interaction between infected non-heading Chinese cabbage and Hyaloperonospora parasitica.

    Science.gov (United States)

    Xiao, Dong; Liu, Shi-Tuo; Wei, Yan-Ping; Zhou, Dao-Yun; Hou, Xi-Lin; Li, Ying; Hu, Chun-Mei

    2016-01-01

    Non-heading Chinese cabbage (Brassica rapa ssp. chinensis) is one of the main green leafy vegetables in the world, especially in China, with significant economic value. Hyaloperonospora parasitica is a fungal pathogen responsible for causing downy mildew disease in Chinese cabbage, which greatly affects its production. The objective of this study was to identify transcriptionally regulated genes during incompatible interactions between non-heading Chinese cabbage and H. parasitica using complementary DNA-amplified fragment length polymorphism (cDNA-AFLP). We obtained 129 reliable differential transcript-derived fragments (TDFs) in a resistant line 'Suzhou Qing'. Among them, 121 upregulated TDFs displayed an expression peak at 24-48 h post inoculation (h.p.i.). Fifteen genes were further selected for validation of cDNA-AFLP expression patterns using quantitative reverse transcription PCR. Results confirmed the altered expression patterns of 13 genes (86.7%) revealed by the cDNA-AFLP. We identified four TDFs related to fungal resistance among the 15 TDFs. Furthermore, comparative analysis of four TDFs between resistant line 'Suzhou Qing' and susceptible line 'Aijiao Huang' showed that transcript levels of TDF14 (BcLIK1_A01) peaked at 48 h.p.i. and 25.1-fold increased in the resistant line compared with the susceptible line. Similarly, transcript levels of the other three genes, TDF42 (BcCAT3_A07), TDF75 (BcAAE3_A06) and TDF88 (BcAMT2_A05) peaked at 24, 48 and 24 h.p.i. with 25.1-, 100- and 15.8-fold increases, respectively. The results suggested that the resistance genes tended to transcribe at higher levels in the resistance line than in the susceptible line, which may provide resistance against pathogen infections. The present study might facilitate elucidating the molecular basis of the infection process and identifying candidate genes for resistance improvement of susceptible cultivars. PMID:27602230

  8. Unconventional Cadherin Localization in Honey Bee Gonads Revealed Through Domain-Specific Apis mellifera E- and N-Cadherin Antibodies Indicates Alternative Functions

    Directory of Open Access Journals (Sweden)

    Klaus Hartfelder

    2012-11-01

    Full Text Available As key factors in intercellular adhesion processes, cadherins play important roles in a plethora of developmental processes, including gametogenesis. In a previous study on cadherin localization in the gonads of honey bees, performed with heterologous pan-cadherin antibodies, we detected these proteins as (i associated with cell membranes, (ii as homogeneously distributed throughout the cytoplasm, and (iii as nuclear foci in both somatic and germline cells, raising the possibility of alternative functions. To further investigate such unusual intracellular cadherin localization we produced specific antibodies against the N- and C-terminal domains of honey bee N- and E-cadherin. A 160 kDa protein was recognized by the E-cadherin antibodies as well as one of approximately 300 kDa from those raised against N-cadherin. In gonad preparations, both proteins were detected as dispersed throughout the cytoplasm and as nuclear foci in both germline and somatic cells of queen and worker ovarioles, as well as in the testioles of drones. This leads us to infer that cadherins may indeed be involved in certain signaling pathways and/or transcriptional regulation during gametogenesis. In late oogenesis stages, immunolabeling for both proteins was observed at the cell cortex, in conformity with a role in cell adhesion. In testioles, E-cadherin was seen in co-localization with fusomes, indicating a possible role in cyst organization. Taken together, the distribution of N- and E-cadherins in honey bee gonads is suggestive of alternative roles for cadherins in gametogenesis of both sexes.

  9. Differential vulnerability to the punishment of cocaine related behaviours: effects of locus of punishment, cocaine taking history and alternative reinforcer availability

    OpenAIRE

    Pelloux, Yann; Murray, Jennifer E.; Everitt, Barry J.

    2014-01-01

    Background: The availability of alternative reinforcement has been shown to reduce drug use, but it remains unclear whether it facilitates a reduction or cessation of drug seeking or taking. Objectives: We compared the effects of punishment of cocaine seeking or taking behaviour after brief or extended cocaine-taking histories when behavioural reallocation was facilitated or not by making available an alternative ingestive reinforcer (sucrose). Methods: In the first experiment, punishme...

  10. Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.

    Directory of Open Access Journals (Sweden)

    Matthew A Oberhardt

    2016-01-01

    Full Text Available Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous 'replacer' gene rescues lethality caused by inactivation of a 'target' gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13. We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG for an essential enzyme (pdxB in production of pyridoxal 5'-phosphate (the active form of Vitamin B6, which we validate experimentally via multicopy suppression. We perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.

  11. An alternative approach to systems of second-order ordinary differential equations with maximal symmetry. Realizations of sl(n + 2 , R) by special functions

    Science.gov (United States)

    Campoamor-Stursberg, R.

    2016-08-01

    Using the general solution of the differential equation x¨(t) +g1(t) x˙ +g2(t) x = 0 , a generic basis of the point-symmetry algebra sl(3 , R) is constructed. Deriving the equation from a time-dependent Lagrangian, the basis elements corresponding to Noether symmetries are deduced. The generalized Lewis invariant is constructed explicitly using a linear combination of Noether symmetries. The procedure is generalized to the case of systems of second-order ordinary differential equations with maximal sl(n + 2 , R) -symmetry, and its possible adaptation to the inhomogeneous non-linear case illustrated by an example.

  12. Alternative security

    International Nuclear Information System (INIS)

    This book contains the following chapters: The Military and Alternative Security: New Missions for Stable Conventional Security; Technology and Alternative Security: A Cherished Myth Expires; Law and Alternative Security: Toward a Just World Peace; Politics and Alternative Security: Toward a More Democratic, Therefore More Peaceful, World; Economics and Alternative Security: Toward a Peacekeeping International Economy; Psychology and Alternative Security: Needs, Perceptions, and Misperceptions; Religion and Alternative Security: A Prophetic Vision; and Toward Post-Nuclear Global Security: An Overview

  13. Quantitative Phosphoproteomic Study Reveals that Protein Kinase A Regulates Neural Stem Cell Differentiation Through Phosphorylation of Catenin Beta-1 and Glycogen Synthase Kinase 3β.

    Science.gov (United States)

    Wang, Shuxin; Li, Zheyi; Shen, Hongyan; Zhang, Zhong; Yin, Yuxin; Wang, Qingsong; Zhao, Xuyang; Ji, Jianguo

    2016-08-01

    Protein phosphorylation is central to the understanding of multiple cellular signaling pathways responsible for regulating the self-renewal and differentiation of neural stem cells (NSCs). Here we performed a large-scale phosphoproteomic analysis of rat fetal NSCs using strong cation exchange chromatography prefractionation and citric acid-assisted two-step enrichment with TiO2 strategy followed by nanoLC-MS/MS analysis. Totally we identified 32,546 phosphosites on 5,091 phosphoproteins, among which 23,945 were class I phosphosites, and quantified 16,000 sites during NSC differentiation. More than 65% of class I phosphosites were novel when compared with PhosphoSitePlus database. Quantification results showed that the early and late stage of NSC differentiation differ greatly. We mapped 69 changed phosphosites on 20 proteins involved in Wnt signaling pathway, including S552 on catenin beta-1 (Ctnnb1) and S9 on glycogen synthase kinase 3β (Gsk3β). Western blotting and real-time PCR results proved that Wnt signaling pathway plays critical roles in NSC fate determination. Furthermore, inhibition and activation of PKA dramatically affected the phosphorylation state of Ctnnb1 and Gsk3β, which regulates the differentiation of NSCs. Our data provides a valuable resource for studying the self-renewal and differentiation of NSCs. Stem Cells 2016;34:2090-2101. PMID:27097102

  14. MEP incentive for onshore wind energy. Study on the robustness of the full load methodology and options for alternative differentiation of the incentive for onshore wind energy

    International Nuclear Information System (INIS)

    The proposed amendment to the Dutch Electricity Law of 1998, called 'environmental quality of electricity production' (MEP), provides operating support through a combination of feed-in tariffs and a reduced ecotax exemption. In order to prevent a free ride of windy locations, the feed-in tariff for onshore wind turbines is limited to a maximum of 18,000 full load hours. Several parties have expressed their concern that this system may possibly provide an incentive to increase the rated power in order to lengthen the period that the feed-in tariff is being received. This report reviews the risks of unintentional side effects of the proposed limitation of 18,000 full load hours. In addition, this report examines the possibilities for further differentiation of the feed-in tariff for onshore wind energy by reviewing methods of differentiation in a number of EU member states

  15. Alternative splicing of the porcine glycogen synthase kinase 3β (GSK-3β gene with differential expression patterns and regulatory functions.

    Directory of Open Access Journals (Sweden)

    Linjie Wang

    Full Text Available BACKGROUND: Glycogen synthase kinase 3 (GSK3α and GSK3β are serine/threonine kinases involved in numerous cellular processes and diverse diseases including mood disorders, Alzheimer's disease, diabetes, and cancer. However, in pigs, the information on GSK3 is very limited. Identification and characterization of pig GSK3 are not only important for pig genetic improvement, but also contribute to the understanding and development of porcine models for human disease prevention and treatment. METHODOLOGY: Five different isoforms of GSK3β were identified in porcine different tissues, in which three isoforms are novel. These isoforms had differential expression patterns in the fetal and adult of the porcine different tissues. The mRNA expression level of GSK3β isoforms was differentially regulated during the course of the insulin treatment, suggesting that different GSK3β isoforms may have different roles in insulin signaling pathway. Moreover, GSK3β5 had a different role on regulating the glycogen synthase activity, phosphorylation and the expression of porcine GYS1 and GYS2 gene compared to other GSK3β isoforms. CONCLUSIONS: We are the first to report five different isoforms of GSK3β identified from the porcine different tissues. Splice variants of GSK3β exhibit differential activity towards glycogen synthase. These results provide new insight into roles of the GSK3β on regulating glycogen metabolism.

  16. Alternative energies; Energies alternatives

    Energy Technology Data Exchange (ETDEWEB)

    Bonal, J.; Rossetti, P

    2007-07-01

    The earth took millions years to made the petroleum, the gas the coal and the uranium. Only a few centuries will be needed to exhaust these fossil fuels and some years to reach expensive prices. Will the wold continue on this way of energy compulsive consumption? The renewable energies and some citizen attitudes are sufficient to break this spiral. This book proposes to discuss these alternative energies. It shows that this attitude must be supported by the government. It takes stock on the more recent information concerning the renewable energies. it develops three main points: the electricity storage, the housing and the transports. (A.L.B.)

  17. Genome-wide analysis of gene expression during adipogenesis in human adipose-derived stromal cells reveals novel patterns of gene expression during adipocyte differentiation.

    Science.gov (United States)

    Ambele, Melvin Anyasi; Dessels, Carla; Durandt, Chrisna; Pepper, Michael Sean

    2016-05-01

    We have undertaken an in-depth transcriptome analysis of adipogenesis in human adipose-derived stromal cells (ASCs) induced to differentiate into adipocytes in vitro. Gene expression was assessed on days 1, 7, 14 and 21 post-induction and genes differentially expressed numbered 128, 218, 253 and 240 respectively. Up-regulated genes were associated with blood vessel development, leukocyte migration, as well as tumor growth, invasion and metastasis. They also shared common pathways with certain obesity-related pathophysiological conditions. Down-regulated genes were enriched for immune response processes. KLF15, LMO3, FOXO1 and ZBTB16 transcription factors were up-regulated throughout the differentiation process. CEBPA, PPARG, ZNF117, MLXIPL, MMP3 and RORB were up-regulated only on days 14 and 21, which coincide with the maturation of adipocytes and could possibly serve as candidates for controlling fat accumulation and the size of mature adipocytes. In summary, we have identified genes that were up-regulated only on days 1 and 7 or days 14 and 21 that could serve as potential early and late-stage differentiation markers. PMID:27108396

  18. Differentiation of Mesenchymal Stem Cells under Hypoxia and Normoxia: Lipid Profiles Revealed by Time-of-Flight Secondary Ion Mass Spectrometry and Multivariate Analysis

    NARCIS (Netherlands)

    Georgi, N.; Cillero-Pastor, B.; Eijkel, G.B.; Chinnagounder Periyasamy, P.; Kiss, A.; Blitterswijk, van C.A.; Post, J.N.; Heeren, R.M.A.; Karperien, H.B.J.

    2015-01-01

    Mesenchymal stem cells (MSC) have the ability to self-renew and differentiate into multiple cell types valuable for clinical treatment of rheumatic pathologies. To study the chondrogenic potential of MSC and identify the conditions that recreate the native cartilage environment, we used time-of-flig

  19. Primary B-cell deficiencies reveal a link between human IL-17-producing CD4 T-cell homeostasis and B-cell differentiation.

    Directory of Open Access Journals (Sweden)

    Rita R Barbosa

    Full Text Available IL-17 is a pro-inflammatory cytokine implicated in autoimmune and inflammatory conditions. The development/survival of IL-17-producing CD4 T cells (Th17 share critical cues with B-cell differentiation and the circulating follicular T helper subset was recently shown to be enriched in Th17 cells able to help B-cell differentiation. We investigated a putative link between Th17-cell homeostasis and B cells by studying the Th17-cell compartment in primary B-cell immunodeficiencies. Common Variable Immunodeficiency Disorders (CVID, defined by defects in B-cell differentiation into plasma and memory B cells, are frequently associated with autoimmune and inflammatory manifestations but we found no relationship between these and Th17-cell frequency. In fact, CVID patients showed a decrease in Th17-cell frequency in parallel with the expansion of activated non-differentiated B cells (CD21(lowCD38(low. Moreover, Congenital Agammaglobulinemia patients, lacking B cells due to impaired early B-cell development, had a severe reduction of circulating Th17 cells. Finally, we found a direct correlation in healthy individuals between circulating Th17-cell frequency and both switched-memory B cells and serum BAFF levels, a crucial cytokine for B-cell survival. Overall, our data support a relationship between Th17-cell homeostasis and B-cell maturation, with implications for the understanding of the pathogenesis of inflammatory/autoimmune diseases and the physiology of B-cell depleting therapies.

  20. Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

    Science.gov (United States)

    In population genetic studies, growing awareness has been raised on non-neutral markers which can provide more estimates of evolutionary differentiation caused by different selections among populations, even though neutral genetic markers have provided unbiased estimates of divergence time and the a...

  1. Genome-wide analysis of gene expression during adipogenesis in human adipose-derived stromal cells reveals novel patterns of gene expression during adipocyte differentiation

    Directory of Open Access Journals (Sweden)

    Melvin Anyasi Ambele

    2016-05-01

    Full Text Available We have undertaken an in-depth transcriptome analysis of adipogenesis in human adipose-derived stromal cells (ASCs induced to differentiate into adipocytes in vitro. Gene expression was assessed on days 1, 7, 14 and 21 post-induction and genes differentially expressed numbered 128, 218, 253 and 240 respectively. Up-regulated genes were associated with blood vessel development, leukocyte migration, as well as tumor growth, invasion and metastasis. They also shared common pathways with certain obesity-related pathophysiological conditions. Down-regulated genes were enriched for immune response processes. KLF15, LMO3, FOXO1 and ZBTB16 transcription factors were up-regulated throughout the differentiation process. CEBPA, PPARG, ZNF117, MLXIPL, MMP3 and RORB were up-regulated only on days 14 and 21, which coincide with the maturation of adipocytes and could possibly serve as candidates for controlling fat accumulation and the size of mature adipocytes. In summary, we have identified genes that were up-regulated only on days 1 and 7 or days 14 and 21 that could serve as potential early and late-stage differentiation markers.

  2. Floral Initiation in Response to Planting Date Reveals the Key Role of Floral Meristem Differentiation Prior to Budding in Canola (Brassica napus L.).

    Science.gov (United States)

    Zhang, Yaofeng; Zhang, Dongqing; Yu, Huasheng; Lin, Baogang; Fu, Ying; Hua, Shuijin

    2016-01-01

    In Brassica napus, floral development is a decisive factor in silique formation, and it is influenced by many cultivation practices including planting date. However, the effect of planting date on floral initiation in canola is poorly understood at present. A field experiment was conducted using a split plot design, in which three planting dates (early, 15 September, middle, 1 October, and late, 15 October) served as main plot and five varieties differing in maturity (1358, J22, Zhongshuang 11, Zheshuang 8, and Zheyou 50) employed as subplot. The purpose of this study was to shed light on the process of floral meristem (FM) differentiation, the influence of planting date on growth period (GP) and floral initiation, and silique formation. The main stages of FM developments can be divided into four stages: first, the transition from shoot apical meristem to FM; second, flower initiation; third, gynoecium and androecium differentiation; and fourth, bud formation. Our results showed that all genotypes had increased GPs from sowing to FM differentiation as planting date was delayed while the GPs from FM differentiation to budding varied year by year except the very early variety, 1358. Based on the number of flowers present at the different reproductive stages, the flowers produced from FM differentiation to budding closely approximated the final silique even though the FM differentiated continuously after budding and peaked generally at the middle flowering stage. The ratio of siliques to maximum flower number ranged from 48 to 80%. These results suggest that (1) the period from FM differentiation to budding is vital for effective flower and silique formation although there was no significant correlation between the length of the period and effective flowers and siliques, and (2) the increased number of flowers from budding were generally ineffective. Therefore, maximizing flower numbers prior to budding will improve silique numbers, and reducing FM degeneration should

  3. Floral Initiation in Response to Planting Date Reveals the Key Role of Floral Meristem Differentiation Prior to Budding in Canola (Brassica napus L.)

    Science.gov (United States)

    Zhang, Yaofeng; Zhang, Dongqing; Yu, Huasheng; Lin, Baogang; Fu, Ying; Hua, Shuijin

    2016-01-01

    In Brassica napus, floral development is a decisive factor in silique formation, and it is influenced by many cultivation practices including planting date. However, the effect of planting date on floral initiation in canola is poorly understood at present. A field experiment was conducted using a split plot design, in which three planting dates (early, 15 September, middle, 1 October, and late, 15 October) served as main plot and five varieties differing in maturity (1358, J22, Zhongshuang 11, Zheshuang 8, and Zheyou 50) employed as subplot. The purpose of this study was to shed light on the process of floral meristem (FM) differentiation, the influence of planting date on growth period (GP) and floral initiation, and silique formation. The main stages of FM developments can be divided into four stages: first, the transition from shoot apical meristem to FM; second, flower initiation; third, gynoecium and androecium differentiation; and fourth, bud formation. Our results showed that all genotypes had increased GPs from sowing to FM differentiation as planting date was delayed while the GPs from FM differentiation to budding varied year by year except the very early variety, 1358. Based on the number of flowers present at the different reproductive stages, the flowers produced from FM differentiation to budding closely approximated the final silique even though the FM differentiated continuously after budding and peaked generally at the middle flowering stage. The ratio of siliques to maximum flower number ranged from 48 to 80%. These results suggest that (1) the period from FM differentiation to budding is vital for effective flower and silique formation although there was no significant correlation between the length of the period and effective flowers and siliques, and (2) the increased number of flowers from budding were generally ineffective. Therefore, maximizing flower numbers prior to budding will improve silique numbers, and reducing FM degeneration should

  4. Alternative additives; Alternative additiver

    Energy Technology Data Exchange (ETDEWEB)

    2007-08-15

    In this project a number of industrial and agricultural waste products have been characterised and evaluated in terms of alkali-getter performance. The intended use is for biomass-fired power stations aiming at reducing corrosion or slagging related problems. The following products have been obtained, characterised and evaluated: 1) Brewery draff 2) Danish de-gassed manure 3) Paper sludge 4) Moulding sand 5) Spent bleaching earth 6) Anorthosite 7) Sand 8) Clay-sludge. Most of the above alternative additive candidates are deemed unsuitable due to insufficient chemical effect and/or expensive requirements for pre-treatment (such as drying and transportation). 3 products were selected for full-scale testing: de-gassed manure, spent bleaching earth and clay slugde. The full scale tests were undertaken at the biomass-fired power stations in Koege, Slagelse and Ensted. Spent bleaching earth (SBE) and clay sludge were the only tested additive candidates that had a proven ability to react with KCl, to thereby reduce Cl-concentrations in deposits, and reduce the deposit flux to superheater tubes. Their performance was shown to nearly as good as commercial additives. De-gassed manure, however, did not evaluate positively due to inhibiting effects of Ca in the manure. Furthermore, de-gassed manure has a high concentration of heavy metals, which imposes a financial burden with regard to proper disposal of the ash by-products. Clay-sludge is a wet clay slurring, and drying and transportation of this product entails substantial costs. Spent bleaching does not require much pre-treatment and is therefore the most promising alternative additive. On the other hand, bleaching earth contains residual plant oil which means that a range of legislation relating to waste combustion comes into play. Not least a waste combustion fee of 330 DKK/tonne. For all alternative (and commercial) additives disposal costs of the increase ash by-products represents a significant cost. This is

  5. The genetic diversity and differentiation of shrimp Fenneropenaeus chinensis in the Yellow Sea revealed by polymorphism in control region of mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    L Wang

    2014-11-01

    Full Text Available Chinese white shrimp Fenneropenaeus chinensis is a commercially important species in northern China and Korea. In the present study, the genetic diversity of five populations collected from Qingdao (QD, Rizhao (RZ of China, and Narodo Island (KN, Taean (KT, Yeongguang (KY of Korea in the Yellow Sea was investigated using the mitochondrial control region (CR. The length of the amplified partial mitochondrial control region (mtCR ranged from 600 to 622 bp, and the sequence variations were distributed among 13 polymorphic sites. The pattern of nucleotide substitution was biased in favour of transitions over transversions in variable sites, including 12 transitions (si, 4 A↔G and 8 T↔C changes and only one was transversion (sv, 1 T↔G changes. Altogether, 24 unique haplotypes were identified from five populations in Yellow Sea. The overall haplotype diversity and nucleotide diversity were 0.368 - 0.421 and 0.052 - 0.079, respectively, and the lowest genetic diversity was found in QD population. There was no differentiation between the two Chinese populations (FST = 0.039. Within the Korean populations, there was a slight differentiation (FST = 0.075, p < 0.05 between KN and KT. The relative bigger differentiation was shown between RZ and KN population (FST = 0.170, p < 0.05. The relative further genetic distance was shown between RZ and KN population as well as between QD and KN population, while the relative closer genetic distance was shown between KT and KY, and between KT and RZ population. The low variability in the mitochondrial control region among F. chinensis in the Yellow Sea indicated the low genetic diversity in comparison to other shrimp species. The results suggested a slight population differentiation among F. chinensis populations. Such information will assist in sustainable use, management, and conservation of the species

  6. sRNA-seq analysis of human embryonic stem cells and definitive endoderm reveals differentially expressed microRNAs and novel IsomiRs with distinct targets.

    Science.gov (United States)

    Hinton, Andrew; Hunter, Shaun E; Afrikanova, Ivka; Jones, G Adam; Lopez, Ana D; Fogel, Gary B; Hayek, Alberto; King, Charles C

    2014-09-01

    MicroRNAs (miRNAs) are noncoding, regulatory RNAs expressed dynamically during differentiation of human embryonic stem cells (hESCs) into defined lineages. Mapping developmental expression of miRNAs during transition from pluripotency to definitive endoderm (DE) should help to elucidate the mechanisms underlying lineage specification and ultimately enhance differentiation protocols. In this report, next generation sequencing was used to build upon our previous analysis of miRNA expression in human hESCs and DE. From millions of sequencing reads, 747 and 734 annotated miRNAs were identified in pluripotent and DE cells, respectively, including 77 differentially expressed miRNAs. Among these, four of the top five upregulated miRNAs were previously undetected in DE. Furthermore, the stem-loop for miR-302a, an important miRNA for both hESCs self-renewal and endoderm specification, produced several highly expressed miRNA species (isomiRs). Overall, isomiRs represented >10% of sequencing reads in >40% of all detected stem-loop arms, suggesting that the impact of these abundant miRNA species may have been overlooked in previous studies. Because of their relative abundance, the role of differential isomiR targeting was studied using the miR-302 cluster as a model system. A miRNA mimetic for miR-302a-5p, but not miR-302a-5p(+3), decreased expression of orthodenticle homeobox 2 (OTX2). Conversely, isomiR 302a-5p(+3) selectively decreased expression of tuberous sclerosis protein 1, but not OTX2, indicating nonoverlapping specificity of miRNA processing variants. Taken together, our characterization of miRNA expression, which includes novel miRNAs and isomiRs, helps establish a foundation for understanding the role of miRNAs in DE formation and selective targeting by isomiRs.

  7. Mountain ridge and sea: Geographic-barrier effects on genetic diversity and differentiation of the Hong Kong newt (Paramesotriton hongkongensis) revealed by AFLP

    OpenAIRE

    Dudgeon, D.; Zhang, YX; He, CZ; Zhang, ZY; Wang, GM

    2011-01-01

    The Hong Kong newt (Paramesotriton hongkongensis) has a restricted distribution in Hong Kong and its adjacent coastal area in China. We employed amplified fragment length polymorphism (AFLP) DNA markers to examine the genetic diversity and differentiation of P. hongkongensis populations (101 individuals) from three streams. Two mainland populations are separated by Tai Mo Shan, the highest peak in Hong Kong. On Hong Kong Island, there is only one population. We investigated whether the marine...

  8. 2D DIGE Does Not Reveal all: A Scotopic Report Suggests Differential Expression of a Single “Calponin Family Member” Protein for Tetany of Sphincters!

    Science.gov (United States)

    Chaudhury, Arun

    2015-01-01

    Using 2D differential gel electrophoresis (DIGE) and mass spectrometry (MS), a recent report by Rattan and Ali (2015) compared proteome expression between tonically contracted sphincteric smooth muscles of the internal anal sphincter (IAS), in comparison to the adjacent rectum [rectal smooth muscles (RSM)] that contracts in a phasic fashion. The study showed the differential expression of a single 23 kDa protein SM22, which was 1.87 fold, overexpressed in RSM in comparison to IAS. Earlier studies have shown differences in expression of different proteins like Rho-associated protein kinase II, myosin light chain kinase, myosin phosphatase, and protein kinase C between IAS and RSM. The currently employed methods, despite its high-throughput potential, failed to identify these well-characterized differences between phasic and tonic muscles. This calls into question the fidelity and validatory potential of the otherwise powerful technology of 2D DIGE/MS. These discrepancies, when redressed in future studies, will evolve this recent report as an important baseline study of “sphincter proteome.” Proteomics techniques are currently underutilized in examining pathophysiology of hypertensive/hypotensive disorders involving gastrointestinal sphincters, including achalasia, gastroesophageal reflux disease (GERD), spastic pylorus, seen during diabetes or chronic chemotherapy, intestinal pseudo-obstruction, and recto-anal incontinence. Global proteome mapping may provide instant snapshot of the complete repertoire of differential proteins, thus expediting to identify the molecular pathology of gastrointestinal motility disorders currently labeled “idiopathic” and facilitating practice of precision medicine. PMID:26151053

  9. Visualization by BiFC of different C/EBPβ dimers and their interaction with HP1α reveals a differential subnuclear distribution of complexes in living cells

    International Nuclear Information System (INIS)

    How the co-ordinated events of gene activation and silencing during cellular differentiation are influenced by spatial organization of the cell nucleus is still poorly understood. Little is known about the molecular mechanisms controlling subnuclear distribution of transcription factors, and their interplay with nuclear proteins that shape chromatin structure. Here we show that C/EBPβ not only associates with pericentromeric heterochromatin but also interacts with the nucleoskeleton upon induction of adipocyte differentiation of 3T3-L1 cells. Different C/EBPβ dimers localize in different nuclear domains. Using BiFC in living cells, we show that LAP (Liver Activating Protein) homodimers localize in euchromatin and heterochromatin. In contrast, LIP (Liver Inhibitory Protein) homodimers localize exclusively in heterochromatin. Importantly, their differential subnuclear distribution mirrors the site for interaction with HP1α. HP1α inhibits LAP transcriptional capacity and occupies the promoter of the C/EBPβ-dependent gene c/ebpα in 3T3-L1 preadipocytes. When adipogenesis is induced, HP1α binding decreases from c/ebpα promoter, allowing transcription. Thus, the equilibrium among different pools of C/EBPβ associated with chromatin or nucleoskeleton, and dynamic changes in their interaction with HP1α, play key roles in the regulation of C/EBP target genes during adipogenesis.

  10. Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes

    Directory of Open Access Journals (Sweden)

    Lee Norman H

    2006-05-01

    Full Text Available Abstract Background The autism spectrum encompasses a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills, and are associated with odd, stereotyped, repetitive behavior and restricted interests. To date, diagnosis of these neurologically based disorders relies predominantly upon behavioral observations often prompted by delayed speech or aberrant behavior, and there are no known genes that can serve as definitive biomarkers for the disorders. Results Here we demonstrate, for the first time, that lymphoblastoid cell lines from monozygotic twins discordant with respect to severity of autism and/or language impairment exhibit differential gene expression patterns on DNA microarrays. Furthermore, we show that genes important to the development, structure, and/or function of the nervous system are among the most differentially expressed genes, and that many of these genes map closely in silico to chromosomal regions containing previously reported autism candidate genes or quantitative trait loci. Conclusion Our results provide evidence that novel candidate genes for autism may be differentially expressed in lymphoid cell lines from individuals with autism spectrum disorders. This finding further suggests the possibility of developing a molecular screen for autism based on expressed biomarkers in peripheral blood lymphocytes, an easily accessible tissue. In addition, gene networks are identified that may play a role in the pathophysiology of autism.

  11. Geophysical variables and behavior: LXXI. Differential contribution of geomagnetic activity to paranormal experiences concerning death and crisis: an alternative to the ESP hypothesis.

    Science.gov (United States)

    Persinger, M A

    1993-04-01

    A total of 621 reports (experienced over an approximately 70-year period) of putative psi experiences concerning death or crisis were differentiated according to traditional labels: telepathic, precognitive, and postmortem phenomena. The 232 telepathic experiences occurred during 24-hour periods in which the global geomagnetic activity was significantly less (quieter) than during the days before or after the experiences; this relationship was not displayed by the 186 precognitive or 203 postmortem cases. Key day differences in geomagnetic activity for the three classes of experiences were equivalent to a correlation of about 0.35. Although content analysis suggests that nocturnal psi experiences and temporal lobe epilepsy may share a similar mechanism, different classes of subjective psi experiences may not be affected by the same stimuli. PMID:8483667

  12. Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis.

    Directory of Open Access Journals (Sweden)

    Rongyan Fan

    Full Text Available The medicinal plant Xanthium strumarium L. (X. strumarium is covered with glandular trichomes, which are the sites for synthesizing pharmacologically active terpenoids such as xanthatin. MicroRNAs (miRNAs are a class of 21-24 nucleotide (nt non-coding RNAs, most of which are identified as regulators of plant growth development. Identification of miRNAs involved in the biosynthesis of plant secondary metabolites remains limited. In this study, high-throughput Illumina sequencing, combined with target gene prediction, was performed to discover novel and conserved miRNAs with potential roles in regulating terpenoid biosynthesis in X. strumarium glandular trichomes. Two small RNA libraries from leaves and glandular trichomes of X. strumarium were established. In total, 1,185 conserved miRNAs and 37 novel miRNAs were identified, with 494 conserved miRNAs and 18 novel miRNAs being differentially expressed between the two tissue sources. Based on the X. strumarium transcriptome data that we recently constructed, 3,307 annotated mRNA transcripts were identified as putative targets of the differentially expressed miRNAs. KEGG (Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that some of the differentially expressed miRNAs, including miR6435, miR5021 and miR1134, might be involved in terpenoid biosynthesis in the X. strumarium glandular trichomes. This study provides the first comprehensive analysis of miRNAs in X. strumarium, which forms the basis for further understanding of miRNA-based regulation on terpenoid biosynthesis.

  13. Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis.

    Science.gov (United States)

    Fan, Rongyan; Li, Yuanjun; Li, Changfu; Zhang, Yansheng

    2015-01-01

    The medicinal plant Xanthium strumarium L. (X. strumarium) is covered with glandular trichomes, which are the sites for synthesizing pharmacologically active terpenoids such as xanthatin. MicroRNAs (miRNAs) are a class of 21-24 nucleotide (nt) non-coding RNAs, most of which are identified as regulators of plant growth development. Identification of miRNAs involved in the biosynthesis of plant secondary metabolites remains limited. In this study, high-throughput Illumina sequencing, combined with target gene prediction, was performed to discover novel and conserved miRNAs with potential roles in regulating terpenoid biosynthesis in X. strumarium glandular trichomes. Two small RNA libraries from leaves and glandular trichomes of X. strumarium were established. In total, 1,185 conserved miRNAs and 37 novel miRNAs were identified, with 494 conserved miRNAs and 18 novel miRNAs being differentially expressed between the two tissue sources. Based on the X. strumarium transcriptome data that we recently constructed, 3,307 annotated mRNA transcripts were identified as putative targets of the differentially expressed miRNAs. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis suggested that some of the differentially expressed miRNAs, including miR6435, miR5021 and miR1134, might be involved in terpenoid biosynthesis in the X. strumarium glandular trichomes. This study provides the first comprehensive analysis of miRNAs in X. strumarium, which forms the basis for further understanding of miRNA-based regulation on terpenoid biosynthesis. PMID:26406988

  14. Comparative Analyses of SUV420H1 Isoforms and SUV420H2 Reveal Differences in Their Cellular Localization and Effects on Myogenic Differentiation

    OpenAIRE

    Tsang, Leanna W. K.; Hu, Ninghe; Underhill, D. Alan

    2010-01-01

    Background Methylation of histone H4 on lysine 20 plays critical roles in chromatin structure and function via mono- (H4K20me1), di- (H4K20me2), and trimethyl (H4K20me3) derivatives. In previous analyses of histone methylation dynamics in mid-gestation mouse embryos, we documented marked changes in H4K20 methylation during cell differentiation. These changes were particularly robust during myogenesis, both in vivo and in cell culture, where we observed a transition from H4K20me1 to H4K20me3. ...

  15. 2D DIGE does not reveal all: A scotopic report suggests differential expression of a single Calponin family member protein for tetany of sphincters!

    Directory of Open Access Journals (Sweden)

    Arun eChaudhury

    2015-06-01

    Full Text Available Using 2D differential gel electrophoresis (DIGE and MS (mass spectrometry, a recent report by Rattan and Ali (2015 compared proteome expression between tonically contracted sphincteric smooth muscles of the internal anal sphincter (IAS, in comparison to the adjacent rectum (RSM, rectal smooth muscles that contracts in a phasic fashion. The study showed the differential expression of a single 23 kDa protein SM22, which was 1.87 fold overexpressed in RSM in comparison to IAS. Earlier studies have shown differences in expression of different proteins like Rho-associated protein kinase II (ROCKII, myosin light chain kinase (MLCK, myosin phosphatase (MYP and protein kinase C (PKC between IAS and RSM. The currently employed methods, despite its high-throughput potential, failed to identify these well-characterized differences between phasic and tonic muscles. This calls into question the fidelity and validatory potential of the otherwise powerful technology of 2D DIGE/MS. These discrepancies, when redressed in future studies, will evolve this recent report as an important baseline study of sphincter proteome. Proteomics techniques are currently underutilized in examining pathophysiology of hypertensive/hypotensive disorders

  16. Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California.

    Science.gov (United States)

    Hull, Joshua M; Keane, John J; Savage, Wesley K; Godwin, Steven A; Shafer, Jo Ann; Jepsen, Eric P; Gerhardt, Rick; Stermer, Chris; Ernest, Holly B

    2010-07-01

    Investigations of regional genetic differentiation are essential for describing phylogeographic patterns and informing management efforts for species of conservation concern. In this context, we investigated genetic diversity and evolutionary relationships among great gray owl (Strix nebulosa) populations in western North America, which includes an allopatric range in the southern Sierra Nevada in California. Based on a total dataset consisting of 30 nuclear microsatellite DNA loci and 1938-base pairs of mitochondrial DNA, we found that Pacific Northwest sampling groups were recovered by frequency and Bayesian analyses of microsatellite data and each population sampled, except for western Canada, showed evidence of recent population bottlenecks and low effective sizes. Bayesian and maximum likelihood phylogenetic analyses of sequence data indicated that the allopatric Sierra Nevada population is also a distinct lineage with respect to the larger species range in North America; we suggest a subspecies designation for this lineage should be considered (Strix nebulosa yosemitensis). Our study underscores the importance of phylogeographic studies for identifying lineages of conservation concern, as well as the important role of Pleistocene glaciation events in driving genetic differentiation of avian fauna. PMID:20193768

  17. Genome-wide study reveals an important role of spontaneous autoimmunity, cardiomyocyte differentiation defect and antiangiogenic activities in gender-specific gene expression in Keshan disease

    Institute of Scientific and Technical Information of China (English)

    He Shulan; Tan Wuhong; Wang Sen; Wu Cuiyan; Wang Pan; Wang Bin; Su Xiaohui

    2014-01-01

    Background Keshan disease (KD) is an endemic cardiomyopathy in China.The etiology of KD is still under debate and there is no effective approach to preventing and curing this disease.Young women of child-bearing age are the most frequent victims in rural areas.The aim of this study was to determine the differences between molecular pathogenic mechanisms in male and female KD sufferers.Methods We extracted RNA from the peripheral blood mononuclear cells of KD patients (12 women and 4 men) and controls (12 women and 4 men).Then the isolated RNA was amplified,labeled and hybridized to Agilent human 4×44k whole genome microarrays.Gene expression was examined using oligonucleotide microarray analysis.A quantitative polymerase chain reaction assay was also performed to validate our microarray results.Results Among the genes differentially expressed in female KD patients we identified:HLA-DOA,HLA-DRA,and HLA-DQA1 associated with spontaneous autoimmunity; BMP5 and BMP7,involved in cardiomyocyte differentiation defect; and ADAMTS 8,CCL23,and TNFSF15,implicated in anti-angiogenic activities.These genes are involved in the canonical pathways and networks recognized for the female KD sufferers and might be related to the pathogenic mechanism of KD.Conclusion Our results might help to explain the higher susceptibility of women to this disease.

  18. Characterization of temperature-sensitive mutants reveals a role for receptor-like kinase SCRAMBLED/STRUBBELIG in coordinating cell proliferation and differentiation during Arabidopsis leaf development.

    Science.gov (United States)

    Lin, Lin; Zhong, Si-Hui; Cui, Xiao-Feng; Li, Jianming; He, Zu-Hua

    2012-12-01

    The balance between cell proliferation and cell differentiation is essential for leaf patterning. However, identification of the factors coordinating leaf patterning and cell growth behavior is challenging. Here, we characterized a temperature-sensitive Arabidopsis mutant with leaf blade and venation defects. We mapped the mutation to the sub-2 allele of the SCRAMBLED/STRUBBELIG (SCM/SUB) receptor-like kinase gene whose functions in leaf development have not been demonstrated. The sub-2 mutant displayed impaired blade development, asymmetric leaf shape and altered venation patterning under high ambient temperature (30°C), but these defects were less pronounced at normal growth temperature (22°C). Loss of SCM/SUB function results in reduced cell proliferation and abnormal cell expansion, as well as altered auxin patterning. SCM/SUB is initially expressed throughout leaf primordia and becomes restricted to the vascular cells, coinciding with its roles in early leaf patterning and venation formation. Furthermore, constitutive expression of the SCM/SUB gene also restricts organ growth by inhibiting the transition from cell proliferation to expansion. We propose the existence of a SCM/SUB-mediated developmental stage-specific signal for leaf patterning, and highlight the importance of the balance between cell proliferation and differentiation for leaf morphogenesis.

  19. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

    Directory of Open Access Journals (Sweden)

    Sha Ky

    2010-08-01

    Full Text Available Abstract Background Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underlying genomic DNA, the epigenome influences the cell's transcriptome and ultimately its function. Existing genomic methods for analyzing cell-type-specific changes in chromatin generally involve two elements: (i a source for purified cells (or nuclei of distinct types, and (ii a specific treatment that partitions or degrades chromatin by activity or structural features. For many cell types of great interest, such assays are limited by our inability to isolate the relevant cell populations in an organism or complex tissue containing an intertwined mixture of other cells. This limitation has confined available knowledge of chromatin dynamics to a narrow range of biological systems (cell types that can be sorted/separated/dissected in large numbers and tissue culture models or to amalgamations of diverse cell types (tissue chunks, whole organisms. Results Transgene-driven expression of DNA/chromatin modifying enzymes provides one opportunity to query chromatin structures in expression-defined cell subsets. In this work we combine in vivo expression of a bacterial DNA adenine methyltransferase (DAM with high throughput sequencing to sample tissue-specific chromatin accessibility on a genome-wide scale. We have applied the method (DALEC: Direct Asymmetric Ligation End Capture towards mapping a cell-type-specific view of genome accessibility as a function of differentiated state. Taking advantage of C. elegans strains expressing the DAM enzyme in diverse tissues (body wall muscle, gut, and hypodermis, our efforts yield a genome-wide dataset measuring chromatin accessibility at each of 538,000 DAM target sites in the C. elegans (diploid genome. Conclusions Validating the DALEC mapping results, we observe a strong association

  20. Genome-wide analysis of the fasciclin-like arabinogalactan protein gene family reveals differential expression patterns, localization and salt stress response in Populus

    Directory of Open Access Journals (Sweden)

    Lina eZang

    2015-12-01

    Full Text Available Fasciclin-like arabinogalactan proteins (FLAs are a subclass of arabinogalactan proteins (AGPs involved in plant growth, development and response to abiotic stress. Although many studies have been performed to identify molecular functions of individual family members, little information is available on genome-wide identification and characterization of FLAs in the genus Populus. Based on genome-wide analysis, we have identified 35 Populus FLAs which were distributed on 16 chromosomes and phylogenetically clustered into four major groups. Gene structure and motif composition were relatively conserved in each group. All the members contained N-terminal signal peptide, 23 of which included predicted glycosylphosphatidylinositol (GPI modification sites and were anchored to plasma membranes. Subcellular localization analysis showed that PtrFLA2/20/26 were localized in cell membrane and cytoplasm of protoplasts from Populus stem-differentiating xylem. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolutionary period which greatly maintained the function of this family. The expression profiles showed that 32 PtrFLAs were differentially expressed in four tissues at four seasons based on publicly available microarray data. 18 FLAs were further verified with qRT-PCR in different tissues, which indicated that PtrFLA1/2/3/7/11/12/20/21/22/24/26/30 were significantly expressed in male and female flowers, suggesting close correlations with the reproductive development. In addition, PtrFLA1/9/10/11/17/21/23/24/26/28 were highly expressed in the stems and differentiating xylem, which may be involved in stem development. To determine salt response of FLAs, qRT-PCR was performed to analyze the expression of 18 genes under salinity stress across two time points. Results demonstrated that all the 18 FLAs were expressed in root tissues; especially, PtrFLA2/12/20/21/24/30 were significantly induced at different time

  1. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

    Directory of Open Access Journals (Sweden)

    Yu Myeong-Hee

    2010-03-01

    Full Text Available Abstract Background Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. Methods Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. Results A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD, and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002. BTD levels were lowered in all cancer grades (I-IV except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940 and progesterone receptor status (p = 0.440 were not associated with the plasma BTD levels. Conclusions Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer.

  2. Monoclonal antibodies to murine thrombospondin-1 and thrombospondin-2 reveal differential expression patterns in cancer and low antigen expression in normal tissues

    Energy Technology Data Exchange (ETDEWEB)

    Bujak, Emil [Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 2, CH-8093 Zurich (Switzerland); Pretto, Francesca; Ritz, Danilo; Gualandi, Laura; Wulhfard, Sarah [Philochem AG, Libernstrasse 3, CH-8112 Otelfingen (Switzerland); Neri, Dario, E-mail: neri@pharma.ethz.ch [Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 2, CH-8093 Zurich (Switzerland)

    2014-09-10

    There is a considerable interest for the discovery and characterization of tumor-associated antigens, which may facilitate antibody-based pharmacodelivery strategies. Thrombospondin-1 and thrombospondin-2 are homologous secreted proteins, which have previously been reported to be overexpressed during remodeling typical for wound healing and tumor progression and to possibly play a functional role in cell proliferation, migration and apoptosis. To our knowledge, a complete immunohistochemical characterization of thrombospondins levels in normal rodent tissues has not been reported so far. Using antibody phage technology, we have generated and characterized monoclonal antibodies specific to murine thrombospondin-1 and thrombospondin-2, two antigens which share 62% aminoacid identity. An immunofluorescence analysis revealed that both antigens are virtually undetectable in normal mouse tissues, except for a weak staining of heart tissue by antibodies specific to thrombospondin-1. The analysis also showed that thrombospondin-1 was strongly expressed in 5/7 human tumors xenografted in nude mice, while it was only barely detectable in 3/8 murine tumors grafted in immunocompetent mice. By contrast, a high-affinity antibody to thrombospondin-2 revealed a much lower level of expression of this antigen in cancer specimens. Our analysis resolves ambiguities related to conflicting reports on thrombosponding expression in health and disease. Based on our findings, thrombospondin-1 (and not thrombospondin-2) may be considered as a target for antibody-based pharmacodelivery strategies, in consideration of its low expression in normal tissues and its upregulation in cancer. - Highlights: • High affinity monoclonal antibodies to murine and human TSP1 and 2 were raised. • Both antigens are virtually undetectable in normal mouse tissues. • Strong positivity of human tumor xenografts for TSP1 was detected. • Study revealed much lower level of TSP2 expression in cancer specimens

  3. Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.

    Directory of Open Access Journals (Sweden)

    Yanan eYang

    2015-09-01

    Full Text Available Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well understood thus far. ‘Starkrimson’ (Pyrus communis L., an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red /green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11-71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2,230 differentially expressed genes (DEGs were identified in red fruit. Gene Ontology (GO terms were defined for 4,886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned ‘Starkrimson’, and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable

  4. Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose.

    Science.gov (United States)

    Schabort, Du Toit W P; Letebele, Precious K; Steyn, Laurinda; Kilian, Stephanus G; du Preez, James C

    2016-01-01

    We investigated the transcriptomic response of a new strain of the yeast Kluyveromyces marxianus, in glucose and xylose media using RNA-seq. The data were explored in a number of innovative ways using a variety of networks types, pathway maps, enrichment statistics, reporter metabolites and a flux simulation model, revealing different aspects of the genome-scale response in an integrative systems biology manner. The importance of the subcellular localisation in the transcriptomic response is emphasised here, revealing new insights. As was previously reported by others using a rich medium, we show that peroxisomal fatty acid catabolism was dramatically up-regulated in a defined xylose mineral medium without fatty acids, along with mechanisms to activate fatty acids and transfer products of β-oxidation to the mitochondria. Notably, we observed a strong up-regulation of the 2-methylcitrate pathway, supporting capacity for odd-chain fatty acid catabolism. Next we asked which pathways would respond to the additional requirement for NADPH for xylose utilisation, and rationalised the unexpected results using simulations with Flux Balance Analysis. On a fundamental level, we investigated the contribution of the hierarchical and metabolic regulation levels to the regulation of metabolic fluxes. Metabolic regulation analysis suggested that genetic level regulation plays a major role in regulating metabolic fluxes in adaptation to xylose, even for the high capacity reactions, which is unexpected. In addition, isozyme switching may play an important role in re-routing of metabolic fluxes in subcellular compartments in K. marxianus. PMID:27315089

  5. Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose.

    Directory of Open Access Journals (Sweden)

    Du Toit W P Schabort

    Full Text Available We investigated the transcriptomic response of a new strain of the yeast Kluyveromyces marxianus, in glucose and xylose media using RNA-seq. The data were explored in a number of innovative ways using a variety of networks types, pathway maps, enrichment statistics, reporter metabolites and a flux simulation model, revealing different aspects of the genome-scale response in an integrative systems biology manner. The importance of the subcellular localisation in the transcriptomic response is emphasised here, revealing new insights. As was previously reported by others using a rich medium, we show that peroxisomal fatty acid catabolism was dramatically up-regulated in a defined xylose mineral medium without fatty acids, along with mechanisms to activate fatty acids and transfer products of β-oxidation to the mitochondria. Notably, we observed a strong up-regulation of the 2-methylcitrate pathway, supporting capacity for odd-chain fatty acid catabolism. Next we asked which pathways would respond to the additional requirement for NADPH for xylose utilisation, and rationalised the unexpected results using simulations with Flux Balance Analysis. On a fundamental level, we investigated the contribution of the hierarchical and metabolic regulation levels to the regulation of metabolic fluxes. Metabolic regulation analysis suggested that genetic level regulation plays a major role in regulating metabolic fluxes in adaptation to xylose, even for the high capacity reactions, which is unexpected. In addition, isozyme switching may play an important role in re-routing of metabolic fluxes in subcellular compartments in K. marxianus.

  6. Differential Expression between Human Dermal Papilla Cells from Balding and Non-Balding Scalps Reveals New Candidate Genes for Androgenetic Alopecia.

    Science.gov (United States)

    Chew, Elaine G Y; Tan, Joanna H J; Bahta, Adiam W; Ho, Bryan S-Y; Liu, Xingliang; Lim, Tze Chiun; Sia, Yee Yen; Bigliardi, Paul L; Heilmann, Stefanie; Wan, Andrew C A; Nöthen, Markus M; Philpott, Michael P; Hillmer, Axel M

    2016-08-01

    Androgenetic alopecia (AGA) is a common heritable and androgen-dependent hair loss condition in men. Twelve genetic risk loci are known to date, but it is unclear which genes at these loci are relevant for AGA. Dermal papilla cells (DPCs) located in the hair bulb are the main site of androgen activity in the hair follicle. Widely used monolayer-cultured primary DPCs in hair-related studies often lack dermal papilla characteristics. In contrast, immortalized DPCs have high resemblance to intact dermal papilla. We derived immortalized human DPC lines from balding (BAB) and non-balding (BAN) scalp. Both BAB and BAN retained high proportions of dermal papilla signature gene and versican protein expression. We performed expression analysis of BAB and BAN and annotated AGA risk loci with differentially expressed genes. We found evidence for AR but not EDA2R as the candidate gene at the AGA risk locus on chromosome X. Further, our data suggest TWIST1 (twist family basic helix-loop-helix transcription factor 1) and SSPN (sarcospan) to be the functionally relevant AGA genes at the 7p21.1 and 12p12.1 risk loci, respectively. Down-regulated genes in BAB compared to BAN were highly enriched for vasculature-related genes, suggesting that deficiency of DPC from balding scalps in fostering vascularization around the hair follicle may contribute to the development of AGA. PMID:27060448

  7. Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

    Science.gov (United States)

    Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

    2016-01-01

    Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression. PMID:26614689

  8. Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

    Science.gov (United States)

    Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

    2016-01-01

    Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression.

  9. Comparative proteomics reveals highly and differentially expressed proteins in field-collected and laboratory-cultured blooming cells of the diatom Skeletonema costatum.

    Science.gov (United States)

    Zhang, Hao; Wang, Da-Zhi; Xie, Zhang-Xian; Zhang, Shu-Fei; Wang, Ming-Hua; Lin, Lin

    2015-10-01

    Diatoms are a major phytoplankton group causing extensive blooms in the ocean. However, little is known about the intracellular biological processes occurring during the blooming period. This study compared the protein profiles of field-collected and laboratory-cultured blooming cells of Skeletonema costatum, and identified highly and differentially expressed proteins using the shotgun proteomic approach. A total of 1372 proteins were confidently identified with two or more peptides. Among them, 222 and 311 proteins were unique to the laboratory and field samples respectively. Proteins involved in photosynthesis, translation, nucleosome assembly, carbohydrate and energy metabolism dominated the protein profiles in both samples. However, different features of specific proteins were also found: proteins participated in light harvesting, photosynthetic pigment biosynthesis, photoprotection, cell division and redox homeostasis were highly detected in the field sample, whereas proteins involved in translation, amino acid and protein metabolic processes, and nitrogen and carbon assimilation presented high detection rates in the laboratory sample. ATP synthase cf1 subunit beta and light harvest complex protein were the most abundant protein in the laboratory and field samples respectively. These results indicated that S. costatum had evolved adaptive mechanisms to the changing environment, and integrating field and laboratory proteomic data should provide comprehensive understanding of bloom mechanisms. PMID:26014042

  10. Proteomic screening of glucose-responsive and glucose non-reponsive MIN-6 beta cells reveals differential expression of protein involved in protein folding, secretion and oxidative stress

    DEFF Research Database (Denmark)

    Dowling, P.; O´Driscoll, L.; O´Sullivan, F.;

    2006-01-01

    The glucose-sensitive insulin-secretion (GSIS) phenotype is relatively unstable in long-term culture of beta cells. The purpose of this study was to investigate relative changes in the proteome between glucose-responsive (low passage) and glucose non-responsive (high passage) murine MIN-6...... pancreatic beta cells. The 2D-DIGE and subsequent DeCyder analysis detected 3351 protein spots in the pH range of 4-7. Comparing MIN-6(H) to MIN-6(L) and using a threshold of 1.2-fold, the number of proteins with a decrease in expression level was 152 (4.5%), similar was 3140 (93.7%) and increased 59 (1.......8%). From the differentially expressed proteins identified in this study, groups of proteins associated with the endoplasmic reticulum (ER) and proteins involved in oxidative stress were found to be significantly decreased in the high-passage (H passage) cells. These proteins included endoplasmic reticulum...

  11. Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile

    Science.gov (United States)

    González, Jorge; Fuentes, Glenda; Alarcón, Diego; Ruiz, Eduardo

    2016-01-01

    Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation. Nothofagus dombeyi (Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories in Nothofagus dombeyi requires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species. PMID:27446942

  12. Alternative Splice in Alternative Lice.

    Science.gov (United States)

    Tovar-Corona, Jaime M; Castillo-Morales, Atahualpa; Chen, Lu; Olds, Brett P; Clark, John M; Reynolds, Stuart E; Pittendrigh, Barry R; Feil, Edward J; Urrutia, Araxi O

    2015-10-01

    Genomic and transcriptomics analyses have revealed human head and body lice to be almost genetically identical; although con-specific, they nevertheless occupy distinct ecological niches and have differing feeding patterns. Most importantly, while head lice are not known to be vector competent, body lice can transmit three serious bacterial diseases; epidemictyphus, trench fever, and relapsing fever. In order to gain insights into the molecular bases for these differences, we analyzed alternative splicing (AS) using next-generation sequencing data for one strain of head lice and one strain of body lice. We identified a total of 3,598 AS events which were head or body lice specific. Exon skipping AS events were overrepresented among both head and body lice, whereas intron retention events were underrepresented in both. However, both the enrichment of exon skipping and the underrepresentation of intron retention are significantly stronger in body lice compared with head lice. Genes containing body louse-specific AS events were found to be significantly enriched for functions associated with development of the nervous system, salivary gland, trachea, and ovarian follicle cells, as well as regulation of transcription. In contrast, no functional categories were overrepresented among genes with head louse-specific AS events. Together, our results constitute the first evidence for transcript pool differences in head and body lice, providing insights into molecular adaptations that enabled human lice to adapt to clothing, and representing a powerful illustration of the pivotal role AS can play in functional adaptation. PMID:26169943

  13. Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica)

    Institute of Scientific and Technical Information of China (English)

    CAI Xingxing; LIU Jing; QIU Yinqiu; ZHAO Wei; SONG Zhiping; LU Baorong

    2007-01-01

    DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers.To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species,we studied 49 Indica,43 Japonica,and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs.Results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%.The scatter plotting data of the principal component analysis (PCA) indicated that:(i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties,in addition to revealing their genetic differentiation;(ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties;and (iii)the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying lndica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly in terms of the Indica-Japonica differentiation.

  14. Genetic diversity of and differentiation among five populations of blunt snout bream (Megalobrama amblycephala revealed by SRAP markers: implications for conservation and management.

    Directory of Open Access Journals (Sweden)

    Wei Ji

    Full Text Available The blunt snout bream (Megalobrama amblycephala is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian and one genetic strain ('Pujiang No. 1' of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h and Shannon's information index (I values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>'Pujiang No. 1'>Yuni Lake. Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations, Nanxian and 'Pujiang No. 1' (cultured population and genetically selected strain, and Yuni Lake (natural population. Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA, with more genetic divergence existing among populations (55.49%, than within populations (44.51%. This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish.

  15. Differential cortical laminar structure revealed by NeuN immunostaining and myeloarchitecture between sulcal and gyral regions independent of sexual dimorphisms in the ferret cerebrum.

    Science.gov (United States)

    Horiuchi-Hirose, Miwa; Sawada, Kazuhiko

    2016-08-01

    The purpose of this study was to quantitatively clarify differences in laminar structure and myeloarchitecture of sulcal and gyral regions of the cerebral cortex of ferrets. Histological sections of cerebrum from male and female ferrets at postnatal day 90 were made at the coronal plane, and were immunostained with anti-NeuN or anti-myelin basic protein (MBP). Thickness was estimated in the entire depth or three strata, that is, layer I, outer (layers II-III) and inner (layers IV-VI) strata of the neocortex in representative five sulcal and seven gyral regions. As with the entire cortical depth, outer and inner strata were significantly thinner in the sulcal bottoms than in the gyral crowns, whereas layer I had about twofold greater thickness in the sulcal bottoms. However, thicknesses of the entire cortical depth and each cortical stratum were not statistically different among five sulcal regions or seven gyral regions examined. By MBP immunostaining, myelin fibers ran tangentially through the superficial regions of layer I in gyral crowns. Those fibers were relatively denser in gyri of frontal and temporal regions, and relatively sparse in gyri of parietal and occipital regions, although their density in any gyri was not different between sexes. These results show a differential laminar structure and myeloarchitecture between the sulcal and gyral regions of the ferret cerebral cortex present in both sexes. Myelination of layer I tangential fibers varied among primary gyri and was weaker in phylogenetically higher-order cortical gyri. Anat Rec, 299:1003-1011, 2016. © 2016 Wiley Periodicals, Inc. PMID:27144367

  16. Transcriptomic analysis reveals differential gene expressions for cell growth and functional secondary metabolites in induced autotetraploid of Chinese woad (Isatis indigotica Fort..

    Directory of Open Access Journals (Sweden)

    Yingying Zhou

    Full Text Available The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14 is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53% unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%(2x vs 4x, 693(0.98%(2x vs 3x, 1045(1.48%(3x vs 4x unigenes were detected to differentially expressed genes (DEGs, including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin, cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites.

  17. Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates

    Directory of Open Access Journals (Sweden)

    Wang Jinkai

    2012-08-01

    Full Text Available Abstract Background The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role of DNA methylation on brain evolution is largely unknown. Results To test if DNA methylation has contributed to the evolution of human brain, with the use of MeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis to identify differentially methylated regions (DMRs in the brain between humans and rhesus macaques. We first identified a total of 150 candidate DMRs by the MeDIP-Chip method, among which 4 DMRs were confirmed by the MassARRAY analysis. All 4 DMRs are within or close to the CpG islands, and a MIR3 repeat element was identified in one DMR, but no repeat sequence was observed in the other 3 DMRs. For the 4 DMR genes, their proteins tend to be conserved and two genes have neural related functions. Bisulfite sequencing and phylogenetic comparison among human, chimpanzee, rhesus macaque and rat suggested several regions of lineage specific DNA methylation, including a human specific hypomethylated region in the promoter of K6IRS2 gene. Conclusions Our study provides a new angle of studying human brain evolution and understanding the evolutionary role of DNA methylation in the central nervous system. The results suggest that the patterns of DNA methylation in the brain are in general similar between humans and non-human primates, and only a few DMRs were identified.

  18. Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins

    Indian Academy of Sciences (India)

    VISHWA JYOTI BARUAH; SIDDHARTHA SANKAR SATAPATHY; BHESH RAJ POWDEL; ROCKTOTPAL KONWARH; ALAK KUMAR BURAGOHAIN; SUVENDRA KUMAR RAY

    2016-09-01

    The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G+C% of the HEG was found to be less in comparison to the genome G+ C% in Crenarchaea, whereas reverse was the case in Euryarchaea. The preponderance of U/A ending codons that code for HEG in Crenarchaea was in sharp contrast to the C/G ended ones in Euryarchaea. The analysis revealed prevalence of U-ending codons even within the WWY (nucleotide ambiguity code) families in Crenarchaea vis-à-vis Euryarchaea, bacteria and Eukarya. No plausible interpretation of the observed disparity could be made either in the context of tRNA gene composition or genome G +C%. The results in this study attested that the preferential biasness for codons in HEG of Crenarchaea might be different from Euryarchaea. The main highlights are (i) varied CUB in the HEG and in the whole genomes in Euryarchaea and Crenarchaea. (ii) Crenarchaea was found to have some unusual optimal codons (OCs) compared to other organisms. (iii) G+ C% (and GC 3) of the HEG were different from the genome G + C% in the two phyla. (iv) Genome G + C% and tRNAgene number failed to explain CUB in Crenarchaea. (v) Translational selection is possibly responsible for A + T rich OCs in Crenarchaea.

  19. Characterization and functional analysis of eugenol O-methyltransferase gene reveal metabolite shifts, chemotype specific differential expression and developmental regulation in Ocimum tenuiflorum L.

    Science.gov (United States)

    Renu, Indu Kumari; Haque, Inamul; Kumar, Manish; Poddar, Raju; Bandopadhyay, Rajib; Rai, Amit; Mukhopadhyay, Kunal

    2014-03-01

    Eugenol-O-methyltransferase (EOMT) catalyzes the conversion of eugenol to methyleugenol in one of the final steps of phenylpropanoid pathway. There are no comprehensive reports on comparative EOMT gene expression and developmental stage specific accumulation of phenylpropenes in Ocimum tenuiflorum. Seven chemotypes, rich in eugenol and methyleugenol, were selected by assessment of volatile metabolites through multivariate data analysis. Isoeugenol accumulated in higher levels during juvenile stage (36.86 ng g(-1)), but reduced sharply during preflowering (8.04 ng g(-1)), flowering (2.29 ng g(-1)) and postflowering stages (0.17 ng g(-1)), whereas methyleugenol content gradually increased from juvenile (12.25 ng g(-1)) up to preflowering (16.35 ng g(-1)) and then decreased at flowering (7.13 ng g(-1)) and post flowering (5.95 ng g(-1)) from fresh tissue. Extreme variations of free intracellular and alkali hydrolysable cell wall released phenylpropanoid compounds were observed at different developmental stages. Analyses of EOMT genomic and cDNA sequences revealed a 843 bp open reading frame and the presence of a 90 bp intron. The translated proteins had eight catalytic domains, the major two being dimerisation superfamily and methyltransferase_2 superfamily. A validated 3D structure of EOMT protein was also determined. The chemotype Ot7 had a reduced reading frame that lacked both dimerisation domains and one of the two protein-kinase-phosphorylation sites; this was also reflected in reduced accumulation of methyleugenol compared to other chemotypes. EOMT transcripts showed enhanced expression in juvenile stage that increased further during preflowering but decreased at flowering and further at postflowering. The expression patterns may possibly be compared and correlated to the amounts of eugenol/isoeugenol and methyleugenol in different developmental stages of all chemotypes.

  20. Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium.

    Directory of Open Access Journals (Sweden)

    Fengxi Yang

    Full Text Available Cymbidium ensifolium belongs to the genus Cymbidium of the orchid family. Owing to its spectacular flower morphology, C. ensifolium has considerable ecological and cultural value. However, limited genetic data is available for this non-model plant, and the molecular mechanism underlying floral organ identity is still poorly understood. In this study, we characterize the floral transcriptome of C. ensifolium and present, for the first time, extensive sequence and transcript abundance data of individual floral organs. After sequencing, over 10 Gb clean sequence data were generated and assembled into 111,892 unigenes with an average length of 932.03 base pairs, including 1,227 clusters and 110,665 singletons. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group terms, the Kyoto Encyclopedia of Genes and Genomes, and the plant transcription factor database. From these annotations, 131 flowering-associated unigenes, 61 CONSTANS-LIKE (COL unigenes and 90 floral homeotic genes were identified. In addition, four digital gene expression libraries were constructed for the sepal, petal, labellum and gynostemium, and 1,058 genes corresponding to individual floral organ development were identified. Among them, eight MADS-box genes were further investigated by full-length cDNA sequence analysis and expression validation, which revealed two APETALA1/AGL9-like MADS-box genes preferentially expressed in the sepal and petal, two AGAMOUS-like genes particularly restricted to the gynostemium, and four DEF-like genes distinctively expressed in different floral organs. The spatial expression of these genes varied distinctly in different floral mutant corresponding to different floral morphogenesis, which validated the specialized roles of them in floral patterning and further supported the effectiveness of our in silico analysis. This dataset generated in our study provides new insights into the molecular mechanisms

  1. Color blobs in cortical areas V1 and V2 of the new world monkey Callithrix jacchus, revealed by non-differential optical imaging.

    Science.gov (United States)

    Valverde Salzmann, Matthias F; Bartels, Andreas; Logothetis, Nikos K; Schüz, Almut

    2012-06-01

    Color vision is reserved to only few mammals, such as Old World monkeys and humans. Most Old World monkeys are trichromats. Among them, macaques were shown to exhibit functional domains of color-selectivity, in areas V1 and V2 of the visual cortex. Such color domains have not yet been shown in New World monkeys. In marmosets a sex-linked dichotomy results in dichromatic and trichromatic genotypes, rendering most male marmosets color-blind. Here we used trichromatic female marmosets to examine the intrinsic signal response in V1 and V2 to chromatic and achromatic stimuli, using optical imaging. To activate the subsystems individually, we used spatially homogeneous isoluminant color opponent (red/green, blue/yellow) and hue versus achromatic flicker (red/gray, green/gray, blue/gray, yellow/gray), as well as achromatic luminance flicker. In contrast to previous optical imaging studies in marmosets, we find clearly segregated color domains, similar to those seen in macaques. Red/green and red/gray flicker were found to be the appropriate stimulus for revealing color domains in single-condition maps. Blue/gray and blue/yellow flicker stimuli resulted in faint patch-patterns. A recently described multimodal vessel mapping approach allowed for an accurate alignment of the functional and anatomical datasets. Color domains were tightly colocalized with cytochrome oxidase blobs in V1 and with thin stripes in V2. Thus, our findings are in accord with 2-Deoxy-D-glucose studies performed in V1 of macaques and studies on color representation in V2. Our results suggest a similar organization of early cortical color processing in trichromats of both Old World and New World monkeys. PMID:22674264

  2. A label-free differential proteomics analysis reveals the effect of melatonin on promoting fruit ripening and anthocyanin accumulation upon postharvest in tomato.

    Science.gov (United States)

    Sun, Qianqian; Zhang, Na; Wang, Jinfang; Cao, Yunyun; Li, Xingsheng; Zhang, Haijun; Zhang, Lei; Tan, Dun-Xian; Guo, Yang-Dong

    2016-09-01

    To better understand the function of melatonin in tomato fruit ripening and quality improvement, a label-free quantitation method was used to investigate the proteins that differ between the control (CK) and 50 μm melatonin treatment (M50) fruits. Proteomics data identified 241 proteins that were significantly influenced by melatonin. These proteins were involved in several ripening-related pathways, including cell wall metabolism, oxidative phosphorylation, carbohydrate, and fatty acid metabolism. Moreover, the application of exogenous melatonin increased eight proteins that are related to anthocyanin accumulation during fruit ripening. Additionally, the affected protein levels correlated with the corresponding gene transcript levels. Further, the total anthocyanin content from M50 increased by 52%, 48%, and 50% at 5, 8, and 13 DAT (day after melatonin treatment), respectively. The melatonin-mediated promotion of fruit ripening and quality might be due to the altered proteins involved in processes associated with ripening. In this work, we indicated that a senescence-related protein was downregulated in the M50 fruit, while a cell apoptosis inhibitor (API5) protein was upregulated. In addition, peroxidases (POD9, POD12, peroxidase p7-like) and catalase (CAT3) significantly increased in the M50 fruits. Based on the previous studies and our data, we inferred that melatonin might be positively related to fruit ripening but negatively related to fruit senescence. This research provides insights into the physiological and molecular mechanisms underlying melatonin-mediated fruit ripening as well as the anthocyanin formation process in tomato fruit at the protein concentration level, and we reveal possible candidates for regulation of anthocyanin formation during fruit ripening.

  3. A family of differentially amplified repetitive DNA sequences in the genus Beta reveals genetic variation in Beta vulgaris subspecies and cultivars.

    Science.gov (United States)

    Kubis, S; Heslop-Harrison, J S; Schmidt, T

    1997-03-01

    Members of a highly abundant restriction satellite family have been isolated from the wild beet species Beta nana. The satellite DNA sequence is characterized by a conserved RsaI restriction site and is present in three of four sections of the genus Beta, namely Nanae, Corollinae, and Beta. It was not detected in species of the evolutionary old section Procumbentes, suggesting its amplification after separation of this section. Sequences of eight monomers were aligned revealing a size variation from 209 to 233 bp and an AT content ranging from 56.5% to 60.5%. The similarity between monomers in B. nana varied from 77.7% to 92.2%. Diverged subfamilies were identified by sequence analysis and Southern hybridization. A comparative study of this repetitive DNA element by fluorescent in situ hybridization and Southern analyses in three representative species was performed showing a variable genomic organization and heterogeneous localizations along metaphase chromosomes both within and between species. In B. nana the copy number of this satellite, with some 30,000 per haploid genome, is more than tenfold higher than in Beta lomatogona and up to 200 times higher than in Beta vulgaris, indicating different levels of sequence amplification during evolution in the genus Beta. In sugar beet (B. vulgaris), the large-scale organization of this tandem repeat was examined by pulsed-field gel electrophoresis. Southern hybridization to genomic DNA digested with DraI demonstrated that satellite arrays are located in AT-rich regions and the tandem repeat is a useful probe for the detection of genetic variation in closely related B. vulgaris cultivars, accessions, and subspecies.

  4. A label-free differential proteomics analysis reveals the effect of melatonin on promoting fruit ripening and anthocyanin accumulation upon postharvest in tomato.

    Science.gov (United States)

    Sun, Qianqian; Zhang, Na; Wang, Jinfang; Cao, Yunyun; Li, Xingsheng; Zhang, Haijun; Zhang, Lei; Tan, Dun-Xian; Guo, Yang-Dong

    2016-09-01

    To better understand the function of melatonin in tomato fruit ripening and quality improvement, a label-free quantitation method was used to investigate the proteins that differ between the control (CK) and 50 μm melatonin treatment (M50) fruits. Proteomics data identified 241 proteins that were significantly influenced by melatonin. These proteins were involved in several ripening-related pathways, including cell wall metabolism, oxidative phosphorylation, carbohydrate, and fatty acid metabolism. Moreover, the application of exogenous melatonin increased eight proteins that are related to anthocyanin accumulation during fruit ripening. Additionally, the affected protein levels correlated with the corresponding gene transcript levels. Further, the total anthocyanin content from M50 increased by 52%, 48%, and 50% at 5, 8, and 13 DAT (day after melatonin treatment), respectively. The melatonin-mediated promotion of fruit ripening and quality might be due to the altered proteins involved in processes associated with ripening. In this work, we indicated that a senescence-related protein was downregulated in the M50 fruit, while a cell apoptosis inhibitor (API5) protein was upregulated. In addition, peroxidases (POD9, POD12, peroxidase p7-like) and catalase (CAT3) significantly increased in the M50 fruits. Based on the previous studies and our data, we inferred that melatonin might be positively related to fruit ripening but negatively related to fruit senescence. This research provides insights into the physiological and molecular mechanisms underlying melatonin-mediated fruit ripening as well as the anthocyanin formation process in tomato fruit at the protein concentration level, and we reveal possible candidates for regulation of anthocyanin formation during fruit ripening. PMID:26820691

  5. Gene profiling of postnatal Mfrprd6 mutant eyes reveals differential accumulation of Prss56, visual cycle and phototransduction mRNAs.

    Science.gov (United States)

    Soundararajan, Ramani; Won, Jungyeon; Stearns, Timothy M; Charette, Jeremy R; Hicks, Wanda L; Collin, Gayle B; Naggert, Jürgen K; Krebs, Mark P; Nishina, Patsy M

    2014-01-01

    Mutations in the membrane frizzled-related protein (MFRP/Mfrp) gene, specifically expressed in the retinal pigment epithelium (RPE) and ciliary body, cause nanophthalmia or posterior microphthalmia with retinitis pigmentosa in humans, and photoreceptor degeneration in mice. To better understand MFRP function, microarray analysis was performed on eyes of homozygous Mfrprd6 and C57BL/6J mice at postnatal days (P) 0 and P14, prior to photoreceptor loss. Data analysis revealed no changes at P0 but significant differences in RPE and retina-specific transcripts at P14, suggesting a postnatal influence of the Mfrprd6 allele. A subset of these transcripts was validated by quantitative real-time PCR (qRT-PCR). In Mfrprd6 eyes, a significant 1.5- to 2.0-fold decrease was observed among transcripts of genes linked to retinal degeneration, including those involved in visual cycle (Rpe65, Lrat, Rgr), phototransduction (Pde6a, Guca1b, Rgs9), and photoreceptor disc morphogenesis (Rpgrip1 and Fscn2). Levels of RPE65 were significantly decreased by 2.0-fold. Transcripts of Prss56, a gene associated with angle-closure glaucoma, posterior microphthalmia and myopia, were increased in Mfrprd6 eyes by 17-fold. Validation by qRT-PCR indicated a 3.5-, 14- and 70-fold accumulation of Prss56 transcripts relative to controls at P7, P14 and P21, respectively. This trend was not observed in other RPE or photoreceptor mutant mouse models with similar disease progression, suggesting that Prss56 upregulation is a specific attribute of the disruption of Mfrp. Prss56 and Glul in situ hybridization directly identified Müller glia in the inner nuclear layer as the cell type expressing Prss56. In summary, the Mfrprd6 allele causes significant postnatal changes in transcript and protein levels in the retina and RPE. The link between Mfrp deficiency and Prss56 up-regulation, together with the genetic association of human MFRP or PRSS56 variants and ocular size, raises the possibility that these genes

  6. Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis.

    Directory of Open Access Journals (Sweden)

    Dung Tien Le

    Full Text Available The availability of complete genome sequence of soybean has allowed research community to design the 66 K Affymetrix Soybean Array GeneChip for genome-wide expression profiling of soybean. In this study, we carried out microarray analysis of leaf tissues of soybean plants, which were subjected to drought stress from late vegetative V6 and from full bloom reproductive R2 stages. Our data analyses showed that out of 46,093 soybean genes, which were predicted with high confidence among approximately 66,000 putative genes, 41,059 genes could be assigned with a known function. Using the criteria of a ratio change > = 2 and a q-value<0.05, we identified 1458 and 1818 upregulated and 1582 and 1688 downregulated genes in drought-stressed V6 and R2 leaves, respectively. These datasets were classified into 19 most abundant biological categories with similar proportions. There were only 612 and 463 genes that were overlapped among the upregulated and downregulated genes, respectively, in both stages, suggesting that both conserved and unconserved pathways might be involved in regulation of drought response in different stages of plant development. A comparative expression analysis using our datasets and that of drought stressed Arabidopsis leaves revealed the existence of both conserved and species-specific mechanisms that regulate drought responses. Many upregulated genes encode either regulatory proteins, such as transcription factors, including those with high homology to Arabidopsis DREB, NAC, AREB and ZAT/STZ transcription factors, kinases and two-component system members, or functional proteins, e.g. late embryogenesis-abundant proteins, glycosyltransferases, glycoside hydrolases, defensins and glyoxalase I family proteins. A detailed analysis of the GmNAC family and the hormone-related gene category showed that expression of many GmNAC and hormone-related genes was altered by drought in V6 and/or R2 leaves. Additionally, the downregulation of

  7. Metamorphic Tectonites and Differential Exhumation Reveal 3D Nature of Extension and Lower Crustal Flow in the Active Woodlark Rift, Papua New Guinea

    Science.gov (United States)

    Little, T. A.; Baldwin, S. L.; Fitzgerald, P. G.; Monteleone, B. D.; Peters, K. J.

    2004-12-01

    The D'Entrecasteaux Islands metamorphic core complexes (MCCs) occur in the Woodlark rift, a continental region where ˜200 km of extension since ˜6 Ma has been focused into a relatively small number of normal faults, some dipping at 12 mm/yr. To the east, an MCC on eastern Normanby Island has top-north footwall mylonites that dip gently SW and that were exhumed during the Pliocene as part of a northward progression of normal faulting that did not arrive at the offshore Moresby Seamount until ˜1.2 Ma (ODP Leg 180 site), relationships that suggest a rolling-hinge style uplift. Importantly, its detachment exposes no rocks deeper than blueschist-facies. Ductile deformation fabrics in the MCCs reveal patterns of lower crustal motion that can be evaluated against seafloor spreading-derived plate motions. Shear fabrics in MCCs closest to the Woodlark spreading ridges, including Normanby and Misima Islands are parallel to the NNE direction of 0.5-3.6 Ma Solomon Sea-Australia spreading. Farther west, lineations in the lower plates of the D'Entrecasteaux MCCs locally deflect ˜40-50° clockwise from this direction. This obliquity is interpreted to reflect inhomogeneous lower crustal extension to the west of the Woodlark spreading ridges. A rift corridor extending ˜100 km to the north of Goodenough and Fergusson Islands is defined by active normal faulting and subsidence of the Trobriand margin. We infer that a previously subducted, locally eclogite-bearing, slab of thinned Australian lower crust to the north of the islands is being pulled out from beneath this zone as it is being sinistrally sheared along its eastern edge. Today the rift zone steps ˜70 km south towards the Papuan Peninsula to define a right-step, an asymmetry that is enhanced by seafloor spreading east of ˜151.4° E. Published focal mechanisms suggest that N-S sinistral shear along the northern Woodlark rift is continuing. In central Normanby Island, ˜2 Ma andesites may have erupted along a transverse

  8. cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici

    Directory of Open Access Journals (Sweden)

    Huang Lili

    2009-06-01

    Full Text Available Abstract Background Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host cells for its reproduction, which makes it difficult to study genes of the pathogen. In spite of its economic importance, little is known about the molecular basis of compatible interaction between the pathogen and wheat host. In this study, we identified wheat and P. striiformis genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-AFLP. Results Of the total 54,912 transcript derived fragments (TDFs obtained using cDNA-AFLP with 64 primer pairs, 2,306 (4.2% displayed altered expression patterns after inoculation, of which 966 showed up-regulated and 1,340 down-regulated. 186 TDFs produced reliable sequences after sequencing of 208 TDFs selected, of which 74 (40% had known functions through BLAST searching the GenBank database. Majority of the latter group had predicted gene products involved in energy (13%, signal transduction (5.4%, disease/defence (5.9% and metabolism (5% of the sequenced TDFs. BLAST searching of the wheat stem rust fungus genome database identified 18 TDFs possibly from the stripe rust pathogen, of which 9 were validated of the pathogen origin using PCR-based assays followed by sequencing confirmation. Of the 186 reliable TDFs, 29 homologous to genes known to play a role in disease/defense, signal transduction or uncharacterized genes were further selected for validation of cDNA-AFLP expression patterns using qRT-PCR analyses. Results confirmed the altered expression patterns of 28 (96.5% genes revealed by the cDNA-AFLP technique. Conclusion The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. Genes involved in compatible interactions between wheat and the

  9. Gene profiling of postnatal Mfrprd6 mutant eyes reveals differential accumulation of Prss56, visual cycle and phototransduction mRNAs.

    Directory of Open Access Journals (Sweden)

    Ramani Soundararajan

    Full Text Available Mutations in the membrane frizzled-related protein (MFRP/Mfrp gene, specifically expressed in the retinal pigment epithelium (RPE and ciliary body, cause nanophthalmia or posterior microphthalmia with retinitis pigmentosa in humans, and photoreceptor degeneration in mice. To better understand MFRP function, microarray analysis was performed on eyes of homozygous Mfrprd6 and C57BL/6J mice at postnatal days (P 0 and P14, prior to photoreceptor loss. Data analysis revealed no changes at P0 but significant differences in RPE and retina-specific transcripts at P14, suggesting a postnatal influence of the Mfrprd6 allele. A subset of these transcripts was validated by quantitative real-time PCR (qRT-PCR. In Mfrprd6 eyes, a significant 1.5- to 2.0-fold decrease was observed among transcripts of genes linked to retinal degeneration, including those involved in visual cycle (Rpe65, Lrat, Rgr, phototransduction (Pde6a, Guca1b, Rgs9, and photoreceptor disc morphogenesis (Rpgrip1 and Fscn2. Levels of RPE65 were significantly decreased by 2.0-fold. Transcripts of Prss56, a gene associated with angle-closure glaucoma, posterior microphthalmia and myopia, were increased in Mfrprd6 eyes by 17-fold. Validation by qRT-PCR indicated a 3.5-, 14- and 70-fold accumulation of Prss56 transcripts relative to controls at P7, P14 and P21, respectively. This trend was not observed in other RPE or photoreceptor mutant mouse models with similar disease progression, suggesting that Prss56 upregulation is a specific attribute of the disruption of Mfrp. Prss56 and Glul in situ hybridization directly identified Müller glia in the inner nuclear layer as the cell type expressing Prss56. In summary, the Mfrprd6 allele causes significant postnatal changes in transcript and protein levels in the retina and RPE. The link between Mfrp deficiency and Prss56 up-regulation, together with the genetic association of human MFRP or PRSS56 variants and ocular size, raises the possibility that

  10. Alternative Treatments

    Science.gov (United States)

    ... Find your chapter: search by state Home > Alzheimer's Disease > Treatments > Alternative Treatments Overview What Is Dementia? What Is Alzheimer's? Younger/Early Onset Facts and Figures Know the 10 Signs Stages Inside the Brain: ...

  11. Cosmic alternatives?

    Science.gov (United States)

    Gregory, Ruth

    2009-04-01

    "Cosmologists are often in error but never in doubt." This pithy characterization by the Soviet physicist Lev Landau sums up the raison d'être of Facts and Speculations in Cosmology. Authors Jayant Narlikar and Geoffrey Burbidge are proponents of a "steady state" theory of cosmology, and they argue that the cosmological community has become fixated on a "Big Bang" dogma, suppressing alternative viewpoints. This book very much does what it says on the tin: it sets out what is known in cosmology, and puts forward the authors' point of view on an alternative to the Big Bang.

  12. Heat reveals faults

    Energy Technology Data Exchange (ETDEWEB)

    Weinreich, Bernhard [Solarschmiede GmbH, Muenchen (Germany). Engineering Dept.

    2010-07-01

    Gremlins cannot hide from the all-revealing view of a thermographic camera, whereby it makes no difference whether it is a roof-mounted system or a megawatt-sized farm. Just as diverse are the range of faults that, with the growing level of expertise, can now be detected and differentiated with even greater detail. (orig.)

  13. iTRAQ Protein Profile Differential Analysis of Dormant and Germinated Grassbur Twin Seeds Reveals that Ribosomal Synthesis and Carbohydrate Metabolism Promote Germination Possibly Through the PI3K Pathway.

    Science.gov (United States)

    Zhang, Guo-Liang; Zhu, Yue; Fu, Wei-Dong; Wang, Peng; Zhang, Rui-Hai; Zhang, Yan-Lei; Song, Zhen; Xia, Gui-Xian; Wu, Jia-He

    2016-06-01

    Grassbur is a destructive and invasive weed in pastures, and its burs can cause gastric damage to animals. The strong adaptability and reproductive potential of grassbur are partly due to a unique germination mechanism whereby twin seeds develop in a single bur: one seed germinates, but the other remains dormant. To investigate the molecular mechanism of seed germination in twin seeds, we used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a dynamic proteomic analysis of germination and dormancy. A total of 1,984 proteins were identified, 161 of which were considered to be differentially accumulated. The differentially accumulated proteins comprised 102 up-regulated and 59 down-regulated proteins. These proteins were grouped into seven functional categories, ribosomal proteins being the predominant group. The authenticity and accuracy of the results were confirmed by enzyme-linked immunosorbent assay (ELISA) and quantitative real-time reverse transcription-PCR (qPCR). A dynamic proteomic analysis revealed that ribosome synthesis and carbohydrate metabolism affect seed germination possibly through the phosphoinositide 3-kinase (PI3K) pathway. As the PI3K pathway is generally activated by insulin, analyses of seeds treated with exogenous insulin by qPCR, ELISA and iTRAQ confirmed that the PI3K pathway can be activated, which suppresses dormancy and promotes germination in twin grassbur seeds. Together, these results show that the PI3K pathway may play roles in stimulating seed germination in grassbur by modulating ribosomal synthesis and carbohydrate metabolism. PMID:27296714

  14. Coseismic fault zone deformation caused by the 2014 Mw=6.2 Nagano-ken-hokubu, Japan, earthquake on the Itoigawa-Shizuoka Tectonic Line revealed with differential LiDAR

    Science.gov (United States)

    Toda, S.; Ishimura, D.; Homma, S.; Mukoyama, S.; Niwa, Y.

    2015-12-01

    The Mw = 6.2 Nagano-ken-hokubu earthquake struck northern Nagano, central Japan, on November 22, 2014, and accompanied a 9-km-long surface rupture mostly along the previously mapped N-NW trending Kamishiro fault, one of the segments of the 150-km-long Itoigawa-Shizuoka Tectonic Line active fault system. While we mapped the rupture and measured vertical displacement of up to 80 cm at the field, interferometric synthetic aperture radar (InSAR) shows densely spaced fringes on the hanging wall side, suggesting westward or uplift movement associated with thrust faulting. The mainshock focal mechanism and aftershock hypocenters indicate the source fault dips to the east but the InSAR images cannot exactly differentiate between horizontal and vertical movements and also lose coherence within and near the fault zone itself. To reveal near-field deformation and shallow fault slip, here we demonstrate a differential LiDAR analysis using a pair of 1 m-resolution pre-event and post-event bare Earth digital terrain models (DTMs) obtained from commercial LiDAR provider. We applied particle image velocity (PIV) method incorporating elevation change to obtain 3-D vectors of coseismic displacements (Mukoyama, 2011, J. Mt. Sci). Despite sporadic noises mostly due to local landslides, we detected up to 1.5 m net movement at the tip of the hanging wall, more than the field measurement of 80 cm. Our result implies that a 9-km-long rupture zone is not a single continuous fault but composed of two bow-shaped fault strands, suggesting a combination of shallow fault dip and modest amount (cultural features across the fault zone. Secondary features, such as subsidiary back-thrust faults confirmed at the field, are also visible as a significant contrast of vector directions and slip amounts.

  15. Growing Alternatives

    DEFF Research Database (Denmark)

    Bagger-Petersen, Mai Corlin

    2014-01-01

    From 2014, Anhui Province will pilot a reform of the residential land market in China, thus integrating rural Anhui in the national housing market. In contrast, artist and activist Ou Ning has proposed the Bishan time money currency, intending to establish an alternative economic circuit in Bishan...

  16. Transcriptome analysis by Illumina high-throughout paired-end sequencing reveals the complexity of differential gene expression during in vitro plantlet growth and flowering in Amaranthus tricolor L.

    Directory of Open Access Journals (Sweden)

    Shengcai Liu

    Full Text Available Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis--based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS, adult seedling (ASS, flower bud (FBS, and flowering (FS stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39% were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the

  17. Outsourcing Alternatives.

    Science.gov (United States)

    Enderle, Jerry

    2001-01-01

    Reveals how outsourcing can save time, money, and headaches and addresses when outsourcing may be the right decision for a school. Recommended criteria for deciding on whether to outsource school services are listed. (GR)

  18. Assessing the role of alternative response rates and reinforcer rates in resistance to extinction of target responding when combining stimuli.

    Science.gov (United States)

    Podlesnik, Christopher A; Bai, John Y H; Skinner, Katherine A

    2016-05-01

    Studies of behavioral momentum reveal that reinforcing an alternative response in the presence of a target response reduces the rate of target responding but increases its persistence, relative to training the target response on its own. Because of the parallels between these studies and differential-reinforcement techniques to reduce problem behavior in clinical settings, alternative techniques to reduce problem behavior without enhancing its persistence are being explored. One potential solution is to train an alternative response in a separate stimulus context from problem behavior before combining the alternative stimulus with the target stimulus. The present study assessed how differences in reinforcement contingencies and rate for alternative responding influenced resistance to extinction of target responding when combining alternative and target stimuli in pigeons. Across three experiments, alternative stimuli signaling a response-reinforcer dependency and greater reinforcer rates more effectively decreased the persistence of target responding when combining alternative and target stimuli within the same extinction tests, but not when compared across separate extinction tests. Overall, these findings reveal that differences in competition between alternative and target responding produced by contingencies of alternative reinforcement could influence the effectiveness of treating problem behavior through combining stimulus contexts. PMID:27193243

  19. Alternative crops

    International Nuclear Information System (INIS)

    Surplus cereal production in the EEC and decreasing product prices, mainly for cereals, has prompted considerable interest for new earnings in arable farming. The objective was to examine whether suggested new crops (fibre, oil, medicinal and alternative grains crops) could be considered as real alternatives. Whether a specific crop can compete economically with cereals and whether there is a market demand for the crop is analyzed. The described possibilities will result in ca. 50,000 hectares of new crops. It is expected that they would not immediately provide increased earnings, but in the long run expected price developments are more positive than for cereals. The area for new crops will not solve the current surplus cereal problem as the area used for new crops is only 3% of that used for cereals. Preconditions for many new crops is further research activities and development work as well as the establishment of processing units and organizational initiatives. Presumably, it is stated, there will then be a basis for a profitable production of new crops for some farmers. (AB) (47 refs.)

  20. Alternative Energies

    Energy Technology Data Exchange (ETDEWEB)

    Planting, A.; De saint Jacob, Y.; Verwijs, H.; Belin, H.; Preesman, L.

    2009-03-15

    In two articles, one interview and one column attention is paid to alternative energies. The article 'A new light on saving energy' discusses the option to save energy by modernising lighting systems in urban areas. The column 'View from Paris' focuses on investment decisions in France with regard to renewable energy and energy savings. The article 'Europe turns a blind eye to big battery' discusses developments in batteries to store energy. The interview concerns fuel cell expert and formerly President of UTC Power Jan van Dokkum. The last article gives a brief overview of the European Energy Research Alliance (EERA) and the challenges this alliance will have to face with regard to climate change and energy security.

  1. Energy alternatives

    International Nuclear Information System (INIS)

    English. A special committe of the Canadian House of Commons was established on 23 May 1980 to investigate the use of alternative energy sources such as 'gasohol', liquified coal, solar energy, methanol, wind and tidal power, biomass, and propane. In its final report, the committee envisions an energy system for Canada based on hydrogen and electricity, using solar and geothermal energy for low-grade heat. The committe was not able to say which method of generating electricty would dominate in the next century, although it recommends that fossil fuels should not be used. The fission process is not specifically discussed, but the outlook for fusion was investigated, and continued governmental support of fusion research is recommended. The report proposes some improvements in governmental energy organizations and programs

  2. Upregulation of RNA Processing Factors in Poorly Differentiated Lung Cancer Cells

    Directory of Open Access Journals (Sweden)

    Kenneth G. Geles

    2016-04-01

    Full Text Available Intratumoral heterogeneity in non–small cell lung cancer (NSCLC has been appreciated at the histological and cellular levels, but the association of less differentiated pathology with poor clinical outcome is not understood at the molecular level. Gene expression profiling of intact human tumors fails to reveal the molecular nature of functionally distinct epithelial cell subpopulations, in particular the tumor cells that fuel tumor growth, metastasis, and disease relapse. We generated primary serum-free cultures of NSCLC and then exposed them to conditions known to promote differentiation: the air-liquid interface (ALI and serum. The transcriptional network of the primary cultures was associated with stem cells, indicating a poorly differentiated state, and worse overall survival of NSCLC patients. Strikingly, the overexpression of RNA splicing and processing factors was a prominent feature of the poorly differentiated cells and was also observed in clinical datasets. A genome-wide analysis of splice isoform expression revealed many alternative splicing events that were specific to the differentiation state of the cells, including an unexpectedly high frequency of events on chromosome 19. The poorly differentiated cells exhibited alternative splicing in many genes associated with tumor progression, as exemplified by the preferential expression of the short isoform of telomeric repeat-binding factor 1 (TERF1, also known as Pin2. Our findings demonstrate the utility of the ALI method for probing the molecular mechanisms that underlie NSCLC pathogenesis and provide novel insight into posttranscriptional mechanisms in poorly differentiated lung cancer cells.

  3. The neurogenetics of alternative splicing

    OpenAIRE

    Vuong, CK; Black, DL; S. Zheng

    2016-01-01

    Alternative precursor-mRNA splicing is a key mechanism for regulating gene expression in mammals and is controlled by specialized RNA-binding proteins. The misregulation of splicing is implicated in multiple neurological disorders. We describe recent mouse genetic studies of alternative splicing that reveal its critical role in both neuronal development and the function of mature neurons. We discuss the challenges in understanding the extensive genetic programmes controlled by proteins that r...

  4. Geometry Revealed

    CERN Document Server

    Berger, Marcel

    2010-01-01

    Both classical geometry and modern differential geometry have been active subjects of research throughout the 20th century and lie at the heart of many recent advances in mathematics and physics. The underlying motivating concept for the present book is that it offers readers the elements of a modern geometric culture by means of a whole series of visually appealing unsolved (or recently solved) problems that require the creation of concepts and tools of varying abstraction. Starting with such natural, classical objects as lines, planes, circles, spheres, polygons, polyhedra, curves, surfaces,

  5. Methods for Characterization of Alternative RNA Splicing.

    Science.gov (United States)

    Harvey, Samuel E; Cheng, Chonghui

    2016-01-01

    Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

  6. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  7. Looking for an Alternative.

    Science.gov (United States)

    Kennedy, Jack

    1999-01-01

    Argues that high school newspapers might do well to create stronger ties with alternative weeklies. Discusses issues of niche marketing, alternative content, and alternative presentation. Notes that high school papers could learn a lot from alternative newspapers. (SR)

  8. Differential characters

    CERN Document Server

    Bär, Christian

    2014-01-01

    Providing a systematic introduction to differential characters as introduced by Cheeger and Simons, this text describes important concepts such as fiber integration, higher dimensional holonomy, transgression, and the product structure in a geometric manner. Differential characters form a model of what is nowadays called differential cohomology, which is the mathematical structure behind the higher gauge theories in physics.  

  9. Quantitative Modeling of the Alternative Pathway of the Complement System.

    Science.gov (United States)

    Zewde, Nehemiah; Gorham, Ronald D; Dorado, Angel; Morikis, Dimitrios

    2016-01-01

    The complement system is an integral part of innate immunity that detects and eliminates invading pathogens through a cascade of reactions. The destructive effects of the complement activation on host cells are inhibited through versatile regulators that are present in plasma and bound to membranes. Impairment in the capacity of these regulators to function in the proper manner results in autoimmune diseases. To better understand the delicate balance between complement activation and regulation, we have developed a comprehensive quantitative model of the alternative pathway. Our model incorporates a system of ordinary differential equations that describes the dynamics of the four steps of the alternative pathway under physiological conditions: (i) initiation (fluid phase), (ii) amplification (surfaces), (iii) termination (pathogen), and (iv) regulation (host cell and fluid phase). We have examined complement activation and regulation on different surfaces, using the cellular dimensions of a characteristic bacterium (E. coli) and host cell (human erythrocyte). In addition, we have incorporated neutrophil-secreted properdin into the model highlighting the cross talk of neutrophils with the alternative pathway in coordinating innate immunity. Our study yields a series of time-dependent response data for all alternative pathway proteins, fragments, and complexes. We demonstrate the robustness of alternative pathway on the surface of pathogens in which complement components were able to saturate the entire region in about 54 minutes, while occupying less than one percent on host cells at the same time period. Our model reveals that tight regulation of complement starts in fluid phase in which propagation of the alternative pathway was inhibited through the dismantlement of fluid phase convertases. Our model also depicts the intricate role that properdin released from neutrophils plays in initiating and propagating the alternative pathway during bacterial infection.

  10. Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

    Directory of Open Access Journals (Sweden)

    Zavolan Mihaela

    2010-10-01

    Full Text Available Abstract Background In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate. Results In order to achieve a greater understanding of NMD regulated gene expression we used 2D-DiGE proteomics technology to examine the changes in protein expression induced in HeLa cells by UPF1 knockdown. QPCR based validation of the corresponding mRNAs, in response to both UPF1 knockdown and cycloheximide treatment, identified 17 bona fide NMD targets. Most of these were associated with bioinformatically predicted NMD activating features, predominantly upstream open reading frames (uORFs. Strikingly, however, the majority of transcripts up-regulated by UPF1 knockdown were either insensitive to, or even down-regulated by, cycloheximide treatment. Furthermore, the mRNA abundance of several down-regulated proteins failed to change upon UPF1 knockdown, indicating that UPF1's role in regulating mRNA and protein abundance is more complex than previously appreciated. Among the bona fide NMD targets, we identified a highly conserved AS-NMD event within the 3' UTR of the HNRNPA2B1 gene. Overexpression of GFP tagged hnRNP A2 resulted in a decrease in endogenous hnRNP A2 and B1 mRNA with a concurrent increase in the NMD sensitive isoforms. Conclusions Despite the large number of changes in protein expression upon UPF1 knockdown, a relatively small fraction of them can be directly attributed to the action of NMD on the corresponding mRNA. From amongst these we have identified a conserved AS-NMD event within HNRNPA2B1 that appears to mediate autoregulation of HNRNPA2B1 expression levels.

  11. Differential auger spectrometry

    Science.gov (United States)

    Strongin, Myron; Varma, Matesh Narayan; Anne, Joshi

    1976-06-22

    Differential Auger spectroscopy method for increasing the sensitivity of micro-Auger spectroanalysis of the surfaces of dilute alloys, by alternately periodically switching an electron beam back and forth between an impurity free reference sample and a test sample containing a trace impurity. The Auger electrons from the samples produce representative Auger spectrum signals which cancel to produce an Auger test sample signal corresponding to the amount of the impurity in the test samples.

  12. Constraint Differentiation

    DEFF Research Database (Denmark)

    Mödersheim, Sebastian Alexander; Basin, David; Viganò, Luca

    2010-01-01

    We introduce constraint differentiation, a powerful technique for reducing search when model-checking security protocols using constraint-based methods. Constraint differentiation works by eliminating certain kinds of redundancies that arise in the search space when using constraints to represent...... results show that constraint differentiation substantially reduces search and considerably improves the performance of OFMC, enabling its application to a wider class of problems....

  13. Differential manifolds

    CERN Document Server

    Kosinski, Antoni A

    2007-01-01

    The concepts of differential topology form the center of many mathematical disciplines such as differential geometry and Lie group theory. Differential Manifolds presents to advanced undergraduates and graduate students the systematic study of the topological structure of smooth manifolds. Author Antoni A. Kosinski, Professor Emeritus of Mathematics at Rutgers University, offers an accessible approach to both the h-cobordism theorem and the classification of differential structures on spheres.""How useful it is,"" noted the Bulletin of the American Mathematical Society, ""to have a single, sho

  14. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  15. Differential meadows

    NARCIS (Netherlands)

    J.A. Bergstra; A. Ponse

    2008-01-01

    A meadow is a zero totalised field (0^{-1}=0), and a cancellation meadow is a meadow without proper zero divisors. In this paper we consider differential meadows, i.e., meadows equipped with differentiation operators. We give an equational axiomatization of these operators and thus obtain a finite b

  16. Genome-wide analysis reveals selective modulation of microRNAs and mRNAs by histone deacetylase inhibitor in B cells induced to undergo class switch DNA recombination and plasma cell differentiation

    Directory of Open Access Journals (Sweden)

    Tian eShen

    2015-12-01

    Full Text Available As we have suggested, epigenetic factors, such as microRNAs (miRNAs, can interact with genetic programs to regulate B cell functions, thereby informing antibody and autoantibody responses. We have shown that histone deacetylase inhibitors (HDI inhibit the differentiation events critical to the maturation of the antibody response: class-switch DNA recombination (CSR, somatic hypermutation (SHM and plasma cell differentiation, by modulating intrinsic B cell mechanisms. HDI repress the expression of AID and Blimp-1, which are critical for CSR/SHM and plasma cell differentiation, respectively, in mouse and human B cells by upregulating selected miRNAs that silenced AICDA/Aicda and PRDM1/Prdm1 mRNAs, as demonstrated by multiple qRT-PCRs (J. Immunol. 193:5933-5950, 2014. To further define the selectivity of HDI-mediated modulation of miRNA and gene expression, we performed genome-wide miRNA-Seq and mRNA-Seq analysis in B cells stimulated by LPS plus IL-4 and treated with HDI or nil. Consistent with what we have shown using qRT-PCR, these HDI-treated B cells displayed reduced expression of Aicda and Prdm1, and increased expression of miR-155, miR-181b and miR-361, which target Aicda, and miR-23b, miR-30a and miR-125b, which target Prdm1. In B cells induced to undergo CSR and plasma cell differentiation, about 23% of over 22,000 mRNAs analyzed were expressed at a significantly high copy number (more than 20 copies/cell. Only 18 (0.36% of these highly expressed mRNAs, including Aicda, Prdm1 and Xbp1, were downregulated by HDI by 50% or more. Further, only 16 (0.30% of the highly expressed mRNAs were upregulated (more than twofold by HDI. The selectivity of HDI-mediated modulation of gene expression was emphasized by unchanged expression of the genes that are involved in regulation, targeting or DNA repair processes of CSR, as well as unchanged expression of the genes encoding epigenetic regulators and factors that are important for cell signaling or

  17. Genome-Wide Analysis Reveals Selective Modulation of microRNAs and mRNAs by Histone Deacetylase Inhibitor in B Cells Induced to Undergo Class-Switch DNA Recombination and Plasma Cell Differentiation.

    Science.gov (United States)

    Shen, Tian; Sanchez, Helia N; Zan, Hong; Casali, Paolo

    2015-01-01

    As we have suggested, epigenetic factors, such as microRNAs (miRNAs), can interact with genetic programs to regulate B cell functions, thereby informing antibody and autoantibody responses. We have shown that histone deacetylase (HDAC) inhibitors (HDI) inhibit the differentiation events critical to the maturation of the antibody response: class-switch DNA recombination (CSR), somatic hypermutation (SHM), and plasma cell differentiation, by modulating intrinsic B cell mechanisms. HDI repress the expression of AID and Blimp-1, which are critical for CSR/SHM and plasma cell differentiation, respectively, in mouse and human B cells by upregulating selected miRNAs that silenced AICDA/Aicda and PRDM1/Prdm1 mRNAs, as demonstrated by multiple qRT-PCRs (J Immunol 193:5933-5950, 2014). To further define the selectivity of HDI-mediated modulation of miRNA and gene expression, we performed genome-wide miRNA-Seq and mRNA-Seq analysis in B cells stimulated by LPS plus IL-4 and treated with HDI or nil. Consistent with what we have shown using qRT-PCR, these HDI-treated B cells displayed reduced expression of Aicda and Prdm1, and increased expression of miR-155, miR-181b, and miR-361, which target Aicda, and miR-23b, miR-30a, and miR-125b, which target Prdm1. In B cells induced to undergo CSR and plasma cell differentiation, about 23% of over 22,000 mRNAs analyzed were expressed at a significantly high copy number (more than 20 copies/cell). Only 18 (0.36%) of these highly expressed mRNAs, including Aicda, Prdm1, and Xbp1, were downregulated by HDI by 50% or more. Further, only 16 (0.30%) of the highly expressed mRNAs were upregulated (more than twofold) by HDI. The selectivity of HDI-mediated modulation of gene expression was emphasized by unchanged expression of the genes that are involved in regulation, targeting, or DNA repair processes of CSR, as well as unchanged expression of the genes encoding epigenetic regulators and factors that are important for cell signaling or

  18. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis.

    Science.gov (United States)

    Cheng, Albert W; Shi, Jiahai; Wong, Piu; Luo, Katherine L; Trepman, Paula; Wang, Eric T; Choi, Heejo; Burge, Christopher B; Lodish, Harvey F

    2014-07-24

    The scope and roles of regulated isoform gene expression during erythroid terminal development are poorly understood. We identified hundreds of differentiation-associated isoform changes during terminal erythropoiesis. Sequences surrounding cassette exons of skipped exon events are enriched for motifs bound by the Muscleblind-like (MBNL) family of splicing factors. Knockdown of Mbnl1 in cultured murine fetal liver erythroid progenitors resulted in a strong block in erythroid differentiation and disrupted the developmentally regulated exon skipping of Ndel1 mRNA, which is bound by MBNL1 and critical for erythroid terminal proliferation. These findings reveal an unanticipated scope of the alternative splicing program and the importance of Mbnl1 during erythroid terminal differentiation.

  19. Laparoscopic real-time en-face differential optical topography of near-surface heterogeneity by using an applicator probe with the maximum-density radially alternating illumination and detection fiber-channels

    CERN Document Server

    Piao, Daqing; Holyoak, G Reed; Patel, Sanjay

    2016-01-01

    We demonstrate a laparoscopic applicator probe and a method thereof for real-time en-face topographic mapping of near-surface heterogeneity for potential use in intraoperative margin assessment during minimally invasive oncological procedures. The probe fits in a 12mm port and houses at its maximum 128 copper-coated 750um fibers that form radially alternating illumination (70 fibers) and detection (58 fibers) channels. By simultaneously illuminating the 70 source channels of the probe that is in contact with a scattering medium and concurrently measuring the light diffusely propagated to the 58 detector channels, the presence of near-surface optical heterogeneities can be resolved in an en-face 9.5mm field-of-view in real-time. Visualization of a subsurface margin of strong attenuation contrast at a depth up to 3mm is demonstrated at one wavelength at a frame rate of 1.25Hz.

  20. Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize

    Directory of Open Access Journals (Sweden)

    Xiaolin eWu

    2015-01-01

    Full Text Available ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5, deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs, late embryogenesis abundant (LEA proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation.

  1. Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize.

    Science.gov (United States)

    Wu, Xiaolin; Gong, Fangping; Yang, Le; Hu, Xiuli; Tai, Fuju; Wang, Wei

    2014-01-01

    ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5), deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs), late embryogenesis abundant (LEA) proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation. PMID:25653661

  2. Differential games

    CERN Document Server

    Friedman, Avner

    2006-01-01

    This volume lays the mathematical foundations for the theory of differential games, developing a rigorous mathematical framework with existence theorems. It begins with a precise definition of a differential game and advances to considerations of games of fixed duration, games of pursuit and evasion, the computation of saddle points, games of survival, and games with restricted phase coordinates. Final chapters cover selected topics (including capturability and games with delayed information) and N-person games.Geared toward graduate students, Differential Games will be of particular interest

  3. Differential topology

    CERN Document Server

    Mukherjee, Amiya

    2015-01-01

    This book presents a systematic and comprehensive account of the theory of differentiable manifolds and provides the necessary background for the use of fundamental differential topology tools. The text includes, in particular, the earlier works of Stephen Smale, for which he was awarded the Fields Medal. Explicitly, the topics covered are Thom transversality, Morse theory, theory of handle presentation, h-cobordism theorem, and the generalised Poincaré conjecture. The material is the outcome of lectures and seminars on various aspects of differentiable manifolds and differential topology given over the years at the Indian Statistical Institute in Calcutta, and at other universities throughout India. The book will appeal to graduate students and researchers interested in these topics. An elementary knowledge of linear algebra, general topology, multivariate calculus, analysis, and algebraic topology is recommended.

  4. Methods for Characterization of Alternative RNA Splicing

    Science.gov (United States)

    Harvey, Samuel E.; Cheng, Chonghui

    2016-01-01

    Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing “minigene” in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest. PMID:26721495

  5. Involvement of Alternative Splicing in Barley Seed Germination.

    Directory of Open Access Journals (Sweden)

    Qisen Zhang

    Full Text Available Seed germination activates many new biological processes including DNA, membrane and mitochondrial repairs and requires active protein synthesis and sufficient energy supply. Alternative splicing (AS regulates many cellular processes including cell differentiation and environmental adaptations. However, limited information is available on the regulation of seed germination at post-transcriptional levels. We have conducted RNA-sequencing experiments to dissect AS events in barley seed germination. We identified between 552 and 669 common AS transcripts in germinating barley embryos from four barley varieties (Hordeum vulgare L. Bass, Baudin, Harrington and Stirling. Alternative 3' splicing (34%-45%, intron retention (32%-34% and alternative 5' splicing (16%-21% were three major AS events in germinating embryos. The AS transcripts were predominantly mapped onto ribosome, RNA transport machineries, spliceosome, plant hormone signal transduction, glycolysis, sugar and carbon metabolism pathways. Transcripts of these genes were also very abundant in the early stage of seed germination. Correlation analysis of gene expression showed that AS hormone responsive transcripts could also be co-expressed with genes responsible for protein biosynthesis and sugar metabolisms. Our RNA-sequencing data revealed that AS could play important roles in barley seed germination.

  6. Involvement of Alternative Splicing in Barley Seed Germination.

    Science.gov (United States)

    Zhang, Qisen; Zhang, Xiaoqi; Wang, Songbo; Tan, Cong; Zhou, Gaofeng; Li, Chengdao

    2016-01-01

    Seed germination activates many new biological processes including DNA, membrane and mitochondrial repairs and requires active protein synthesis and sufficient energy supply. Alternative splicing (AS) regulates many cellular processes including cell differentiation and environmental adaptations. However, limited information is available on the regulation of seed germination at post-transcriptional levels. We have conducted RNA-sequencing experiments to dissect AS events in barley seed germination. We identified between 552 and 669 common AS transcripts in germinating barley embryos from four barley varieties (Hordeum vulgare L. Bass, Baudin, Harrington and Stirling). Alternative 3' splicing (34%-45%), intron retention (32%-34%) and alternative 5' splicing (16%-21%) were three major AS events in germinating embryos. The AS transcripts were predominantly mapped onto ribosome, RNA transport machineries, spliceosome, plant hormone signal transduction, glycolysis, sugar and carbon metabolism pathways. Transcripts of these genes were also very abundant in the early stage of seed germination. Correlation analysis of gene expression showed that AS hormone responsive transcripts could also be co-expressed with genes responsible for protein biosynthesis and sugar metabolisms. Our RNA-sequencing data revealed that AS could play important roles in barley seed germination.

  7. Investigating typographic differentiation

    DEFF Research Database (Denmark)

    Beier, Sofie

    2016-01-01

    Text designers are likely to benefit from guidance on how to use typographic differentiation for emphasis. Three experiments use purposely-designed fonts to explore the size and nature of differences in the stylistic characteristics of fonts (weight, width, contrast, italic) which affect letter...... identification. Results indicate that words set in bold and expanded fonts, when alternated with words set in a Neutral test font, may impair performance, whereas changing to italic does not. Possible explanations are explored through measuring the physical and perceptual similarities of the test fonts...

  8. Global affine differential geometry of hypersurfaces

    CERN Document Server

    Li, An-Min; Zhao, Guosong; Hu, Zejun

    2015-01-01

    This book draws a colorful and widespread picture of global affine hypersurface theory up to the most recent state. Moreover, the recent development revealed that affine differential geometry- as differential geometry in general- has an exciting intersection area with other fields of interest, like partial differential equations, global analysis, convex geometry and Riemann surfaces.

  9. Blood cell morphology : controversies and alternatives

    NARCIS (Netherlands)

    Meer, Wim van der

    2006-01-01

    In this thesis we describe controversial morphologic features in both microscopic and automated differentiation of blood cells. In addition, we have investigated alternative methods to overcome these shortcomings. Furthermore we describe the variance of microscopic counting of band cells and variant

  10. The Differential Gene Expression Pattern of Mycobacterium tuberculosis in Response to Capreomycin and PA-824 versus First-Line TB Drugs Reveals Stress- and PE/PPE-Related Drug Targets

    Directory of Open Access Journals (Sweden)

    Li M. Fu

    2009-01-01

    Full Text Available Tuberculosis is a leading infectious disease causing millions of deaths each year. How to eradicate mycobacterial persistence has become a central research focus for developing next-generation TB drugs. Yet, the knowledge in this area is fundamentally limited and only a few drugs, notably capreomycin and PA-824, have been shown to be active against non-replicating persistent TB bacilli. In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. Our study has identified 42 genes specifically induced by capreomycin and PA-824. Many of these genes are related to stress responses. In terms of the distribution of identified genes in a specific category relative to the whole genome, only the categories of PE/PPE and conserved hypotheticals have statistical significance. Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. Further biological elucidation of their roles in mycobacterial persistence is warranted.

  11. Improvements in differentiation unfolding of radiation spectra

    International Nuclear Information System (INIS)

    Differentiation unfolding is widely used for measurements of neutron spectra in reactors using proton-recoil proportional counters and for measurements of neutron and gamma-ray spectra using scintillators. Current differentiation unfolding codes use various least-squares fits of polynomials to estimate the derivative of numerical data. Simple examples are used to illustrate the errors in unfolded energy spectra that result from the use of least-squares differentiation. An alternative method of numerical differentiation is presented; this method is shown to be free of the errors that result from least-squares differentiation

  12. Differential geometry

    CERN Document Server

    Guggenheimer, Heinrich W

    1977-01-01

    This is a text of local differential geometry considered as an application of advanced calculus and linear algebra. The discussion is designed for advanced undergraduate or beginning graduate study, and presumes of readers only a fair knowledge of matrix algebra and of advanced calculus of functions of several real variables. The author, who is a Professor of Mathematics at the Polytechnic Institute of New York, begins with a discussion of plane geometry and then treats the local theory of Lie groups and transformation groups, solid differential geometry, and Riemannian geometry, leading to a

  13. Product and Quotient Rules from Logarithmic Differentiation

    Science.gov (United States)

    Chen, Zhibo

    2012-01-01

    A new application of logarithmic differentiation is presented, which provides an alternative elegant proof of two basic rules of differentiation: the product rule and the quotient rule. The proof can intrigue students, help promote their critical thinking and rigorous reasoning and deepen their understanding of previously encountered concepts. The…

  14. Complementary and Alternative Medicine

    Science.gov (United States)

    ... Help a Friend Who Cuts? Complementary and Alternative Medicine KidsHealth > For Teens > Complementary and Alternative Medicine Print ... replacement. continue How Is CAM Different From Conventional Medicine? Conventional medicine is based on scientific knowledge of ...

  15. Alternative medicine - pain relief

    Science.gov (United States)

    Alternative medicine refers to treatments that are used instead of conventional (standard) ones. If you use an alternative ... considered complementary therapy. There are many forms of ... Acupuncture involves stimulating certain acupoints on the body ...

  16. Genomic and proteomic analyses reveal multiple homologs of genes encoding enzymes of the methanol:coenzyme M methyltransferase system that are differentially expressed in methanol- and acetate-grown Methanosarcina thermophila.

    Science.gov (United States)

    Ding, Yan-Huai R; Zhang, Shi-Ping; Tomb, Jean-Francois; Ferry, James G

    2002-09-24

    Each of the genomic sequences of Methanosarcina acetivorans, Methanosarcina mazei, and Methanosarcina thermophila revealed two homologs of mtaA, three homologs of mtaB, and three homologs of mtaC encoding enzymes specific for methanogenesis from methanol. Two-dimensional gel electrophoretic analyses of polypeptides from M. thermophila established that methanol induces the expression of mtaA-1, mtaB-1, mtaB-2, mtaB-3, mtaC-1, mtaC-2, and mtaC-3 whereas mtaB-3 and mtaC-3 are constitutively expressed in acetate-grown cells. The gene product of one of three mttC homologs, encoding trimethylamine-specific methyltransferase I, was detected in methanol- but not acetate-grown M. thermophila. A postulated role for the multiple homologs is discussed. PMID:12393212

  17. Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein

    Directory of Open Access Journals (Sweden)

    Hunt Kelly K

    2006-03-01

    Full Text Available Abstract Background Isotope-coded affinity tag (ICAT tandem mass spectrometry (MS allows for qualitative and quantitative analysis of paired protein samples. We sought to determine whether ICAT technology could quantify and identify differential expression of tumor-specific proteins in nipple aspirate fluid (NAF from the tumor-bearing and contralateral disease-free breasts of patients with unilateral early-stage breast cancer. Methods Paired NAF samples from 18 women with stage I or II unilateral invasive breast carcinoma and 4 healthy volunteers were analyzed using ICAT labeling, sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE, liquid chromatography, and MS. Proteins were identified by sequence database analysis. Western blot analysis of NAF from an independent sample set from 12 women (8 with early-stage breast cancer and 4 healthy volunteers was also performed. Results 353 peptides were identified from tandem mass spectra and matched to peptide sequences in the National Center for Biotechnology Information database. Equal numbers of peptides were up- versus down-regulated. Alpha2HS-glycoprotein [Heavy:Light (H:L ratio 0.63] was underexpressed in NAF from tumor-bearing breasts, while lipophilin B (H:L ratio 1.42, beta-globin (H:L ratio 1.98, hemopexin (H:L ratio 1.73, and vitamin D-binding protein precursor (H:L ratio 1.82 were overexpressed. Western blot analysis of pooled samples of NAF from healthy volunteers versus NAF from women with breast cancer confirmed the overexpression of vitamin D-binding protein in tumor-bearing breasts. Conclusion ICAT tandem MS was able to identify and quantify differences in specific protein expression between NAF samples from tumor-bearing and disease-free breasts. Proteomic screening techniques using ICAT and NAF may be used to find markers for diagnosis of breast cancer.

  18. Punishment and Alternative Strategies for Decreasing a Behavior.

    Science.gov (United States)

    Vought, James J.

    1984-01-01

    Provides an overview on the subject of punishment and alternative procedures to decelerate a behavior. Describes differential reinforcement, extinction, satiation, corrective feedback, using peers as models and rearranging the environment as positive and nonaversive procedures for decreasing a behavior. (LLL)

  19. Introductory course on differential equations

    CERN Document Server

    Gorain, Ganesh C

    2014-01-01

    Introductory Course on DIFFERENTIAL EQUATIONS provides an excellent exposition of the fundamentals of ordinary and partial differential equations and is ideally suited for a first course of undergraduate students of mathematics, physics and engineering. The aim of this book is to present the elementary theories of differential equations in the forms suitable for use of those students whose main interest in the subject are based on simple mathematical ideas. KEY FEATURES: Discusses the subject in a systematic manner without sacrificing mathematical rigour. A variety of exercises drill the students in problem solving in view of the mathematical theories explained in the book. Worked out examples illustrated according to the theories developed in the book with possible alternatives. Exhaustive collection of problems and the simplicity of presentation differentiate this book from several others. Material contained will help teachers as well as aspiring students of different competitive examinations.

  20. Differential topology

    CERN Document Server

    Margalef-Roig, J

    1992-01-01

    ...there are reasons enough to warrant a coherent treatment of the main body of differential topology in the realm of Banach manifolds, which is at the same time correct and complete. This book fills the gap: whenever possible the manifolds treated are Banach manifolds with corners. Corners add to the complications and the authors have carefully fathomed the validity of all main results at corners. Even in finite dimensions some results at corners are more complete and better thought out here than elsewhere in the literature. The proofs are correct and with all details. I see this book as a reliable monograph of a well-defined subject; the possibility to fall back to it adds to the feeling of security when climbing in the more dangerous realms of infinite dimensional differential geometry. Peter W. Michor

  1. Medaka tert produces multiple variants with differential expression during differentiation in vitro and in vivo

    Directory of Open Access Journals (Sweden)

    Feng Rao, Tiansu Wang, Mingyou Li, Zhendong Li, Ni Hong, Haobin Zhao, Yan Yan, Wenqing Lu, Tiansheng Chen, Weijia Wang, Menghuat Lim, Yongming Yuan, Ling Liu, Lingbing Zeng, Qiwei Wei, Guijun Guan, Changming Li, Yunhan Hong

    2011-01-01

    Full Text Available Embryonic stem (ES cells have immortality for self-renewal and pluripotency. Differentiated human cells undergo replicative senescence. In human, the telomerase reverse transcriptase (Tert, namely the catalytic subunit of telomerase, exhibits differential expression to regulate telomerase activity governing cellular immortality or senescence, and telomerase activity or tert expression is a routine marker of pluripotent ES cells. Here we have identified the medaka tert gene and determined its expression and telomerase activity in vivo and in vitro. We found that the medaka tert locus produces five variants called terta to terte encoding isoforms TertA to TertE. The longest TertA consists of 1090 amino acid residues and displays a maximum of 34% identity to the human TERT and all the signature motifs of the Tert family. TertB to TertE are novel isoforms and have considerable truncation due to alternative splicing. The terta RNA is ubiquitous in embryos, adult tissues and cell lines, and accompanies ubiquitous telomerase activity in vivo and in vitro as revealed by TRAP assays. The tertb RNA was restricted to the testis, absent in embryos before gastrulation and barely detectable in various cell lines The tertc transcript was absent in undifferentiated ES cells but became evident upon ES cell differentiation, in vivo it was barely detectable in early embryos and became evident when embryogenesis proceeds. Therefore, ubiquitous terta expression correlates with ubiquitous telomerase activity in medaka, and expression of other tert variants appears to delineate cell differentiation in vitro and in vivo.

  2. On an Alternative Cosmology

    CERN Document Server

    Vankov, A

    1998-01-01

    The suggested alternative cosmology is based on the idea of barion symmetric universe, in which our home universe is a representative of multitude of typical matter and antimatter universes. This alternative concept gives a physically reasonable explanation of all major problems of the Standard Cosmological Model. Classification Code MSC: Cosmology 524.8 Key words: standard cosmological model, alternative cosmology, barionic symmetry, typical universe, quasars, cosmic rays.

  3. Polyphase alternating codes

    CERN Document Server

    Markkanen, Markku

    2007-01-01

    This work introduces a method for constructing polyphase alternating codes in which the length of a code transmission cycle can be $p^m$ or $p-1$, where $p$ is a prime number and $m$ is a positive integer. The relevant properties leading to the construction alternating codes and the algorithm for generating alternating codes is described. Examples of all practical and some not that practical polyphase code lengths are given.

  4. Alternative Solar Indices

    Energy Technology Data Exchange (ETDEWEB)

    Lantz, L.J.

    1980-07-01

    Possible alternative Solar Indices which could either be a perturbation from the currently defined Solar Index or possible indices based on current technologies for other media markets are discussed. An overview is given of the current project, including the logic that was utilized in defining its current structure and then alternative indices and definitions are presented and finally, recommendations are made for adopting alternative indices.

  5. Complex Alternative Splicing

    OpenAIRE

    Park, Jung Woo; Graveley, Brenton R.

    2007-01-01

    Alternative splicing is a powerful means of controlling gene expression and increasing protein diversity. Most genes express a limited number of mRNA isoforms, but there are several examples of genes that use alternative splicing to generate hundreds, thousands, and even tens of thousands of isoforms. Collectively such genes are considered to undergo complex alternative splicing. The best example is the Drosophila Down syndrome cell adhesion molecule (Dscam) gene, which can generate 38,016 is...

  6. ALTERNATING DIRECTION FINITE ELEMENT METHOD FOR SOME REACTION DIFFUSION MODELS

    Institute of Scientific and Technical Information of China (English)

    江成顺; 刘蕴贤; 沈永明

    2004-01-01

    This paper is concerned with some nonlinear reaction - diffusion models. To solve this kind of models, the modified Laplace finite element scheme and the alternating direction finite element scheme are established for the system of patrical differential equations. Besides, the finite difference method is utilized for the ordinary differential equation in the models. Moreover, by the theory and technique of prior estimates for the differential equations, the convergence analyses and the optimal L2- norm error estimates are demonstrated.

  7. Differential fat harvesting

    Directory of Open Access Journals (Sweden)

    Sebastian Torres Farr

    2014-12-01

    Full Text Available Aim: Volume replacement with fillers is regularly performed with the use of diverse volumetric materials to correct different structures around the face, depending on the volume enhancement required and the thickness of the soft tissue envelope. Differential fat harvesting and posterior grafting is performed to place the correct fat parcel size for each target area, expanding the potential applications of fat. Methods: Sixty patients consecutively recruited on a first come basis undergone a facial fat grafting procedure, in private practice setting between March 2012 and October 2013. Fat grafting quantity and quality was predicted for each case. Differential harvesting was performed, with 2 fat parcels size. Processing was performed through washing. Fat infiltration was carried out through small cannulas or needles depending on the treated area. Outcomes were analysed both by the physicians and the patients at 7 days, 1 month, 3 months and 6 months through a perceived satisfaction questionnaire. Parameters considered were downtime or discomfort, skin benefits, volume restoration, reabsorption rate estimated and overall improvement. Results: Full facial differential fat grafting procedure lasted an average of 1.5-2.5 h. Average downtime was 3-4 days. Follow-up was performed to a minimum of 6 months. Both patient and physician overall satisfaction rates were mostly excellent. Adverse events like lumps or irregularities were not encountered. Conclusion: Differential fat harvesting and posterior grafting is a valid alternative, to expand the repertoire of fat use, allow a more homogeneous effect, reduce the potential complications, speed up the process, improve graft survival, and to enhance overall aesthetic outcome.

  8. Alternative Devices for Taking Insulin

    Science.gov (United States)

    ... KB). Alternate Language URL Alternative Devices for Taking Insulin Page Content On this page: What alternative devices ... the skin. [ Top ] What alternative devices for taking insulin are available? Insulin pens provide a convenient, easy- ...

  9. Compensating Differentials for Sexual Harassment

    OpenAIRE

    Joni Hersch

    2011-01-01

    Workplace sexual harassment is illegal, but many workers report that they have been sexually harassed. Exposure to the risk of sexual harassment may decrease productivity, which would reduce wages. Alternatively, workers may receive a compensating differential for exposure to sexual harassment, which would increase wages. Data on claims of sexual harassment filed with the Equal Employment Opportunity Commission are used to calculate the first measures of sexual harassment risks by industry, a...

  10. Alternative health insurance schemes

    DEFF Research Database (Denmark)

    Keiding, Hans; Hansen, Bodil O.

    2002-01-01

    In this paper, we present a simple model of health insurance with asymmetric information, where we compare two alternative ways of organizing the insurance market. Either as a competitive insurance market, where some risks remain uninsured, or as a compulsory scheme, where however, the level...... competitive insurance; this situation turns out to be at least as good as either of the alternatives...

  11. Intronic Alus influence alternative splicing.

    Directory of Open Access Journals (Sweden)

    Galit Lev-Maor

    Full Text Available Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome.

  12. Biochemical Analyses of Sorghum Varieties Reveal Differential Responses to Drought

    OpenAIRE

    Chukwuma C Ogbaga; Piotr Stepien; Dyson, Beth C.; Nicholas J W Rattray; Ellis, David I.; Royston Goodacre; Johnson, Giles N.

    2016-01-01

    We have examined the biochemical responses of two sorghum cultivars of differing drought tolerance, Samsorg 17 (more drought tolerant) and Samsorg 40 (less drought tolerant), to sustained drought. Plants were exposed to different degrees of drought and then maintained at that level for five days. Responses were examined in terms of metabolic changes and the expression of drought induced proteins - Heat Shock Proteins (HSPs) and dehydrins (DHNs). Generalised phenotypic changes were studied usi...

  13. Trophic specialisations in alternative heterochronic morphs

    OpenAIRE

    Denoël, Mathieu; Schabetsberger, Robert; Joly, Pierre

    2004-01-01

    Polymorphisms are suspected of reducing competition among conspecifics in heterogeneous environments by allowing differential resource use. However the adaptive significance of alternative morphs has been poorly documented. The aim of this study is to determine food partitioning of two heterochronic morphs of the Alpine newt, Triturus alpestris, in mountain lakes. The morphs differ in the functional morphology of their feeding apparatus. Only paedomorphs are able to expel water during prey su...

  14. Common but Differentiated Responsibilities:Burden Sharing Based on Alternative Emission of Global Harvested Wood Products Carbon Pool%共同但有区别责任:基于全球HWP碳库替代减排的责任分担

    Institute of Scientific and Technical Information of China (English)

    杨红强; 张小标

    2015-01-01

    “Common but Differentiated Responsibilities”is the main principal of emission reduction bur⁃den sharing among countries under the context of global response to climate change.Currently,developed coun⁃tries do not reflect upon their technological efficiency on advantages in harvested wood products( HWP ) carbon pool storage.Definite burden sharing is urgent in alternative emission of global HWP carbon pool.From the per⁃spective of“capacity to pay principal”,with 4 scenarios based on economic development and rate of technologi⁃cal efficiency promoting of 20 representative HWP producing countries in the world,this study analyzed chan⁃ges of global HWP carbon pool and respective burden shares between 2010—2030 with GFPM.Results show that:①Technological efficiency is an important factor that promotes global HWP carbon pool,and if developed countries promote their technological efficiency at a given faster rate compared with average rate of sample countries,the global HWP carbon pool will get an increment of 2.9×103 TgC.②The capacity of alternative e⁃mission of HWP carbon pool in developed countries are relatively stronger,and as a result,developed countries should undertake 76%-97% share of the responsibility.Developing countries'burden share is 11% to 31% of those of developed countries respectively.③United States,Sweden,Finland and Germany are major countries that should undertake the alternative emission responsibility of global HWP carbon pool.Meanwhile,China’ s alternative emission of HWP carbon pool is an important contribution and burden share in future response to climate change.%从“减排能力原则”的视角,依据全球20个代表性HWP生产国的经济发展水平和技术效率提升速率设置4个分析情景,使用GFPM模型模拟并评价2010—2030年全球HWP碳库变动和相应的责任分担。研究表明:①技术效率是提升全球HWP碳库水平的重要因素,发达国家若以既定于样本国

  15. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  16. HL-LHC alternatives

    CERN Document Server

    Tomás, R; White, S

    2014-01-01

    The HL-LHC parameters assume unexplored regimes for hadron colliders in various aspects of accelerator beam dynamics and technology. This paper reviews three alternatives that could potentially improve the LHC performance: (i) the alternative filling scheme 8b+4e, (ii) the use of a 200 MHz RF system in the LHC and (iii) the use of proton cooling methods to reduce the beam emittance (at top energy and at injection). The alternatives are assessed in terms of feasibility, pros and cons, risks versus benefits and the impact on beam availability.

  17. Overexpression of Oct4 in porcine ovarian stem/stromal cells enhances differentiation of oocyte-like cells in vitro and ovarian follicular formation in vivo

    OpenAIRE

    Lee, Yeon-Mi; Kim, Tae-ho; Lee, Jeong-Hyeon; Lee, Won-Jae; Jeon, Ryoung-Hoon; Jang, Si-Jung; Ock, Sun-A; Lee, Sung-Lim; Park, Bong-Wook; RHO, Gyu-Jin

    2016-01-01

    Background Recent findings have revealed that the female gonad may have regenerative activity with having germ line stem cells in juveniles and adults. Application of these germ line stem cells could be an alternative therapy for reproductive disorders in regenerative medicine. Methods To enhance the potency of differentiation into oocyte-like cells (OLCs) and folliculogenesis, we overexpressed Oct4 in ovarian stem/stromal cell (OvSCs) and examined the cellular properties related to stemness ...

  18. Alternative polyadenylation: New insights from global analyses

    OpenAIRE

    Shi, Yongsheng

    2012-01-01

    Recent global studies revealed that mRNA alternative polyadenylation (APA) is widespread in eukaryotic transcriptomes and is an important mechanism for gene regulation. APA deregulation has been found in a variety of diseases. This article reviews recent progress in the field and provides a global perspective on the prevalence, mechanisms, and functional impact of APA.

  19. Seal design alternatives study

    International Nuclear Information System (INIS)

    This report presents the results from a study of various sealing alternatives for the WIPP sealing system. Overall, the sealing system has the purpose of reducing to the extent possible the potential for fluids (either gas or liquid) from entering or leaving the repository. The sealing system is divided into three subsystems: drift and panel seals within the repository horizon, shaft seals in each of the four shafts, and borehole seals. Alternatives to the baseline configuration for the WIPP seal system design included evaluating different geometries and schedules for seal component installations and the use of different materials for seal components. Order-of-magnitude costs for the various alternatives were prepared as part of the study. Firm recommendations are not presented, but the advantages and disadvantages of the alternatives are discussed. Technical information deficiencies are identified and studies are outlined which can provide required information

  20. Evaluation of Expenditure Alternates

    Science.gov (United States)

    Poehlein, Gary W.; And Others

    1973-01-01

    Illustrates a system of calculating dollar expenditures over periods of time in terms of present value. The system enables planners, school boards, and administrators to compare expenditure alternatives as a decisionmaking factor. (Author)

  1. Alternatives to Nursing Homes

    Science.gov (United States)

    ... this website may not be available. Alternatives to nursing homes Before you make any decisions about long ... live and what help you may need. A nursing home may not be your only choice. Discharge ...

  2. Alternative disinfectant water treatments

    Science.gov (United States)

    Alternative disinfestant water treatments are disinfestants not as commonly used by the horticultural industry. Chlorine products that produce hypochlorous acid are the main disinfestants used for treating irrigation water. Chlorine dioxide will be the primary disinfestant discussed as an alternativ...

  3. Vaginal dryness alternative treatments

    Science.gov (United States)

    ... a day. Soybeans contain plant-based substances called isoflavones. These substances have an effect on the body ... soy for vasomotor symptoms: the Herbal Alternatives for Menopause (HALT) Study. Menopause . 2008;15(1):51-58. ...

  4. An alternative currency

    OpenAIRE

    Frendo, Mario; Duca, Edward

    2013-01-01

    Malta- a tiny island, a minute social reality, a precursory canovaccio of European unification- has a unique asset it ought to be prouder of: culture. http://www.um.edu.mt/think/an-alternative-currency/

  5. Alternative fuel information sources

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    This short document contains a list of more than 200 US sources of information (Name, address, phone number, and sometimes contact) related to the use of alternative fuels in automobiles and trucks. Electric-powered cars are also included.

  6. Seal design alternatives study

    Energy Technology Data Exchange (ETDEWEB)

    Van Sambeek, L.L. [RE/SPEC Inc., Rapid City, SD (US); Luo, D.D.; Lin, M.S.; Ostrowski, W.; Oyenuga, D. [Parsons Brinckerhoff Quade & Douglas, Inc., San Francisco, CA (US)

    1993-06-01

    This report presents the results from a study of various sealing alternatives for the WIPP sealing system. Overall, the sealing system has the purpose of reducing to the extent possible the potential for fluids (either gas or liquid) from entering or leaving the repository. The sealing system is divided into three subsystems: drift and panel seals within the repository horizon, shaft seals in each of the four shafts, and borehole seals. Alternatives to the baseline configuration for the WIPP seal system design included evaluating different geometries and schedules for seal component installations and the use of different materials for seal components. Order-of-magnitude costs for the various alternatives were prepared as part of the study. Firm recommendations are not presented, but the advantages and disadvantages of the alternatives are discussed. Technical information deficiencies are identified and studies are outlined which can provide required information.

  7. Alternative fuel cycles

    International Nuclear Information System (INIS)

    Uranium resource utilization and economic considerations provide incentives to study alternative fuel cycles as future options to the PHWR natural uranium cycle. Preliminary studies to define the most favourable alternatives and their possible introduction dates are discussed. The important and uncertain components which influence option selection are reviewed, including nuclear capacity growth, uranium availability and demand, economic potential, and required technological developments. Finally, a summary of Ontario Hydro's program to further assess cycle selection and define development needs is given. (auth)

  8. Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

    KAUST Repository

    Ding, Feng

    2014-06-04

    Background: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.Results: To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.Conclusions: Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress. 2014 Ding et al.; licensee BioMed Central Ltd.

  9. Shape Morphing of Complex Geometries Using Partial Differential Equations

    Directory of Open Access Journals (Sweden)

    Gabriela González Castro

    2007-11-01

    Full Text Available An alternative technique for shape morphing using a surface generating method using partial differential equations is outlined throughout this work. The boundaryvalue nature that is inherent to this surface generation technique together with its mathematical properties are hereby exploited for creating intermediate shapes between an initial shape and a final one. Four alternative shape morphing techniques are proposed here. The first one is based on the use of a linear combination of the boundary conditions associated with the initial and final surfaces, the second one consists of varying the Fourier mode for which the PDE is solved whilst the third results from a combination of the first two. The fourth of these alternatives is based on the manipulation of the spine of the surfaces, which is computed as a by-product of the solution. Results of morphing sequences between two topologically nonequivalent surfaces are presented. Thus, it is shown that the PDE based approach for morphing is capable of obtaining smooth intermediate surfaces automatically in most of the methodologies presented in this work and the spine has been revealed as a powerful tool for morphing surfaces arising from the method proposed here.

  10. Differential reinforcement with and without instructional fading.

    OpenAIRE

    Ringdahl, Joel E; Kitsukawa, Kana; Andelman, Marc S; Call, Nathan; Winborn, Lisa; Barretto, Anjali; Reed, Gregory K

    2002-01-01

    We evaluated a differential-reinforcement-based treatment package for the reduction of problem behavior during instructional situations. Differential reinforcement of alternative behavior (DRA; compliance) was implemented across two conditions. During one condition, instructions were presented approximately once every other minute. This condition was considered the terminal goal for treatment. During the second condition, the rate of instructions was gradually increased (beginning at zero and...

  11. Understanding stem cell differentiation through self-organization theory.

    Science.gov (United States)

    Qu, K; Ortoleva, P

    2008-02-21

    The mechanism underling stem cells' key property, the ability to either divide into two replicate cells or a replicate and a differentiated daughter, still is not understood. We tested a hypothesis that stem cell asymmetric division/differentiation is spontaneously created by the coupling of processes within each daughter and the resulting biochemical feedbacks via the exchange of molecules between them during mitotic division. We developed a mathematical/biochemical model that accounts for dynamic processes accompanying division, including signaling initiation and transcriptional, translational and post-translational (TTP) reactions. Analysis of this model shows that it could explain how stem cells make the decision to divide symmetrically or asymmetrically under different microenvironmental conditions. The analysis also reveals that a stem cell can be induced externally to transition to an alternative state that does not have the potentiality to have the option to divide symmetrically or asymmetrically. With this model, we initiated a search of large databases of transcriptional regulatory network (TRN), protein-protein interaction, and cell signaling pathways. We found 12 subnetworks (motifs) that could support human stem cell asymmetric division. A prime example of the discoveries made possible by this tool, two groups of the genes in the genetic model are revealed to be strongly over-represented in a database of cancer-related genes. PMID:18076908

  12. Alternative fuels for vehicles; Alternative drivmidler

    Energy Technology Data Exchange (ETDEWEB)

    2012-02-15

    Up until 2020 and onwards the analysis indicates that especially electricity, biogas and natural gas as propellants is economically attractive compared to conventional gasoline and diesel while other fuels have the same or higher costs for petrol and diesel. Especially biogas and electricity will also offer significant reductions in CO{sub 2} emissions, but also hydrogen, methanol, DME and to a lesser extent the second generation bioethanol and most of the other alternative fuels reduce CO{sub 2} emissions. Use of the traditional food-based first generation biofuels involves, at best, only modest climate benefits if land use changes are counted, and at worst, significant negative climate effects. Natural gas as a propellant involves a moderate climate gain, but may play a role for building infrastructure and market for gaseous fuels in large fleets, thereby contributing to the phasing in of biogas for transport. The electric-based automotive fuels are the most effective due to a high efficiency of the engine and an increasing proportion of wind energy in the electricity supply. The methanol track also has a relatively high efficiency. Among the others, the track based on diesel engines (biodiesel) is more effective than the track based on gasoline/Otto engines (gas and ethanol) as a result of the diesel engine's better efficiency. For the heavy vehicles all the selected alternative fuels to varying degrees reduce emissions of CO{sub 2}, particularly DME based on wood. The only exception to this is - as for passenger cars - the propellant synthetic diesel based on coal. (LN).

  13. Fetal mesenchymal stromal cells differentiating towards chondrocytes acquire a gene expression profile resembling human growth plate cartilage.

    Directory of Open Access Journals (Sweden)

    Sandy A van Gool

    Full Text Available We used human fetal bone marrow-derived mesenchymal stromal cells (hfMSCs differentiating towards chondrocytes as an alternative model for the human growth plate (GP. Our aims were to study gene expression patterns associated with chondrogenic differentiation to assess whether chondrocytes derived from hfMSCs are a suitable model for studying the development and maturation of the GP. hfMSCs efficiently formed hyaline cartilage in a pellet culture in the presence of TGFβ3 and BMP6. Microarray and principal component analysis were applied to study gene expression profiles during chondrogenic differentiation. A set of 232 genes was found to correlate with in vitro cartilage formation. Several identified genes are known to be involved in cartilage formation and validate the robustness of the differentiating hfMSC model. KEGG pathway analysis using the 232 genes revealed 9 significant signaling pathways correlated with cartilage formation. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development.

  14. Alternative Green Solvents Project

    Science.gov (United States)

    Maloney, Phillip R.

    2012-01-01

    Necessary for safe and proper functioning of equipment. Mainly halogenated solvents. Tetrachloride, Trichloroethylene (TCE), CFC-113. No longer used due to regulatory/safety concerns. Precision Cleaning at KSC: Small % of total parts. Used for liquid oxygen (LOX) systems. Dual solvent process. Vertrel MCA (decafluoropentane (DFP) and trons-dichloroethylene) HFE-7100. DFP has long term environmental concerns. Project Goals: a) Identify potential replacements. b) 22 wet chemical processes. c) 3 alternative processes. d) Develop test procedures. e) Contamination and cleaning. f) Analysis. g) Use results to recommend alternative processes. Conclusions: a) No alternative matched Vertrel in this study. b) No clear second place solvent. c) Hydrocarbons- easy; Fluorinated greases- difficult. d) Fluorinated component may be needed in replacement solvent. e) Process may need to make up for shortcoming of the solvent. f) Plasma and SCC02 warrant further testing.

  15. Catalysis for alternative energy generation

    CERN Document Server

    2012-01-01

    Summarizes recent problems in using catalysts in alternative energy generation and proposes novel solutions  Reconsiders the role of catalysis in alternative energy generation  Contributors include catalysis and alternative energy experts from across the globe

  16. Genome-wide analysis of alternative transcripts in human breast cancer

    Science.gov (United States)

    Wen, Ji; Toomer, Kevin H.

    2016-01-01

    Transcript variants play a critical role in diversifying gene expression. Alternative splicing is a major mechanism for generating transcript variants. A number of genes have been implicated in breast cancer pathogenesis with their aberrant expression of alternative transcripts. In this study, we performed genome-wide analyses of transcript variant expression in breast cancer. With RNA-Seq data from 105 patients, we characterized the transcriptome of breast tumors, by pairwise comparison of gene expression in the breast tumor versus matched healthy tissue from each patient. We identified 2839 genes, ~10 % of protein-coding genes in the human genome, that had differential expression of transcript variants between tumors and healthy tissues. The validity of the computational analysis was confirmed by quantitative RT-PCR assessment of transcript variant expression from four top candidate genes. The alternative transcript profiling led to classification of breast cancer into two subgroups and yielded a novel molecular signature that could be prognostic of patients’ tumor burden and survival. We uncovered nine splicing factors (FOX2, MBNL1, QKI, PTBP1, ELAVL1, HNRNPC, KHDRBS1, SFRS2, and TIAR) that were involved in aberrant splicing in breast cancer. Network analyses for the coordinative patterns of transcript variant expression identified twelve “hub” genes that differentiated the cancerous and normal transcriptomes. Dysregulated expression of alternative transcripts may reveal novel biomarkers for tumor development. It may also suggest new therapeutic targets, such as the “hub” genes identified through the network analyses of transcript variant expression, or splicing factors implicated in the formation of the tumor transcriptome. PMID:25913416

  17. Domestic energy alternatives

    International Nuclear Information System (INIS)

    These alternatives include biomass, clean coal, geothermal, hydropower, natural gas, nuclear, solar and photovoltaic, and wind. With the current, volatile situation in the Middle East, this nation's political leaders appear to be left scratching their heads in their attempts to come up with new, sound, energy policies to reduce our dependence on foreign oil. Therefore, the FORTNIGHTLY's editorial staff thought that this might be an opportune time to briefly examine some home-grown and environmentally responsible fuel alternatives to black gold. While some of these electricity-producing technologies are still on the horizon, others are available now

  18. Alternative Interpretation for the Eberswalde Delta, Holden NE Crater, Mars

    Science.gov (United States)

    Fedo, C. M.; Finkelstein, D. B.; Moersch, J. E.

    2008-03-01

    Examination of HiRISE images from the Eberswalde Delta reveal that it is hard to identify sedimentologic and stratigraphic components of a fluvio-deltaic system, leaving open alternative interpretations for the origin of the strata and geomorphpology.

  19. Alternative and Integrative Medicine

    Science.gov (United States)

    ... are the healthcare rituals practiced by a given culture (eg, Asian, Indian, African). Homeopathic Medicine: This alternative medicine system is based on the principle that “like cures like.” In other words, the same substance ... American Brain Tumor Association 8550 W. Bryn Mawr Ave. ...

  20. Alternative Energy Busing

    Science.gov (United States)

    LaFee, Scott

    2012-01-01

    In recent years, school districts have converted portions of their bus fleets to cleaner-burning, sometimes cheaper, alternative fossil fuels, such as compressed natural gas or propane. Others have adopted biodiesel, which combines regular diesel with fuel derived from organic sources, usually vegetable oils or animal fats. The number of biodiesel…

  1. Compensated pulsed alternator

    International Nuclear Information System (INIS)

    This invention relates to an electromechanical energy converter with inertial energy storage. The device, a single phase, two or multi-pole alternator with stationary field coils, and a rotating armature is provided. The rotor itself may be of laminated steel for slower pulses or for faster pulses should be nonmagnetic and electrically nonconductive in order to allow rapid penetration of the field as the armature coil rotates. The armature coil comprises a plurality of power generating conductors mounted on the rotor. The alternator may also include a stationary or counterrotating compensating coil to increase the output voltage thereof and to reduce the internal impedance of the alternator at the moment of peak output. As the machine voltage rises sinusoidally, an external trigger switch is adapted to be closed at the appropriate time to create the desired output current from said alternator to an external load circuit, and as the output current passes through zero a self-commutating effect is provided to allow the switch to disconnect the generator from the external circuit

  2. Alternatives to Violence.

    Science.gov (United States)

    Children Today, 1994

    1994-01-01

    Notes that our capacity to diffuse conflict rests in our ability to recognize and verbalize feelings, develop empathy, and think of alternatives to violence. Explores the influence of role models and culture on violence and how the media can use violent images effectively in helping us confront a culture of violence. (HTH)

  3. Alternatives to Traditional Notation.

    Science.gov (United States)

    Gaare, Mark

    1997-01-01

    Provides a introduction and overview to alternative music notation systems. Describes guitar tablature, accordion tablature, klavarskribo (a keyboard notational system developed by Cornelius Pot, a Dutch engineer), and the digital piano roll. Briefly discusses the history of notation reform and current efforts. Includes examples from scores. (MJP)

  4. Energy conversion alternatives study

    Science.gov (United States)

    Shure, L. T.

    1979-01-01

    Comparison of coal based energy systems is given. Study identifies and compares various advanced energy conversion systems using coal or coal derived fuels for baselaoad electric power generation. Energy Conversion Alternatives Study (ECAS) reports provede government, industry, and general public with technically consistent basis for comparison of system's options of interest for fossilfired electric-utility application.

  5. Alternatives in solar energy

    Science.gov (United States)

    Schueler, D. G.

    1978-01-01

    Although solar energy has the potential of providing a significant source of clean and renewable energy for a variety of applications, it is expected to penetrate the nation's energy economy very slowly. The alternative solar energy technologies which employ direct collection and conversion of solar radiation as briefly described.

  6. Solving Partial Differential Equations Using a New Differential Evolution Algorithm

    Directory of Open Access Journals (Sweden)

    Natee Panagant

    2014-01-01

    Full Text Available This paper proposes an alternative meshless approach to solve partial differential equations (PDEs. With a global approximate function being defined, a partial differential equation problem is converted into an optimisation problem with equality constraints from PDE boundary conditions. An evolutionary algorithm (EA is employed to search for the optimum solution. For this approach, the most difficult task is the low convergence rate of EA which consequently results in poor PDE solution approximation. However, its attractiveness remains due to the nature of a soft computing technique in EA. The algorithm can be used to tackle almost any kind of optimisation problem with simple evolutionary operation, which means it is mathematically simpler to use. A new efficient differential evolution (DE is presented and used to solve a number of the partial differential equations. The results obtained are illustrated and compared with exact solutions. It is shown that the proposed method has a potential to be a future meshless tool provided that the search performance of EA is greatly enhanced.

  7. Boolean Differential Operators

    OpenAIRE

    Catumba, Jorge; Diaz, Rafael

    2012-01-01

    We consider four combinatorial interpretations for the algebra of Boolean differential operators. We show that each interpretation yields an explicit matrix representation for Boolean differential operators.

  8. Detecting differential usage of exons from RNA-seq data

    OpenAIRE

    Anders, Simon; Reyes, Alejandro; Huber, Wolfgang

    2012-01-01

    RNA-seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons between conditions, cell types, or tissues. We present DEXSeq, a statistical method to test for differential exon usage in RNA-seq data. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biologic...

  9. Conservation Laws of Differential Equations in Finance

    Institute of Scientific and Technical Information of China (English)

    QIN Mao-Chang; MEI Feng-Xiang; SHANG Mei

    2005-01-01

    Conservation laws of some differential equations in fiance are studied in this paper. This method does not involve the use or existence of a variational principle. As an alternative, linearize the given equation and find adjoint equation of the linearized equation, the conservation laws can be constructed directly from the symmetries and adjoint symmetries of the associated linearized equation and its adjoint equation.

  10. INTERNATIONAL SPECIALIZATION AND VERTICAL DIFFERENTIATION

    Directory of Open Access Journals (Sweden)

    Furia Donatella

    2010-07-01

    Full Text Available During the last decades, market segmentation and intra-industry trade have become increasingly relevant. The underlying hypothesis of our work is that distinct articles have heterogeneous potential for vertical differentiation, implying that different patterns of international specialization should be identifiable. We carry out an analysis on revealed comparative advantage (through the Lafay Index in specific sectors of interest. Then we highlight the emergence of diverse degrees of product quality differentiation among sectors (through the Relative Quality Index. Results confirm our hypothesis. Indeed it appears that only certain goods, for which the pace of either creative or technological innovation (or both is particularly fast, present a high degree of vertical differentiation and market segmentation. This allows countries to specialize in a particular product variety and gain market power position for that variety. These findings should be taken in due consideration when designing trade policies.

  11. Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

    KAUST Repository

    Roy, S.

    2015-06-27

    Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages. Transcription factor (TF) binding motif activity analysis revealed four motifs, NFKB1_REL_RELA, IRF1,2, IRF7 and TBP that are commonly activated but have distinct activity dynamics in M1 and M2 activation. We observe matching changes in the expression profiles of the corresponding TFs and show that only a restricted set of TFs change expression. There is an overall drastic and transient up-regulation in M1 and a weaker and more sustainable up-regulation in M2. Novel TFs, such as Thap6, Maff, (M1) and Hivep1, Nfil3, Prdm1, (M2) among others, were suggested to be involved in the activation processes. Additionally, 52 (M1) and 67 (M2) novel differentially expressed genes and, for the first time, several differentially expressed long non-coding RNA (lncRNA) transcriptome markers were identified. In conclusion, the finding of novel motifs, TFs and protein-coding and lncRNA genes is an important step forward to fully understand the transcriptional machinery of macrophage activation.

  12. Differentiation Therapy of Acute Myeloid Leukemia

    Directory of Open Access Journals (Sweden)

    Elzbieta Gocek

    2011-05-01

    Full Text Available Acute Myeloid Leukemia (AML is a predominant acute leukemia among adults, characterized by accumulation of malignantly transformed immature myeloid precursors. A very attractive way to treat myeloid leukemia, which is now called ‘differentiation therapy’, was proposed as in vitro studies have shown that a variety of agents stimulate differentiation of the cell lines isolated from leukemic patients. One of the differentiation-inducing agents, all-trans retinoic acid (ATRA, which can induce granulocytic differentiation in myeloid leukemic cell lines, has been introduced into clinics to treat patients with acute promyelocytic leukemia (APL in which a PML-RARA fusion protein is generated by a t(15;17(q22;q12 chromosomal translocation. Because differentiation therapy using ATRA has significantly improved prognosis for patients with APL, many efforts have been made to find alternative differentiating agents. Since 1,25-dihydroxyvitamin D3 (1,25D is capable of inducing in vitro monocyte/macrophage differentiation of myeloid leukemic cells, clinical trials have been performed to estimate its potential to treat patients with AML or myelodysplastic syndrome (MDS. Unfortunately therapeutic concentrations of 1,25D can induce potentially fatal systemic hypercalcemia, thus limiting clinical utility of that compound. Attempts to overcome this problem have focused on the synthesis of 1,25D analogs (VDAs which retain differentiation inducing potential, but lack its hypercalcemic effects. This review aims to discuss current problems and potential solutions in differentiation therapy of AML.

  13. Differentiation Therapy of Acute Myeloid Leukemia

    Energy Technology Data Exchange (ETDEWEB)

    Gocek, Elzbieta; Marcinkowska, Ewa, E-mail: ema@cs.uni.wroc.pl [Department of Biotechnology, University of Wroclaw, ul Tamka 2, Wroclaw 50-137 (Poland)

    2011-05-16

    Acute Myeloid Leukemia (AML) is a predominant acute leukemia among adults, characterized by accumulation of malignantly transformed immature myeloid precursors. A very attractive way to treat myeloid leukemia, which is now called ‘differentiation therapy’, was proposed as in vitro studies have shown that a variety of agents stimulate differentiation of the cell lines isolated from leukemic patients. One of the differentiation-inducing agents, all-trans retinoic acid (ATRA), which can induce granulocytic differentiation in myeloid leukemic cell lines, has been introduced into clinics to treat patients with acute promyelocytic leukemia (APL) in which a PML-RARA fusion protein is generated by a t(15;17)(q22;q12) chromosomal translocation. Because differentiation therapy using ATRA has significantly improved prognosis for patients with APL, many efforts have been made to find alternative differentiating agents. Since 1,25-dihydroxyvitamin D{sub 3} (1,25D) is capable of inducing in vitro monocyte/macrophage differentiation of myeloid leukemic cells, clinical trials have been performed to estimate its potential to treat patients with AML or myelodysplastic syndrome (MDS). Unfortunately therapeutic concentrations of 1,25D can induce potentially fatal systemic hypercalcemia, thus limiting clinical utility of that compound. Attempts to overcome this problem have focused on the synthesis of 1,25D analogs (VDAs) which retain differentiation inducing potential, but lack its hypercalcemic effects. This review aims to discuss current problems and potential solutions in differentiation therapy of AML.

  14. Alternative Splicing of Type II Procollagen: IIB or not IIB?

    OpenAIRE

    McAlinden, Audrey

    2014-01-01

    Over two decades ago, two isoforms of the type II procollagen gene (COL2A1) were discovered. These isoforms, named IIA and IIB, are generated in a developmentally-regulated manner by alternative splicing of exon 2. Chondroprogenitor cells synthesize predominantly IIA isoforms (containing exon 2) while differentiated chondrocytes produce mainly IIB transcripts (devoid of exon 2). Importantly, this IIA-to-IIB alternative splicing switch occurs only during chondrogenesis. More recently, two othe...

  15. Alternative mRNA Splicing: Control by Combination

    OpenAIRE

    Mabon, Stephen A; Tom Misteli

    2005-01-01

    Alternative splicing in mammalian cells has been suggested to be largely controlled by combinatorial binding of basal splicing factors to pre-mRNA templates. This model predicts that distinct sets of pre-mRNA splicing factors are associated with alternatively spliced transcripts. However, no experimental evidence for differential recruitment of splicing factors to transcripts with distinct splicing fates is available. Here we have used quantitative single-cell imaging to test this key predict...

  16. Differential rotation in a solar-driven quasi-axisymmetric circulation. [of planetary atmospheres

    Science.gov (United States)

    Mayr, H. G.; Harris, I.; Chan, K. L.

    1984-01-01

    The concept of a quasi-axisymmetric circulation is used to explore the global scale dynamics of planetary atmospheres. A numerical circulation model applicable to Jupiter is presented, and an analytical study is performed elucidating the conditions leading to differential rotation in an atmosphere which is convectively unstable. A linear system forced by solar differential heating is considered, with nonlinear effects arising from advection being represented in the form of eddy diffusion. An empirical, latitudinal spectrum of the observed zonal wind field on Jupiter is discussed. Numerical solutions are presented which reveal banded wind fields with alternating and equatorial zonal jets and a multicellular Ferrel-Thomson meridional circulation consistent with the observed cloud striations on Jupiter. The vertical derivatives are parameterized to construct a simplified one-layer model.

  17. Stat3 and G-CSF-induced myeloid differentiation.

    Science.gov (United States)

    Chakraborty, A; Tweardy, D J

    1998-08-01

    Granulocyte colony-stimulating factor (G-CSF) is the cytokine critical for directing neutrophilic granulocyte differentiation. Early G-CSF signaling events in myeloid cells involves activation of STATs, proteins that serve the dual function of signal transduction and activation of transcription, especially the activation of Stat3. A dominant-negative mutant construct of Stat3 inhibited G-CSF-mediated neutrophilic differentiation indicating that Stat3 is a essential component for driving the G-CSF-mediated differentiation program in myeloid cells. Three isoforms of Stat3 have been identified, alpha(p92), beta(p83) and gamma(p72) each derived from a single gene. Stat3alpha is the predominant isoform expressed in most cells. Stat3beta is derived from Stat3alpha by alternative RNA splicing. Stat3gamma is derived from Stat3alpha by limited proteolysis. Mapping of Stat3alpha and Stat3beta activation in M1 murine myeloid leukemia cells revealed that their optimal activation required G-CSFR constructs containing both Y704 and Y744. These amino acid residues has previously been demonstrated to be essential for G-CSF-induced differentiation in this cells. Phosphopeptide affinity and phosphopeptide inhibition studies indicate that Stat3alpha and Stat3beta are recruited to the G-CSF receptor complex through their interaction with the receptor at phosphotyrosines Y704 and Y744. Y744 is followed at the +3 position by Cys (C). This sequence YXXC, represents a novel motif implicated in the recruitment and activation of Stat3alpha, Stat3beta and Stat3gamma by the hG-CSFR. Structurally, Stat3alpha, Stat3beta and Stat3gamma differ from each other in their C-terminal transactivation domain. In the beta isoform, the Stat3alpha transactivation domain is replaced by 7 amino acid residues which enable Stat3beta to interact with c-Jun. In the gamma isoform, the Stat3alpha transactivation domain is removed by limited proteolysis creating a dominant negative isoform. In immature human

  18. Extensive alternative splicing of the repressor element silencing transcription factor linked to cancer.

    Directory of Open Access Journals (Sweden)

    Guo-Lin Chen

    Full Text Available The repressor element silencing transcription factor (REST is a coordinate transcriptional and epigenetic regulator which functions as a tumor suppressor or an oncogene depending on cellular context, and a truncated splice variant REST4 has been linked to various types of cancer. We performed a comprehensive analysis of alternative splicing (AS of REST by rapid amplification of cDNA ends and PCR amplification of cDNAs from various tissues and cell lines with specific primers. We identified 8 novel alternative exons including an alternate last exon which doubles the REST gene boundary, along with numerous 5'/3' splice sites and ends in the constitutive exons. With the combination of various splicing patterns (e.g. exon skipping and alternative usage of the first and last exons that are predictive of altered REST activity, at least 45 alternatively spliced variants of coding and non-coding mRNA were expressed in a species- and cell-type/tissue-specific manner with individual differences. By examining the repertoire of REST pre-mRNA splicing in 27 patients with kidney, liver and lung cancer, we found that all patients without exception showed differential expression of various REST splice variants between paired tumor and adjacent normal tissues, with striking cell-type/tissue and individual differences. Moreover, we revealed that exon 3 skipping, which causes no frame shift but loss of a domain essential for nuclear translocation, was affected by pioglitazone, a highly selective activator of the peroxisome proliferator-activated receptor gamma (PPARγ which contributes to cell differentiation and tumorigenesis besides its metabolic actions. Accordingly, this study demonstrates an extensive AS of REST pre-mRNA which redefines REST gene boundary and structure, along with a general but differential link between REST pre-mRNA splicing and various types of cancer. These findings advance our understanding of the complex, context-dependent regulation of

  19. Nonferromagnetic linear variable differential transformer

    Science.gov (United States)

    Ellis, James F.; Walstrom, Peter L.

    1977-06-14

    A nonferromagnetic linear variable differential transformer for accurately measuring mechanical displacements in the presence of high magnetic fields is provided. The device utilizes a movable primary coil inside a fixed secondary coil that consists of two series-opposed windings. Operation is such that the secondary output voltage is maintained in phase (depending on polarity) with the primary voltage. The transducer is well-suited to long cable runs and is useful for measuring small displacements in the presence of high or alternating magnetic fields.

  20. Signaled alternative reinforcement and the persistence of operant behavior.

    Science.gov (United States)

    Bland, Vikki J; Bai, John Y H; Fullerton, Jane A; Podlesnik, Christopher A

    2016-07-01

    Differential reinforcement of alternative behavior (DRA) is a treatment designed to eliminate problem behavior by reinforcing an alternative behavior at a higher rate. Availability of alternative reinforcement may be signaled, as with Functional Communication Training, or unsignaled. Whether or not alternative reinforcement is signaled could influence both the rate and persistence of problem behavior. The present study investigated whether signaling the availability of alternative reinforcement affects the rate and persistence of a concurrently available target response with pigeons. Three components of a multiple concurrent schedule arranged equal reinforcement rates for target responding. Two of the components also arranged equal reinforcement rates for an alternative response. In one DRA component, a discrete stimulus signaled the availability of response-contingent alternative reinforcement by changing the keylight color upon reinforcement availability. In the other DRA component, availability of alternative reinforcement was not signaled. Target responding was most persistent in the unsignaled DRA component when disrupted by satiation, free food presented between components, and extinction, relative to the signaled DRA and control components. These findings suggest the discrete stimulus functionally separated the availability of alternative reinforcement from the discriminative stimuli governing target responding. These findings provide a novel avenue to explore in translational research assessing whether signaling the availability of alternative reinforcement with DRA treatments reduces the persistence of problem behavior. PMID:27282131

  1. Adaptive Alternating Minimization Algorithms

    CERN Document Server

    Niesen, Urs; Wornell, Gregory

    2007-01-01

    The classical alternating minimization (or projection) algorithm has been successful in the context of solving optimization problems over two variables or equivalently of finding a point in the intersection of two sets. The iterative nature and simplicity of the algorithm has led to its application to many areas such as signal processing, information theory, control, and finance. A general set of sufficient conditions for the convergence and correctness of the algorithm is quite well-known when the underlying problem parameters are fixed. In many practical situations, however, the underlying problem parameters are changing over time, and the use of an adaptive algorithm is more appropriate. In this paper, we study such an adaptive version of the alternating minimization algorithm. As a main result of this paper, we provide a general set of sufficient conditions for the convergence and correctness of the adaptive algorithm. Perhaps surprisingly, these conditions seem to be the minimal ones one would expect in ...

  2. [Alternatives to animal testing].

    Science.gov (United States)

    Fabre, Isabelle

    2009-11-01

    The use of alternative methods to animal testing are an integral part of the 3Rs concept (refine, reduce, replace) defined by Russel & Burch in 1959. These approaches include in silico methods (databases and computer models), in vitro physicochemical analysis, biological methods using bacteria or isolated cells, reconstructed enzyme systems, and reconstructed tissues. Emerging "omic" methods used in integrated approaches further help to reduce animal use, while stem cells offer promising approaches to toxicologic and pathophysiologic studies, along with organotypic cultures and bio-artificial organs. Only a few alternative methods can so far be used in stand-alone tests as substitutes for animal testing. The best way to use these methods is to integrate them in tiered testing strategies (ITS), in which animals are only used as a last resort. PMID:20669543

  3. Alternatives to Higgs scalars

    International Nuclear Information System (INIS)

    We discuss alternatives to the Higgs Scalar doublet Φ of the minimal standard model. In particular we review technicolor (TC) and extended technicolor (ETC), and show that the threat of flavour changing neutral currents (FCNC's) is avoided by walking TC and/or strongly coupled ETC. The phenomenology of minimal TC and the techni-family is discussed. Finally we consider the possibility that the Higgs doublet Φ is a composite bound state of quarks from the third (or fourth) family

  4. Alternatives to ECMO.

    OpenAIRE

    Donn, S M

    1994-01-01

    The past decade has witnessed technological advancements which are unparalleled in neonatology. ECMO has been demonstrated to be a powerful rescue treatment, but has perhaps been overutilised and is not universally available. Alternative treatments have been shown to be both safe and efficacious in the management of infants with respiratory failure. Direct head to head clinical trials will probably be necessary to establish appropriate criteria and indications for use, given the wide diversit...

  5. Alternative approaches in IVF

    OpenAIRE

    Fauser, Bart; Bouchard, P.; Coelingh Bennink, H.J.; Collins, John; Devroey, P.; Evers, Johannes; Van Steirteghem, A

    2002-01-01

    textabstractVarious new developments in clinical and basic science which may impact on IVF in the near or distant future will be discussed in this review. These key areas include the regulation of early follicle development and the extended in-vitro culture of oocytes and embryos. Moreover, alternative compounds and ovarian stimulation protocols will be discussed, along with highlights in the development of the cryopreservation of excess oocytes or embryos. Finally, the health economics of IV...

  6. Metamaterials critique and alternatives

    CERN Document Server

    Munk, Ben A

    2009-01-01

    A Convincing and Controversial Alternative Explanation of Metamaterials with a Negative Index of Refraction In a book that will generate both support and controversy, one of the world's foremost authorities on periodic structures addresses several of the current fashions in antenna design-most specifically, the popular subject of double negative metamaterials. Professor Munk provides a comprehensive theoretical electromagnetic investigation of the issues and concludes that many of the phenomena claimed by researchers may be impossible. While denying the existence of negative refractio

  7. Outlook for alternative transportation fuels

    Energy Technology Data Exchange (ETDEWEB)

    Gushee, D.E. [Univ. of Illinois, Chicago, IL (United States)

    1996-12-31

    This presentation provides a brief review of regulatory issues and Federal programs regarding alternative fuel use in automobiles. A number of U.S. DOE initiatives and studies aimed at increasing alternative fuels are outlined, and tax incentives in effect at the state and Federal levels are discussed. Data on alternative fuel consumption and alternative fuel vehicle use are also presented. Despite mandates, tax incentives, and programs, it is concluded alternative fuels will have minimal market penetration. 7 refs., 5 tabs.

  8. Alternative Energy Sources

    CERN Document Server

    Michaelides, Efstathios E (Stathis)

    2012-01-01

    Alternative Energy Sources is designed to give the reader, a clear view of the role each form of alternative energy may play in supplying the energy needs of the human society in the near and intermediate future (20-50 years).   The two first chapters on energy demand and supply and environmental effects, set the tone as to why the widespread use of alternative energy is essential for the future of human society. The third chapter exposes the reader to the laws of energy conversion processes, as well as the limitations of converting one energy form to another. The sections on exergy give a succinct, quantitative background on the capability/potential of each energy source to produce power on a global scale. The fourth, fifth and sixth chapters are expositions of fission and fusion nuclear energy. The following five chapters (seventh to eleventh) include detailed descriptions of the most common renewable energy sources – wind, solar, geothermal, biomass, hydroelectric – and some of the less common sources...

  9. State alternative route designations

    Energy Technology Data Exchange (ETDEWEB)

    1989-07-01

    Pursuant to the Hazardous Materials Transportation Act (HMTA), the Department of Transportation (DOT) has promulgated a comprehensive set of regulations regarding the highway transportation of high-level radioactive materials. These regulations, under HM-164 and HM-164A, establish interstate highways as the preferred routes for the transportation of radioactive materials within and through the states. The regulations also provide a methodology by which a state may select alternative routes. First,the state must establish a ``state routing agency,`` defined as an entity authorized to use the state legal process to impose routing requirements on carriers of radioactive material (49 CFR 171.8). Once identified, the state routing agency must select routes in accordance with Large Quantity Shipments of Radioactive Materials or an equivalent routing analysis. Adjoining states and localities should be consulted on the impact of proposed alternative routes as a prerequisite of final route selection. Lastly, the states must provide written notice of DOT of any alternative route designation before the routes are deemed effective.

  10. State alternative route designations

    Energy Technology Data Exchange (ETDEWEB)

    1989-07-01

    Pursuant to the Hazardous Materials Transportation Act (HMTA), the Department of Transportation (DOT) has promulgated a comprehensive set of regulations regarding the highway transportation of high-level radioactive materials. These regulations, under HM-164 and HM-164A, establish interstate highways as the preferred routes for the transportation of radioactive materials within and through the states. The regulations also provide a methodology by which a state may select alternative routes. First,the state must establish a state routing agency,'' defined as an entity authorized to use the state legal process to impose routing requirements on carriers of radioactive material (49 CFR 171.8). Once identified, the state routing agency must select routes in accordance with Large Quantity Shipments of Radioactive Materials or an equivalent routing analysis. Adjoining states and localities should be consulted on the impact of proposed alternative routes as a prerequisite of final route selection. Lastly, the states must provide written notice of DOT of any alternative route designation before the routes are deemed effective.

  11. Alternative Fuels: Research Progress

    Directory of Open Access Journals (Sweden)

    Maher A.R. Sadiq Al-Baghdadi

    2013-01-01

    Full Text Available Chapter 1: Pollutant Emissions and Combustion Characteristics of Biofuels and Biofuel/Diesel Blends in Laminar and Turbulent Gas Jet Flames. R. N. Parthasarathy, S. R. Gollahalli Chapter 2: Sustainable Routes for The Production of Oxygenated High-Energy Density Biofuels from Lignocellulosic Biomass. Juan A. Melero, Jose Iglesias, Gabriel Morales, Marta Paniagua Chapter 3: Optical Investigations of Alternative-Fuel Combustion in an HSDI Diesel Engine. T. Huelser, M. Jakob, G. Gruenefeld, P. Adomeit, S. Pischinger Chapter 4: An Insight into Biodiesel Physico-Chemical Properties and Exhaust Emissions Based on Statistical Elaboration of Experimental Data. Evangelos G. Giakoumis Chapter 5: Biodiesel: A Promising Alternative Energy Resource. A.E. Atabani Chapter 6: Alternative Fuels for Internal Combustion Engines: An Overview of the Current Research. Ahmed A. Taha, Tarek M. Abdel-Salam, Madhu Vellakal Chapter 7: Investigating the Hydrogen-Natural Gas Blends as a Fuel in Internal Combustion Engine. ?lker YILMAZ Chapter 8: Conversion of Bus Diesel Engine into LPG Gaseous Engine; Method and Experiments Validation. M. A. Jemni , G. Kantchev , Z. Driss , R. Saaidia , M. S. Abid Chapter 9: Predicting the Combustion Performance of Different Vegetable Oils-Derived Biodiesel Fuels. Qing Shu, ChangLin Yu Chapter 10: Production of Gasoline, Naphtha, Kerosene, Diesel, and Fuel Oil Range Fuels from Polypropylene and Polystyrene Waste Plastics Mixture by Two-Stage Catalytic Degradation using ZnO. Moinuddin Sarker, Mohammad Mamunor Rashid

  12. DIF Trees: Using Classification Trees to Detect Differential Item Functioning

    Science.gov (United States)

    Vaughn, Brandon K.; Wang, Qiu

    2010-01-01

    A nonparametric tree classification procedure is used to detect differential item functioning for items that are dichotomously scored. Classification trees are shown to be an alternative procedure to detect differential item functioning other than the use of traditional Mantel-Haenszel and logistic regression analysis. A nonparametric…

  13. Double object constructions and dative / accusative alternations in Spanish and Catalan: A unified account

    Directory of Open Access Journals (Sweden)

    Anna Pineda

    2013-06-01

    Full Text Available This paper has a twofold aim: to present a unified analysis of ditransitive constructions and transitivity alternations (dative/accusative alternations in Spanish. As for the first phenomenon, and more concretely the purported existence in Spanish of something comparable to the English dative alternation, we will show the weaknesses of what we consider an analysis fruit of the tendency consisting of finding in the Romance area an exact reflex of English facts. Therefore, we will refute the hypothesis defended by several authors (Masullo 1992, Demonte 1995, Romero 1997, Cuervo 2003a,b according to which Spanish ditransitive constructions with dative clitic doubling correspond to double object constructions (DOC, whereas non-doubled constructions correspond to the so-called prepositional constructions (PC, or to-dative, in English. After a careful and exhaustive examination of the data, we will argue that Spanish (and Catalan ditransitive constructions instantiate DOC, whether they bear clitic doubling or not.  Pronominalization facts in Catalan, a language which preserves prepositional clitics, will support this analysis, based on the postulation of an affectedness/possession restriction with gradual implementation. As for the second phenomenon of study, the existence of true case alternations in Spanish, we will argue that we are dealing with a kind of variation constrained by the same restriction (or a version of it which acts in the realm of ditransitive predicates. Here, also, Catalan data will reveal crucial for our analysis. Crucially, we will show that what lies behind Spanish and Catalan dative/accusative alternation is an instance of Differential Indirect Object Marking (DIOM

  14. The Competitiveness of Alternative Hydrogen Pathways

    DEFF Research Database (Denmark)

    Hansen, Anders Chr.

    to transport services and in market competitiveness and societal competitiveness. The major societal competitive advantage of hydrogen is its convertibility to electricity and from any other source of energy. This enables a flexible use of natural gas and primary electricity as transport fuels. The major......The paper surveys the literature on the competitiveness of alternative hydrogen pathways in the transport sector. The competitiveness of the alternative systems can be differentiated in the “well-to-tank (WtT)” and “tank-to-wheel (TtW)” sections of the pathway transforming primary energy...... advantage in market competitiveness is the energy efficiency of the fuel cell. This advantage is, however, to some extent balanced by the costs associated with conversion, transport, and storage. The balance between these factors required for market competitiveness is identified....

  15. Alternative medicine and general practitioners in The Netherlands: towards acceptance and integration.

    OpenAIRE

    Visser, G.J.; Peters, L.

    1990-01-01

    A questionnaire on alternative medicine was sent to 600 general practitioners in the Netherlands. Most of the 360 (60%) GPs who replied expressed on interest in alternative practice; and 47% revealed that they used one or more alternative methods themselves, most often homoeopathy. However, the number of patients given alternative treatment by each doctor was small. Almost all (90%) of the GPs referred patients to alternative practitioners. There is no reason to assume that GPs make use of al...

  16. Differential Hybrid Games

    OpenAIRE

    Platzer, André

    2015-01-01

    This article introduces differential hybrid games, which combine differential games with hybrid games. In both kinds of games, two players interact with continuous dynamics. The difference is that hybrid games also provide all the features of hybrid systems and discrete games, but only deterministic differential equations. Differential games, instead, provide differential equations with continuous-time game input by both players, but not the luxury of hybrid games, such as mode switches and d...

  17. Osteogenic differentiation of stem cells from human exfoliated deciduous teeth on poly(ε-caprolactone) nanofibers containing strontium phosphate

    Energy Technology Data Exchange (ETDEWEB)

    Su, Wen-Ta, E-mail: f10549@ntut.edu.tw [Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan (China); Wu, Pai-Shuen [Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan (China); Huang, Te-Yang [Department of Orthopedic Surgery, Mackay Memorial Hospital, Taipei, Taiwan (China)

    2015-01-01

    Mimicking the architecture of the extracellular matrix is an effective strategy for tissue engineering. Composite nanofibers similar to natural bone structure can be prepared via an electrospinning technique and used in biomedical applications. Stem cells from human exfoliated deciduous teeth (SHEDs) can differentiate into multiple cell lineages, such as cells that are alternative sources of stem cells for tissue engineering. Strontium has important functions in bone remodeling; for example, this element can simulate bone formation and decrease bone resorption. Incorporating strontium phosphate into nanofibers provides a potential material for bone tissue engineering. This study investigated the potential of poly(ε-caprolactone) (PCL) nanofibers coated or blended with strontium phosphate for the osteogenic differentiation of SHEDs. Cellular morphology and MTT assay revealed that nanofibers effectively support cellular attachment, spreading, and proliferation. Strontium-loaded PCL nanofibers exhibited higher expressions of collagen type I, alkaline phosphatase, biomineralization, and bone-related genes than pure PCL nanofibers during the osteogenic differentiation of SHEDs. This study demonstrated that strontium can be an effective inducer of osteogenesis for SHEDs. Understanding the function of bioceramics (such as strontium) is useful in designing and developing strategies for bone tissue engineering. - Highlights: • SHEDs have been considered as alternative sources of adult stem cells in tissue engineering. • Strontium phosphate into nanofibers provides a potential material for bone tissue engineering. • Nanofibers coated or blended with strontium phosphate for the osteogenic differentiation of SHEDs.

  18. Endogenous Choice Between Horizontal and Vertical Product Differentiation

    OpenAIRE

    Lambertini, Luca

    1993-01-01

    The endogenous choice between two alternative kinds of product differentiation is addressed in a duopoly model where firms are free to locate along the real axis, while consumers are distributed along a linear city of finite length. It turns out that the nature of differentiation may be heavily affected by the sequence of decisions. If firms simultaneously choose first locations and then prices, product differentiation at equilibrium is horizontal. If instead one firm acts as a Stackelberg le...

  19. Quantifying asymmetry: ratios and alternatives.

    Science.gov (United States)

    Franks, Erin M; Cabo, Luis L

    2014-08-01

    Traditionally, the study of metric skeletal asymmetry has relied largely on univariate analyses, utilizing ratio transformations when the goal is comparing asymmetries in skeletal elements or populations of dissimilar dimensions. Under this approach, raw asymmetries are divided by a size marker, such as a bilateral average, in an attempt to produce size-free asymmetry indices. Henceforth, this will be referred to as "controlling for size" (see Smith: Curr Anthropol 46 (2005) 249-273). Ratios obtained in this manner often require further transformations to interpret the meaning and sources of asymmetry. This model frequently ignores the fundamental assumption of ratios: the relationship between the variables entered in the ratio must be isometric. Violations of this assumption can obscure existing asymmetries and render spurious results. In this study, we examined the performance of the classic indices in detecting and portraying the asymmetry patterns in four human appendicular bones and explored potential methodological alternatives. Examination of the ratio model revealed that it does not fulfill its intended goals in the bones examined, as the numerator and denominator are independent in all cases. The ratios also introduced strong biases in the comparisons between different elements and variables, generating spurious asymmetry patterns. Multivariate analyses strongly suggest that any transformation to control for overall size or variable range must be conducted before, rather than after, calculating the asymmetries. A combination of exploratory multivariate techniques, such as Principal Components Analysis, and confirmatory linear methods, such as regression and analysis of covariance, appear as a promising and powerful alternative to the use of ratios. PMID:24842694

  20. Signaling involved in stem cell reprogramming and differentiation

    Institute of Scientific and Technical Information of China (English)

    Shihori; Tanabe

    2015-01-01

    Stem cell differentiation is regulated by multiple signaling events. Recent technical advances have reve-aled that differentiated cells can be reprogrammed into stem cells. The signals involved in stem cell pro-gramming are of major interest in stem cell research. The signaling mechanisms involved in regulating stem cell reprogramming and differentiation are the subject of intense study in the field of life sciences. In this review,the molecular interactions and signaling pathways related to stem cell differentiation are discussed.

  1. Alternate fuels; Combustibles alternos

    Energy Technology Data Exchange (ETDEWEB)

    Romero Paredes R, Hernando; Ambriz G, Juan Jose [Universidad Autonoma Metropolitana. Iztapalapa (Mexico)

    2003-07-01

    In the definition and description of alternate fuels we must center ourselves in those technological alternatives that allow to obtain compounds that differ from the traditional ones, in their forms to be obtained. In this article it is tried to give an overview of alternate fuels to the conventional derivatives of petroleum and that allow to have a clear idea on the tendencies of modern investigation and the technological developments that can be implemented in the short term. It is not pretended to include all the tendencies and developments of the present world, but those that can hit in a relatively short term, in accordance with agreed with the average life of conventional fuels. Nevertheless, most of the conversion principles are applicable to the spectrum of carbonaceous or cellulosic materials which are in nature, are cultivated or wastes of organic origin. Thus one will approach them in a successive way, the physical, chemical and biological conversions that can take place in a production process of an alternate fuel or the same direct use of the fuel such as burning the sweepings derived from the forests. [Spanish] En la definicion y descripcion de combustibles alternos nos debemos centrar en aquellas alternativas tecnologicas que permitan obtener compuestos que difieren de los tradicionales, al menos en sus formas de ser obtenidos. En este articulo se pretende dar un panorama de los combustibles alternos a los convencionales derivados del petroleo y que permita tener una idea clara sobre las tendencias de la investigacion moderna y los desarrollos tecnologicos que puedan ser implementados en el corto plazo. No se pretende abarcar todas las tendencias y desarrollos del mundo actual, sino aquellas que pueden impactar en un plazo relativamente corto, acordes con la vida media de los combustibles convencionales. Sin embargo, la mayor parte de los principios de conversion son aplicables al espectro de materiales carbonaceos o celulosicos los cuales se

  2. Alternate fusion concepts

    International Nuclear Information System (INIS)

    This review summarizes the status of alternate fusion concepts and plans for their future. The concepts selected for review are those employing electromagnetic confinement for which there have been reasonable predictions of net energy gain from pure fusion and which have shown significant recent development or are the subjects of ongoing international activity. They include advanced tokamaks, stellarators, the spherical torus, reversed-field pinch and dense z-field pinch devices, field reversed configuration, and spheromaks. In addition, an overall view of the status of each concept with respect to achieving ignition and to reactor designs is presented

  3. Alternate transportation system

    Science.gov (United States)

    Zertuche, Tony; Mckinnie, James

    1988-01-01

    Three missions have been identified by NASA for a Space Shuttle-supplementing Alternate Transportation System (ATS) encompassing combinations of booster vehicles, crew modules, and service modules: (1) to achieve manned access to orbit for Space Station crew rotation every 90 days, (2) the lofting of a logistics module resupplying the Space Station every 180 days, and (3) the simultaneous launch of both crews and logistics to the Space Station. A reentry glider is considered, in conjunction with the Space Shuttle's unmanned cargo version and the Apollo manned capsule, as an important ATS element. The Titan IV/NUS is used as a booster.

  4. Polyphase alternating codes

    OpenAIRE

    M. Markkanen; Vierinen, J.; Markkanen, J.

    2007-01-01

    We present a new class of alternating codes. Instead of the customary binary phase codes, the new codes utilize either p or p–1 phases, where p is a prime number. The first class of codes has code length pm, where m is a positive integer, the second class has code length p–1. We give an actual construction algorithm, and explain the principles behind it. We ...

  5. Polyphase alternating codes

    Directory of Open Access Journals (Sweden)

    M. Markkanen

    2008-08-01

    Full Text Available We present a new class of alternating codes. Instead of the customary binary phase codes, the new codes utilize either p or p–1 phases, where p is a prime number. The first class of codes has code length pm, where m is a positive integer, the second class has code length p–1. We give an actual construction algorithm, and explain the principles behind it. We handle a few specific examples in detail. The new codes offer an enlarged collection of code lengths for radar experiments.

  6. Indigenous Representation and Alternative Schooling: Prioritising an Epistemology of Relationality

    Science.gov (United States)

    Keddie, Amanda

    2014-01-01

    This paper draws on a case study of a small alternative Indigenous school in Queensland, Australia. From the perspective of several of the school's Indigenous Elders, the paper foregrounds the significance of group differentiation at the school on the basis of Indigenous representation. However, it also considers how such…

  7. Technology-Based Classroom Assessments: Alternatives to Testing

    Science.gov (United States)

    Salend, Spencer J.

    2009-01-01

    Although many teachers are using new technologies to differentiate instruction and administer tests, educators are also employing a range of technology-based resources and strategies to implement a variety of classroom assessments as alternatives to standardized and teacher-made testing. Technology-based classroom assessments focus on the use of…

  8. Axiomatic differential geometry II-2 - differential forms

    OpenAIRE

    Nishimura, Hirokazu

    2013-01-01

    We refurbish our axiomatics of differential geometry introduced in [Mathematics for Applications,, 1 (2012), 171-182]. Then the notion of Euclideaness can naturally be formulated. The principal objective in this paper is to present an adaptation of our theory of differential forms developed in [International Journal of Pure and Applied Mathematics, 64 (2010), 85-102] to our present axiomatic framework.

  9. Axiomatic Differential Geometry Ⅱ-2: Differential Forms

    OpenAIRE

    Nishimura, Hirokazu

    2013-01-01

    We refurbish our axiomatics of differential geometry introduced in [arXiv 1203.3911]. Then the notion of Euclideaness can naturally be formulated. The principal objective in this paper is to present an adaptation of our theory of differential forms developed in [International Journal of Pure and Applied Mathematics, 64 (2010), 85-102] to our present axiomatic framework.

  10. Some differential equations in synthetic differential geometry

    OpenAIRE

    Kock, Anders; Reyes, Gonzalo E.

    2001-01-01

    Some differential equations are considered in the context of Synthetic Differential Geometry. Here, this means that not only nilpotent infinitesimals, but also the formation of function spaces, is exploited. In particular, we utilize distribution spaces in our study of wave and heat equations.

  11. Differential selection after duplication in mammalian developmental genes.

    Science.gov (United States)

    Dermitzakis, E T; Clark, A G

    2001-04-01

    Gene duplication provides the opportunity for subsequent refinement of distinct functions of the duplicated copies. Either through changes in coding sequence or changes in regulatory regions, duplicate copies appear to obtain new or tissue-specific functions. If this divergence were driven by natural selection, we would expect duplicated copies to have differentiated patterns of substitutions. We tested this hypothesis using genes that duplicated before the human/mouse split and whose orthologous relations were clear. The null hypothesis is that the number of amino acid changes between humans and mice was distributed similarly across different paralogs. We used a method modified from Tang and Lewontin to detect heterogeneity in the amino acid substitution pattern between those different paralogs. Our results show that many of the paralogous gene pairs appear to be under differential selection in the human/mouse comparison. The properties that led to diversification appear to have arisen before the split of the human and mouse lineages. Further study of the diverged genes revealed insights regarding the patterns of amino acid substitution that resulted in differences in function and/or expression of these genes. This approach has utility in the study of newly identified members of gene families in genomewide data mining and for contrasting the merits of alternative hypotheses for the evolutionary divergence of function of duplicated genes. PMID:11264407

  12. Alternate Gauge Electroweak Model

    CERN Document Server

    Dalton, Bill

    2010-01-01

    We describe an alternate gauge electroweak model that permits neutrinos with mass, and at the same time explains why right-handed neutrinos do not appear in weak interactions. This is a local gauge theory involving a space [V ] of three scalar functions. The standard Lagrangian density for the Yang-Mills field part and Higgs doublet remain invariant. A ma jor change is made in the transformation and corresponding Lagrangian density parts involving the right-handed leptons. A picture involving two types of right-handed leptons emerges. A dichotomy of matter on the [V ] space corresponds to coupled and uncoupled right-handed Leptons. Here, we describe a covariant dipole-mode solution in which the neutral bosons A{\\mu} and Z{\\mu} produce precessions on [V ]. The W {\\pm} {\\mu} bosons provide nutations on [V ], and consequently, provide transitions between the coupled and uncoupled regions. To elucidate the [V ] space matter dichotomy, and to generate the boson masses, we also provide an alternate potential Lagran...

  13. Automatic differentiation bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Corliss, G.F. (comp.)

    1992-07-01

    This is a bibliography of work related to automatic differentiation. Automatic differentiation is a technique for the fast, accurate propagation of derivative values using the chain rule. It is neither symbolic nor numeric. Automatic differentiation is a fundamental tool for scientific computation, with applications in optimization, nonlinear equations, nonlinear least squares approximation, stiff ordinary differential equation, partial differential equations, continuation methods, and sensitivity analysis. This report is an updated version of the bibliography which originally appeared in Automatic Differentiation of Algorithms: Theory, Implementation, and Application.

  14. Alternative Medicine and Your Child

    Science.gov (United States)

    ... to Know About Zika & Pregnancy Complementary and Alternative Medicine KidsHealth > For Parents > Complementary and Alternative Medicine Print ... works. previous continue How CAM Differs From Traditional Medicine CAM is frequently distinguished by its holistic methods, ...

  15. Pea Island Alternatives Development Report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this Alternatives Development Report is to outline,in broad scope, the options, tools and alternatives available to the US Fish and Wildlife Service...

  16. Alternative splicing and muscular dystrophy

    OpenAIRE

    Pistoni, Mariaelena; Ghigna, Claudia; Gabellini, Davide

    2010-01-01

    Alternative splicing of pre-mRNAs is a major contributor to proteomic diversity and to the control of gene expression in higher eukaryotic cells. For this reasons, alternative splicing is tightly regulated in different tissues and developmental stages and its disruption can lead to a wide range of human disorders. The aim of this review is to focus on the relevance of alternative splicing for muscle function and muscle disease. We begin by giving a brief overview of alternative splicing, musc...

  17. Culture belief based multi-objective hybrid differential evolutionary algorithm in short term hydrothermal scheduling

    International Nuclear Information System (INIS)

    Highlights: ► Culture belief is integrated into multi-objective differential evolution. ► Chaotic sequence is imported to improve evolutionary population diversity. ► The priority of convergence rate is proved in solving hydrothermal problem. ► The results show the quality and potential of proposed algorithm. - Abstract: A culture belief based multi-objective hybrid differential evolution (CB-MOHDE) is presented to solve short term hydrothermal optimal scheduling with economic emission (SHOSEE) problem. This problem is formulated for compromising thermal cost and emission issue while considering its complicated non-linear constraints with non-smooth and non-convex characteristics. The proposed algorithm integrates a modified multi-objective differential evolutionary algorithm into the computation model of culture algorithm (CA) as well as some communication protocols between population space and belief space, three knowledge structures in belief space are redefined according to these problem-solving characteristics, and in the differential evolution a chaotic factor is embedded into mutation operator for avoiding the premature convergence by enlarging the search scale when the search trajectory reaches local optima. Furthermore, a new heuristic constraint-handling technique is utilized to handle those complex equality and inequality constraints of SHOSEE problem. After the application on hydrothermal scheduling system, the efficiency and stability of the proposed CB-MOHDE is verified by its more desirable results in comparison to other method established recently, and the simulation results also reveal that CB-MOHDE can be a promising alternative for solving SHOSEE.

  18. ALTERNATIVE FUELS FOR DIESEL ENGINES

    Directory of Open Access Journals (Sweden)

    Jacek Caban

    2013-12-01

    Full Text Available This paper presents the development and genesis of the use of alternative fuels in internal combustion ignition engines. Based on the analysis of the literature, this article shows various alternative fuels used in Poland and all over the world. Furthermore, this article describes the research directions for alternative fuels use in road transport powered by diesel engines.

  19. ALTERNATIVE FUELS FOR DIESEL ENGINES

    OpenAIRE

    Jacek Caban; Agata Gniecka; Lukáš Holeša

    2013-01-01

    This paper presents the development and genesis of the use of alternative fuels in internal combustion ignition engines. Based on the analysis of the literature, this article shows various alternative fuels used in Poland and all over the world. Furthermore, this article describes the research directions for alternative fuels use in road transport powered by diesel engines.

  20. Electrochemistry reveals archaeological materials

    OpenAIRE

    Costa, Virginia; Leyssens, Karen; Adriaens, Annemie; Richard, N.; Scholz, Fritz

    2010-01-01

    The characterization of materials constituting cultural artefacts is a challenging step in their conservation, due to the object’s uniqueness and the reduced number of conservation institutes able to supply non-destructive analysis. We propose an alternative analytical tool, which combines accessibility (low cost and portable) and high sensitivity, based on electrochemical linear sweep voltammetry (LSV) with paraffin impregnated graphite electrode (PIGE). To investigate the composition of “wh...

  1. Alternative Modernities for Colonial Korea

    Directory of Open Access Journals (Sweden)

    Steven Lee

    2016-06-01

    Full Text Available Sunyoung Park. The Proletarian Wave: Literature and Leftist Culture in Colonial Korea, 1910–1945. Cambridge, MA: Harvard University Asia Center, 2015. 348 pp. $50 (cloth. Vladimir Tikhonov. Modern Korea and Its Others: Perceptions of the Neighbouring Countries and Korean Modernity. London: Routledge, 2016. 218 pp. $160 (cloth. It has become a global scholarly undertaking: how to rethink modernity so as to decouple it from Westernization (Chakrabarty 2000. Strategies have included foregrounding the plurality of history to disrupt linear progress; positing non-Western centers of modernity in, say, Moscow or Shanghai; and tracing anticolonial circuits connecting Asia to Africa to Latin America. The two recent books under review here add colonial-era Korea to such far-reaching discussions by situating the country across national boundaries. Interestingly, one connecting thread here is the alternative world system provided by the interwar, Soviet-oriented Left. The result is an unsettling of binaries that subsequently became entrenched during the Cold War: for example, north-south, socialist-nationalist, and, for literature, realist-modernist. But more broadly, pervading both books is the sense that history could have turned out differently—that revisiting northeast Asia’s porous borders in the early twentieth century reveals the Korean peninsula’s lost, internationalist potential...

  2. Revealing a steroid receptor ligand as a unique PPARγagonist

    Institute of Scientific and Technical Information of China (English)

    Shengchen Lin; Ying Han; Yuzhe Shi; Hui Rong; Songyang Zheng; Shikan Jin; Shu-Yong Lin; Sheng-Cai Lin; Yong Li

    2012-01-01

    Peroxisome proliferator-activated receptor gamma (PPARγ) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs.We report here the identification of a steroid receptor ligand,RU-486,as an unexpected PPARγ agonist,thereby uncovering a novel signaling route for this steroid drug.Similar to rosiglitazone,RU486 modulates the expression of key PPARγ target genes and promotes adipocyte differentiation,but with a lower adipogenic activity.Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPARγ ligand-binding pocket with distinctive properties and epitopes,providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs.Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPARγligands in the treatment of insulin resistance.

  3. Revealing a steroid receptor ligand as a unique PPAR[gamma] agonist

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Shengchen; Han, Ying; Shi, Yuzhe; Rong, Hui; Zheng, Songyang; Jin, Shikan; Lin, Shu-Yong; Lin, Sheng-Cai; Li, Yong (Pitt); (Xiamen)

    2012-06-28

    Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPAR{gamma} agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPAR{gamma} target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPAR{gamma} ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPAR{gamma} ligands in the treatment of insulin resistance.

  4. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

    Science.gov (United States)

    Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

    2014-01-01

    Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

  5. Eye contact reveals a relationship between Neuroticism and anterior EEG asymmetry.

    Science.gov (United States)

    Uusberg, Helen; Allik, Jüri; Hietanen, Jari K

    2015-07-01

    Although anterior functional brain asymmetry has been linked to individual differences in affect and motivation, its relations with the Five Factor Model personality traits remain unclear. We investigated anterior EEG alpha-activity asymmetry in response to variable degrees of social contact induced by different gaze directions of a "live" model. Neuroticism was negatively related to the anterior EEG asymmetry scores in response to direct gaze, indicating that higher levels of Neuroticism were associated with avoidance-related, relative right-sided functional brain asymmetry. Neuroticism was also related to behavioral direct gaze avoidance and subjective averted gaze preference. These relationships arose primarily from the Withdrawal aspect factor, suggesting that two subdomains of Neuroticism may be differentially related to approach-avoidance tendencies. These findings demonstrate that experimental manipulations of social contact can reveal personality related differences in anterior EEG asymmetry responsiveness, offering a motivationally salient alternative to resting state measures. PMID:25980386

  6. Alternative tsunami models

    Energy Technology Data Exchange (ETDEWEB)

    Tan, A; Lyatskaya, I [Department of Physics, Alabama A and M University, Normal, AL 35762 (United States)], E-mail: arjun.tan@aamu.edu

    2009-01-15

    The interesting papers by Margaritondo (2005 Eur. J. Phys. 26 401) and by Helene and Yamashita (2006 Eur. J. Phys. 27 855) analysed the great Indian Ocean tsunami of 2004 using a simple one-dimensional canal wave model, which was appropriate for undergraduate students in physics and related fields of discipline. In this paper, two additional, easily understandable models, suitable for the same level of readership, are proposed: one, a two-dimensional model in flat space, and two, the same on a spherical surface. The models are used to study the tsunami produced by the central Kuril earthquake of November 2006. It is shown that the two alternative models, especially the latter one, give better representations of the wave amplitude, especially at far-flung locations. The latter model further demonstrates the enhancing effect on the amplitude due to the curvature of the Earth for far-reaching tsunami propagation.

  7. Alternatives to neoliberalism?

    DEFF Research Database (Denmark)

    Warring, Niels; Ahrenkiel, Annegrethe; Nielsen, Birger Steen;

    This paper will discuss the consequences of neoliberal governance in Danish day care centres, the social educators’ response, and the possible development of alternatives based on collective participation of social educators and union representatives. We will show how important and unnoticed...... professional competencies come under pressure, and how collective interest representation is challenged. We will discuss how concepts of “gestural knowledge”, “coherence” and “rhythm” open for a new understanding of professional competence. And we will conclude that the social educators and their unions have...... the possibility to contribute to the development of a new welfare paradigm. The paper is based on material from two research projects (Ahrenkiel et al. 2009, 2011) involving social educators and union representatives in day care institutions. We have observed everyday work activities in day care...

  8. Alternate laser fusion drivers

    International Nuclear Information System (INIS)

    One objective of research on inertial confinement fusion is the development of a power generating system based on this concept. Realization of this goal will depend on the availability of a suitable laser or other system to drive the power plant. The primary laser systems used for laser fusion research, Nd3+: Glass and CO2, have characteristics which may preclude their use for this application. Glass lasers are presently perceived to be incapable of sufficiently high average power operation and the CO2 laser may be limited by and issues associated with target coupling. These general perceptions have encouraged a search for alternatives to the present systems. The search for new lasers has been directed generally towards shorter wavelengths; most of the new lasers discovered in the past few years have been in the visible and ultraviolet region of the spectrum. Virtually all of them have been advocated as the most promising candidate for a fusion driver at one time or another

  9. LIU: exploring alternative ideas

    CERN Document Server

    Damerau, H; Garoby, R; Gilardoni, S; Hancock, S; Mikulec, B; Papaphilippou, Y; Rumolo, G; Shaposhnikova, E; Tomas, R

    2014-01-01

    The baseline upgrade scenarios for the injector complex cover the connection of Linac4 to the PSB, the increase of the PSB-PS transfer energy from 1 . 4 GeV to 2 GeV and the major SPS RF upgrade during LS2. The achievable beam characteristics will nonetheless remain below the expectation of the HL-LHC project. Therefore, alternative or additional options like, e.g., special bunch distributions, the use of injection optics optimized for high space charge or extra RF systems will be discussed. The expected beam parameters, possible implementation and impact on beam availability for these more exotic options will be analysed and compared to the LIU baseline plan. Moreover, the potential interest of further batch compression schemes will be evaluated.

  10. An Alternative to Tensors

    Science.gov (United States)

    Brown, Eric

    2008-10-01

    Some of the most beautiful and complex theories in physics are formulated in the language of tensors. While powerful, these methods are sometimes daunting to the uninitiated. I will introduce the use of Clifford Algebra as a practical alternative to the use of tensors. Many physical quantities can be represented in an indexless form. The boundary between the classical and the quantum worlds becomes a little more transparent. I will review some key concepts, and then talk about some of the things that I am doing with this interesting and powerful tool. Of note to some will be the development of rigid body dynamics for a game engine. Others may be interested in expressing the connection on a spin bundle. My intent is to prove to the audience that there exists an accessible mathematical tool that can be employed to probe the most difficult of topics in physics.

  11. Differential reinforcement with and without instructional fading.

    Science.gov (United States)

    Ringdahl, Joel E; Kitsukawa, Kana; Andelman, Marc S; Call, Nathan; Winborn, Lisa; Barretto, Anjali; Reed, Gregory K

    2002-01-01

    We evaluated a differential-reinforcement-based treatment package for the reduction of problem behavior during instructional situations. Differential reinforcement of alternative behavior (DRA; compliance) was implemented across two conditions. During one condition, instructions were presented approximately once every other minute. This condition was considered the terminal goal for treatment. During the second condition, the rate of instructions was gradually increased (beginning at zero and ending when instruction rate was similar to the first condition). Results indicated that DRA with instructional fading resulted in less problem behavior than DRA without instructional fading. These results are similar to previous studies regarding the utility of instructional fading.

  12. functional-differential inequalities

    Directory of Open Access Journals (Sweden)

    Ludwik Byszewski

    1995-01-01

    Full Text Available A theorem about a system of strong impulsive degenerate nonlinear parabolic functional-differential inequalities in an arbitrary parabolic set is proved. As a consequence of the theorem, some theorems about impulsive degenerate nonlinear parabolic differential inequalities and the uniqueness of a classical solution of an impulsive degenerate nonlinear parabolic differential problem are established.

  13. Alternative medicines for AIDS in resource-poor settings: insights from exploratory anthropological studies in Asia and Africa.

    Science.gov (United States)

    Hardon, Anita; Desclaux, Alice; Egrot, Marc; Simon, Emmanuelle; Micollier, Evelyne; Kyakuwa, Margaret

    2008-01-01

    The emergence of alternative medicines for AIDS in Asia and Africa was discussed at a satellite symposium and the parallel session on alternative and traditional treatments of the AIDSImpact meeting, held in Marseille, in July 2007. These medicines are heterogeneous, both in their presentation and in their geographic and cultural origin. The sessions focused on the role of these medications in selected resource poor settings in Africa and Asia now that access to anti-retroviral therapy is increasing. The aims of the sessions were to (1) identify the actors involved in the diffusion of these alternative medicines for HIV/AIDS, (2) explore uses and forms, and the way these medicines are given legitimacy, (3) reflect on underlying processes of globalisation and cultural differentiation, and (4) define priority questions for future research in this area. This article presents the insights generated at the meeting, illustrated with some findings from the case studies (Uganda, Senegal, Benin, Burkina Faso, China and Indonesia) that were presented. These case studies reveal the wide range of actors who are involved in the marketing and supply of alternative medicines. Regulatory mechanisms are weak. The efficacy claims of alternative medicines often reinforce a biomedical paradigm for HIV/AIDS, and fit with a healthy living ideology promoted by AIDS care programs and support groups. The AIDSImpact session concluded that more interdisciplinary research is needed on the experience of people living with HIV/AIDS with these alternative medicines, and on the ways in which these products interact (or not) with anti-retroviral therapy at pharmacological as well as psychosocial levels. PMID:18616794

  14. Alternative medicines for AIDS in resource-poor settings: Insights from exploratory anthropological studies in Asia and Africa

    Directory of Open Access Journals (Sweden)

    Simon Emmanuelle

    2008-07-01

    Full Text Available Abstract The emergence of alternative medicines for AIDS in Asia and Africa was discussed at a satellite symposium and the parallel session on alternative and traditional treatments of the AIDSImpact meeting, held in Marseille, in July 2007. These medicines are heterogeneous, both in their presentation and in their geographic and cultural origin. The sessions focused on the role of these medications in selected resource poor settings in Africa and Asia now that access to anti-retroviral therapy is increasing. The aims of the sessions were to (1 identify the actors involved in the diffusion of these alternative medicines for HIV/AIDS, (2 explore uses and forms, and the way these medicines are given legitimacy, (3 reflect on underlying processes of globalisation and cultural differentiation, and (4 define priority questions for future research in this area. This article presents the insights generated at the meeting, illustrated with some findings from the case studies (Uganda, Senegal, Benin, Burkina Faso, China and Indonesia that were presented. These case studies reveal the wide range of actors who are involved in the marketing and supply of alternative medicines. Regulatory mechanisms are weak. The efficacy claims of alternative medicines often reinforce a biomedical paradigm for HIV/AIDS, and fit with a healthy living ideology promoted by AIDS care programs and support groups. The AIDSImpact session concluded that more interdisciplinary research is needed on the experience of people living with HIV/AIDS with these alternative medicines, and on the ways in which these products interact (or not with anti-retroviral therapy at pharmacological as well as psychosocial levels.

  15. Alternative medicine and general practitioners in The Netherlands: towards acceptance and integration.

    NARCIS (Netherlands)

    Visser, G.J.; Peters, L.

    1990-01-01

    A questionnaire on alternative medicine was sent to 600 general practitioners in the Netherlands. Most of the 360 (60%) GPs who replied expressed on interest in alternative practice; and 47% revealed that they used one or more alternative methods themselves, most often homoeopathy. However, the numb

  16. Transcriptomics comparison between porcine adipose and bone marrow mesenchymal stem cells during in vitro osteogenic and adipogenic differentiation.

    Directory of Open Access Journals (Sweden)

    Elisa Monaco

    Full Text Available Bone-marrow mesenchymal stem cells (BMSC are considered the gold standard for use in tissue regeneration among mesenchymal stem cells (MSC. The abundance and ease of harvest make the adipose-derived stem cells (ASC an attractive alternative to BMSC. The aim of the present study was to compare the transcriptome of ASC and BMSC, respectively isolated from subcutaneous adipose tissue and femur of 3 adult pigs, during in vitro osteogenic and adipogenic differentiation for up to four weeks. At 0, 2, 7, and 21 days of differentiation RNA was extracted for microarray analysis. A False Discovery Rate ≤0.05 for overall interactions effect and P<0.001 between comparisons were used to determine differentially expressed genes (DEG. Ingenuity Pathway Analysis and DAVID performed the functional analysis of the DEG. Functional analysis of highest expressed genes in MSC and genes more expressed in MSC vs. fully differentiated tissues indicated low immunity and high angiogenic capacity. Only 64 genes were differentially expressed between ASC and BMSC before differentiation. The functional analysis uncovered a potential larger angiogenic, osteogenic, migration, and neurogenic capacity in BMSC and myogenic capacity in ASC. Less than 200 DEG were uncovered between ASC and BMSC during differentiation. Functional analysis also revealed an overall greater lipid metabolism in ASC, while BMSC had a greater cell growth and proliferation. The time course transcriptomic comparison between differentiation types uncovered <500 DEG necessary to determine cell fate. The functional analysis indicated that osteogenesis had a larger cell proliferation and cytoskeleton organization with a crucial role of G-proteins. Adipogenesis was driven by PPAR signaling and had greater angiogenesis, lipid metabolism, migration, and tumorigenesis capacity. Overall the data indicated that the transcriptome of the two MSC is relatively similar across the conditions studied. In addition

  17. Considering alternative calculations of weight suppression.

    Science.gov (United States)

    Schaumberg, Katherine; Anderson, Lisa M; Reilly, Erin E; Gorrell, Sasha; Anderson, Drew A; Earleywine, Mitch

    2016-01-01

    Weight suppression (WS)--the difference between an individual's highest adult weight and current weight-relates to eating pathology and weight gain; however, there are several methodological issues associated with its calculation. The current study presents four alternative methods of calculating WS and tests whether these methods differentially relate to maladaptive outcomes. Alternative methods of calculation included: (1) change in BMI units; (2) BMI category change; (3) percent change in weight; and (4) two different uses of regression residuals. A sample of undergraduate students (N=631) completed self-report measures of eating pathology, current and past weight, and teasing. Measures included the Eating Disorder Examination-Questionnaire and the Perceptions of Teasing Scale. Results indicated that components of WS, current weight and highest weight, were strongly related in the present sample. The traditional method of calculating WS was related to eating pathology, binge eating and teasing for both males and females. However, WS indices orthogonal to the highest weight did not correlate with eating pathology and teasing in both males and females; for females, WS indices orthogonal to current weight were also unrelated to eating pathology. Findings suggest that the link between WS and eating pathology is mitigated after accounting for an individual's highest weight. Future research should continue to assess the reliability and clinical utility of this construct and consider using alternative WS calculations. PMID:26643591

  18. Differential evolution in electromagnetics

    CERN Document Server

    Qing, Anyong

    2010-01-01

    Differential evolution has proven itself a very simple while very powerful stochastic global optimizer. It has been applied to solve problems in many scientific and engineering fields. This book focuses on applications of differential evolution in electromagnetics to showcase its achievement and capability in solving synthesis and design problems in electromagnetics.Topics covered in this book include:*A comprehensive up-to-date literature survey on differential evolution*A systematic description of differential evolution*A topical review on applications of differential evolution in electromag

  19. Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis

    Science.gov (United States)

    Jiang, Qiang; Yang, Chun Hong; Zhang, Yan; Sun, Yan; Li, Rong Ling; Wang, Chang Fa; Zhong, Ji Feng; Huang, Jin Ming

    2016-01-01

    Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine–cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5′ splicing and alternative 3ʹ splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis. PMID:27459697

  20. Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis.

    Science.gov (United States)

    Wang, Xiu Ge; Ju, Zhi Hua; Hou, Ming Hai; Jiang, Qiang; Yang, Chun Hong; Zhang, Yan; Sun, Yan; Li, Rong Ling; Wang, Chang Fa; Zhong, Ji Feng; Huang, Jin Ming

    2016-01-01

    Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine-cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5' splicing and alternative 3' splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis. PMID:27459697

  1. Differentiation and Molecular Properties of Mesenchymal Stem Cells Derived from Murine Induced Pluripotent Stem Cells Derived on Gelatin or Collagen.

    Science.gov (United States)

    Obara, Chizuka; Takizawa, Kazuya; Tomiyama, Kenichi; Hazawa, Masaharu; Saotome-Nakamura, Ai; Gotoh, Takaya; Yasuda, Takeshi; Tajima, Katsushi

    2016-01-01

    The generation of induced-pluripotential stem cells- (iPSCs-) derived mesenchymal stem cells (iMSCs) is an attractive and promising approach for preparing large, uniform batches of applicable MSCs that can serve as an alternative cell source of primary MSCs. Appropriate culture surfaces may influence their growth and differentiation potentials during iMSC derivation. The present study compared molecular properties and differentiation potential of derived mouse iPS-MSCs by deriving on gelatin or collagen-coated surfaces. The cells were derived by a one-step method and expressed CD73 and CD90, but CD105 was downregulated in iMSCs cultured only on gelatin-coated plates with increasing numbers of passages. A pairwise scatter analysis revealed similar expression of MSC-specific genes in iMSCs derived on gelatin and on collagen surfaces as well as in primary mouse bone marrow MSCs. Deriving iMSCs on gelatin and collagen dictated their osteogenic and adipose differentiation potentials, respectively. Derived iMSCs on gelatin upregulated Bmp2 and Lif prior to induction of osteogenic or adipose differentiation, while PPARγ was upregulated by deriving on collagen. Our results suggest that extracellular matrix components such as gelatin biases generated iMSC differentiation potential towards adipose or bone tissue in their derivation process via up- or downregulation of these master genes. PMID:27642306

  2. Modified Chebyshev Collocation Method for Solving Differential Equations

    Directory of Open Access Journals (Sweden)

    M Ziaul Arif

    2015-05-01

    Full Text Available This paper presents derivation of alternative numerical scheme for solving differential equations, which is modified Chebyshev (Vieta-Lucas Polynomial collocation differentiation matrices. The Scheme of modified Chebyshev (Vieta-Lucas Polynomial collocation method is applied to both Ordinary Differential Equations (ODEs and Partial Differential Equations (PDEs cases. Finally, the performance of the proposed method is compared with finite difference method and the exact solution of the example. It is shown that modified Chebyshev collocation method more effective and accurate than FDM for some example given.

  3. Digital differential confocal microscopy based on spatial shift transformation.

    Science.gov (United States)

    Liu, J; Wang, Y; Liu, C; Wilson, T; Wang, H; Tan, J

    2014-11-01

    Differential confocal microscopy is a particularly powerful surface profilometry technique in industrial metrology due to its high axial sensitivity and insensitivity to noise. However, the practical implementation of the technique requires the accurate positioning of point detectors in three-dimensions. We describe a simple alternative based on spatial transformation of a through-focus series of images obtained from a homemade beam scanning confocal microscope. This digital differential confocal microscopy approach is described and compared with the traditional Differential confocal microscopy approach. The ease of use of the digital differential confocal microscopy system is illustrated by performing measurements on a 3D standard specimen. PMID:25303106

  4. Digital differential confocal microscopy based on spatial shift transformation.

    Science.gov (United States)

    Liu, J; Wang, Y; Liu, C; Wilson, T; Wang, H; Tan, J

    2014-11-01

    Differential confocal microscopy is a particularly powerful surface profilometry technique in industrial metrology due to its high axial sensitivity and insensitivity to noise. However, the practical implementation of the technique requires the accurate positioning of point detectors in three-dimensions. We describe a simple alternative based on spatial transformation of a through-focus series of images obtained from a homemade beam scanning confocal microscope. This digital differential confocal microscopy approach is described and compared with the traditional Differential confocal microscopy approach. The ease of use of the digital differential confocal microscopy system is illustrated by performing measurements on a 3D standard specimen.

  5. The nuclear power alternative

    International Nuclear Information System (INIS)

    The Director General of the IAEA stressed the need for energy policies and other measures which would help to slow and eventually halt the present build-up of carbon dioxide, methane and other so-called greenhouse gases, which are held to cause global warming. He urged that nuclear power and various other sources of energy, none of which contribute to global warming, should not be seen as alternatives, but should all be used to counteract the greenhouse effect. He pointed out that the commercially used renewable energies, apart from hydropower, currently represent only 0.3% of the world's energy consumption and, by contrast, the 5% of the world's energy consumption coming from nuclear power is not insignificant. Dr. Blix noted that opposition for nuclear power stems from fear of accidents and concern about the nuclear wastes. But no generation of electricity, whether by coal, hydro, gas or nuclear power, is without some risk. He emphasized that safety can never be a static concept, and that many new measures are being taken by governments and by the IAEA to further strengthen the safety of nuclear power

  6. Hospital diversification: evaluating alternatives.

    Science.gov (United States)

    Hammer, L

    1987-05-01

    The appropriateness of diversification as a growth strategy for hospitals is discussed, and planning for diversification is described. Because new forms of health-care delivery are now in direct competition with hospitals, many hospitals are confronting environmental pressures and preparing for future survival through diversification. To explore the potential risks and benefits of diversification, the hospital must identify opportunities for new business ventures. Diversification can be "related," through an expansion of the primary product line (health care), or "unrelated," into areas not directly associated with health care. The hospital must establish specific criteria for evaluating each diversification alternative, and the two or three most attractive options should be analyzed further through a financial feasibility study. The hospital should also seek legal advice to determine the implications of diversification for maintenance of tax status, antitrust limitations, and applicability of certificate of need. Although diversification may not be appropriate for every institution, hospitals should consider it as a strategy for increasing their revenue base, confronting environmental pressures, and securing future survival. PMID:3300300

  7. Detecting alternative graph clusterings.

    Science.gov (United States)

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network.

  8. Hospital diversification: evaluating alternatives.

    Science.gov (United States)

    Hammer, L

    1987-05-01

    The appropriateness of diversification as a growth strategy for hospitals is discussed, and planning for diversification is described. Because new forms of health-care delivery are now in direct competition with hospitals, many hospitals are confronting environmental pressures and preparing for future survival through diversification. To explore the potential risks and benefits of diversification, the hospital must identify opportunities for new business ventures. Diversification can be "related," through an expansion of the primary product line (health care), or "unrelated," into areas not directly associated with health care. The hospital must establish specific criteria for evaluating each diversification alternative, and the two or three most attractive options should be analyzed further through a financial feasibility study. The hospital should also seek legal advice to determine the implications of diversification for maintenance of tax status, antitrust limitations, and applicability of certificate of need. Although diversification may not be appropriate for every institution, hospitals should consider it as a strategy for increasing their revenue base, confronting environmental pressures, and securing future survival.

  9. Alternative nuclear technologies

    Science.gov (United States)

    Schubert, E.

    1981-10-01

    The lead times required to develop a select group of nuclear fission reactor types and fuel cycles to the point of readiness for full commercialization are compared. Along with lead times, fuel material requirements and comparative costs of producing electric power were estimated. A conservative approach and consistent criteria for all systems were used in estimates of the steps required and the times involved in developing each technology. The impact of the inevitable exhaustion of the low- or reasonable-cost uranium reserves in the United States on the desirability of completing the breeder reactor program, with its favorable long-term result on fission fuel supplies, is discussed. The long times projected to bring the most advanced alternative converter reactor technologies the heavy water reactor and the high-temperature gas-cooled reactor into commercial deployment when compared to the time projected to bring the breeder reactor into equivalent status suggest that the country's best choice is to develop the breeder. The perceived diversion-proliferation problems with the uranium plutonium fuel cycle have workable solutions that can be developed which will enable the use of those materials at substantially reduced levels of diversion risk.

  10. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  11. Dynamics of laser-guided alternating current high voltage discharges

    Science.gov (United States)

    Daigle, J.-F.; Théberge, F.; Lassonde, P.; Kieffer, J.-C.; Fujii, T.; Fortin, J.; Châteauneuf, M.; Dubois, J.

    2013-10-01

    The dynamics of laser-guided alternating current high voltage discharges are characterized using a streak camera. Laser filaments were used to trigger and guide the discharges produced by a commercial Tesla coil. The streaking images revealed that the dynamics of the guided alternating current high voltage corona are different from that of a direct current source. The measured effective corona velocity and the absence of leader streamers confirmed that it evolves in a pure leader regime.

  12. Pedagogical Implications in the Thermal Analysis of Uniform Annular Fins: Alternative Analytic Solutions by Series.

    Science.gov (United States)

    Campo, Antonio; Rodriguez, Franklin

    1998-01-01

    Presents two alternative computational procedures for solving the modified Bessel equation of zero order: the Frobenius method, and the power series method coupled with a curve fit. Students in heat transfer courses can benefit from these alternative procedures; a course on ordinary differential equations is the only mathematical background that…

  13. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

    Energy Technology Data Exchange (ETDEWEB)

    Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla; Conboy, John G.

    2008-11-07

    In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.

  14. Alternative Genres of IS Research

    DEFF Research Database (Denmark)

    Avital, Michel; Mathiassen, Lars; Crowston, Kevin;

    2012-01-01

    perspectives, research methods, semantic framing, literary styles, and media of expression. Overall, the application of alternative genres is considered to be a generative act that provides an opportunity to take a fresh look and to gain deeper understanding of the subject matter. Nonetheless, paradoxically......The potential value of alternative genres in IS research is the core question that drives this panel discussion. The term “Alternative Genres” refers to unconventional forms of thinking, doing, and communicating scholarship and practice. It relates to innovation with respect to epistemological...... the prevailing genres have much inertia, in spite of the inherent boundary spanning nature of alternative genres. Building on their own recent empirical research, the panelists will debate the potential value of alternative genres as unconventional modality of IS scholarship and how alternative genres might...

  15. Differential splicing using whole-transcript microarrays

    Directory of Open Access Journals (Sweden)

    Robinson Mark D

    2009-05-01

    Full Text Available Abstract Background The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0 ST (sense target platform, with versions for Human, Mouse and Rat, is designed primarily to probe every known or predicted exon. The smaller Gene 1.0 ST array is designed as an expression microarray but still interrogates expression with probes along the full length of each well-characterized transcript. We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events. Results We propose a strategy to score differential splicing by using the auxiliary information from fitting the statistical model, RMA (robust multichip analysis. RMA partitions the probe-level data into probe effects and expression levels, operating robustly so that if a small number of probes behave differently than the rest, they are downweighted in the fitting step. We argue that adjacent poorly fitting probes for a given sample can be evidence of differential splicing and have designed a statistic to search for this behaviour. Using a public tissue panel dataset, we show many examples of tissue-specific alternative splicing. Furthermore, we show that evidence for putative alternative splicing has a strong correspondence between the Gene 1.0 ST and Exon 1.0 ST platforms. Conclusion We propose a new approach, FIRMAGene, to search for differentially spliced genes using the Gene 1.0 ST platform. Such an analysis complements the search for differential expression. We validate the method by illustrating several known examples and we note some of the challenges in interpreting the probe-level data. Software implementing our methods is freely available as an R package.

  16. Alternative fuelds in urban fleets

    Energy Technology Data Exchange (ETDEWEB)

    Lindsay, T.

    1994-12-31

    In this presentation the author addresses four main objectives. They are to: discuss programs that are driving the introduction of alternative fuels into fleet operations in urban areas around the country; define alternative fuels; quantify the present use and future projections on alternative fuel vehicles (AVFs) in the Chicago metropolitan statistical area; and discuss benefits of increased use of alternative fuels in urban areas. Factors which touch on these points include: present domestic dependence on petroleum for autos, with usage exceeding production; the large populations in urban areas which do not meet Clean Air Standards; recent legislative initiatives which give guidance and aid in the adoption of such strategies.

  17. Alternative fuelds in urban fleets

    International Nuclear Information System (INIS)

    In this presentation the author addresses four main objectives. They are to: discuss programs that are driving the introduction of alternative fuels into fleet operations in urban areas around the country; define alternative fuels; quantify the present use and future projections on alternative fuel vehicles (AVFs) in the Chicago metropolitan statistical area; and discuss benefits of increased use of alternative fuels in urban areas. Factors which touch on these points include: present domestic dependence on petroleum for autos, with usage exceeding production; the large populations in urban areas which do not meet Clean Air Standards; recent legislative initiatives which give guidance and aid in the adoption of such strategies

  18. Private Housing or Alternative Financing?

    Science.gov (United States)

    Bruno, Nick

    1999-01-01

    Explores the history of privatizing university housing and some current financing options, including use of developer and private foundations. Examples of successful alternative financing methods are highlighted. (GR)

  19. Alternative value chains for rare earths

    DEFF Research Database (Denmark)

    Machacek, Erika; Fold, Niels

    2014-01-01

    The 2011 peak in rare earth element (REE) prices revealed a vast knowledge gap on the REE-based industry considered to be almost monopolized by Chinese players. A global value chain (GVC) framework is used to provide an understanding of value-adding segments of REE in their transformation from mine...... to market but inquiries on the currently most-advanced company strategies for alternative REE supplies form the cornerstone of this paper. The Anglo-REE deposit developer strategies are aligned with the value-adding segments and different approaches to integration and co-optation of REE processing...

  20. Applications of Differential Geometry to Cartography

    Science.gov (United States)

    Benitez, Julio; Thome, Nestor

    2004-01-01

    This work introduces an application of differential geometry to cartography. The mathematical aspects of some geographical projections of Earth surface are revealed together with some of its more important properties. An important problem since the discovery of the 'spherical' form of the Earth is how to compose a reliable map of the surface of…