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Sample records for relative transcript abundance

  1. Transcript Abundance of Photorhabdus Insect-Related (Pir Toxin in Manduca sexta and Galleria mellonella Infections

    Directory of Open Access Journals (Sweden)

    Anaïs Castagnola

    2016-09-01

    Full Text Available In this study, we assessed pirAB toxin transcription in Photorhabdus luminescens laumondii (strain TT01 (Enterobacteriaceae by comparing mRNA abundance under in vivo and in vitro conditions. In vivo assays considered both natural and forced infections with two lepidopteran hosts: Galleria mellonella and Manduca sexta. Three portals of entry were utilized for the forced infection assays: (a integument; (b the digestive route (via mouth and anus; and (c the tracheal route (via spiracles. We also assessed plu4093-2 transcription during the course of a natural infection; this is when the bacteria are delivered by Heterorhabditis bacteriophora nematodes. Transcript abundance in G. mellonella was higher than in M. sexta at two of the observed time points: 15 and 18 h. Expression of pirAB plu4093-2 reached above endogenous control levels at 22 h in G. mellonella but not in M. sexta. Overall, pirAB plu4093-2 transcripts were not as highly expressed in M. sexta as in G. mellonella, from 15 to 22 h. This is the first study to directly compare pirAB plu4093-2 toxin transcript production considering different portals of entry.

  2. Proposed Method for Estimating Health-Promoting Glucosinolates and Hydrolysis Products in Broccoli (Brassica oleracea var. italica) Using Relative Transcript Abundance.

    Science.gov (United States)

    Becker, Talon M; Jeffery, Elizabeth H; Juvik, John A

    2017-01-18

    Due to the importance of glucosinolates and their hydrolysis products in human nutrition and plant defense, optimizing the content of these compounds is a frequent breeding objective for Brassica crops. Toward this goal, we investigated the feasibility of using models built from relative transcript abundance data for the prediction of glucosinolate and hydrolysis product concentrations in broccoli. We report that predictive models explaining at least 50% of the variation for a number of glucosinolates and their hydrolysis products can be built for prediction within the same season, but prediction accuracy decreased when using models built from one season's data for prediction of an opposing season. This method of phytochemical profile prediction could potentially allow for lower phytochemical phenotyping costs and larger breeding populations. This, in turn, could improve selection efficiency for phase II induction potential, a type of chemopreventive bioactivity, by allowing for the quick and relatively cheap content estimation of phytochemicals known to influence the trait.

  3. Light regimes differentially affect baseline transcript abundance of stress-axis and (neurodevelopment-related genes in zebrafish (Danio rerio, Hamilton 1822 AB and TL larvae

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    Ruud van den Bos

    2017-11-01

    Full Text Available Many strains of zebrafish (Danio rerio are readily available. Earlier we observed differences between AB and Tupfel long-fin (TL larvae regarding baseline hypothalamus-pituitary-interrenal (HPI axis activity and (neurodevelopment. Light regimes, i.e. 14 h light:10 h dark and 24 h continuous dark or light, affect hatching rate and larval growth. Here, we assessed baseline transcript abundance of HPI-axis-related genes and (neurodevelopment-related genes of AB and TL larvae (5 days post fertilisation using these light regimes. A principal component analysis revealed that in AB larvae the baseline expression of HPI-axis-related genes was higher the more hours of light, while the expression of (neurodevelopment-related genes was higher under 14 h light:10 h dark than under both continuous light or dark. In TL larvae, a complex pattern emerged regarding baseline expression of HPI-axis-related and (neurodevelopment-related genes. These data extend data of earlier studies by showing that light regimes affect gene-expression in larvae, and more importantly so, strengthen the notion of differences between larvae of the AB and TL strain. The latter finding adds to the growing database of phenotypical differences between zebrafish of the AB and TL strain.

  4. Detecting novel low-abundant transcripts in Drosophila

    DEFF Research Database (Denmark)

    Lee, Sanggyu; Bao, Jingyue; Zhou, Guolin

    2005-01-01

    Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244......,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts...... in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Udgivelsesdato: 2005-Jun...

  5. Transcriptional profiling of cells sorted by RNA abundance

    NARCIS (Netherlands)

    Klemm, Sandy; Semrau, Stefan; Wiebrands, Kay; Mooijman, Dylan; Faddah, Dina A; Jaenisch, Rudolf; van Oudenaarden, Alexander

    We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of

  6. Ethylene and pollination decrease transcript abundance of an ethylene receptor gene in Dendrobium petals.

    Science.gov (United States)

    Thongkum, Monthathip; Burns, Parichart; Bhunchoth, Anjana; Warin, Nuchnard; Chatchawankanphanich, Orawan; van Doorn, Wouter G

    2015-03-15

    We studied the expression of a gene encoding an ethylene receptor, called Ethylene Response Sensor 1 (Den-ERS1), in the petals of Dendrobium orchid flowers. Transcripts accumulated during the young floral bud stage and declined by the time the flowers had been open for several days. Pollination or exposure to exogenous ethylene resulted in earlier flower senescence, an increase in ethylene production and a lower Den-ERS1 transcript abundance. Treatment with 1-methylcyclopropene (1-MCP), an inhibitor of the ethylene receptor, decreased ethylene production and resulted in high transcript abundance. The literature indicates two kinds of ethylene receptor genes with regard to the effects of ethylene. One group shows ethylene-induced down-regulated transcription, while the other has ethylene-induced up-regulation. The present gene is an example of the first group. The 5' flanking region showed binding sites for Myb and myb-like, homeodomain, MADS domain, NAC, TCP, bHLH and EIN3-like transcription factors. The binding site for the EIN3-like factor might explain the ethylene effect on transcription. A few other transcription factors (RAV1 and NAC) seem also related to ethylene effects. Copyright © 2015 Elsevier GmbH. All rights reserved.

  7. Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L

    DEFF Research Database (Denmark)

    Rozenfeld, Christoffer; Butts, Ian A.E.; Tomkiewicz, Jonna

    2016-01-01

    -tubulin, insulin-like growth factor 2 (igf2), nucleoplasmin (npm2), prohibitin 2 (phb2), phosphatidylinositol glycan biosynthesis class F protein 5 (pigf5), and carnitine O-palmitoyltransferase liver isoform-like 1 (cpt1) are associated with embryonic developmental competence in other teleosts. Here, the relations...... and no hatching groups for any of the selected genes at 0, 2.5, and 5 HPF. However, at 30 HPF the hatch group showed significantly higher abundance of cpt1a, cpt1b, β-tubulin, phb2, and pigf5 transcripts than the no hatch group. Therefore, these results indicate that up-regulation of the transcription...

  8. Intergenic disease-associated regions are abundant in novel transcripts.

    Science.gov (United States)

    Bartonicek, N; Clark, M B; Quek, X C; Torpy, J R; Pritchard, A L; Maag, J L V; Gloss, B S; Crawford, J; Taft, R J; Hayward, N K; Montgomery, G W; Mattick, J S; Mercer, T R; Dinger, M E

    2017-12-28

    Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS single nucleotide polymorphisms (SNPs) and associated haplotype blocks are in intronic and intergenic regions, hindering their functional evaluation. While some of these risk-susceptibility regions encompass cis-regulatory sites, their transcriptional potential has never been systematically explored. To detect rare tissue-specific expression, we employed the transcript-enrichment method CaptureSeq on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic haploblocks associated with 392 traits and diseases, covering 73.9 Mb (2.2%) of the human genome. We show that a large proportion (85%) of disease-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific and enriched for GWAS SNPs as well as epigenetic markers of active transcription and enhancer activity. Similarly, we captured transcriptomes from 13 melanomas, targeting nine melanoma-associated haploblocks, and characterized 31 novel melanoma-specific transcripts that include fusion proteins, novel exons and non-coding RNAs, one-third of which showed allelically imbalanced expression. This resource of previously unreported transcripts in disease-associated regions ( http://gwas-captureseq.dingerlab.org ) should provide an important starting point for the translational community in search of novel biomarkers, disease mechanisms, and drug targets.

  9. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

    KAUST Repository

    Lescot, Magali

    2015-11-27

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

  10. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

    KAUST Repository

    Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier; Ludicone, Daniele; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki

    2015-01-01

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

  11. Genetic variations in GPSM3 associated with protection from rheumatoid arthritis affect its transcript abundance.

    Science.gov (United States)

    Gall, B J; Wilson, A; Schroer, A B; Gross, J D; Stoilov, P; Setola, V; Watkins, C M; Siderovski, D P

    2016-03-01

    G protein signaling modulator 3 (GPSM3) is a regulator of G protein-coupled receptor signaling, with expression restricted to leukocytes and lymphoid organs. Previous genome-wide association studies have highlighted single-nucleotide polymorphisms (SNPs; rs204989 and rs204991) in a region upstream of the GPSM3 transcription start site as being inversely correlated to the prevalence of rheumatoid arthritis (RA)-this association is supported by the protection afforded to Gpsm3-deficient mice in models of inflammatory arthritis. Here, we assessed the functional consequences of these polymorphisms. We collected biospecimens from 50 volunteers with RA diagnoses, 50 RA-free volunteers matched to the aforementioned group and 100 unmatched healthy young volunteers. We genotyped these individuals for GPSM3 (rs204989, rs204991), CCL21 (rs2812378) and HLA gene region (rs6457620) polymorphisms, and found no significant differences in minor allele frequencies between the RA and disease-free cohorts. However, we identified that individuals homozygous for SNPs rs204989 and rs204991 had decreased GPSM3 transcript abundance relative to individuals homozygous for the major allele. In vitro promoter activity studies suggest that SNP rs204989 is the primary cause of this decrease in transcript levels. Knockdown of GPSM3 in THP-1 cells, a human monocytic cell line, was found to disrupt ex vivo migration to the chemokine MCP-1.

  12. An Increase of Abundance and Transcriptional Activity for Acinetobacter junii Post Wastewater Treatment

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    Muhammad Raihan Jumat

    2018-04-01

    Full Text Available A membrane bioreactor (MBR-based wastewater treatment plant (WWTP in Saudi Arabia is assessed over a five-month period in 2015 and once in 2017 for bacterial diversity and transcriptional activity using metagenomics, metatranscriptomics and real time quantitative polymerase chain reaction (RT-qPCR. Acinetobacter spp. are shown to be enriched in the chlorinated effluent. Members of the Acinetobacter genus are the most abundant in the effluent and chlorinated effluent. At the species level, Acinetobacter junii have higher relative abundances post MBR and chlorination. RNA-seq analysis show that, in A. junii, 288 genes and 378 genes are significantly upregulated in the effluent and chlorinated effluent, respectively, with 98 genes being upregulated in both. RT-qPCR of samples in 2015 and 2017 confirm the upregulation observed in RNA-seq. Analysis of the 98 genes show that majority of the upregulated genes are involved in cellular repair and metabolism followed by resistance, virulence, and signaling. Additionally, two different subpopulations of A. junii are observed in the effluent and chlorinated effluent. The upregulation of cellular repair and metabolism genes, and the formation of different subpopulations of A. junii in both effluents provide insights into the mechanisms employed by A. junii to persist in the conditions of a WWTP.

  13. An Increase of Abundance and Transcriptional Activity for Acinetobacter junii Post Wastewater Treatment

    KAUST Repository

    Jumat, Muhammad

    2018-04-11

    A membrane bioreactor (MBR)-based wastewater treatment plant (WWTP) in Saudi Arabia is assessed over a five-month period in 2015 and once in 2017 for bacterial diversity and transcriptional activity using metagenomics, metatranscriptomics and real time quantitative polymerase chain reaction (RT-qPCR). Acinetobacter spp. are shown to be enriched in the chlorinated effluent. Members of the Acinetobacter genus are the most abundant in the effluent and chlorinated effluent. At the species level, Acinetobacter junii have higher relative abundances post MBR and chlorination. RNA-seq analysis show that, in A. junii, 288 genes and 378 genes are significantly upregulated in the effluent and chlorinated effluent, respectively, with 98 genes being upregulated in both. RT-qPCR of samples in 2015 and 2017 confirm the upregulation observed in RNA-seq. Analysis of the 98 genes show that majority of the upregulated genes are involved in cellular repair and metabolism followed by resistance, virulence, and signaling. Additionally, two different subpopulations of A. junii are observed in the effluent and chlorinated effluent. The upregulation of cellular repair and metabolism genes, and the formation of different subpopulations of A. junii in both effluents provide insights into the mechanisms employed by A. junii to persist in the conditions of a WWTP.

  14. An Increase of Abundance and Transcriptional Activity for Acinetobacter junii Post Wastewater Treatment

    KAUST Repository

    Jumat, Muhammad; Haroon, Muhammad; Aljassim, Nada I.; Cheng, Hong; Hong, Pei-Ying

    2018-01-01

    A membrane bioreactor (MBR)-based wastewater treatment plant (WWTP) in Saudi Arabia is assessed over a five-month period in 2015 and once in 2017 for bacterial diversity and transcriptional activity using metagenomics, metatranscriptomics and real time quantitative polymerase chain reaction (RT-qPCR). Acinetobacter spp. are shown to be enriched in the chlorinated effluent. Members of the Acinetobacter genus are the most abundant in the effluent and chlorinated effluent. At the species level, Acinetobacter junii have higher relative abundances post MBR and chlorination. RNA-seq analysis show that, in A. junii, 288 genes and 378 genes are significantly upregulated in the effluent and chlorinated effluent, respectively, with 98 genes being upregulated in both. RT-qPCR of samples in 2015 and 2017 confirm the upregulation observed in RNA-seq. Analysis of the 98 genes show that majority of the upregulated genes are involved in cellular repair and metabolism followed by resistance, virulence, and signaling. Additionally, two different subpopulations of A. junii are observed in the effluent and chlorinated effluent. The upregulation of cellular repair and metabolism genes, and the formation of different subpopulations of A. junii in both effluents provide insights into the mechanisms employed by A. junii to persist in the conditions of a WWTP.

  15. The flavonoid pathway in tomato seedlings: transcript abundance and the modeling of metabolite dynamics.

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    Marian Groenenboom

    Full Text Available Flavonoids are secondary metabolites present in all terrestrial plants. The flavonoid pathway has been extensively studied, and many of the involved genes and metabolites have been described in the literature. Despite this extensive knowledge, the functioning of the pathway in vivo is still poorly understood. Here, we study the flavonoid pathway using both experiments and mathematical models. We measured flavonoid metabolite dynamics in two tissues, hypocotyls and cotyledons, during tomato seedling development. Interestingly, the same backbone of interactions leads to very different accumulation patterns in the different tissues. Initially, we developed a mathematical model with constant enzyme concentrations that described the metabolic networks separately in both tissues. This model was unable to fit the measured flavonoid dynamics in the hypocotyls, even if we allowed unrealistic parameter values. This suggested us to investigate the effect of transcript abundance on flavonoid accumulation. We found that the expression of candidate flavonoid genes varies considerably with time. Variation in transcript abundance results in enzymatic variation, which could have a large effect on metabolite accumulation. Candidate transcript abundance was included in the mathematical model as representative for enzyme concentration. We fitted the resulting model to the flavonoid dynamics in the cotyledons, and tested it by applying it to the data from hypocotyls. When transcript abundance is included, we are indeed able to explain flavonoid dynamics in both tissues. Importantly, this is possible under the biologically relevant restriction that the enzymatic properties estimated by the model are conserved between the tissues.

  16. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea

    KAUST Repository

    Moitinho-Silva, Lucas; Bayer, Kristina; Cannistraci, Carlo; Giles, Emily; Ryu, Tae Woo; Seridi, Loqmane; Ravasi, Timothy; Hentschel, Ute T E

    2013-01-01

    Marine sponges are generally classified as high microbial abundance (HMA) and low microbial abundance (LMA) species. Here, 16S rRNA amplicon sequencing was applied to investigate the diversity, specificity and transcriptional activity of microbes

  17. An Assay in Microtitre Plates for Absolute Abundance of Chicken Interferon Alpha Transcripts

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    Renata Novak Kujundžić

    2010-01-01

    Full Text Available Immunosuppression of commercial chickens is a serious animal health and economic problem in the poultry industry. The major causes of the immunosuppression are viruses that suppress transcription of interferon genes, especially interferon alpha. There is a need for monitoring immunosuppression in commercially bred chickens. For this purpose, the absolute abundance of interferon alpha transcripts can be measured in blood of chickens by a suitable assay. Such an assay was used to estimate abundance of chicken interferon alpha in a sample of splenic cells induced with polyinosinic polycytidylic acid. The abundance measured was 29 ± 2 attomoles/µg total RNA. This assay can be performed in microtitre plates using samples collected from chickens in poultry houses.

  18. Relative Abundance of Adult Mosquitoes in University of Abuja Main ...

    African Journals Online (AJOL)

    Relative Abundance of Adult Mosquitoes in University of Abuja Main ... relative abundance of adult mosquitoes in four selected sites in University of Abuja ... These results indicated that vectors of mosquito-borne diseases are breeding in the ...

  19. Impacts of different exposure scenarios on transcript abundances in Danio rerio embryos when investigating the toxicological burden of riverine sediments.

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    Kerstin Bluhm

    Full Text Available PURPOSE: Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript abundance in zebrafish embryos exposed to whole sediment samples and corresponding organic extracts in order to identify the impact of different exposure pathways on sediment toxicity. MATERIALS AND METHODS: Danio rerio embryos were exposed to sublethal concentrations of three sediment samples from the Danube River, Germany. The sediment samples were investigated both as freeze-dried samples and as organic extracts. Silica dust and a process control of the extraction procedure were used as references. After exposure, mRNA was isolated and changes in profiles of gene expression levels were examined by an oligonucleotide microarray. The microarray results were compared with bioassays, chemical analysis of the sediments and profiles of gene expression levels induced by several single substances. RESULTS AND DISCUSSION: The microarray approach elucidated significant changes in the abundance of transcripts in exposed zebrafish embryos compared to the references. Generally, results could be related to Ah-receptor-mediated effects as confirmed by bioassays and chemical analysis of dioxin-like contaminants, as well as to exposure to stress-inducing compounds. Furthermore, the results indicated that mixtures of chemicals, as present in sediment and extract samples, result in complex changes of gene expression level profiles difficult to compare with profiles induced by single chemical substances. Specifically, patterns of transcript abundances were less influenced by the chemical composition at the sampling site compared t the method of exposure (sediment/extract. This effect might be related to different bioavailability of chemicals. CONCLUSIONS: The apparent

  20. Targeted reduction of highly abundant transcripts using pseudo-random primers.

    Science.gov (United States)

    Arnaud, Ophélie; Kato, Sachi; Poulain, Stéphane; Plessy, Charles

    2016-04-01

    Transcriptome studies based on quantitative sequencing can estimate levels of gene expression by measuring target RNA abundance in sequencing libraries. Sequencing costs are proportional to the total number of sequenced reads, and in order to cover rare RNAs, considerable quantities of abundant and identical reads are needed. This major limitation can be addressed by depleting a proportion of the most abundant sequences from the library. However, such depletion strategies involve either extra handling of the input RNA sample or use of a large number of reverse transcription primers, termed not-so-random (NSR) primers, which are costly to synthesize. Taking advantage of the high tolerance of reverse transcriptase to mis-prime, we found that it is possible to use as few as 40 pseudo-random (PS) reverse transcription primers to decrease the rate of undesirable abundant sequences within a library without affecting the overall transcriptome diversity. PS primers are simple to design and can be used to deplete several undesirable RNAs simultaneously, thus creating a flexible tool for enriching transcriptome libraries for rare transcript sequences.

  1. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea

    KAUST Repository

    Moitinho-Silva, Lucas

    2013-08-20

    Marine sponges are generally classified as high microbial abundance (HMA) and low microbial abundance (LMA) species. Here, 16S rRNA amplicon sequencing was applied to investigate the diversity, specificity and transcriptional activity of microbes associated with an LMA sponge (Stylissa carteri), an HMA sponge (Xestospongia testudinaria) and sea water collected from the central Saudi Arabia coast of the Red Sea. Altogether, 887 068 denoised sequences were obtained, of which 806 661 sequences remained after quality control. This resulted in 1477 operational taxonomic units (OTUs) that were assigned to 27 microbial phyla. The microbial composition of S. carteri was more similar to that of sea water than to that of X. testudinaria, which is consistent with the observation that the sequence data set of S. carteri contained many more possibly sea water sequences (~24%) than the X. testudinaria data set (~6%). The most abundant OTUs were shared between all three sources (S. carteri, X. testudinaria, sea water), while rare OTUs were unique to any given source. Despite this high degree of overlap, each sponge species contained its own specific microbiota. The X. testudinaria-specific bacterial taxa were similar to those already described for this species. A set of S. carteri-specific bacterial taxa related to Proteobacteria and Nitrospira was identified, which are likely permanently associated with S. carteri. The transcriptional activity of sponge-associated microorganisms correlated well with their abundance. Quantitative PCR revealed the presence of Poribacteria, representing typical sponge symbionts, in both sponge species and in sea water; however, low transcriptional activity in sea water suggested that Poribacteria are not active outside the host context. © 2013 John Wiley & Sons Ltd.

  2. De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

    Science.gov (United States)

    Keilwagen, Jens; Grau, Jan; Paponov, Ivan A; Posch, Stefan; Strickert, Marc; Grosse, Ivo

    2011-02-10

    Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan compendium based on experimental data from micro-array, ChIP-chip, ChIP-DSL, and DamID as well as Gene Ontology data. Finally, we apply Dispom to find binding sites differentially abundant in promoters of auxin-responsive genes extracted from Arabidopsis thaliana microarray data, and we find a motif that can be interpreted as a refined auxin responsive element predominately positioned in the 250-bp region upstream of the transcription start site. Using an independent data set of auxin-responsive genes, we find in genome-wide predictions that the refined motif is more specific for auxin-responsive genes than the canonical auxin-responsive element. In general, Dispom can be used to find differentially abundant motifs in sequences of any origin. However, the positional distribution learned by Dispom is especially beneficial if all sequences are aligned to some anchor point like the transcription start site in case of promoter sequences. We demonstrate that the combination of searching for differentially abundant motifs and inferring a position distribution from the data is beneficial for de-novo motif discovery. Hence, we make the tool freely available as a component of the open

  3. A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance

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    Wang Xiaowei

    2008-12-01

    Full Text Available Abstract Background Quantitative polymerase chain reaction (QPCR is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specific amplification of non-target genes has frequently been a problem. Although several online databases have been created for the storage and retrieval of experimentally validated primers, only a few thousand primer pairs are currently present in existing databases and the primers are not designed for use under a common PCR thermal profile. Results We previously reported the implementation of an algorithm to predict PCR primers for most known human and mouse genes. We now report the use of that resource to identify 17483 pairs of primers that have been experimentally verified to amplify unique sequences corresponding to distinct murine transcripts. The primer pairs have been validated by gel electrophoresis, DNA sequence analysis and thermal denaturation profile. In addition to the validation studies, we have determined the uniformity of amplification using the primers and the technical reproducibility of the QPCR reaction using the popular and inexpensive SYBR Green I detection method. Conclusion We have identified an experimentally validated collection of murine primer pairs for PCR and QPCR which can be used under a common PCR thermal profile, allowing the evaluation of transcript abundance of a large number of genes in parallel. This feature is increasingly attractive for confirming and/or making more precise data trends observed from experiments performed with DNA microarrays.

  4. Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume.

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    Brian L Zielinski

    transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function.

  5. In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme

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    Iqbal M Javed

    2008-09-01

    Full Text Available Abstract Background Sudden death syndrome (SDS of soybean (Glycine max L. Merr. is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv. Due to the complexity and length of the soybean-Fusarium interaction, the molecular mechanisms underlying plant resistance and susceptibility to the pathogen are not fully understood. F. virguliforme has a very wide host range for the ability to cause root rot and a very narrow host range for the ability to cause a leaf scorch. Arabidopsis thaliana is a host for many types of phytopathogens including bacteria, fungi, viruses and nematodes. Deciphering the variations among transcript abundances (TAs of functional orthologous genes of soybean and A. thaliana involved in the interaction will provide insights into plant resistance to F. viguliforme. Results In this study, we reported the analyses of microarrays measuring TA in whole plants after A. thaliana cv 'Columbia' was challenged with fungal pathogen F. virguliforme. Infection caused significant variations in TAs. The total number of increased transcripts was nearly four times more than that of decreased transcripts in abundance. A putative resistance pathway involved in responding to the pathogen infection in A. thaliana was identified and compared to that reported in soybean. Conclusion Microarray experiments allow the interrogation of tens of thousands of transcripts simultaneously and thus, the identification of plant pathways is likely to be involved in plant resistance to Fusarial pathogens. Dissection of the set functional orthologous genes between soybean and A. thaliana enabled a broad view of the functional relationships and molecular interactions among plant genes involved in F. virguliforme resistance.

  6. Impacts of Different Exposure Scenarios on Transcript Abundances in Danio rerio Embryos when Investigating the Toxicological Burden of Riverine Sediments.

    NARCIS (Netherlands)

    Bluhm, K.; Otte, J; Yang, L.; Zinsmeister, C.; Legradi, J.B.; Keiter, S.; Kosmehl, T.; Braunbeck, T.; Straehle, U.; Hollert, H.

    2014-01-01

    Purpose: Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio) embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript

  7. Axion: Mass -- Dark Matter Abundance Relation

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The axion is a hypothetical particle which would explain why QCD is approximately T-conserving, and is also an excellent Cold Dark Matter candidate. It should be possible to make a clean theoretical prediction relating the dark matter density in axions and the axion mass (under reasonable assumptions about inflation). But the axion's early-Universe dynamics, which establish its density as dark matter, are unexpectedly rich in a way which is only starting to yield to quantitative numerical study.

  8. types and abundance of arthropod fauna in relation to physico ...

    African Journals Online (AJOL)

    DJFLEX

    TYPES AND ABUNDANCE OF ARTHROPOD FAUNA IN RELATION ... The occurrence of arthropods associated with the bottom sediment of Warri River was investigated, and samples were collected ..... to analysis of the vegetation on Danish.

  9. mRNA Transcript abundance during plant growth and the influence of Li(+) exposure.

    Science.gov (United States)

    Duff, M C; Kuhne, W W; Halverson, N V; Chang, C-S; Kitamura, E; Hawthorn, L; Martinez, N E; Stafford, C; Milliken, C E; Caldwell, E F; Stieve-Caldwell, E

    2014-12-01

    Lithium (Li) toxicity in plants is, at a minimum, a function of Li(+) concentration, exposure time, species and growth conditions. Most plant studies with Li(+) focus on short-term acute exposures. This study examines short- and long-term effects of Li(+) exposure in Arabidopsis with Li(+) uptake studies and measured shoot mRNA transcript abundance levels in treated and control plants. Stress, pathogen-response and arabinogalactan protein genes were typically more up-regulated in older (chronic, low level) Li(+)-treatment plants and in the much younger plants from acute high-level exposures. The gene regulation behavior of high-level Li(+) resembled prior studies due to its influence on: inositol synthesis, 1-aminocyclopropane-1-carboxylate synthases and membrane ion transport. In contrast, chronically-exposed plants had gene regulation responses that were indicative of pathogen, cold, and heavy-metal stress, cell wall degradation, ethylene production, signal transduction, and calcium-release modulation. Acute Li(+) exposure phenocopies magnesium-deficiency symptoms and is associated with elevated expression of stress response genes that could lead to consumption of metabolic and transcriptional energy reserves and the dedication of more resources to cell development. In contrast, chronic Li(+) exposure increases expression signal transduction genes. The identification of new Li(+)-sensitive genes and a gene-based "response plan" for acute and chronic Li(+) exposure are delineated. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  10. Relative abundance of desert tortoises on the Nevada Test Site

    International Nuclear Information System (INIS)

    Rautenstrauch, K.R.; O'Farrell, T.P.

    1993-01-01

    Seven hundred fifty-nine transects having a total length of 1,191 km were walked during 1981--1986 to determine the distribution and relative abundance of desert tortoises (Gopherus agassizii) on the Nevada Test Site (NTS). The abundance of tortoises on NTS was low to very low relative to other populations in the Mojave Desert. Sign of tortoises was found from 880 to 1,570 m elevation and was more abundant above 1,200 m than has been reported previously for Nevada. Tortoises were more abundant on NTS on the upper alluvial fans and slopes of mountains than in valley bottoms. They also were more common on or near limestone and dolomite mountains than on mountains of volcanic origin

  11. The raccoon polyomavirus genome and tumor antigen transcription are stable and abundant in neuroglial tumors.

    Science.gov (United States)

    Brostoff, Terza; Dela Cruz, Florante N; Church, Molly E; Woolard, Kevin D; Pesavento, Patricia A

    2014-11-01

    Raccoon polyomavirus (RacPyV) is associated with 100% of neuroglial tumors in free-ranging raccoons. Other tumor-associated polyomaviruses (PyVs), including simian virus 40 (SV40), murine PyV, and Merkel cell PyV, are found integrated in the host genome in neoplastic cells, where they constitutively express splice variants of the tumor antigen (TAg) gene. We have previously reported that RacPyV exists only as an episome (nonintegrated) in neuroglial tumors. Here, we have investigated TAg transcription in primary tumor tissue by transcriptome analysis, and we identified the alternatively spliced TAg transcripts for RacPyV. We also determined that TAg was highly transcribed relative to host cellular genes. We further colocalized TAg DNA and mRNA by in situ hybridization and found that the majority of tumor cells showed positive staining. Lastly, we examined the stability of the viral genome and TAg transcription by quantitative reverse transcriptase PCR in cultured tumor cells in vitro and in a mouse xenograft model. When tumor cells were cultured in vitro, TAg transcription increased nearly 2 log-fold over that of parental tumor tissue by passage 17. Both episomal viral genome and TAg transcription were faithfully maintained in culture and in tumors arising from xenotransplantation of cultured cells in mice. This study represents a minimal criterion for RacPyV's association with neuroglial tumors and a novel mechanism of stability for a polyomavirus in cancer. The natural cycle of polyomaviruses in mammals is to persist in the host without causing disease, but they can cause cancer in humans or in other animals. Because this is an unpredictable and rare event, the oncogenic potential of polyomavirus is primarily evaluated in laboratory animal models. Recently, raccoon polyomavirus (RacPyV) was identified in neuroglial tumors of free-ranging raccoons. Viral copy number was consistently high in these tumors but was low or undetectable in nontumor tissue or in

  12. Relative abundance of mosquito species in Katsina Metropolis ...

    African Journals Online (AJOL)

    A study was conducted on the relative abundance of mosquito species, around selected areas of Katsina metropolis, Katsina State, Nigeria during the months of January, February, April and June 2010. Mosquitoes were collected from five sampling sites: Kofar Durbi, Kofar Kaura, Kofar Marusa, GRA and Layout. These were ...

  13. Species Composition, Relative Abundance and Distribution of the ...

    African Journals Online (AJOL)

    Species Composition, Relative Abundance and Distribution of the Avian Fauna of Entoto Natural Park and Escarpment, Addis Ababa. ... Eucalyptus plantation, soil erosion, deforestation, habitat fragmentation, settlement and land degradation were the main threats for the distribution of birds in the present study area.

  14. Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays

    Science.gov (United States)

    Hahn, Cassidy M.; Iwanowicz, Luke R.; Cornman, Robert S.; Mazik, Patricia M.; Blazer, Vicki S.

    2016-01-01

    Environmental studies increasingly identify the presence of both contaminants of emerging concern (CECs) and legacy contaminants in aquatic environments; however, the biological effects of these compounds on resident fishes remain largely unknown. High throughput methodologies were employed to establish partial transcriptomes for three wild-caught, non-model fish species; smallmouth bass (Micropterus dolomieu), white sucker (Catostomus commersonii) and brown bullhead (Ameiurus nebulosus). Sequences from these transcriptome databases were utilized in the development of a custom nCounter CodeSet that allowed for direct multiplexed measurement of 50 transcript abundance endpoints in liver tissue. Sequence information was also utilized in the development of quantitative real-time PCR (qPCR) primers. Cross-species hybridization allowed the smallmouth bass nCounter CodeSet to be used for quantitative transcript abundance analysis of an additional non-model species, largemouth bass (Micropterus salmoides). We validated the nCounter analysis data system with qPCR for a subset of genes and confirmed concordant results. Changes in transcript abundance biomarkers between sexes and seasons were evaluated to provide baseline data on transcript modulation for each species of interest.

  15. Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays.

    Science.gov (United States)

    Hahn, Cassidy M; Iwanowicz, Luke R; Cornman, Robert S; Mazik, Patricia M; Blazer, Vicki S

    2016-12-01

    Environmental studies increasingly identify the presence of both contaminants of emerging concern (CECs) and legacy contaminants in aquatic environments; however, the biological effects of these compounds on resident fishes remain largely unknown. High throughput methodologies were employed to establish partial transcriptomes for three wild-caught, non-model fish species; smallmouth bass (Micropterus dolomieu), white sucker (Catostomus commersonii) and brown bullhead (Ameiurus nebulosus). Sequences from these transcriptome databases were utilized in the development of a custom nCounter CodeSet that allowed for direct multiplexed measurement of 50 transcript abundance endpoints in liver tissue. Sequence information was also utilized in the development of quantitative real-time PCR (qPCR) primers. Cross-species hybridization allowed the smallmouth bass nCounter CodeSet to be used for quantitative transcript abundance analysis of an additional non-model species, largemouth bass (Micropterus salmoides). We validated the nCounter analysis data system with qPCR for a subset of genes and confirmed concordant results. Changes in transcript abundance biomarkers between sexes and seasons were evaluated to provide baseline data on transcript modulation for each species of interest. Published by Elsevier Inc.

  16. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

    Science.gov (United States)

    Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

    2016-01-01

    We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

  17. A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinated genes accompanies its sedentary parasitic phase

    Directory of Open Access Journals (Sweden)

    Overall Christopher C

    2007-04-01

    Full Text Available Abstract Background Heterodera glycines (soybean cyst nematode [SCN], the major pathogen of Glycine max (soybean, undergoes muscle degradation (sarcopenia as it becomes sedentary inside the root. Many genes encoding muscular and neuromuscular components belong to the uncoordinated (unc family of genes originally identified in Caenorhabditis elegans. Previously, we reported a substantial decrease in transcript abundance for Hg-unc-87, the H. glycines homolog of unc-87 (calponin during the adult sedentary phase of SCN. These observations implied that changes in the expression of specific muscle genes occurred during sarcopenia. Results We developed a bioinformatics database that compares expressed sequence tag (est and genomic data of C. elegans and H. glycines (CeHg database. We identify H. glycines homologs of C. elegans unc genes whose protein products are involved in muscle composition and regulation. RT-PCR reveals the transcript abundance of H. glycines unc homologs at mobile and sedentary stages of its lifecycle. A prominent reduction in transcript abundance occurs in samples from sedentary nematodes for homologs of actin, unc-60B (cofilin, unc-89, unc-15 (paromyosin, unc-27 (troponin I, unc-54 (myosin, and the potassium channel unc-110 (twk-18. Less reduction is observed for the focal adhesion complex gene Hg-unc-97. Conclusion The CeHg bioinformatics database is shown to be useful in identifying homologs of genes whose protein products perform roles in specific aspects of H. glycines muscle biology. Our bioinformatics comparison of C. elegans and H. glycines genomic data and our Hg-unc-87 expression experiments demonstrate that the transcript abundance of specific H. glycines homologs of muscle gene decreases as the nematode becomes sedentary inside the root during its parasitic feeding stages.

  18. EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

    Science.gov (United States)

    Lee, Soohyun; Seo, Chae Hwa; Alver, Burak Han; Lee, Sanghyuk; Park, Peter J

    2015-09-03

    RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost. We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods. EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.

  19. Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli' (Pyrus sinkiangensis Yu) by digital transcript abundance measurements.

    Science.gov (United States)

    Qi, Xiaoxiao; Wu, Jun; Wang, Lifen; Li, Leiting; Cao, Yufen; Tian, Luming; Dong, Xingguang; Zhang, Shaoling

    2013-10-23

    'Kuerlexiangli' (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit shape and quality. Although several studies have looked into the physiological aspects of the calyx abscission process, the underlying molecular mechanisms remain unknown. In order to better understand the molecular basis of the process of calyx abscission, materials at three critical stages of regulation, with 6000 × Flusilazole plus 300 × PBO treatment (calyx abscising treatment) and 50 mg.L-1GA3 treatment (calyx persisting treatment), were collected and cDNA fragments were sequenced using digital transcript abundance measurements to identify candidate genes. Digital transcript abundance measurements was performed using high-throughput Illumina GAII sequencing on seven samples that were collected at three important stages of the calyx abscission process with chemical agent treatments promoting calyx abscission and persistence. Altogether more than 251,123,845 high quality reads were obtained with approximately 8.0 M raw data for each library. The values of 69.85%-71.90% of clean data in the digital transcript abundance measurements could be mapped to the pear genome database. There were 12,054 differentially expressed genes having Gene Ontology (GO) terms and associating with 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. The differentially expressed genes correlated with calyx abscission were mainly involved in photosynthesis, plant hormone signal transduction, cell wall modification, transcriptional regulation, and carbohydrate metabolism. Furthermore, candidate calyx abscission-specific genes, e.g. Inflorescence deficient in abscission gene, were identified. Quantitative real-time PCR was used to confirm the digital transcript abundance measurements results. We identified candidate genes that showed highly dynamic changes in

  20. Relation between grade and abundance of manganese nodules

    Digital Repository Service at National Institute of Oceanography (India)

    Sudhakar, M.

    Data from more than 1000 locations in the Central Indian Ocean Basin (CIOB) where both bulk nodule chemistry and abundance were determined and utilized to study the relationship between grade and abundance of manganese nodule deposits. Grade...

  1. Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function.

    Directory of Open Access Journals (Sweden)

    Cheryl Hemingway

    Full Text Available The WHO estimates around a million children contract tuberculosis (TB annually with over 80 000 deaths from dissemination of infection outside of the lungs. The insidious onset and association with skin test anergy suggests failure of the immune system to both recognise and respond to infection. To understand the immune mechanisms, we studied genome-wide whole blood RNA expression in children with TB meningitis (TBM. Findings were validated in a second cohort of children with TBM and pulmonary TB (PTB, and functional T-cell responses studied in a third cohort of children with TBM, other extrapulmonary TB (EPTB and PTB. The predominant RNA transcriptional response in children with TBM was decreased abundance of multiple genes, with 140/204 (68% of all differentially regulated genes showing reduced abundance compared to healthy controls. Findings were validated in a second cohort with concordance of the direction of differential expression in both TBM (r2 = 0.78 p = 2x10-16 and PTB patients (r2 = 0.71 p = 2x10-16 when compared to a second group of healthy controls. Although the direction of expression of these significant genes was similar in the PTB patients, the magnitude of differential transcript abundance was less in PTB than in TBM. The majority of genes were involved in activation of leucocytes (p = 2.67E-11 and T-cell receptor signalling (p = 6.56E-07. Less abundant gene expression in immune cells was associated with a functional defect in T-cell proliferation that recovered after full TB treatment (p<0.0003. Multiple genes involved in T-cell activation show decreased abundance in children with acute TB, who also have impaired functional T-cell responses. Our data suggest that childhood TB is associated with an acquired immune defect, potentially resulting in failure to contain the pathogen. Elucidation of the mechanism causing the immune paresis may identify new treatment and prevention strategies.

  2. Knock-down of transcript abundance of a family of Kunitz proteinase inhibitor genes in white clover (Trifolium repens) reveals a redundancy and diversity of gene function.

    Science.gov (United States)

    Islam, Afsana; Leung, Susanna; Burgess, Elisabeth P J; Laing, William A; Richardson, Kim A; Hofmann, Rainer W; Dijkwel, Paul P; McManus, Michael T

    2015-12-01

    The transcriptional regulation of four phylogenetically distinct members of a family of Kunitz proteinase inhibitor (KPI) genes isolated from white clover (Trifolium repens; designated Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5) has been investigated to determine their wider functional role. The four genes displayed differential transcription during seed germination, and in different tissues of the mature plant, and transcription was also ontogenetically regulated. Heterologous over-expression of Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5 in Nicotiana tabacum retarded larval growth of the herbivore Spodoptera litura, and an increase in the transcription of the pathogenesis-related genes PR1 and PR4 was observed in the Tr-KPI1 and Tr-KPI4 over-expressing lines. RNA interference (RNAi) knock-down lines in white clover displayed significantly altered vegetative growth phenotypes with inhibition of shoot growth and a stimulation of root growth, while knock-down of Tr-KPI1, Tr-KPI2 and Tr-KPI5 transcript abundance also retarded larval growth of S. litura. Examination of these RNAi lines revealed constitutive stress-associated phenotypes as well as altered transcription of cellular signalling genes. These results reveal a functional redundancy across members of the KPI gene family. Further, the regulation of transcription of at least one member of the family, Tr-KPI2, may occupy a central role in the maintenance of a cellular homeostasis. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  3. Relative foraminiferan abundance as an indicator of seagrass sediment health:

    Science.gov (United States)

    Cajandig, P.; Quiros, A.; Nolan, H.; Tallman, R.; Cooper, N.; Ayala, J.; Courtier, C.

    2013-12-01

    Authors: Patrick Cajandig*, Jose Ayala**, Nathaniel Cooper**, Catherine Courtier**, Hannah Nolan**, Rachelle Tallman**, T.E. Angela L. Quiros** * Davis High-School CA, **University of California Santa Cruz, Ecology and Evolutionary Biology Department Seagrasses are a key component in coastal ecosystems. Found in shallow marine environments, they make a large contribution to coastal ecosystem health by sustaining water quality, stabilizing the sea bottom, and providing habitat as well as food for other organisms. Seagrasses accumulate tiny grains of sediment, increasing water clarity. Just like barren hills are prone to erosion compared to vegetated, rooted down hills, we find a similar situation in the ocean. Seagrasses have broad roots that extend vertically and horizontally to help stabilize the seabed. Seagrasses support a whole ecosystem, because some organisms feed off of the seagrass alone, while others feed off the inhabitants of the seagrass. The quality of sediment is a vital part of seagrass health, just like nutrient rich soils are important to land plants. But what in seagrass sediment is a good indication of health? We hypothesize that seagrass health measures such as percent cover and seagrass species diversity are related to the abundance of foraminiferans relative to other seagrass sediment components. My mentor, T. E. Angela L. Quiros, from the University of California, Santa Cruz (UCSC), collected the sediment samples from seagrass beds in the Philippines. Samples were dried and brought to UCSC for sediment sieving. We used different sized sieves to sort the sediment. These sieves ranged from coarse to very fine sieves (Phi -2.0 (coarse) through +3.0 (fine) going in 0.5 intervals on a log scale). We weighed the sediment that was caught in each tray and separated them into bags of different size classes. To analyze each sample, we subsampled four size classes (Phi's -2.0, -1.5,-1.0, 0.0), and used a dissecting scope to identify and then weigh the

  4. Dominance behaviour in a non-aggressive flatfish, Senegalese sole (Solea senegalensis and brain mRNA abundance of selected transcripts.

    Directory of Open Access Journals (Sweden)

    Elvira Fatsini

    Full Text Available Dominance is defined as the preferential access to limited resources. The present study aimed to characterise dominance in a non-aggressive flatfish species, the Senegalese sole (Solea senegalensis by 1 identifying dominance categories and associated behaviours and 2 linking dominance categories (dominant and subordinate with the abundance of selected mRNA transcripts in the brain. Early juveniles (n = 74, 37 pairs were subjected to a dyadic dominance test, related to feeding, and once behavioural phenotypes had been described the abundance of ten selected mRNAs related to dominance and aggressiveness was measured in the brain. Late juveniles were subjected to two dyadic dominance tests (n = 34, 17 pairs, related to feeding and territoriality and one group test (n = 24, 4 groups of 6 fish. Sole feeding first were categorized as dominant and sole feeding second or not feeding as subordinate. Three social behaviours (i. "Resting the head" on another fish, ii. "Approaching" another fish, iii. "Swimming above another" fish were associated with dominance of feeding. Two other variables (i. Total time occupying the preferred area during the last 2 hours of the 24 h test, ii. Organisms occupying the preferred area when the test ended were representative of dominance in the place preference test. In all tests, dominant fish compared to subordinate fish displayed a significantly higher number of the behaviours "Rest the head" and "Approaches". Moreover, dominant sole dominated the sand at the end of the test, and in the group test dominated the area close to the feed delivery point before feed was delivered. The mRNA abundance of the selected mRNAs related to neurogenesis (nrd2 and neuroplasticity (c-fos in dominant sole compared to subordinate were significantly different. This is the first study to characterise dominance categories with associated behaviours and mRNA abundance in Senegalese sole and provides tools to study dominance related problems in

  5. Resistance-related gene transcription and antioxidant enzyme ...

    African Journals Online (AJOL)

    The two tobacco relatives of Nicotiana alata and Nicotiana longiflora display a high level of resistance against Colletotrichum nicotianae and the two genes NTF6 and NtPAL related to pathogen defense transcription were higher in N. alata and N. longiflora than the commercial cv. K326. Inoculation with C. nicotianae ...

  6. Relative abundance and distribution of bacteria in the gut of ...

    African Journals Online (AJOL)

    Escherichia coli, Aeromonas hydrophila, Salmonella typhi and Pseudomonas aeruginosa were the most abundant species in the samples from Epe Lagoon while Escherichia coli, Aeromonas hydrophila, Proteus vulgaris and Pseudomonas aeruginosa were predominant in Badagry Creek. It was noteworthy that Citrobacter ...

  7. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein coding...... regions, the map of transcripts is very complex due to small transcripts from the flanking ends of the transcription unit, the use of multiple start and stop sites for the main transcript, production of multiple functional RNA molecules from the same primary transcript, and RNA molecules made...... by independent transcription from within the unit. In genomic regions separating those that encode proteins or highly abundant RNA molecules with known function, transcripts are generally of low abundance and short-lived. In most of these cases, it is unclear to what extent a function is related to transcription...

  8. Transcriptional profiling of immune-related genes in Pacific white shrimp (Litopenaeus vannamei) during ontogenesis.

    Science.gov (United States)

    Quispe, Ruth L; Justino, Emily B; Vieira, Felipe N; Jaramillo, Michael L; Rosa, Rafael D; Perazzolo, Luciane M

    2016-11-01

    We have performed here a gene expression analysis to determine the developmental stage at the main genes involved in crustacean immune response begin to be expressed and their changes in mRNA abundance during shrimp development. By using a quantitative PCR-based approach, we have measured the mRNA abundance of 24 immune-related genes from different functional categories in twelve developmental stages ranging from fertilized eggs to larval and postlarval stages and also in juveniles. We showed for the first time that the main genes from the RNAi-based post-transcriptional pathway involved in shrimp antiviral immunity are transcribed in all developmental stages, but exhibit a diverse pattern of gene expression during shrimp ontogenesis. On the other hand, hemocyte-expressed genes mainly involved in antimicrobial defenses appeared to be transcribed in larval stages, indicating that hematopoiesis initiates early in development. Moreover, transcript levels of some genes were early detected in fertilized eggs at 0-4 h post-spawning, suggesting a maternal contribution of immune-related transcripts to shrimp progeny. Altogether, our results provide important clues regarding the ontogenesis of hemocytes as well the establishment of antiviral and antimicrobial defenses in shrimp. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Influence of culture medium composition on relative mRNA abundances in domestic cat embryos.

    Science.gov (United States)

    Hribal, R; Jewgenow, K; Braun, B C; Comizzoli, P

    2013-04-01

    Different culture conditions have been used to produce domestic cat embryos. As part of the in vitro procedures, the medium composition significantly affects the quality of the embryo development also. Quality assessments based on cleavage kinetics and blastomere symmetry are useful, but embryos also can differ in their relative gene expression patterns despite similar morphological characteristics. The aim of this study was to compare cat embryos produced with two different in vitro culture systems routinely used in two different laboratories [Smithsonian Conservation Biology Institute, Washington D.C., USA (SCBI) and Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (IZW)]. Specifically, relative mRNA expression patterns of critical genes for pre-implantation embryo development were assessed in both conditions. Embryos were produced in parallel in both culture systems by IVF using frozen-thawed ejaculated semen in the United States and fresh epididymal sperm in Germany. Success of embryo development in vitro was recorded as well as relative mRNA abundances [DNA methyltransferases 1 and 3A (DNMT1, DNMT3A), gap junction protein alpha 1 (GJA1), octamer-binding transcription factor 4 [OCT4], insulin-like growth factors 1 and 2 receptors (IGF1R, IGF2R), beta-actin (ACTB)] in pools of days 4-5 morulae by semi-quantitative RT-PCR assay. Percentages of cleaved embryos were similar (p > 0.05) between both culture systems, regardless of the location. OCT4 mRNA abundance was higher (p culture system compared with those from the IZW system when epididymal sperm was used for IVF. No clear correlation between the expression pattern and the culture system could be found for all other genes. It is suggested that OCT4 expression might be affected by the media composition in some conditions and can be the indicator of a better embryo quality. © 2012 Blackwell Verlag GmbH.

  10. The abundance properties of nearby late-type galaxies. II. The relation between abundance distributions and surface brightness profiles

    International Nuclear Information System (INIS)

    Pilyugin, L. S.; Grebel, E. K.; Zinchenko, I. A.; Kniazev, A. Y.

    2014-01-01

    The relations between oxygen abundance and disk surface brightness (OH–SB relation) in the infrared W1 band are examined for nearby late-type galaxies. The oxygen abundances were presented in Paper I. The photometric characteristics of the disks are inferred here using photometric maps from the literature through bulge-disk decomposition. We find evidence that the OH–SB relation is not unique but depends on the galactocentric distance r (taken as a fraction of the optical radius R 25 ) and on the properties of a galaxy: the disk scale length h and the morphological T-type. We suggest a general, four-dimensional OH–SB relation with the values r, h, and T as parameters. The parametric OH–SB relation reproduces the observed data better than a simple, one-parameter relation; the deviations resulting when using our parametric relation are smaller by a factor of ∼1.4 than that of the simple relation. The influence of the parameters on the OH–SB relation varies with galactocentric distance. The influence of the T-type on the OH–SB relation is negligible at the centers of galaxies and increases with galactocentric distance. In contrast, the influence of the disk scale length on the OH–SB relation is at a maximum at the centers of galaxies and decreases with galactocentric distance, disappearing at the optical edges of galaxies. Two-dimensional relations can be used to reproduce the observed data at the optical edges of the disks and at the centers of the disks. The disk scale length should be used as a second parameter in the OH–SB relation at the center of the disk while the morphological T-type should be used as a second parameter in the relation at optical edge of the disk. The relations between oxygen abundance and disk surface brightness in the optical B and infrared K bands at the center of the disk and at optical edge of the disk are also considered. The general properties of the abundance–surface brightness relations are similar for the three

  11. Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters.

    Science.gov (United States)

    Sawers, Ruairidh J H; Svane, Simon F; Quan, Clement; Grønlund, Mette; Wozniak, Barbara; Gebreselassie, Mesfin-Nigussie; González-Muñoz, Eliécer; Chávez Montes, Ricardo A; Baxter, Ivan; Goudet, Jerome; Jakobsen, Iver; Paszkowski, Uta

    2017-04-01

    Plant interactions with arbuscular mycorrhizal fungi have long attracted interest for their potential to promote more efficient use of mineral resources in agriculture. Their use, however, remains limited by a lack of understanding of the processes that determine the outcome of the symbiosis. In this study, the impact of host genotype on growth response to mycorrhizal inoculation was investigated in a panel of diverse maize lines. A panel of 30 maize lines was evaluated with and without inoculation with arbuscular mycorrhizal fungi. The line Oh43 was identified to show superior response and, along with five other reference lines, was characterized in greater detail in a split-compartment system, using 33 P to quantify mycorrhizal phosphorus uptake. Changes in relative growth indicated variation in host capacity to profit from the symbiosis. Shoot phosphate content, abundance of root-internal and -external fungal structures, mycorrhizal phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters varied among lines. Superior response in Oh43 is correlated with extensive development of root-external hyphae, accumulation of specific Pht1 transcripts and high phosphorus uptake by mycorrhizal plants. The data indicate that host genetic factors influence fungal growth strategy with an impact on plant performance. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  12. Moderate nutrient restriction influences transcript abundance of genes impacting production efficiencies of beef cattle in fetal liver, muscle, and cerebrum by d 50 of gestation

    Science.gov (United States)

    We hypothesized that a moderate maternal nutrient restriction during the first 50 d of gestation in beef heifers would affect transcript abundance of genes impacting production efficiency phenotypes in fetal liver, muscle, and cerebrum. Fourteen Angus-cross heifers were estrus synchronized and assig...

  13. Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters

    DEFF Research Database (Denmark)

    Sawers, Ruairidh J H; Svane, Simon F; Quan, Clement

    2016-01-01

    content, abundance of intra-radical and root-external fungal structures, mycorrhizal phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters varied among lines. Larger growth responses in Oh43 were correlated with extensive development of root-external hyphae...

  14. Archaeal and bacterial H-GDGTs are abundant in peat and their relative abundance is positively correlated with temperature

    Science.gov (United States)

    Naafs, B. D. A.; McCormick, D.; Inglis, G. N.; Pancost, R. D.; T-GRES Peat Database Collaborators

    2018-04-01

    Glycerol monoalkyl glycerol tetraether lipids (GMGTs; also called 'H-GDGTs') differ from the more commonly studied glycerol dialkyl glycerol tetraether (GDGTs) in that they have an additional covalent bond that links the two alkyl chains. Six different archaeal isoprenoidal H-GDGTs (H-isoGDGTs) and one branched H-GDGT (H-brGDGT), presumably produced by bacteria, have previously been found. However, the function of H-GDGTs in both domains of life is unknown. It is thought that the formation of this additional covalent bond results in enhanced membrane stability, accounting for the high abundance of H-GDGTs in extreme environments such as geothermal settings, but so far there has been little evidence to support this hypothesis. Here we report the distribution of H-GDGTs in a global peat database (n = 471) with a broad range in mean annual air temperature (MAAT) and pH. This is the first finding of H-GDGTs in soils (specifically, peat), highlighting that H-GDGTs are widespread in mesophilic settings. In addition, we report the presence of two new H-brGDGTs with one (H-1034) and two (H-1048) additional methyl groups, respectively. Our results suggest that the relative abundance of both bacterial and archaeal H-GDGTs compared to regular GDGTs is related to temperature with the highest relative abundance of H-GDGTs in tropical peats. Although other factors besides temperature likely also play a role, these results do support the hypothesis that H-GDGTs are an adaptation to temperature to maintain membrane stability. The observation that both bacterial and archaeal membrane lipids respond to temperature indicates the same adaption across the lipid divide between these two domains of life, suggesting parallel or convergent evolution (potentially facilitated by lateral gene transfer).

  15. Transcriptional regulation of genes related to progesterone production.

    Science.gov (United States)

    Mizutani, Tetsuya; Ishikane, Shin; Kawabe, Shinya; Umezawa, Akihiro; Miyamoto, Kaoru

    2015-01-01

    Steroid hormones are synthesized from cholesterol in various tissues, mainly in the adrenal glands and gonads. Because these lipid-soluble steroid hormones immediately diffuse through the cells in which they are produced, their secretion directly reflects the activity of the genes related to their production. Progesterone is important not only for luteinization and maintenance of pregnancy, but also as a substrate for most other steroids. Steroidogenic acute regulatory protein (STAR), cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc), and 3β-hydroxysteroid dehydrogenase/Δ(5)-Δ(4) isomerase (3β-HSD) are well-known proteins essential for progesterone production. In addition to them, glutathione S-transferase A1-1 and A3-3 are shown to exert Δ(5)-Δ(4) isomerization activity to produce progesterone in a cooperative fashion with 3β-HSD. 5-Aminolevulinic acid synthase 1, ferredoxin 1, and ferredoxin reductase also play a role in steroidogenesis as accessory factors. Members of the nuclear receptor 5A (NR5A) family (steroidogenic factor 1 and liver receptor homolog 1) play a crucial role in the transcriptional regulation of these genes. The NR5A family activates these genes by binding to NR5A responsive elements present within their promoter regions, as well as to the elements far from their promoters. In addition, various NR5A-interacting proteins including peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α), nuclear receptor subfamily 0, group B, member 1 (DAX-1), and CCAAT/enhancer-binding proteins (C/EBP) are involved in the transcription of NR5A target genes and regulate the transcription either positively or negatively under both basal and tropic hormone-stimulated conditions. In this review, we describe the transcriptional regulation of genes related to progesterone production.

  16. Distribution and relative abundance of the marine catfish (Siluriformes, Ariidae) in Sepetiba Bay, Rio de Janeiro

    OpenAIRE

    Azevedo, Márcia Cristina Costa de; Araújo, Francisco Gerson; Cruz Filho, Antônio Gomes da; Santos, Alexandre Clístenes de Alcântara

    1998-01-01

    Marine catfish (Ariidae) are abundant resources in otter trawl fisheries carried out at Sepetiba Bay, Rio de Janeiro (Lat. 22º54, 23º04'S; Long. 43º34 44º10'W). Relative abundance and distribution were assessed, based in 158 fishing sampling at seven sites in the Bay, between July-1993 e June-1996. Five species were recorded in the following abundance rank order: Genidens genidens (Valenciennes, 1839), Caihorops spixii (Agassiz,1829), Sciadeichthys lunisculis (Valenciennes, 1840), Nelunia bar...

  17. Regulation of an H-ras-related transcript by parathyroid hormone in rat osteosarcoma cells

    Science.gov (United States)

    Scott, D. K.; Weaver, W. R.; Clohisy, J. C.; Brakenhoff, K. D.; Kahn, A. J.; Partridge, N. C.

    1992-01-01

    The rat osteosarcoma cell line UMR 106-01 is a commonly used model system for the study of osteoblast function. However, it also expresses a phenotype characteristic of transformed cells. To test whether the latter could be accounted for by aberrant oncogene expression, we probed Northern blots of UMR and other osteoblastic cells with a panel of oncogene probes. These blots, when probed with a cDNA specific for v-H-ras, revealed a 7.0-kilobase (kb) H-ras-related transcript (designated HRRT) in UMR 106-01 cells that was not expressed in other osteoblastic cells. Osteoblast-enriched calvarial cells expressed the typical 1.1-kb H-ras mRNA, which was absent in UMR cells. Additionally, Western blots of lysates of UMR cells documented the presence of three proteins immunologically related to H-rasp21. To determine whether HRRT represented a recombinant retrovirus product, Northern blots were probed with a cDNA specific for the highly conserved gag-pol region of Moloney murine leukemia virus. These blots showed parallel cross-reactivity with an apparently identical transcript of 7.0 kb. The 7.0-kb transcripts detected by both v-H-ras and gag-pol probes declined to the same extent after treatment with concentrations of PTH known to inhibit proliferation of these cells. PTH regulated the abundance of HRRT in a time- and dose-dependent manner, with greatest repression of the transcript after 8 h of treatment with 10(-8) M PTH. The decrease in HRRT could not be completely accounted for by changes in transcriptional activity, as determined by nuclear run-on assays.(ABSTRACT TRUNCATED AT 250 WORDS).

  18. The relative abundance of desert tortoises on the Nevada Test Site within ecological landform units

    International Nuclear Information System (INIS)

    Woodward, R.; Rautenstrauch, K.R.; Hall, D.B.; Ostler, W.K.

    1998-09-01

    Sign-survey transects were sampled in 1996 to better determine the relative abundance of desert tortoises on the Nevada Test Site (NTS). These transects were sampled within ecological land-form units (ELUs), which are small, ecologically homogeneous units of land. Two-hundred and six ELUs were sampled by walking 332 transects totaling 889 kilometers (km). These ELUs covered 528 km 2 . Two-hundred and eight-one sign were counted. An average of 0.32 sign was found per km walked. Seventy percent of the area sampled had a very low abundance of tortoises, 29% had a low abundance, and 1% had a moderate abundance. A revised map of the relative abundance of desert tortoise on the NTS is presented. Within the 1,330 km 2 of desert tortoise habitat on the NTS, 49% is classified as having no tortoises or a very low abundance, 18% has a low or moderate abundance, 12% is unclassified land being used by the Yucca Mountain Site Characterization Project, and the remaining 21% still has an unknown abundance of desert tortoises. Based on the results of this work, the amount of tortoise habitat previously classified as having an unknown or low-moderate abundance, and on which clearance surveys and on-site monitoring was required, has been reduced by 20%

  19. Fear or food - abundance of red fox in relation to occurrence of lynx and wolf.

    Science.gov (United States)

    Wikenros, Camilla; Aronsson, Malin; Liberg, Olof; Jarnemo, Anders; Hansson, Jessica; Wallgren, Märtha; Sand, Håkan; Bergström, Roger

    2017-08-22

    Apex predators may affect mesopredators through intraguild predation and/or supply of carrion from their prey, causing a trade-off between avoidance and attractiveness. We used wildlife triangle snow-tracking data to investigate the abundance of red fox (Vulpes vulpes) in relation to lynx (Lynx lynx) and wolf (Canis lupus) occurrence as well as land composition and vole (Microtus spp.) density. Data from the Swedish wolf-monitoring system and VHF/GPS-collared wolves were used to study the effect of wolf pack size and time since wolf territory establishment on fox abundance. Bottom-up processes were more influential than top-down effects as the proportion of arable land was the key indicator of fox abundance at the landscape level. At this spatial scale, there was no effect of wolf abundance on fox abundance, whereas lynx abundance had a positive effect. In contrast, at the wolf territory level there was a negative effect of wolves on fox abundance when including detailed information of pack size and time since territory establishment, whereas there was no effect of lynx abundance. This study shows that different apex predator species may affect mesopredator abundance in different ways and that the results may be dependent on the spatiotemporal scale and resolution of the data.

  20. Relative abundance and diel variation of zooplankton from south west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Santhakumari, V.; Peter, K.J.

    abundant group, of which calanoids predominated. A swarm of the hydromedusan species, Aequorea conica, (181/m sup(-3)) was seen at night. Quantitative and qualitative variations of various zooplankton groups from six stations in relation to selected physico...

  1. In-Depth Global Analysis of Transcript Abundance Levels in Porcine Alveolar Macrophages Following Infection with Porcine Reproductive and Respiratory Syndrome Virus

    Directory of Open Access Journals (Sweden)

    Laura C. Miller

    2010-01-01

    Full Text Available Porcine reproductive and respiratory syndrome virus (PRRSV is a major pathogen of swine worldwide and causes considerable economic loss. Identifying specific cell signaling or activation pathways that associate with variation in PRRSV replication and macrophage function may lead to identification of novel gene targets for the control of PRRSV infection. Serial Analysis of Gene Expression (SAGE was used to create and survey the transcriptome of in vitro mock-infected and PRRSV strain VR-2332-infected porcine alveolar macrophages (PAM at 0, 6, 12, 16, and 24 hours after infection. The transcriptome data indicated changes in transcript abundance occurring in PRRSV-infected PAMs over time after infection with more than 590 unique tags with significantly altered transcript abundance levels identified (P<.01. Strikingly, innate immune genes (whose transcript abundances are typically altered in response to other pathogens or insults including IL-8, CCL4, and IL-1β showed no or very little change at any time point following infection.

  2. Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site

    OpenAIRE

    Brunnschweiler, Juerg M.; Abrantes, Kátya G.; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-...

  3. Relative abundance of mesopredators and size of oak patches in the cross-timbers ecoregion

    Science.gov (United States)

    Disney, M.R.; Hellgren, E.C.; Davis, C.A.; Leslie, David M.; Engle, David M.

    2008-01-01

    Mesopredators (e.g., raccoon Procyon lotor, Virginia opossum Didelphis virginiana, striped skunk Mephitis mephitis) have received considerable attention because of links to population declines in birds via increased nest predation, especially in landscapes fragmented by anthropogenic forces. Relationships of abundance of mesopredators to size of habitat patches have received less attention than relationships to other metrics of fragmentation, particularly edge characteristics. We tested the hypothesis that relative abundance of mesopredators (e.g., raccoons and Virginia opossums) was related negatively to size of forest patch. We delineated 15 patches of oak (Quercus) forest ranging from 0.2 to 55.3 ha within a grassland-woodland mosaic in the cross-timbers ecoregion of Oklahoma. Scent stations and live traps within these patches were used to index relative abundance of mesopredators in summers 2003 and 2004. Both indices of relative abundance were related weakly and negatively to area of forest patch. However, rate of capture and visitation to scent station were not correlated consistently throughout the study. Our results suggested that the two methods to index abundance provided separate information on functional and numerical responses to size of patch. Our evidence that mesopredators within the cross timbers were more likely to be in smaller patches of oak forest may have implications to success of avian nesting in these patches.

  4. [Mammals' camera-trapping in Sierra Nanchititla, Mexico: relative abundance and activity patterns].

    Science.gov (United States)

    Monroy-Vilchis, Octavio; Zarco-González, Martha M; Rodríguez-Soto, Clarita; Soria-Díaz, Leroy; Urios, Vicente

    2011-03-01

    Species conservation and their management depend on the availability of their population behavior and changes in time. This way, population studies include aspects such as species abundance and activity pattern, among others, with the advantage that nowadays new technologies can be applied, in addition to common methods. In this study, we used camera-traps to obtain the index of relative abundance and to establish activity pattern of medium and large mammals in Sierra Nanchititla, Mexico. The study was conducted from December 2003 to May 2006, with a total sampling effort of 4 305 trap-days. We obtained 897 photographs of 19 different species. Nasua narica, Sylvilagus floridanus and Urocyon cinereoargenteus were the most abundant, in agreement with the relative abundance index (RAI, number of independent records/100 trap-days), and according to previous studies with indirect methods in the area. The activity patterns of the species showed that 67% of them are nocturnal, except Odocoileus virginianus, Nasua narica and others. Some species showed differences with previously reported patterns, which are related with seasonality, resources availability, organism sex, principally. The applied method contributed with reliable data about relative abundance and activity patterns.

  5. Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury

    Directory of Open Access Journals (Sweden)

    Monesi Nadia

    2007-07-01

    Full Text Available Abstract Background The sequencing of the D.melanogaster genome revealed an unexpected small number of genes (~ 14,000 indicating that mechanisms acting on generation of transcript diversity must have played a major role in the evolution of complex metazoans. Among the most extensively used mechanisms that accounts for this diversity is alternative splicing. It is estimated that over 40% of Drosophila protein-coding genes contain one or more alternative exons. A recent transcription map of the Drosophila embryogenesis indicates that 30% of the transcribed regions are unannotated, and that 1/3 of this is estimated as missed or alternative exons of previously characterized protein-coding genes. Therefore, the identification of the variety of expressed transcripts depends on experimental data for its final validation and is continuously being performed using different approaches. We applied the Open Reading Frame Expressed Sequence Tags (ORESTES methodology, which is capable of generating cDNA data from the central portion of rare transcripts, in order to investigate the presence of hitherto unnanotated regions of Drosophila transcriptome. Results Bioinformatic analysis of 1,303 Drosophila ORESTES clusters identified 68 sequences derived from unannotated regions in the current Drosophila genome version (4.3. Of these, a set of 38 was analysed by polyA+ northern blot hybridization, validating 17 (50% new exons of low abundance transcripts. For one of these ESTs, we obtained the cDNA encompassing the complete coding sequence of a new serine protease, named SP212. The SP212 gene is part of a serine protease gene cluster located in the chromosome region 88A12-B1. This cluster includes the predicted genes CG9631, CG9649 and CG31326, which were previously identified as up-regulated after immune challenges in genomic-scale microarray analysis. In agreement with the proposal that this locus is co-regulated in response to microorganisms infection, we show

  6. Correlations of carotenoid content and transcript abundances for fibrillin and carotenogenic enzymes in Capsicum annum fruit pericarp.

    Science.gov (United States)

    Kilcrease, James; Rodriguez-Uribe, Laura; Richins, Richard D; Arcos, Juan Manuel Garcia; Victorino, Jesus; O'Connell, Mary A

    2015-03-01

    The fruits of Capsicum spp. are especially rich sites for carotenoid synthesis and accumulation, with cultivar-specific carotenoid accumulation profiles. Differences in chromoplast structure as well as carotenoid biosynthesis are correlated with distinct carotenoid accumulations and fruit color. In the present study, the inheritance of chromoplast shape, carotenoid accumulation profiles, and transcript levels of four genes were measured. Comparisons of these traits were conducted using fruit from contrasting variants, Costeño Amarillo versus Costeño Red, and from F1 hybrids; crosses between parental lines with novel versions of these traits. Intermediate chromoplast shapes were observed in the F1, but no association between specific carotenoid accumulation and chromoplast shape was detected. Increased total carotenoid content was associated with increased β-carotene and violaxanthin content. Transcript levels for phytoene synthase (Psy) and β-carotene hydroxylase (CrtZ-2) were positively correlated with increased levels of specific carotenoids. No correlation was detected between transcript levels of capsanthin/capsorubin synthase (Ccs) and carotenoid composition or chromoplast shape. Transcript levels of fibrillin, were differentially correlated with specific carotenoids, negatively correlated with accumulation of capsanthin, and positively correlated with violaxanthin. The regulation of carotenoid accumulation in chromoplasts in Capsicum fruit continues to be a complex process with multiple steps for control. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Differential transcript abundance and genotypic variation of four putative allergen-encoding gene families in melting peach

    NARCIS (Netherlands)

    Yang, Z.; Ma, Y.; Chen, L.; Xie, R.; Zhang, X.; Zhang, B.; Lu, M.; Wu, S.; Gilissen, L.J.W.J.; Ree, van R.; Gao, Z.

    2011-01-01

    We analysed the temporal and spatial transcript expression of the panel of 18 putative isoallergens from four gene families (Pru p 1–4) in the peach fruit, anther and leaf of two melting cultivars, to gain insight into their expression profiles and to identify the key family members. Genotypic

  8. Sex ratios, mating frequencies and relative abundance of sympatric millipedes in the genus Chersastus (Diplopoda: Pachybolidae

    Directory of Open Access Journals (Sweden)

    Mark Ian Cooper

    2014-12-01

    Full Text Available Three hypotheses exist for explaining climbing behavior in millipedes: 1 waterlogging, 2 detritus limiting, and 3 mate avoidance. Data of sex ratios, mating frequency and relative abundance are provided to suggest an alternative explanation for the pattern in sympatric forest millipedes. Sex ratio differences - from equality - were tested using a G-test comparing millipedes on and above ground. Mating frequencies were calculated based on the percentage of paired individuals. Relative abundance may correlate with male-biases in the sex ratios. All three factors suggest Chersastus inscriptus has a higher reproductive potential than C. anulatus. This is evidence for mating hotspots.

  9. ABCC5, ERCC2, XPA and XRCC1 transcript abundance levels correlate with cisplatin chemoresistance in non-small cell lung cancer cell lines

    Directory of Open Access Journals (Sweden)

    Khuder Sadik A

    2005-05-01

    Full Text Available Abstract Background Although 40–50% of non-small cell lung cancer (NSCLC tumors respond to cisplatin chemotherapy, there currently is no way to prospectively identify potential responders. The purpose of this study was to determine whether transcript abundance (TA levels of twelve selected DNA repair or multi-drug resistance genes (LIG1, ERCC2, ERCC3, DDIT3, ABCC1, ABCC4, ABCC5, ABCC10, GTF2H2, XPA, XPC and XRCC1 were associated with cisplatin chemoresistance and could therefore contribute to the development of a predictive marker. Standardized RT (StaRT-PCR, was employed to assess these genes in a set of NSCLC cell lines with a previously published range of sensitivity to cisplatin. Data were obtained in the form of target gene molecules relative to 106 β-actin (ACTB molecules. To cancel the effect of ACTB variation among the different cell lines individual gene expression values were incorporated into ratios of one gene to another. Each two-gene ratio was compared as a single variable to chemoresistance for each of eight NSCLC cell lines using multiple regression. In an effort to validate these results, six additional lines then were evaluated. Results Following validation, single variable models best correlated with chemoresistance (p ERCC2/XPC, ABCC5/GTF2H2, ERCC2/GTF2H2, XPA/XPC and XRCC1/XPC. All single variable models were examined hierarchically to achieve two variable models. The two variable model with the highest correlation was (ABCC5/GTF2H2, ERCC2/GTF2H2 with an R2 value of 0.96 (p Conclusion These results provide markers suitable for assessment of small fine needle aspirate biopsies in an effort to prospectively identify cisplatin resistant tumors.

  10. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    Science.gov (United States)

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  11. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    Directory of Open Access Journals (Sweden)

    Juerg M Brunnschweiler

    Full Text Available Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive

  12. The relative importance of water temperature and residence time in predicting cyanobacteria abundance in regulated rivers.

    Science.gov (United States)

    Cha, YoonKyung; Cho, Kyung Hwa; Lee, Hyuk; Kang, Taegu; Kim, Joon Ha

    2017-11-01

    Despite a growing awareness of the problems associated with cyanobacterial blooms in rivers, and particularly in regulated rivers, the drivers of bloom formation and abundance in rivers are not well understood. We developed a Bayesian hierarchical model to assess the relative importance of predictors of summer cyanobacteria abundance, and to test whether the relative importance of each predictor varies by site, using monitoring data from 16 sites in the four major rivers of South Korea. The results suggested that temperature and residence time, but not nutrient levels, are important predictors of summer cyanobacteria abundance in rivers. Although the two predictors were of similar significance across the sites, the residence time was marginally better in accounting for the variation in cyanobacteria abundance. The model with spatial hierarchy demonstrated that temperature played a consistently significant role at all sites, and showed no effect from site-specific factors. In contrast, the importance of residence time varied significantly from site to site. This variation was shown to depend on the trophic state, indicated by the chlorophyll-a and total phosphorus levels. Our results also suggested that the magnitude of weir inflow is a key factor determining the cyanobacteria abundance under baseline conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Relative abundance and size of coastal sharks derived from commercial shark longline catch and effort data.

    Science.gov (United States)

    Carlson, J K; Hale, L F; Morgan, A; Burgess, G

    2012-04-01

    In the north-west Atlantic Ocean, stock assessments conducted for some commercially harvested coastal sharks indicate declines from 64 to 80% with respect to virgin population levels. While the status of commercially important species is available, abundance trend information for other coastal shark species in the north-west Atlantic Ocean are unavailable. Using a generalized linear modelling (GLM) approach, a relative abundance index was derived from 1994 to 2009 using observer data collected in a commercial bottom longline fishery. Trends in abundance and average size were estimated for bull shark Carcharhinus leucas, spinner shark Carcharhinus brevipinna, tiger shark Galeocerdo cuvier and lemon shark Negaprion brevirostris. Increases in relative abundance for all shark species ranged from 14% for C. brevipinna, 12% for C. leucas, 6% for N. brevirostris and 3% for G. cuvier. There was no significant change in the size at capture over the time period considered for all species. While the status of shark populations should not be based exclusively on abundance trend information, but ultimately on stock assessment models, results from this study provide some cause for optimism on the status of these coastal shark species. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

  14. Multidirectional abundance shifts among North American birds and the relative influence of multifaceted climate factors.

    Science.gov (United States)

    Huang, Qiongyu; Sauer, John R; Dubayah, Ralph O

    2017-09-01

    Shifts in species distributions are major fingerprint of climate change. Examining changes in species abundance structures at a continental scale enables robust evaluation of climate change influences, but few studies have conducted these evaluations due to limited data and methodological constraints. In this study, we estimate temporal changes in abundance from North American Breeding Bird Survey data at the scale of physiographic strata to examine the relative influence of different components of climatic factors and evaluate the hypothesis that shifting species distributions are multidirectional in resident bird species in North America. We quantify the direction and velocity of the abundance shifts of 57 permanent resident birds over 44 years using a centroid analysis. For species with significant abundance shifts in the centroid analysis, we conduct a more intensive correlative analysis to identify climate components most strongly associated with composite change of abundance within strata. Our analysis focus on two contrasts: the relative importance of climate extremes vs. averages, and of temperature vs. precipitation in strength of association with abundance change. Our study shows that 36 species had significant abundance shifts over the study period. The average velocity of the centroid is 5.89 km·yr -1 . The shifted distance on average covers 259 km, 9% of range extent. Our results strongly suggest that the climate change fingerprint in studied avian distributions is multidirectional. Among 6 directions with significant abundance shifts, the northwestward shift was observed in the largest number of species (n = 13). The temperature/average climate model consistently has greater predictive ability than the precipitation/extreme climate model in explaining strata-level abundance change. Our study shows heterogeneous avian responses to recent environmental changes. It highlights needs for more species-specific approaches to examine contributing

  15. Weed management practices affect the diversity and relative abundance of physic nut mites.

    Science.gov (United States)

    Saraiva, Althiéris de Sousa; Sarmento, Renato A; Erasmo, Eduardo A L; Pedro-Neto, Marçal; de Souza, Danival José; Teodoro, Adenir V; Silva, Daniella G

    2015-03-01

    Crop management practices determine weed community, which in turn may influence patterns of diversity and abundance of associated arthropods. This study aimed to evaluate whether local weed management practices influence the diversity and relative abundance of phytophagous and predatory mites, as well as mites with undefined feeding habits--of the families Oribatidae and Acaridae--in a physic nut (Jatropha curcas L.) plantation subjected to (1) within-row herbicide spraying and between-row mowing; (2) within-row herbicide spraying and no between-row mowing; (3) within-row weeding and between-row mowing; (4) within-row weeding and no between-row mowing; and (5) unmanaged (control). The herbicide used was glyphosate. Herbicide treatments resulted in higher diversity and relative abundance of predatory mites and mites with undefined feeding habit on physic nut shrubs. This was probably due to the toxic effects of the herbicide on mites or to removal of weeds. Within-row herbicide spraying combined with between-row mowing was the treatment that most contributed to this effect. Our results show that within-row weeds harbor important species of predatory mites and mites with undefined feeding habit. However, the dynamics of such mites in the system can be changed according to the weed management practice applied. Among the predatory mites of the family Phytoseiidae Amblydromalus sp. was the most abundant, whereas Brevipalpus phoenicis was the most frequent phytophagous mite and an unidentified oribatid species was the most frequent mite with undefined feeding habit.

  16. Penguin tissue as a proxy for relative krill abundance in East Antarctica during the Holocene.

    Science.gov (United States)

    Huang, Tao; Sun, Liguang; Long, Nanye; Wang, Yuhong; Huang, Wen

    2013-09-30

    Antarctic krill (Euphausia superba) is a key component of the Southern Ocean food web. It supports a large number of upper trophic-level predators, and is also a major fishery resource. Understanding changes in krill abundance has long been a priority for research and conservation in the Southern Ocean. In this study, we performed stable isotope analyses on ancient Adélie penguin tissues and inferred relative krill abundance during the Holocene epoch from paleodiets of Adélie penguin (Pygoscelis adeliae), using inverse of δ¹⁵N (ratio of ¹⁵N/¹⁴N) value as a proxy. We find that variations in krill abundance during the Holocene are in accord with episodes of regional climate changes, showing greater krill abundance in cold periods. Moreover, the low δ¹⁵N values found in modern Adélie penguins indicate relatively high krill availability, which supports the hypothesis of krill surplus in modern ages due to recent hunt for krill-eating seals and whales by humans.

  17. Xe isotopic abundances in enstatite meteorites and relations to other planetary reservoirs

    International Nuclear Information System (INIS)

    Lee, Jee-Yon; Marti, Kurt; Wacker, John F.

    2009-01-01

    This paper describes the interpretation of xenon that was measured in the Abee meteorite. Reported Xe isotopic abundances in enstatite chondrites (EC's) show some variability, and this makes comparisons to other solar system reservoirs rather difficult. In contrast, we find uniform Xe isotopic abundances in the EC chondrite Abee for a variety of clasts, except for 128 Xe and 129 Xe, the isotopes affected by neutron capture in I and by extinct 129 I. We report averages for the studied clasts which are consistent within error limits with OC-Xe and with the Q-Xe signature. On the other hand, the elemental abundance ratios Ar/Xe are variable between clasts. A strongly reducing environment which is indicated for enstatite meteorites was generally assumed to be consistent with conditions existing in the early inner solar system. Xe isotopic abundances in SNC meteorites from Mars and also those in some terrestrial wells show that distinct isotopic reservoirs coexisted on the same planets. In particular, the Xe isotopic signatures in terrestrial well gases show the presence of a minor distinct component in two of the reported four well gases. These authors suggested that the extra component represents solar Xe, but we show that also a meteoritic xenon reservoir of the Abee-Xe structure is an option. The reported Xe data in Ar-rich (subsolar) EC's show isotopic abundances slightly lighter than those in Abee-Xe, but the relative abundances of Ar, Kr, and Xe indicate only a minor component of elementally unfractionated solar Xe. The elemental ratios suggest rather a different origin for these gases: the loading of solar particles into grain surfaces during exposure at elevated temperatures during accretion of matter in the inner solar system. A model of this type was suggested for the accretion of gases now observed in the atmosphere on Venus. We note that disks of crystalline silicates (including enstatite and olivine) have been observed in T Tauri stars during their early

  18. Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon.

    Science.gov (United States)

    Lemay, Matthew A; Russello, Michael A

    2014-11-04

    Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with

  19. Weed-Species Abundance and Diversity Indices in Relation to Tillage Systems and Fertilization

    Directory of Open Access Journals (Sweden)

    Ilias S. Travlos

    2018-04-01

    Full Text Available Weeds pose a major threat to world agriculture by reducing detrimentally crop yield and quality. However, at the same time, weeds are major interacting components of the agroecosystems. Abundance and diversity of weeds vary significantly among the several communities. In order to evaluate each community's structure and the interactions among them, several population indices are used as key tools. In parallel, various cultivation and land management strategies, such as tillage and fertilization, are commonly used in terms of integrated weed management. Estimating the response of weed species on those practices is crucial for both biodiversity maintenance and alternative weed control methods. Many experiments have confirmed the fundamental role of tillage intensity and nutrition supply in weed species' abundance and diversity. For instance, in some studies, the abundance of perennial weeds was doubled under reduced tillage intensity. In addition, higher values of Shannon-Weiner and Pielou indices were reported in the PK fertilization treatment compared to the control and NK fertilization treatments. The objective of this paper is to provide a brief overview of the key results of these experiments and summarize the part of the literature related to the effect of tillage systems and fertilization on weed species abundance and diversity. Such knowledge could contribute to the sound design and implementation of integrated weed management programs which in turn may lead to a decrease in the density of serious and noxious weeds and an increase in the overall balance of agroecosystems.

  20. Modeled distribution and abundance of a pelagic seabird reveal trends in relation to fisheries

    Science.gov (United States)

    Renner, Martin; Parrish, Julia K.; Piatt, John F.; Kuletz, Kathy J.; Edwards, Ann E.; Hunt, George L.

    2013-01-01

    The northern fulmar Fulmarus glacialis is one of the most visible and widespread seabirds in the eastern Bering Sea and Aleutian Islands. However, relatively little is known about its abundance, trends, or the factors that shape its distribution. We used a long-term pelagic dataset to model changes in fulmar at-sea distribution and abundance since the mid-1970s. We used an ensemble model, based on a weighted average of generalized additive model (GAM), multivariate adaptive regression splines (MARS), and random forest models to estimate the pelagic distribution and density of fulmars in the waters of the Aleutian Archipelago and Bering Sea. The most important predictor variables were colony effect, sea surface temperature, distribution of fisheries, location, and primary productivity. We calculated a time series from the ratio of observed to predicted values and found that fulmar at-sea abundance declined from the 1970s to the 2000s at a rate of 0.83% (± 0.39% SE) per annum. Interpolating fulmar densities on a spatial grid through time, we found that the center of fulmar distribution in the Bering Sea has shifted north, coinciding with a northward shift in fish catches and a warming ocean. Our study shows that fisheries are an important, but not the only factor, shaping fulmar distribution and abundance trends in the eastern Bering Sea and Aleutian Islands.

  1. Nature's starships. I. Observed abundances and relative frequencies of amino acids in meteorites

    International Nuclear Information System (INIS)

    Cobb, Alyssa K.; Pudritz, Ralph E.

    2014-01-01

    The class of meteorites called carbonaceous chondrites are examples of material from the solar system which have been relatively unchanged from the time of their initial formation. These meteorites have been classified according to the temperatures and physical conditions of their parent planetesimals. We collate available data on amino acid abundance in these meteorites and plot the concentrations of different amino acids for each meteorite within various meteorite subclasses. We plot average concentrations for various amino acids across meteorites separated by subclass and petrologic type. We see a predominance in the abundance and variety of amino acids in CM2 and CR2 meteorites. The range in temperature corresponding to these subclasses indicates high degrees of aqueous alteration, suggesting aqueous synthesis of amino acids. Within the CM2 and CR2 subclasses, we identify trends in relative frequencies of amino acids to investigate how common amino acids are as a function of their chemical complexity. These two trends (total abundance and relative frequencies) can be used to constrain formation parameters of amino acids within planetesimals. Our organization of the data supports an onion shell model for the temperature structure of planetesimals. The least altered meteorites (type 3) and their amino acids originated near cooler surface regions. The most active amino acid synthesis likely took place at intermediate depths (type 2). The most altered materials (type 1) originated furthest toward parent body cores. This region is likely too hot to either favor amino acid synthesis or for amino acids to be retained after synthesis.

  2. Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Göttert, Hendrikje; Mattiazzi Usaj, Mojca; Rosebrock, Adam P; Andrews, Brenda J

    2018-01-01

    Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains. We also present an alternative pipeline for the analysis of R-SGA output strains using flow cytometry of cells in liquid culture. Data normalization for both pipelines is discussed.

  3. Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa.

    Science.gov (United States)

    Sonnleitner, Elisabeth; Valentini, Martina; Wenner, Nicolas; Haichar, Feth el Zahar; Haas, Dieter; Lapouge, Karine

    2012-01-01

    The opportunistic human pathogen Pseudomonas aeruginosa is able to utilize a wide range of carbon and nitrogen compounds, allowing it to grow in vastly different environments. The uptake and catabolism of growth substrates are organized hierarchically by a mechanism termed catabolite repression control (Crc) whereby the Crc protein establishes translational repression of target mRNAs at CA (catabolite activity) motifs present in target mRNAs near ribosome binding sites. Poor carbon sources lead to activation of the CbrAB two-component system, which induces transcription of the small RNA (sRNA) CrcZ. This sRNA relieves Crc-mediated repression of target mRNAs. In this study, we have identified novel targets of the CbrAB/Crc system in P. aeruginosa using transcriptome analysis in combination with a search for CA motifs. We characterized four target genes involved in the uptake and utilization of less preferred carbon sources: estA (secreted esterase), acsA (acetyl-CoA synthetase), bkdR (regulator of branched-chain amino acid catabolism) and aroP2 (aromatic amino acid uptake protein). Evidence for regulation by CbrAB, CrcZ and Crc was obtained in vivo using appropriate reporter fusions, in which mutation of the CA motif resulted in loss of catabolite repression. CbrB and CrcZ were important for growth of P. aeruginosa in cystic fibrosis (CF) sputum medium, suggesting that the CbrAB/Crc system may act as an important regulator during chronic infection of the CF lung.

  4. Fluorescent peptide biosensor for probing the relative abundance of cyclin-dependent kinases in living cells.

    Directory of Open Access Journals (Sweden)

    Laetitia Kurzawa

    Full Text Available Cyclin-dependant kinases play a central role in coordinating cell growth and division, and in sustaining proliferation of cancer cells, thereby constituting attractive pharmacological targets. However, there are no direct means of assessing their relative abundance in living cells, current approaches being limited to antigenic and proteomic analysis of fixed cells. In order to probe the relative abundance of these kinases directly in living cells, we have developed a fluorescent peptide biosensor with biligand affinity for CDKs and cyclins in vitro, that retains endogenous CDK/cyclin complexes from cell extracts, and that bears an environmentally-sensitive probe, whose fluorescence increases in a sensitive fashion upon recognition of its targets. CDKSENS was introduced into living cells, through complexation with the cell-penetrating carrier CADY2 and applied to assess the relative abundance of CDK/Cyclins through fluorescence imaging and ratiometric quantification. This peptide biosensor technology affords direct and sensitive readout of CDK/cyclin complex levels, and reports on differences in complex formation when tampering with a single CDK or cyclin. CDKSENS further allows for detection of differences between different healthy and cancer cell lines, thereby enabling to distinguish cells that express high levels of these heterodimeric kinases, from cells that present decreased or defective assemblies. This fluorescent biosensor technology provides information on the overall status of CDK/Cyclin complexes which cannot be obtained through antigenic detection of individual subunits, in a non-invasive fashion which does not require cell fixation or extraction procedures. As such it provides promising perspectives for monitoring the response to therapeutics that affect CDK/Cyclin abundance, for cell-based drug discovery strategies and fluorescence-based cancer diagnostics.

  5. A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

    Science.gov (United States)

    Dick, Jeffrey M.; Shock, Everett L.

    2013-01-01

    Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the

  6. Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: a first proposal using Shannon's entropy.

    Science.gov (United States)

    Ricotta, Carlo

    2003-01-01

    Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.

  7. Allergen relative abundance in several wheat varieties as revealed via a targeted quantitative approach using MS.

    Science.gov (United States)

    Rogniaux, Hélène; Pavlovic, Marija; Lupi, Roberta; Lollier, Virginie; Joint, Mathilde; Mameri, Hamza; Denery, Sandra; Larré, Colette

    2015-05-01

    Food allergy has become a major health issue in developed countries, therefore there is an urgent need to develop analytical methods able to detect and quantify with a good sensitivity and reliability some specific allergens in complex food matrices. In this paper, we present a targeted MS/MS approach to compare the relative abundance of the major recognized wheat allergens in the salt-soluble (albumin/globulin) fraction of wheat grains. Twelve allergens were quantified in seven wheat varieties, selected from three Triticum species: T. aestivum (bread wheat), T. durum (durum wheat), and T. monococcum. The allergens were monitored from one or two proteotypic peptides and their relative abundance was deduced from the intensity of one fragment measured in MS/MS. Whereas the abundance of some of the targeted allergens was quite stable across the genotypes, others like alpha-amylase inhibitors showed clear differences according to the wheat species, in accordance with the results of earlier functional studies. This study enriches the scarce knowledge available on allergens content in wheat genotypes, and brings new perspectives for food safety and plant breeding. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia.

    Science.gov (United States)

    Kaysheva, Anna L; Kopylov, Artur T; Ponomarenko, Elena A; Kiseleva, Olga I; Teryaeva, Nadezhda B; Potapov, Alexander A; Izotov, Alexander А; Morozov, Sergei G; Kudryavtseva, Valeria Yu; Archakov, Alexander I

    2018-03-01

    A comparative protein profile analysis of 17 blood plasma samples from patients with ischemia and 20 samples from healthy volunteers was carried out using ultra-high resolution mass spectrometry. The analysis of measurements was performed using the proteomics search engine OMSSA. Normalized spectrum abundance factor (NSAF) in the biological samples was assessed using SearchGUI. The findings of mass spectrometry analysis of the protein composition of blood plasma samples demonstrate that the depleted samples are quite similar in protein composition and relative abundance of proteins. By comparing them with the control samples, we have found a small group of 44 proteins characteristic of the blood plasma samples from patients with chronic cerebral ischemia. These proteins contribute to the processes of homeostasis maintenance, including innate immune response unfolding, the response of a body to stress, and contribution to the blood clotting cascade.

  9. The relative contribution of climate to changes in lesser prairie-chicken abundance

    Science.gov (United States)

    Ross, Beth E.; Haukos, David A.; Hagen, Christian A.; Pitman, James

    2016-01-01

    Managing for species using current weather patterns fails to incorporate the uncertainty associated with future climatic conditions; without incorporating potential changes in climate into conservation strategies, management and conservation efforts may fall short or waste valuable resources. Understanding the effects of climate change on species in the Great Plains of North America is especially important, as this region is projected to experience an increased magnitude of climate change. Of particular ecological and conservation interest is the lesser prairie-chicken (Tympanuchus pallidicinctus), which was listed as “threatened” under the U.S. Endangered Species Act in May 2014. We used Bayesian hierarchical models to quantify the effects of extreme climatic events (extreme values of the Palmer Drought Severity Index [PDSI]) relative to intermediate (changes in El Niño Southern Oscillation) and long-term climate variability (changes in the Pacific Decadal Oscillation) on trends in lesser prairie-chicken abundance from 1981 to 2014. Our results indicate that lesser prairie-chicken abundance on leks responded to environmental conditions of the year previous by positively responding to wet springs (high PDSI) and negatively to years with hot, dry summers (low PDSI), but had little response to variation in the El Niño Southern Oscillation and the Pacific Decadal Oscillation. Additionally, greater variation in abundance on leks was explained by variation in site relative to broad-scale climatic indices. Consequently, lesser prairie-chicken abundance on leks in Kansas is more strongly influenced by extreme drought events during summer than other climatic conditions, which may have negative consequences for the population as drought conditions intensify throughout the Great Plains.

  10. Species richness and relative abundance of birds in natural and anthropogenic fragments of Brazilian Atlantic forest

    Directory of Open Access Journals (Sweden)

    Luiz dos Anjos

    2004-06-01

    Full Text Available Bird communities were studied in two types of fragmented habitat of Atlantic forest in the State of Paraná, southern Brazil; one consisted of forest fragments that were created as a result of human activities (forest remnants, the other consisted of a set of naturally occurring forest fragments (forest patches. Using quantitative data obtained by the point counts method in 3 forest patches and 3 forest remnants during one year, species richness and relative abundance were compared in those habitats, considering species groups according to their general feeding habits. Insectivores, omnivores, and frugivores presented similar general tendencies in both habitats (decrease of species number with decreasing size and increasing isolation of forest fragment. However, these tendencies were different, when considering the relative abundance data: the trunk insectivores presented the highest value in the smallest patch while the lowest relative abundance was in the smallest remnant. In the naturally fragmented landscape, time permitted that the loss of some species of trunk insectivores be compensated for the increase in abundance of other species. In contrast, the remnants essentially represented newly formed islands that are not yet at equilibrium and where future species losses would make them similar to the patches.Comunidades de aves foram estudadas em duas regiões fragmentadas de floresta Atlântica no Estado do Paraná, sul do Brasil; uma região é constituída de fragmentos florestais que foram criados como resultado de atividades humanas (remanescentes florestais e a outra de um conjunto de fragmentos florestais naturais (manchas de floresta. Usando dados quantitativos (o método de contagens pontuais previamente obtidos em 3 manchas de floresta e em 3 remanescentes florestais durante um ano, a riqueza e a abundância relativa de aves foram comparadas naqueles habitats considerando as espécies pelos seus hábitos alimentares. Inset

  11. Relative abundance estimations of Chengal trees in a tropical rainforest by using modified canopy fractional cover (mCFC)

    International Nuclear Information System (INIS)

    Hassan, N

    2014-01-01

    Tree species composition estimations are important to sustain forest management. This study estimates relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of tree species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying tree species composition

  12. Relative abundance estimations of chengal tree in a tropical rainforest by using modified Canopy Fractional Cover (mCFC)

    International Nuclear Information System (INIS)

    Hassan, N

    2014-01-01

    Tree species composition estimations are important to sustain forest management. This study challenged estimates of relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of trees species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying trees species composition

  13. Size matters: abundance matching, galaxy sizes, and the Tully-Fisher relation in EAGLE

    Science.gov (United States)

    Ferrero, Ismael; Navarro, Julio F.; Abadi, Mario G.; Sales, Laura V.; Bower, Richard G.; Crain, Robert A.; Frenk, Carlos S.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

    2017-02-01

    The Tully-Fisher relation (TFR) links the stellar mass of a disc galaxy, Mstr, to its rotation speed: it is well approximated by a power law, shows little scatter, and evolves weakly with redshift. The relation has been interpreted as reflecting the mass-velocity scaling (M ∝ V3) of dark matter haloes, but this interpretation has been called into question by abundance-matching (AM) models, which predict the galaxy-halo mass relation to deviate substantially from a single power law and to evolve rapidly with redshift. We study the TFR of luminous spirals and its relation to AM using the EAGLE set of Λ cold dark matter (ΛCDM) cosmological simulations. Matching both relations requires disc sizes to satisfy constraints given by the concentration of haloes and their response to galaxy assembly. EAGLE galaxies approximately match these constraints and show a tight mass-velocity scaling that compares favourably with the observed TFR. The TFR is degenerate to changes in galaxy formation efficiency and the mass-size relation; simulations that fail to match the galaxy stellar mass function may fit the observed TFR if galaxies follow a different mass-size relation. The small scatter in the simulated TFR results because, at fixed halo mass, galaxy mass and rotation speed correlate strongly, scattering galaxies along the main relation. EAGLE galaxies evolve with lookback time following approximately the prescriptions of AM models and the observed mass-size relation of bright spirals, leading to a weak TFR evolution consistent with observation out to z = 1. ΛCDM models that match both the abundance and size of galaxies as a function of stellar mass have no difficulty reproducing the observed TFR and its evolution.

  14. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece

    2012-11-28

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  15. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece; Rashid, Mamoon; Pain, Arnab

    2012-01-01

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  16. Fear or food ? abundance of red fox in relation to occurrence of lynx and wolf

    OpenAIRE

    Wikenros, Camilla; Aronsson, Malin; Liberg, Olof; Jarnemo, Anders; Hansson, Jessica; Wallgren, M?rtha; Sand, H?kan; Bergstr?m, Roger

    2017-01-01

    Apex predators may affect mesopredators through intraguild predation and/or supply of carrion from their prey, causing a trade-off between avoidance and attractiveness. We used wildlife triangle snow-tracking data to investigate the abundance of red fox (Vulpes vulpes) in relation to lynx (Lynx lynx) and wolf (Canis lupus) occurrence as well as land composition and vole (Microtus spp.)?density. Data from the Swedish wolf-monitoring system and VHF/GPS-collared wolves were used to study the eff...

  17. Effects of Pb(Ⅱ) exposure on Chlorella protothecoides and Chlorella vulgaris growth, malondialdehyde, and photosynthesis-related gene transcription.

    Science.gov (United States)

    Xiong, Bang; Zhang, Wei; Chen, Lin; Lin, Kuang-Fei; Guo, Mei-Jin; Wang, Wei-Liang; Cui, Xin-Hong; Bi, Hua-Song; Wang, Bin

    2014-11-01

    Greater exposure to Pb(Ⅱ) increases the likelihood of harmful effects in the environment. In this study, the aquatic unicellular alga Chlorella protothecoides (C. protothecoides) and Chlorella vulgaris (C. vulgaris) were chosen to assess the acute and chronic toxicity of Pb(Ⅱ) exposure. Results of the observations show dose-response relationships could be clearly observed between Pb(Ⅱ) concentration and percentage inhibition (PI). Exposure to Pb(Ⅱ) increased malondialdehyde (MDA) content by up to 4.22 times compared with the control, suggesting that there was some oxidative damage. ANOVA analysis shows that Pb(Ⅱ) decreased chlorophyll (chl) content, indicating marked concentration-dependent relationships, and the lowest levels of chl a, chl b, and total-chl were 14.53, 18.80, and 17.95% of the controls, respectively. A real-time PCR assay suggests the changes in transcript abundances of three photosynthetic-related genes. After 120 h exposure Pb(Ⅱ) reduced the transcript abundance of rbcL, psaB, and psbC, and the relative abundances of the three genes of C. protothecoides and C. vulgaris in response to Pb(Ⅱ) were 54.66-98.59, 51.68-95.59, 37.89-95.48, 36.04-94.94, 41.19-91.20, and 58.75-96.80% of those of the controls, respectively. As for 28 d treatments, the three genes displayed similar inhibitory trend. This research provides a basic understanding of Pb(Ⅱ) toxicity to aquatic organisms. Copyright © 2013 Wiley Periodicals, Inc.

  18. Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

    Science.gov (United States)

    Kamke, Janine; Soni, Priya; Li, Yang; Ganesh, Siva; Kelly, William J; Leahy, Sinead C; Shi, Weibing; Froula, Jeff; Rubin, Edward M; Attwood, Graeme T

    2017-08-08

    Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH 4 /kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures. Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were affiliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing effect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade. This is the first report of bacterial type III secretion system genes being associated with high

  19. Abundance of thraustochytridsand bacteria in the equatorial Indian Ocean, in relation totransparent exopolymeric particles (TEPs)

    Digital Repository Service at National Institute of Oceanography (India)

    Damare, V.; Raghukumar, S.

    Thraustochytrid protists are often abundant in coastal waters. However, their population dynamics and substrate preferences in the oceanic water column are poorly understood.We studied the abundance and distribution of thraustochytrids, bacteria...

  20. Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan.

    Science.gov (United States)

    Shakir, Muhammad Mussadiq; Ahmed, Sohail

    2015-05-01

    Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops (p arthropods according to abundance, i.e., highly abundant (Collembola, Acarina, Myripoda, Hymenoptera), moderately abundant (Orthoptera, Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface arthropods were the major contributors of variation in overall

  1. Gray whale distribution relative to benthic invertebrate biomass and abundance: Northeastern Chukchi Sea 2009-2012

    Science.gov (United States)

    Brower, Amelia A.; Ferguson, Megan C.; Schonberg, Susan V.; Jewett, Stephen C.; Clarke, Janet T.

    2017-10-01

    The shallow continental shelf waters of the Bering and Chukchi seas are the northernmost foraging grounds of North Pacific gray whales (Eschrichtius robustus). Benthic amphipods are considered the primary prey of gray whales in these waters, although no comprehensive quantitative analysis has been performed to support this assumption. Gray whale relative abundance, distribution, and behavior in the northeastern Chukchi Sea (69°-72°N, 155-169°W) were documented during aerial surveys in June-October 2009-2012. Concurrently, vessel-based benthic infaunal sampling was conducted in the area in July-August 2009-10, September 2011, and August 2012. Gray whales were seen in the study area each month that surveys were conducted, with the majority of whales feeding. Statistical analyses confirm that the highest densities of feeding gray whales were associated with high benthic amphipod abundance, primarily within 70 km of shore from Point Barrow to Icy Cape, in water whales were not seen in 40-km×40-km cells containing benthic sampling stations with 85 m-2 or fewer amphipods. Continuing broad-scale aerial surveys in the Chukchi Sea and prey sampling near feeding gray whales will be an important means to monitor and document ongoing and predicted ecosystem changes.

  2. Relative abundance and species richness of cerambycid beetles in partial cut and uncut bottomland hardwood forests

    Science.gov (United States)

    Newell, P.; King, S.

    2009-01-01

    Partial cutting techniques are increasingly advocated and used to create habitat for priority wildlife. However, partial cutting may or may not benefit species dependent on deadwood; harvesting can supplement coarse woody debris in the form of logging slash, but standing dead trees may be targeted for removal. We sampled cerambycid beetles during the spring and summer of 2006 and 2007 with canopy malaise traps in 1- and 2-year-old partial cut and uncut bottomland hardwood forests of Louisiana. We captured a total of 4195 cerambycid beetles representing 65 species. Relative abundance was higher in recent partial cuts than in uncut controls and with more dead trees in a plot. Total species richness and species composition were not different between treatments. The results suggest partial cuts with logging slash left on site increase the abundance of cerambycid beetles in the first few years after partial cutting and that both partial cuts and uncut forest should be included in the bottomland hardwood forest landscape.

  3. Increased abundance of ADAM9 transcripts in the blood is associated with tissue damage [version 2; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Darawan Rinchai

    2016-10-01

    Full Text Available Background: Members of the ADAM (a disintegrin and metalloprotease domain family have emerged as critical regulators of cell-cell signaling during development and homeostasis. ADAM9 is consistently overexpressed in various human cancers, and has been shown to play an important role in tumorigenesis. However, little is known about the involvement of ADAM9 during immune-mediated processes. Results: Mining of an extensive compendium of transcriptomic datasets identified important gaps in knowledge regarding the possible role of ADAM9 in immunological homeostasis and inflammation: 1 The abundance of ADAM9 transcripts in the blood was increased in patients with acute infection but, 2 changed very little after in vitro exposure to a wide range of pathogen-associated molecular patterns (PAMPs. 3 Furthermore it was found to increase significantly in subjects as a result of tissue injury or tissue remodeling, in absence of infectious processes. Conclusions: Our findings indicate that ADAM9 may constitute a valuable biomarker for the assessment of tissue damage, especially in clinical situations where other inflammatory markers are confounded by infectious processes.

  4. Expression of mink cell focus-forming murine leukemia virus-related transcripts in AKR mice

    International Nuclear Information System (INIS)

    Khan, A.S.; Laigret, F.; Rodi, C.P.

    1987-01-01

    The authors used a synthetic 16-base-pair mink cell focus-forming (MCF) env-specific oligomer as radiolabeled probe to study MCF murine leukemia virus (MuLV)-related transcripts in brain, kidney, liver, spleen, and thymus tissues of AKR mice ranging from 5 weeks to 6 months (mo) of age. Tissue-specific expression of poly(A) + RNAs was seen. In addition, all the tissues tested contained 3.0-kb messages. The transcription of these MCF-related mRNAs was independent of the presence of ecotropic and xenotropic MuLVs. In general, expression of the MCF env-related transcripts appeared to peak at 2 mo of age; these messages were barely detectable in brain, kidney, liver, and spleen tissues after 2 mo and in thymus tissue after 4 mo of age. All of the subgenomic MCF env-related mRNAs appeared to contain the 190-base-pair cellular DNA insert, characteristic of the long terminal repeats associated with endogenous MCF env-related proviruses. No genomic-size (8.4-kb) transcripts corresponding to endogenous MCF-related proviruses were detected. An 8.4-kb MCF env-related mRNA was first seen at 3 mo of age, exclusively in thymus tissue. This species most likely represents the first appearance of a recombinant MCF-related MuLV genome. The transcripts which were detected in thymus tissue might be involved in the generation of leukemogenic MCF viruses

  5. Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.

    Directory of Open Access Journals (Sweden)

    K V Srividhya

    Full Text Available BACKGROUND: Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. METHODOLOGY: Earlier dinucleotide relative abundance (DRA have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. CONCLUSIONS: The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences.

  6. Myocardin-related transcription factors are required for cardiac development and function

    OpenAIRE

    Mokalled, Mayssa H.; Carroll, Kelli J.; Cenik, Bercin K.; Chen, Beibei; Liu, Ning; Olson, Eric N.; Bassel-Duby, Rhonda

    2015-01-01

    Myocardin-Related Transcription Factors A and B (MRTF-A and MRTF-B) are highly homologous proteins that function as powerful coactivators of serum response factor (SRF), a ubiquitously expressed transcription factor essential for cardiac development. The SRF/MRTF complex binds to CArG boxes found in the control regions of genes that regulate cytoskeletal dynamics and muscle contraction, among other processes. While SRF is required for heart development and function, the role of MRTFs in the d...

  7. Measurements of periods, relative abundances and absolute yields of delayed neutrons from fast neutron induced fission of {sup 237}Np

    Energy Technology Data Exchange (ETDEWEB)

    Piksaikine, V. [Institute of Physics and Power Engineering, Obninsk (Russian Federation)

    1997-03-01

    The experimental method for measurements of the delayed neutron yields and period is presented. The preliminary results of the total yield, relative abundances and periods are shown comparing with the previously reported values. (J.P.N.)

  8. Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

    KAUST Repository

    Scarascia, Giantommaso; Cheng, Hong; Harb, Moustapha; Hong, Pei-Ying

    2017-01-01

    for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study

  9. Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study.

    Science.gov (United States)

    Borgo, Francesca; Verduci, Elvira; Riva, Alessandra; Lassandro, Carlotta; Riva, Enrica; Morace, Giulia; Borghi, Elisa

    2017-02-01

    Differences in relative proportions of gut microbial communities in adults have been correlated with intestinal diseases and obesity. In this study we evaluated the gut microbiota biodiversity, both bacterial and fungal, in obese and normal-weight school-aged children. We studied 28 obese (mean age 10.03 ± 0.68) and 33 age- and sex-matched normal-weight children. BMI z-scores were calculated, and the obesity condition was defined according to the WHO criteria. Fecal samples were analyzed by 16S rRNA amplification followed by denaturing gradient gel electrophoresis (DGGE) analysis and sequencing. Real-time polymerase chain reaction (PCR) was performed to quantify the most representative microbial species and genera. DGGE profiles showed high bacterial biodiversity without significant correlations with BMI z-score groups. Compared to bacterial profiles, we observed lower richness in yeast species. Sequence of the most representative bands gave back Eubacterium rectale, Saccharomyces cerevisiae, Candida albicans, and C. glabrata as present in all samples. Debaryomyces hansenii was present only in two obese children. Obese children revealed a significantly lower abundance in Akkermansia muciniphyla, Faecalibacterium prausnitzii, Bacteroides/Prevotella group, Candida spp., and Saccharomyces spp. (P = 0.031, P = 0.044, P = 0.003, P = 0.047, and P = 0.034, respectively). Taking into account the complexity of obesity, our data suggest that differences in relative abundance of some core microbial species, preexisting or diet driven, could actively be part of its etiology. This study improved our knowledge about the fungal population in the pediatric school-age population and highlighted the need to consider the influence of cross-kingdom relationships.

  10. Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

    KAUST Repository

    Scarascia, Giantommaso

    2017-04-04

    Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. Conclusions: Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.

  11. Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance

    Science.gov (United States)

    Wilson, T.L.; Odei, J.B.; Hooten, M.B.; Edwards, T.C.

    2010-01-01

    Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

  12. Combined effect of copper and cadmium on Chlorella vulgaris growth and photosynthesis-related gene transcription

    International Nuclear Information System (INIS)

    Qian Haifeng; Li Jingjing; Sun Liwei; Chen Wei; Sheng, G. Daniel; Liu Weiping; Fu Zhengwei

    2009-01-01

    Chlorella vulgaris was tested to assess their toxicities in freshwater contaminated by the metal compounds of copper (Cu) and cadmium (Cd), both singly and combined. Exposure to 0.5 and 1.5 μM Cu or 1.0 and 2.0 μM Cd alone significantly decreased algal growth and chlorophyll content and increased reactive oxygen species (ROS) content. Two-way ANOVA analysis shows that the combination of these two metal compounds decreased cell growth, chlorophyll content and increased ROS content synergistically. The highest algal cell inhibition was 78.55%, the lowest levels of chl a, chl b and total-chl were 10.59%, 33.33% and 17.94% of the control, respectively. The highest increase in ROS was 9.15-fold greater than that of the control when exposed to Cu(1.5) + Cd(2.0). Real-time PCR shows that Cu and Cd reduced the transcript abundance of psbA and rbcL, but without a synergistic interaction, whereas Cu and Cd increased the transcript abundance of psaB synergistically. These results demonstrate that Cu and Cd independently inhibit PSII activity and CO 2 assimilation, but synergistically increase ROS content to disrupt chlorophyll synthesis and inhibit cell growth.

  13. Combined effect of copper and cadmium on Chlorella vulgaris growth and photosynthesis-related gene transcription

    Energy Technology Data Exchange (ETDEWEB)

    Qian Haifeng; Li Jingjing; Sun Liwei; Chen Wei; Sheng, G. Daniel; Liu Weiping [College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032 (China); Fu Zhengwei, E-mail: azwfu2003@yahoo.com.cn [College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032 (China)

    2009-08-13

    Chlorella vulgaris was tested to assess their toxicities in freshwater contaminated by the metal compounds of copper (Cu) and cadmium (Cd), both singly and combined. Exposure to 0.5 and 1.5 {mu}M Cu or 1.0 and 2.0 {mu}M Cd alone significantly decreased algal growth and chlorophyll content and increased reactive oxygen species (ROS) content. Two-way ANOVA analysis shows that the combination of these two metal compounds decreased cell growth, chlorophyll content and increased ROS content synergistically. The highest algal cell inhibition was 78.55%, the lowest levels of chl a, chl b and total-chl were 10.59%, 33.33% and 17.94% of the control, respectively. The highest increase in ROS was 9.15-fold greater than that of the control when exposed to Cu(1.5) + Cd(2.0). Real-time PCR shows that Cu and Cd reduced the transcript abundance of psbA and rbcL, but without a synergistic interaction, whereas Cu and Cd increased the transcript abundance of psaB synergistically. These results demonstrate that Cu and Cd independently inhibit PSII activity and CO{sub 2} assimilation, but synergistically increase ROS content to disrupt chlorophyll synthesis and inhibit cell growth.

  14. Effects of exposure to 17{alpha}-ethynylestradiol during larval development on growth, sexual differentiation, and abundances of transcripts in the liver of the wood frog (Lithobates sylvaticus)

    Energy Technology Data Exchange (ETDEWEB)

    Tompsett, Amber R., E-mail: amber.tompsett@usask.ca [Toxicology Centre, University of Saskatchewan, Saskatoon, SK (Canada); Wiseman, Steve; Higley, Eric [Toxicology Centre, University of Saskatchewan, Saskatoon, SK (Canada); Giesy, John P. [Toxicology Centre, University of Saskatchewan, Saskatoon, SK (Canada); Dept. of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK (Canada); Dept. of Biology and Chemistry and State Key Laboratory for Marine Pollution, City University of Hong Kong, Hong Kong, Special Administrative Region (Hong Kong); Hecker, Markus [Toxicology Centre, University of Saskatchewan, Saskatoon, SK (Canada); School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK (Canada)

    2013-01-15

    Populations of amphibians are in decline in certain locations around the world, and the possible contribution of environmental contaminants, including estrogenic compounds, to these declines is of potential concern. In the current study, responses of the wood frog (Lithobates sylvaticus) to exposure to 17{alpha}-ethynylestradiol (EE2), the synthetic estrogen used in oral contraceptives, during the larval period were characterized. Exposure of L. sylvaticus to 1.08, 9.55, or 80.9 {mu}g EE2/L had no effects on survival, growth, or metamorphic endpoints monitored in the current study. However, there were significant effects of exposure to EE2 on phenotypic sex ratios. In general, lesser proportions of L. sylvaticus developed as phenotypic males and greater proportions developed as phenotypic females or with mixed sex phenotypes at all concentrations of EE2 tested. Utilizing the data collected in the current study, the EC{sub 50} for complete feminization of L. sylvaticus was determined to be 7.7 {mu}g EE2/L, and the EC{sub 50} for partial feminization was determined to be 2.3 {mu}g EE2/L. In addition, after chronic exposure, abundances of transcripts of vitellogenin A2, high density lipoprotein binding protein, and 7-dehydrocholesterol reductase were 1.8-280-fold greater in livers from L. sylvaticus exposed to EE2 compared to controls. Overall, there were significant effects of exposure to all concentrations of EE2 tested, the least of which was within about 2-fold of estrogen equivalent concentrations previously measured in the environment.

  15. Effects of exposure to 17α-ethynylestradiol during larval development on growth, sexual differentiation, and abundances of transcripts in the liver of the wood frog (Lithobates sylvaticus)

    International Nuclear Information System (INIS)

    Tompsett, Amber R.; Wiseman, Steve; Higley, Eric; Giesy, John P.; Hecker, Markus

    2013-01-01

    Populations of amphibians are in decline in certain locations around the world, and the possible contribution of environmental contaminants, including estrogenic compounds, to these declines is of potential concern. In the current study, responses of the wood frog (Lithobates sylvaticus) to exposure to 17α-ethynylestradiol (EE2), the synthetic estrogen used in oral contraceptives, during the larval period were characterized. Exposure of L. sylvaticus to 1.08, 9.55, or 80.9 μg EE2/L had no effects on survival, growth, or metamorphic endpoints monitored in the current study. However, there were significant effects of exposure to EE2 on phenotypic sex ratios. In general, lesser proportions of L. sylvaticus developed as phenotypic males and greater proportions developed as phenotypic females or with mixed sex phenotypes at all concentrations of EE2 tested. Utilizing the data collected in the current study, the EC 50 for complete feminization of L. sylvaticus was determined to be 7.7 μg EE2/L, and the EC 50 for partial feminization was determined to be 2.3 μg EE2/L. In addition, after chronic exposure, abundances of transcripts of vitellogenin A2, high density lipoprotein binding protein, and 7-dehydrocholesterol reductase were 1.8–280-fold greater in livers from L. sylvaticus exposed to EE2 compared to controls. Overall, there were significant effects of exposure to all concentrations of EE2 tested, the least of which was within about 2-fold of estrogen equivalent concentrations previously measured in the environment.

  16. Coyote abundance in relation to habitat characteristics in Sierra San Luis, Sonora, Mexico

    Science.gov (United States)

    Eduardo Ponce Guevara; Karla Pelz Serrano; Carlos A. Lopez Gonzalez

    2005-01-01

    Coyotes have expanded their historical distribution range because of anthropogenic activities and habitat transformation, where forests have been considered marginal habitat. We tested the relationship between vegetation structure and coyote abundance in different habitat types. We expected to find a higher abundance in open lands than in thicker areas. We used scent...

  17. Constraints on the Mass–Richness Relation from the Abundance and Weak Lensing of SDSS Clusters

    Science.gov (United States)

    Murata, Ryoma; Nishimichi, Takahiro; Takada, Masahiro; Miyatake, Hironao; Shirasaki, Masato; More, Surhud; Takahashi, Ryuichi; Osato, Ken

    2018-02-01

    We constrain the scaling relation between optical richness (λ) and halo mass (M) for a sample of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters within the context of the Planck cosmological model. We use a forward modeling approach where we model the probability distribution of optical richness for a given mass, P({ln}λ | M). To model the abundance and the stacked lensing profiles, we use an emulator specifically built to interpolate the halo mass function and the stacked lensing profile for an arbitrary set of halo mass and redshift, which is calibrated based on a suite of high-resolution N-body simulations. We apply our method to 8312 SDSS redMaPPer clusters with 20 ≤ λ ≤ 100 and 0.10 ≤ z λ ≤ 0.33 and show that the lognormal distribution model for P(λ | M), with four free parameters, well reproduces the measured abundances and lensing profiles simultaneously. The constraints are characterized by the mean relation, (M)=A+B{ln}(M/{M}pivot}), with A={3.207}-0.046+0.044 and B={0.993}-0.055+0.041 (68% CL), where the pivot mass scale M pivot = 3 × 1014 h ‑1 M ⊙, and the scatter {σ }lnλ | M}={σ }0+q{ln}(M/{M}pivot}) with {σ }0={0.456}-0.039+0.047 and q=-{0.169}-0.026+0.035. We find that a large scatter in halo masses is required at the lowest-richness bins (20 ≤ λ ≲ 30) in order to reproduce the measurements. Without such a large scatter, the model prediction for the lensing profiles tends to overestimate the measured amplitudes. This might imply a possible contamination of intrinsically low-richness clusters due to the projection effects. Such a low-mass halo contribution is significantly reduced when applying our method to the sample of 30 ≤ λ ≤ 100.

  18. Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan

    Science.gov (United States)

    Shakir, Muhammad Mussadiq; Ahmed, Sohail

    2015-05-01

    Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops ( p Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface arthropods were the major contributors of variation in overall abundance in extreme temperature months while microarthropods in low-temperature months. CCA analysis revealed the occurrence of

  19. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

    Directory of Open Access Journals (Sweden)

    Yingying Zhu

    Full Text Available Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish or non-meat proteins (casein or soy for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota.

  20. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

    Science.gov (United States)

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota.

  1. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces

    Science.gov (United States)

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota. PMID:27042829

  2. Yield in almond is related more to the abundance of flowers than the relative number of flowers that set fruit

    Directory of Open Access Journals (Sweden)

    Sergio Tombesi

    2016-11-01

    Full Text Available Almond tree yield is a function of the number of flowers on a tree and the percentage of flowers that set fruit. Almonds are borne on spurs (short proleptic shoots that can have both leaves and flowers. Almond tree spur dynamics research has documented that previous year spur leaf area is a predictive parameter for year-to-year spur survival, spur flowering and to a lesser extent spur fruiting, while previous year fruit bearing has a negative impact on subsequent year flowering. However, a question remained about whether yields are more dependent on flower numbers or relative fruit set of the flowers that are present. The aim of the present work was to compare the importance of flower abundance with that of relative fruit set in determining the productivity of a population of tagged spurs in almond trees over a 6-year period. Overall tree yield among years was more sensitive to total number of flowers on a tree rather than relative fruit set. These results emphasize the importance of maintaining large populations of healthy flowering spurs for sustained high production in almond orchards.

  3. Relation of desert pupfish abundance to selected environmental variables in natural and manmade habitats in the Salton Sea basin

    Science.gov (United States)

    Martin, B.A.; Saiki, M.K.

    2005-01-01

    We assessed the relation between abundance of desert pupfish, Cyprinodon macularius, and selected biological and physicochemical variables in natural and manmade habitats within the Salton Sea Basin. Field sampling in a natural tributary, Salt Creek, and three agricultural drains captured eight species including pupfish (1.1% of the total catch), the only native species encountered. According to Bray-Curtis resemblance functions, fish species assemblages differed mostly between Salt Creek and the drains (i.e., the three drains had relatively similar species assemblages). Pupfish numbers and environmental variables varied among sites and sample periods. Canonical correlation showed that pupfish abundance was positively correlated with abundance of western mosquitofish, Gambusia affinis, and negatively correlated with abundance of porthole livebearers, Poeciliopsis gracilis, tilapias (Sarotherodon mossambica and Tilapia zillii), longjaw mudsuckers, Gillichthys mirabilis, and mollies (Poecilia latipinnaandPoecilia mexicana). In addition, pupfish abundance was positively correlated with cover, pH, and salinity, and negatively correlated with sediment factor (a measure of sediment grain size) and dissolved oxygen. Pupfish abundance was generally highest in habitats where water quality extremes (especially high pH and salinity, and low dissolved oxygen) seemingly limited the occurrence of nonnative fishes. This study also documented evidence of predation by mudsuckers on pupfish. These findings support the contention of many resource managers that pupfish populations are adversely influenced by ecological interactions with nonnative fishes. ?? Springer 2005.

  4. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    Science.gov (United States)

    Keeley, Jon E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  5. Phytoplankton abundance in relation to the quality of the coastal water – Arabian Gulf, Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Mostafa Abdel Mohsen El Gammal

    2017-12-01

    Full Text Available Phytoplankton abundance in relation to some physicochemical characters of the costal water of Arabian Gulf (Saudi Arabia was studied for one year. The sampling program included 15 locations in Dammam, Saihat, Al-Qatif, Al-Awamia and Safwa. Water samples were analyzed monthly for these parameters; temperature, pH, salinity, dissolved oxygen, nitrite, nitrate, ammonia, carbon dioxide, total chloride, reactive orthophosphate and total phosphorus and alkalinity, also phytoplankton communities were identified and Chlorophyll a was estimated. The results showed that, the high phytoplankton density attaining the maximum (190.3 × 104/m3 during May and June, and the minimum (10.4 × 104/m3 during November and December. Forty Five species belonging to 5 phytoplankton groups were recorded. Bacillariophyceae was the first dominant group forming 48% of the total phytoplankton communities (23 species. The dominant species of Bacillariophyceae were Pleurosigma strigosum, Pleurosigma elongatum, Lyrella clavata, Rhizosolenia shrubsolei, Cylindrotheca closterium, Nitzschia panduriform, Nitzschia longissimia, Amphora sp and Stephanopyxis. Dinophyceae was the second dominant group and formed 31% of the total phytoplankton communities (10 species; the dominant species were Ceratium fusus, Heterosigma sp, Ceratium furca, Prorocentrum triestium, Protoperidinium sp, Gyrodinium spirale, Noctiluca scintillans and Scrippsiella trochoidea. Cyanophyceae formed 13% (5 species where Nostoc sp, Oscillatoria and Merismopedia sp were the dominant species. Chlorophyceae had 8% (6 species; Scendesmus sp., Chlorella sp., Chlamydomonas sp., Dunaliella salina and Nannochloropsis sp were the dominant species. The Euglinophyceae was rare only one species (Euglina sp. The relationship was positive between the phytoplankton, chlorophyll a and carbon dioxide while negative amongst dissolved oxygen and total nitrogen. This research indicated that the relation between water quality

  6. Hippocampal CA1 transcriptional profile of sleep deprivation: relation to aging and stress.

    Directory of Open Access Journals (Sweden)

    Nada M Porter

    Full Text Available Many aging changes seem similar to those elicited by sleep-deprivation and psychosocial stress. Further, sleep architecture changes with age suggest an age-related loss of sleep. Here, we hypothesized that sleep deprivation in young subjects would elicit both stress and aging-like transcriptional responses.F344 rats were divided into control and sleep deprivation groups. Body weight, adrenal weight, corticosterone level and hippocampal CA1 transcriptional profiles were measured. A second group of animals was exposed to novel environment stress (NES, and their hippocampal transcriptional profiles measured. A third cohort exposed to control or SD was used to validate transcriptional results with Western blots. Microarray results were statistically contrasted with prior transcriptional studies. Microarray results pointed to sleep pressure signaling and macromolecular synthesis disruptions in the hippocampal CA1 region. Animals exposed to NES recapitulated nearly one third of the SD transcriptional profile. However, the SD-aging relationship was more complex. Compared to aging, SD profiles influenced a significant subset of genes. mRNA associated with neurogenesis and energy pathways showed agreement between aging and SD, while immune, glial, and macromolecular synthesis pathways showed SD profiles that opposed those seen in aging.We conclude that although NES and SD exert similar transcriptional changes, selective presynaptic release machinery and Homer1 expression changes are seen in SD. Among other changes, the marked decrease in Homer1 expression with age may represent an important divergence between young and aged brain response to SD. Based on this, it seems reasonable to conclude that therapeutic strategies designed to promote sleep in young subjects may have off-target effects in the aged. Finally, this work identifies presynaptic vesicular release and intercellular adhesion molecular signatures as novel therapeutic targets to counter

  7. Variation in the Abundance of OsHAK1 Transcript Underlies the Differential Salinity Tolerance of an indica and a japonica Rice Cultivar

    Directory of Open Access Journals (Sweden)

    Guang Chen

    2018-01-01

    Full Text Available Salinity imposes a major constraint over the productivity of rice. A set of chromosome segment substitution lines (CSSLs, derived from a cross between the japonica type cultivar (cv. Nipponbare (salinity sensitive and the indica type cv. 9311 (moderately tolerant, was scored using a hydroponics system for their salinity tolerance at the seedling stage. Two of the CSSLs, which share a ∼1.2 Mbp stretch of chromosome 4 derived from cv. Nipponbare, were as sensitive to the stress as cv. Nipponbare itself. Fine mapping based on an F2 population bred from a backcross between one of these CSSLs and cv. 9311 narrowed this region to 95 Kbp, within which only one gene (OsHAK1 exhibited a differential (lower transcript abundance in cv. Nipponbare and the two CSSLs compared to in cv. 9311. The gene was up-regulated by exposure to salinity stress both in the root and the shoot, while a knockout mutant proved to be more salinity sensitive than its wild type with respect to its growth at both the vegetative and reproductive stages. Seedlings over-expressing OsHAK1 were more tolerant than wild type, displaying a superior photosynthetic rate, a higher leaf chlorophyll content, an enhanced accumulation of proline and a reduced level of lipid peroxidation. At the transcriptome level, the over-expression of OsHAK1 stimulated a number of stress-responsive genes as well as four genes known to be involved in Na+ homeostasis and the salinity response (OsHKT1;5, OsSOS1, OsLti6a and OsLti6b. When the stress was applied at booting through to maturity, the OsHAK1 over-expressors out-yielded wild type by 25%, and no negative pleiotropic effects were expressed in plants gown under non-saline conditions. The level of expression of OsHAK1 was correlated with Na+/K+ homeostasis, which implies that the gene should be explored a target for molecular approaches to the improvement of salinity tolerance in rice.

  8. Allelic Variations at Four Major Maturity E Genes and Transcriptional Abundance of the E1 Gene Are Associated with Flowering Time and Maturity of Soybean Cultivars

    Science.gov (United States)

    Wang, Yueqiang; Chen, Xin; Ren, Haixiang; Yang, Jiayin; Cheng, Wen; Zong, Chunmei; Gu, Heping; Qiu, Hongmei; Wu, Hongyan; Zhang, Xingzheng; Cui, Tingting; Xia, Zhengjun

    2014-01-01

    The time to flowering and maturity are ecologically and agronomically important traits for soybean landrace and cultivar adaptation. As a typical short-day crop, long day conditions in the high-latitude regions require soybean cultivars with photoperiod insensitivity that can mature before frost. Although the molecular basis of four major E loci (E1 to E4) have been deciphered, it is not quite clear whether, or to what degree, genetic variation and the expression level of the four E genes are associated with the time to flowering and maturity of soybean cultivars. In this study, we genotyped 180 cultivars at E1 to E4 genes, meanwhile, the time to flowering and maturity of those cultivars were investigated at six geographic locations in China from 2011 to 2012 and further confirmed in 2013. The percentages of recessive alleles at E1, E2, E3 and E4 loci were 38.34%, 84.45%, 36.33%, and 7.20%, respectively. Statistical analysis showed that allelic variations at each of four loci had a significant effect on flowering time as well as maturity. We classified the 180 cultivars into eight genotypic groups based on allelic variations of the four major E loci. The genetic group of e1-nf representing dysfunctional alleles at the E1 locus flowered earliest in all the geographic locations. In contrast, cultivars in the E1E2E3E4 group originated from the southern areas flowered very late or did not flower before frost at high latitude locations. The transcriptional abundance of functional E1 gene was significantly associated with flowering time. However, the ranges of time to flowering and maturity were quite large within some genotypic groups, implying the presence of some other unknown genetic factors that are involved in control of flowering time or maturity. Known genes (e.g. E3 and E4) and other unknown factors may function, at least partially, through regulation of the expression of the E1 gene. PMID:24830458

  9. The ubiquitin ligase SEVEN IN ABSENTIA (SINA) ubiquitinates a defense-related NAC transcription factor and is involved in defense signaling.

    Science.gov (United States)

    Miao, Min; Niu, Xiangli; Kud, Joanna; Du, Xinran; Avila, Julian; Devarenne, Timothy P; Kuhl, Joseph C; Liu, Yongsheng; Xiao, Fangming

    2016-07-01

    We recently identified a defense-related tomato (Solanum lycopersicum) NAC (NAM, ATAF1,2, CUC2) transcription factor, NAC1, that is subjected to ubiquitin-proteasome system-dependent degradation in plant cells. In this study, we identified a tomato ubiquitin ligase (termed SEVEN IN ABSENTIA3; SINA3) that ubiquitinates NAC1, promoting its degradation. We conducted coimmunoprecipitation and bimolecular fluorescence complementation to determine that SINA3 specifically interacts with the NAC1 transcription factor in the nucleus. Moreover, we found that SINA3 ubiquitinates NAC1 in vitro and promotes NAC1 degradation via polyubiquitination in vivo, indicating that SINA3 is a ubiquitin ligase that ubiquitinates NAC1, promoting its degradation. Our real-time PCR analysis indicated that, in contrast to our previous finding that NAC1 mRNA abundance increases upon Pseudomonas infection, the SINA3 mRNA abundance decreases in response to Pseudomonas infection. Moreover, using Agrobacterium-mediated transient expression, we found that overexpression of SINA3 interferes with the hypersensitive response cell death triggered by multiple plant resistance proteins. These results suggest that SINA3 ubiquitinates a defense-related NAC transcription factor for degradation and plays a negative role in defense signaling. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  10. Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters

    DEFF Research Database (Denmark)

    Sawers, Ruairidh J. H.; Svane, Simon; Quan, Clement

    2017-01-01

    -internal and -external fungal structures, mycorrhizal phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters varied among lines. Superior response in Oh43 is correlated with extensive development of root-external hyphae, accumulation of specific Pht1 transcripts and high...

  11. Financial development and oil resource abundance-growth relations: evidence from panel data.

    Science.gov (United States)

    Law, Siong Hook; Moradbeigi, Maryam

    2017-10-01

    This study investigates whether financial development dampens the negative impact of oil resource abundance on economic growth. Because of substantial cross-sectional dependence in our data, which contain a core sample of 63 oil-producing countries from 1980 through 2010, we use the common correlated effect mean group (CCEMG) estimator to account for the high degree of heterogeneity and drop the outlier countries. The empirical results reveal that oil resource abundance affects the growth rate in output contingent on the degree of development in financial markets. More developed financial markets can channel the revenues from oil into more productive activities and thus offset the negative effects of oil resource abundance on economic growth. Thus, better financial development can reverse resource curse or enhance resource blessing in oil-rich economies.

  12. Identification of transcripts related to high egg production in the chicken hypothalamus and pituitary gland.

    Science.gov (United States)

    Shiue, Yow-Ling; Chen, Lih-Ren; Chen, Chih-Feng; Chen, Yi-Ling; Ju, Jhy-Phen; Chao, Ching-Hsien; Lin, Yuan-Ping; Kuo, Yu-Ming; Tang, Pin-Chi; Lee, Yen-Pai

    2006-09-15

    To identify transcripts related to high egg production expressed specifically in the hypothalamus and pituitary gland of the chicken, two subtracted cDNA libraries were constructed. Two divergently selected strains of Taiwan Country Chickens (TCCs), B (sire line) and L2 (dam line) were used; they had originated from a single population and were further subjected (since 1982) to selection for egg production to 40 wk of age and body weight/comb size, respectively. A total of 324 and 370 clones were identified from the L2-B (L2-subtract-B) and the B-L2 subtracted cDNA libraries, respectively. After sequencing and annotation, 175 and 136 transcripts that represented 53 known and 65 unknown non-redundant sequences were characterized in the L2-B subtracted cDNA library. Quantitative reverse-transcription (RT)-PCR was used to screen the mRNA expression levels of 32 randomly selected transcripts in another 78 laying hens from five different strains. These strains included the two original strains (B and L2) used to construct the subtracted cDNA libraries and an additional three commercial strains, i.e., Black- and Red-feather TCCs and Single-Comb White Leghorn (WL) layer. The mRNA expression levels of 16 transcripts were significantly higher in the L2 than in the B strain, whereas the mRNA expression levels of nine transcripts, BDH, NCAM1, PCDHA@, PGDS, PLAG1, PRL, SAR1A, SCG2 and STMN2, were significantly higher in two high egg production strains, L2 and Single-Comb WL; this indicated their usefulness as molecular markers of high egg production.

  13. Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats.

    Science.gov (United States)

    Lee, Sang-Im; Lee, Hyunna; Jablonski, Piotr G; Choe, Jae Chun; Husby, Magne

    2017-01-01

    Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the

  14. The relative influence of prey abundance and co-breeders on the ...

    African Journals Online (AJOL)

    This study investigates if the reproductive performance of polyandrous Pale Chanting-goshawks, Melierax canorus, is governed by the abundance of dominant rodent-prey species or a co-breeding male participating fully in prey being delivered to the female and young. Polyandrous trios in prey-rich habitat, the only habitat ...

  15. Woodland pond salamander abundance in relation to forest management and environmental conditions in northern Wisconsin

    Science.gov (United States)

    Deahn M. Donner; Christine A. Ribic; Albert J. Beck; Dale Higgins; Dan Eklund; Susan. Reinecke

    2015-01-01

    Woodland ponds are important landscape features that help sustain populations of amphibians that require this aquatic habitat for successful reproduction. Species abundance patterns often reflect site-specific differences in hydrology, physical characteristics, and surrounding vegetation. Large-scale processes such as changing land cover and environmental conditions...

  16. A nondestructive technique to monitor the relative abundance of terrestrial salamanders

    Science.gov (United States)

    Richard M. DeGraaf; Mariko. Yamasaki

    1992-01-01

    Salamanders are abundant vertebrates in many forest ecosystems, and their annual biomass production can be important in forest food webs (Pough et al. 1987). Population densities of eastern redback salamanders (Plethodon cinereus) can exceed 2 individuals/m2 in deciduous forests of the United States (Heatwole 1962, Jaeger 1980...

  17. Killer whale presence in relation to naval sonar activity and prey abundance in northern Norway

    NARCIS (Netherlands)

    Kuningas, S.; Kvadsheim, P.H.; Lam, F.P.A.; Miller, P.J.O.

    2013-01-01

    In this study, retrospective data on naval sonar activity and prey abundance were correlated with killer whale sightings within a fjord basin in northern Norway. In addition, passive acoustic and visual marine mammal surveys were conducted before, during, and after a specific navy exercise in 2006.

  18. Relative abundance of resident versus oceanic zooplankton over an interisland reef

    International Nuclear Information System (INIS)

    Alldredge, A.L.; King, J.M.

    1979-01-01

    Zooplankton were collected from various substrate types. Densities were determined and results indicated that demersal plankton were abundant on the Japtan reef flat. Behavioral mechanisms were exhibited by many organisms including swimming near the substrate or in the lees of coral heads. Demersal plankton may provide an important food source for nocturnally foraging fishes

  19. Seasonal variation in copepod abundance in relation to other zooplanktonic groups in the northwestern Mediterranean

    NARCIS (Netherlands)

    Kouwenberg, Juliana H.M.

    1993-01-01

    Abundance of adult copepods and late copepodid stages from the upper 50 m in the Golfe du Lion (N.W. Mediterranean) was studied by the author in 1986, 1987, and 1988 for each season. Altogether 87 stations at 22 fixed locations were sampled in the frame of the multidisciplinary French/Spanish

  20. Variation in local abundance and species richness of stream fishes in relation to dispersal barriers: Implications for management and conservation

    Science.gov (United States)

    Nislow, K.H.; Hudy, M.; Letcher, B.H.; Smith, E.P.

    2011-01-01

    1.Barriers to immigration, all else being equal, should in principle depress local abundance and reduce local species richness. These issues are particularly relevant to stream-dwelling species when improperly designed road crossings act as barriers to migration with potential impacts on the viability of upstream populations. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population- and community-level effects can be difficult to detect. 2.In this study, we tested the effects of potential barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, U.S.A. Fishes were sampled using simple standard techniques above- and below road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species and that variable effects on abundance would translate into lower species richness. 3.Supporting these predictions, the statistical model that best accounted for variation in abundance and species richness included a significant interaction between location (upstream or downstream of crossing) and type (passable or impassable crossing). Stream sections located above predicated impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. 4.Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In turn, these results suggest that when measured at

  1. Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests

    Directory of Open Access Journals (Sweden)

    Rosario A. Marroquin-Flores

    2017-08-01

    Full Text Available Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2,150–2,460 m. We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%, the highest proportion of which were infected with Haemoproteus (20.9%, followed by Leucocytozoon (13.4%, then Plasmodium (8.0%. We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium. When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27 of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six, while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI [43–98]; thus, we may have already sampled ∼60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the

  2. Longitudinal patterns in flathead catfish relative abundance and length at age within a large river: Effects of an urban gradient

    Science.gov (United States)

    Paukert, C.P.; Makinster, A.S.

    2009-01-01

    We investigated the spatial variation of flathead catfish (Pylodictis olivaris) relative abundance and growth in the 274 km long Kansas River to determine if population dynamics of catfish are related to urbanization. Electrofishing was conducted at 462 random sites throughout the river in summer, 2005-2006 to collect fish. Relative abundance of age 1 fish (???200mm), subadult (>200-400mm) and adult fish (>400 mm) ranged from 0.34 to 14.67 fish h-1, mean length at age 1 was 165 (range: 128-195) mm total length (TL) and mean length at age 3 was 376 mm TL (range: 293-419mm TL). The proportion of land use within 200 m of the river edge was between 0 and 0.54 urban. River reaches with high relative abundance of age 1 flathead catfish had high relative abundance of subadult and adult catfish. River reaches with fast flathead catfish growth to age 1 had fast growth to age 3. High urban land use and riprap in the riparian area were evident in river reaches near the heavily populated Kansas City and Topeka, Kansas, USA. Reaches with increased number of log jams and islands had decreased riparian agriculture. Areas of low urbanization had faster flathead catfish growth (r = 0.67, p = 0.005). Relative abundance of flathead catfish was higher in more agricultural areas (r = -0.57, p = 0.02). Changes in land use in riverine environments may alter population dynamics of a fish species within a river. Spatial differences in population dynamics need to be considered when evaluating riverine fish populations. Published in 2008 by John Wiley & Sons Ltd.

  3. Transcriptional effects of glucocorticoid receptors in the dentate gyrus increase anxiety-related behaviors.

    Directory of Open Access Journals (Sweden)

    Nadège Sarrazin

    Full Text Available The Glucocorticoid Receptor (GR is a transcription factor ubiquitously expressed in the brain. Activation of brain GRs by high levels of glucocorticoid (GC hormones modifies a large variety of physiological and pathological-related behaviors. Unfortunately the specific cellular targets of GR-mediated behavioral effects of GC are still largely unknown. To address this issue, we generated a mutated form of the GR called DeltaGR. DeltaGR is a constitutively transcriptionally active form of the GR that is localized in the nuclei and activates transcription without binding to glucocorticoids. Using the tetracycline-regulated system (Tet-OFF, we developed an inducible transgenic approach that allows the expression of the DeltaGR in specific brain areas. We focused our study on a mouse line that expressed DeltaGR almost selectively in the glutamatergic neurons of the dentate gyrus (DG of the hippocampus. This restricted expression of the DeltaGR increased anxiety-related behaviors without affecting other behaviors that could indirectly influence performance in anxiety-related tests. This behavioral phenotype was also associated with an up-regulation of the MAPK signaling pathway and Egr-1 protein in the DG. These findings identify glutamatergic neurons in the DG as one of the cellular substrate of stress-related pathologies.

  4. Iron Abundance in the Prototype PG 1159 Star, GW Vir Pulsator PG 1159-035, and Related Objects

    Science.gov (United States)

    Werner, K.; Rauch, T.; Kruk, J. W.; Kurucz, R. L.

    2011-01-01

    We performed an iron abundance determination of the hot, hydrogen deficient post-AGB star PG 1159-035. which is the prototype of the PG 1159 spectral class and the GW Vir pulsators, and of two related objects (PG 1520+525, PG 1144+005), based on the first detection of Fe VIII lines in stellar photospheres. In another PG 1159 star. PG 1424+535. we detect Fe VII lines. In all four stars, each within T(sub eff) = 110,000-150,000 K, we find a solar iron abundance. This result agrees with our recent abundance analysis of the hottest PG 1159 stars (T(sub eff) = 150,000-200,000 K) that exhibit Fe x lines. On the whole, we find that the PG 1159 stars are not significantly iron deficient, in contrast to previous notions.

  5. Rapid Upregulation of Orai1 Abundance in the Plasma Membrane of Platelets Following Activation with Thrombin and Collagen Related Peptide

    Directory of Open Access Journals (Sweden)

    Guilai Liu

    2015-11-01

    Full Text Available Background: Blood platelets accomplish primary hemostasis following vascular injury and contribute to the orchestration of occlusive vascular disease. Platelets are activated by an increase of cytosolic Ca2+-activity ([Ca2+]i, which is accomplished by Ca2+-release from intracellular stores and subsequent store operated Ca2+ entry (SOCE through Ca2+ release activated Ca2+ channel moiety Orai1. Powerful activators of platelets include thrombin and collagen related peptide (CRP, which are in part effective by activation of small G- protein Rac1. The present study explored the influence of thrombin and CRP on Orai1 protein abundance and cytosolic Ca2+-activity ([Ca2+]i in platelets drawn from wild type mice. Methods: Orai1 protein surface abundance was quantified utilizing CF™488A conjugated antibodies, and [Ca2+]i was determined with Fluo3-fluorescence. Results: In resting platelets, Orai1 protein abundance and [Ca2+]i were low. Thrombin (0.02 U/ml and CRP (5ug/ml within 2 min increased [Ca2+]i and Orai1 protein abundance at the platelet surface. [Ca2+]i was further increased by Ca2+ ionophore ionomycin (1 µM and by store depletion with the sarcoendoplasmatic Ca2+ ATPase inhibitor thapsigargin (1 µM. However, Orai1 protein abundance at the platelet surface was not significantly affected by ionomycin and only slightly increased by thapsigargin. The effect of thrombin and CRP on Orai1 abundance and [Ca2+]i was significantly blunted by Rac1 inhibitor NSC23766 (50 µM. Conclusion: The increase of [Ca2+]i following stimulation of platelets with thrombin and collagen related peptide is potentiated by ultrarapid Rac1 sensitive translocation of Orai1 into the cell membrane.

  6. Abundance of plankton population densities in relation to bottom soil textural types in aquaculture ponds

    Directory of Open Access Journals (Sweden)

    F. Siddika

    2012-06-01

    Full Text Available Plankton is an important food item of fishes and indicator for the productivity of a water body. The present study was conducted to evaluate the effects of bottom soil textural conditions on abundance of plankton in aquaculture pond. The experiment was carried out using three treatments, i.e., ponds bottom with sandy loam (T1, with loam (T2 and with clay loam (T3. The ranges of water quality parameters analyzed were suitable for the growth of plankton during the experimental period. Similarly, chemical properties of soil were also within suitable ranges and every parameter showed higher ranges in T2. A total 20 genera of phytoplankton were recorded belonged to Chlorophyceae (7, Cyanophyceae (5, Bacillariophyceae (5, Euglenophyceae (2 and Dinophyceae (1. On the other hand, total 13 genera of zooplankton were recorded belonged to Crustacea (7 and Rotifera (6. The highest ranges of phytoplankton and zooplankton densities were found in T2 where low to medium-type bloom was observed during the study period. Consequently, the mean abundance of plankton (phytoplankton and zooplankton density was significantly highest in T2. The highest abundance of plankton in the T2 indicated that pond bottom with loamy soil is suitable for the growth and production of plankton in aquaculture ponds.

  7. Relative expression of the products of glyoxylate bypass operon: contributions of transcription and translation.

    OpenAIRE

    Chung, T; Resnik, E; Stueland, C; LaPorte, D C

    1993-01-01

    Although the genes of the aceBAK operon are expressed from the same promoter, the relative cellular levels of their products are approximately 0.3:1:0.003. Gene and operon fusions with lacZ were constructed to characterize this differential expression. The upshift in expression between aceB and aceA resulted from differences in translational efficiency. In contrast, inefficient translation and premature transcriptional termination contributed to the downshift in expression between aceA and ac...

  8. Differences in relative amounts of two novel mutant HEXA transcripts in a juvenile TSD Druze patient

    Energy Technology Data Exchange (ETDEWEB)

    Drucker, L.; Navon, R. [Tel Aviv Univ. (Israel)]|[Sapir Medical Center, Kfar Sava (Israel)

    1994-09-01

    An Israeli-Druze patient with juvenile Tay-Sachs disease, born to first cousins, was found to be a compound heterozygote for two novel mutant HEXA alleles. SSCP analysis of the parents` genomic DNA revealed alterations in both exons 5 and 8. Direct sequencing showed a novel missense mutation T{sup 835}{r_arrow}C (Ser{sup 279}{r_arrow}Pro) in exon 8, of maternal origin. The mutant allele of paternal origin carried a novel double mutation in exon 5, (i) a C{sup 496} deletion, resulting in a frameshift and eventually a stop codon, (ii) a C{sup 496}{r_arrow}G transition which is a silent mutation. Both these latter mutations occur in the same codon. New restriction sites for ScrFI were introduced into the two mutant alleles, enabling rapid screening for their presence. In order to detect differences of the relative levels of the transcripts originating from the two mutant alleles, we applied allele-specific transcripts polymerase chain reaction (AST-PCR) to the RNA extractions prepared from the heterozygous parents (each carry a normal and mutant allele). In order to distinguish between the transcripts originating from the normal allele and those originating from each of the mutant alleles, the transcripts were digested by ScrFI. A severe depletion of the mRNA coded by the allele carrying the mutation in exon 5 was found. The phenomena corresponds with citations in the literature in cases of stop mutations. The allele carrying the transversion in exon 8, contrary to our expectations, also had a distinctly lower level of transcripts. The AST-PCR approach offers a molecular tool to study allele-specific gene expression in heterozygous individuals.

  9. NFE2-Related Transcription Factor 2 Coordinates Antioxidant Defense with Thyroglobulin Production and Iodination in the Thyroid Gland.

    Science.gov (United States)

    Ziros, Panos G; Habeos, Ioannis G; Chartoumpekis, Dionysios V; Ntalampyra, Eleni; Somm, Emmanuel; Renaud, Cédric O; Bongiovanni, Massimo; Trougakos, Ioannis P; Yamamoto, Masayuki; Kensler, Thomas W; Santisteban, Pilar; Carrasco, Nancy; Ris-Stalpers, Carrie; Amendola, Elena; Liao, Xiao-Hui; Rossich, Luciano; Thomasz, Lisa; Juvenal, Guillermo J; Refetoff, Samuel; Sykiotis, Gerasimos P

    2018-06-01

    The thyroid gland has a special relationship with oxidative stress. While generation of oxidative substances is part of normal iodide metabolism during thyroid hormone synthesis, the gland must also defend itself against excessive oxidation in order to maintain normal function. Antioxidant and detoxification enzymes aid thyroid cells to maintain homeostasis by ameliorating oxidative insults, including during exposure to excess iodide, but the factors that coordinate their expression with the cellular redox status are not known. The antioxidant response system comprising the ubiquitously expressed NFE2-related transcription factor 2 (Nrf2) and its redox-sensitive cytoplasmic inhibitor Kelch-like ECH-associated protein 1 (Keap1) defends tissues against oxidative stress, thereby protecting against pathologies that relate to DNA, protein, and/or lipid oxidative damage. Thus, it was hypothesized that Nrf2 should also have important roles in maintaining thyroid homeostasis. Ubiquitous and thyroid-specific male C57BL6J Nrf2 knockout (Nrf2-KO) mice were studied. Plasma and thyroids were harvested for evaluation of thyroid function tests by radioimmunoassays and of gene and protein expression by real-time polymerase chain reaction and immunoblotting, respectively. Nrf2-KO and Keap1-KO clones of the PCCL3 rat thyroid follicular cell line were generated using CRISPR/Cas9 technology and were used for gene and protein expression studies. Software-predicted Nrf2 binding sites on the thyroglobulin enhancer were validated by site-directed in vitro mutagenesis and chromatin immunoprecipitation. The study shows that Nrf2 mediates antioxidant transcriptional responses in thyroid cells and protects the thyroid from oxidation induced by iodide overload. Surprisingly, it was also found that Nrf2 has a dramatic impact on both the basal abundance and the thyrotropin-inducible intrathyroidal abundance of thyroglobulin (Tg), the precursor protein of thyroid hormones. This effect is mediated

  10. Temporal Patterns in the Abundance of a Critically Endangered Marsupial Relates to Disturbance by Roads and Agriculture.

    Science.gov (United States)

    Yeatman, Georgina J; Wayne, Adrian F; Mills, Harriet R; Prince, Jane

    2016-01-01

    The aim of this study was to investigate how landscape disturbance associated with roads, agriculture and forestry influenced temporal patterns in woylie (Bettongia penicillata) abundance before, during and after periods of rapid population change. Data were collected from an area of approximately 140,000 ha of forest within the Upper Warren region in south-western Australia. Woylie abundance was measured using cage trapping at 22 grid and five transect locations with varying degrees of landscape disturbance between 1994 and 2012. We found evidence that the distribution and abundance of woylies over time appears to be related to the degree of fragmentation by roads and proximity to agriculture. Sites furthest from agriculture supported a greater abundance of woylies and had slower rates of population decline. Sites with fewer roads had a greater abundance of woylies generally and a greater rate of increase in abundance after the implementation of invasive predator control. The results of this study suggest that landscape disturbance is less important at peak population densities, but during times of environmental and population change, sites less dissected by roads and agriculture better support woylie populations. This may be due to the role these factors play in increasing the vulnerability of woylies to introduced predators, population fragmentation, weed species invasion, mortality from road collisions or a reduction in available habitat. Strategies that reduce the impact of disturbance on woylie populations could include the rationalisation of forest tracks and consolidation of contiguous habitat through the acquisition of private property. Reducing the impact of disturbance in the Upper Warren region could improve the resilience of this critically important woylie population during future environmental change.

  11. Diet and condition of mesopredators on coral reefs in relation to shark abundance.

    Science.gov (United States)

    Barley, Shanta C; Meekan, Mark G; Meeuwig, Jessica J

    2017-01-01

    Reef sharks may influence the foraging behaviour of mesopredatory teleosts on coral reefs via both risk effects and competitive exclusion. We used a "natural experiment" to test the hypothesis that the loss of sharks on coral reefs can influence the diet and body condition of mesopredatory fishes by comparing two remote, atoll-like reef systems, the Rowley Shoals and the Scott Reefs, in northwestern Australia. The Rowley Shoals are a marine reserve where sharks are abundant, whereas at the Scott Reefs numbers of sharks have been reduced by centuries of targeted fishing. On reefs where sharks were rare, the gut contents of five species of mesopredatory teleosts largely contained fish while on reefs with abundant sharks, the same mesopredatory species consumed a larger proportion of benthic invertebrates. These measures of diet were correlated with changes in body condition, such that the condition of mesopredatory teleosts was significantly poorer on reefs with higher shark abundance. Condition was defined as body weight, height and width for a given length and also estimated via several indices of condition. Due to the nature of natural experiments, alternative explanations cannot be discounted. However, the results were consistent with the hypothesis that loss of sharks may influence the diet and condition of mesopredators and by association, their fecundity and trophic role. Regardless of the mechanism (risk effects, competitive release, or other), our findings suggest that overfishing of sharks has the potential to trigger trophic cascades on coral reefs and that further declines in shark populations globally should be prevented to protect ecosystem health.

  12. Diet and condition of mesopredators on coral reefs in relation to shark abundance.

    Directory of Open Access Journals (Sweden)

    Shanta C Barley

    Full Text Available Reef sharks may influence the foraging behaviour of mesopredatory teleosts on coral reefs via both risk effects and competitive exclusion. We used a "natural experiment" to test the hypothesis that the loss of sharks on coral reefs can influence the diet and body condition of mesopredatory fishes by comparing two remote, atoll-like reef systems, the Rowley Shoals and the Scott Reefs, in northwestern Australia. The Rowley Shoals are a marine reserve where sharks are abundant, whereas at the Scott Reefs numbers of sharks have been reduced by centuries of targeted fishing. On reefs where sharks were rare, the gut contents of five species of mesopredatory teleosts largely contained fish while on reefs with abundant sharks, the same mesopredatory species consumed a larger proportion of benthic invertebrates. These measures of diet were correlated with changes in body condition, such that the condition of mesopredatory teleosts was significantly poorer on reefs with higher shark abundance. Condition was defined as body weight, height and width for a given length and also estimated via several indices of condition. Due to the nature of natural experiments, alternative explanations cannot be discounted. However, the results were consistent with the hypothesis that loss of sharks may influence the diet and condition of mesopredators and by association, their fecundity and trophic role. Regardless of the mechanism (risk effects, competitive release, or other, our findings suggest that overfishing of sharks has the potential to trigger trophic cascades on coral reefs and that further declines in shark populations globally should be prevented to protect ecosystem health.

  13. The relative importance of pollinator abundance and species richness for the temporal variance of pollination services.

    Science.gov (United States)

    Genung, Mark A; Fox, Jeremy; Williams, Neal M; Kremen, Claire; Ascher, John; Gibbs, Jason; Winfree, Rachael

    2017-07-01

    The relationship between biodiversity and the stability of ecosystem function is a fundamental question in community ecology, and hundreds of experiments have shown a positive relationship between species richness and the stability of ecosystem function. However, these experiments have rarely accounted for common ecological patterns, most notably skewed species abundance distributions and non-random extinction risks, making it difficult to know whether experimental results can be scaled up to larger, less manipulated systems. In contrast with the prolific body of experimental research, few studies have examined how species richness affects the stability of ecosystem services at more realistic, landscape scales. The paucity of these studies is due in part to a lack of analytical methods that are suitable for the correlative structure of ecological data. A recently developed method, based on the Price equation from evolutionary biology, helps resolve this knowledge gap by partitioning the effect of biodiversity into three components: richness, composition, and abundance. Here, we build on previous work and present the first derivation of the Price equation suitable for analyzing temporal variance of ecosystem services. We applied our new derivation to understand the temporal variance of crop pollination services in two study systems (watermelon and blueberry) in the mid-Atlantic United States. In both systems, but especially in the watermelon system, the stronger driver of temporal variance of ecosystem services was fluctuations in the abundance of common bee species, which were present at nearly all sites regardless of species richness. In contrast, temporal variance of ecosystem services was less affected by differences in species richness, because lost and gained species were rare. Thus, the findings from our more realistic landscapes differ qualitatively from the findings of biodiversity-stability experiments. © 2017 by the Ecological Society of America.

  14. Distribution and relative abundance of large whales in a former whaling ground off eastern South America

    Directory of Open Access Journals (Sweden)

    Artur Andriolo

    2010-10-01

    Full Text Available Ship-based sighting surveys for cetaceans were conducted in the former whaling ground off the northeastern coast of Brazil. The cruises took place in winter and spring of 1998-2001 with the objectives of investigating current distribution and abundance of cetaceans, particularly large whale species taken during whaling. In 1998 the survey were conducted between the parallels 5°30'W and 9°S and the 200 m isobath and the meridian 033°W. A total of about 3,100 nm were surveyed between 1998 and 2001 Surveys were conducted using line transect methods from about 5-10°S, and from the coast to 33°W. A total of 151 sightings (203 individuals of large whales were recorded on effort. The Antarctic minke whale - Balaenoptera bonaerensis (Burmeister, 1867 was the most frequently sighted species (97 groups/132 individuals; Sighting Rate [SR] = 0.031 groups/nm, being recorded only in offshore waters. Density gradually increased from August to October. Minke whales were distributed throughout the area, both to the north and the south of former whaling ground. Sighting data indicate this is the most abundant species, particularly in the area beyond the continental shelf break. Breeding behavior was observed for Antarctic minke whales, but few groups containing calves were recorded (4.3% of the groups sighted on effort. Three other large whale species were recorded in low numbers: the Bryde's whale - Balaenoptera edeni (Anderson, 1879¹; the sei whale, B. borealis (Lesson, 1828, and the sperm, Physeter macrocephalus (Linnaeus, 1758. Sei, Bryde and sperm whales were regularly caught during whaling operations, but are rare in the area, suggesting they were depleted by whaling and have yet to recover to their pre-explotation abundance. In contrast, minke whales are abundant in this area, suggesting that either they were not substantially depleted, or that they have recovered rapidly. Blue whale, Balaenoptera musculus (Linnaeus, 1758, and fin whale, B. physalus

  15. Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches.

    Science.gov (United States)

    Oster, Ryan J; Wijesinghe, Rasanthi U; Haack, Sheridan K; Fogarty, Lisa R; Tucker, Taaja R; Riley, Stephen C

    2014-12-16

    Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10 E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

  16. Golden alga presence and abundance are inversely related to salinity in a high-salinity river ecosystem, Pecos River, USA

    Science.gov (United States)

    Israël, Natascha M.D.; VanLandeghem, Matthew M.; Denny, Shawn; Ingle, John; Patino, Reynaldo

    2014-01-01

    Prymnesium parvum (golden alga, GA) is a toxigenic harmful alga native to marine ecosystems that has also affected brackish inland waters. The first toxic bloom of GA in the western hemisphere occurred in the Pecos River, one of the saltiest rivers in North America. Environmental factors (water quality) associated with GA occurrence in this basin, however, have not been examined. Water quality and GA presence and abundance were determined at eight sites in the Pecos River basin with or without prior history of toxic blooms. Sampling was conducted monthly from January 2012 to July 2013. Specific conductance (salinity) varied spatiotemporally between 4408 and 73,786 mS/cm. Results of graphical, principal component (PCA), and zero-inflated Poisson (ZIP) regression analyses indicated that the incidence and abundance of GA are reduced as salinity increases spatiotemporally. LOWESS regression and correlation analyses of archived data for specific conductance and GA abundance at one of the study sites retrospectively confirmed the negative association between these variables. Results of PCA also suggested that at <15,000 mS/cm, GA was present at a relatively wide range of nutrient (nitrogen and phosphorus) concentrations whereas at higher salinity, GA was observed only at mid-to-high nutrient levels. Generally consistent with earlier studies, results of ZIP regression indicated that GA presence is positively associated with organic phosphorus and in samples where GA is present, GA abundance is positively associated with organic nitrogen and negatively associated with inorganic nitrogen. This is the first report of an inverse relation between salinity and GA presence and abundance in riverine waters and of interaction effects of salinity and nutrients in the field. These observations contribute to a more complete understanding of environmental conditions that influence GA distribution in inland waters.

  17. Impact of improving dietary amino acid balance for lactating sows on efficiency of dietary amino acid utilization and transcript abundance of genes encoding lysine transporters in mammary tissue

    DEFF Research Database (Denmark)

    Huber, L; de Lange, C F M; Ernst, Cathy

    2016-01-01

    Lactating multiparous Yorkshire sows (n = 64) were used in 2 experiments to test the hypothesis that reducing dietary CP intake and improving AA balance through crystalline AA (CAA) supplementation improves apparent dietary AA utilization efficiency for milk production and increases transcript ab...

  18. Utilizing individual fish biomass and relative abundance models to map environmental niche associations of adult and juvenile targeted fishes.

    Science.gov (United States)

    Galaiduk, Ronen; Radford, Ben T; Harvey, Euan S

    2018-06-21

    Many fishes undergo ontogenetic habitat shifts to meet their energy and resource needs as they grow. Habitat resource partitioning and patterns of habitat connectivity between conspecific fishes at different life-history stages is a significant knowledge gap. Species distribution models were used to examine patterns in the relative abundance, individual biomass estimates and environmental niche associations of different life stages of three iconic West Australian fishes. Continuous predictive maps describing the spatial distribution of abundance and individual biomass of the study species were created as well predictive hotspot maps that identify possible areas for aggregation of individuals of similar life stages of multiple species (i.e. spawning grounds, fisheries refugia or nursery areas). The models and maps indicate that processes driving the abundance patterns could be different from the body size associated demographic processes throughout an individual's life cycle. Incorporating life-history in the spatially explicit management plans can ensure that critical habitat of the vulnerable stages (e.g. juvenile fish, spawning stock) is included within proposed protected areas and can enhance connectivity between various functional areas (e.g. nursery areas and adult populations) which, in turn, can improve the abundance of targeted species as well as other fish species relying on healthy ecosystem functioning.

  19. Distribution and abundance of juvenile demersal fishes in relation to summer hypoxia and other environmental variables in coastal Oregon, USA

    Science.gov (United States)

    Sobocinski, Kathryn L.; Ciannelli, Lorenzo; Wakefield, W. Waldo; Yergey, Matthew E.; Johnson-Colegrove, Angela

    2018-05-01

    The juvenile demersal fish assemblage along the Pacific Northwest coast has received little attention relative to adult life history stages since pioneering work in the 1970s. Increasing severity of hypoxia along the Oregon coast in recent years has prompted investigations into the response of biota in this region. We used summer data (2008-2013) from a beam trawl survey targeting juvenile demersal fishes in soft-bottom habitats along the Oregon coast to describe patterns of distribution and abundance at fixed sampling stations (from 30 m to 100 m depth). We relate the assemblage and abundance of the common species to environmental variables and analyze condition of recently settled fish (improve our understanding of this community, especially in light of changing environmental drivers such as decreasing pH, warming water, and episodic periods of low dissolved oxygen coinciding with settlement for many species.

  20. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  1. Evaluation of alternative age-based methods for estimating relative abundance from survey data in relation to assessment models

    DEFF Research Database (Denmark)

    Berg, Casper Willestofte; Nielsen, Anders; Kristensen, Kasper

    2014-01-01

    Indices of abundance from fishery-independent trawl surveys constitute an important source of information for many fish stock assessments. Indices are often calculated using area stratified sample means on age-disaggregated data, and finally treated in stock assessment models as independent...... observations. We evaluate a series of alternative methods for calculating indices of abundance from trawl survey data (delta-lognormal, delta-gamma, and Tweedie using Generalized Additive Models) as well as different error structures for these indices when used as input in an age-based stock assessment model...... the different indices produced. The stratified mean method is found much more imprecise than the alternatives based on GAMs, which are found to be similar. Having time-varying index variances is found to be of minor importance, whereas the independence assumption is not only violated but has significant impact...

  2. Data-poor management of African lion hunting using a relative index of abundance.

    Science.gov (United States)

    Edwards, Charles T T; Bunnefeld, Nils; Balme, Guy A; Milner-Gulland, E J

    2014-01-07

    Sustainable management of terrestrial hunting requires managers to set quotas restricting offtake. This often takes place in the absence of reliable information on the population size, and as a consequence, quotas are set in an arbitrary fashion, leading to population decline and revenue loss. In this investigation, we show how an indirect measure of abundance can be used to set quotas in a sustainable manner, even in the absence of information on population size. Focusing on lion hunting in Africa, we developed a simple algorithm to convert changes in the number of safari days required to kill a lion into a quota for the following year. This was tested against a simulation model of population dynamics, accounting for uncertainties in demography, observation, and implementation. Results showed it to reliably set sustainable quotas despite these uncertainties, providing a robust foundation for the conservation of hunted species.

  3. Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches

    Science.gov (United States)

    Oster, Ryan J.; Wijesinghe, Rasanthi U.; Fogarty, Lisa Reynolds; Haack, Sheridan K.; Fogarty, Lisa R.; Tucker, Taaja R.; Riley, Stephen

    2014-01-01

    Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

  4. Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling

    Directory of Open Access Journals (Sweden)

    Wang Yubing

    2012-12-01

    Full Text Available Abstract Background Brown planthopper (BPH, Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF are up-stream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. Results We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT. We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1. We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC of more than 2.0 (P10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. Conclusions We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants protect themselves by reducing their metabolic level to inhibit feeding by BPH and prevent damage from water and nutrient loss. We have selected 21 TF genes related to BPH resistance for further analyses to understand the molecular responses to BPH feeding in rice.

  5. G-actin sequestering protein thymosin-β4 regulates the activity of myocardin-related transcription factor.

    Science.gov (United States)

    Morita, Tsuyoshi; Hayashi, Ken'ichiro

    2013-08-02

    Myocardin-related transcription factors (MRTFs) are robust coactivators of serum response factor (SRF). MRTFs contain three copies of the RPEL motif at their N-terminus, and they bind to monomeric globular actin (G-actin). Previous studies illustrate that G-actin binding inhibits MRTF activity by preventing the MRTFs nuclear accumulation. In the living cells, the majority of G-actin is sequestered by G-actin binding proteins that prevent spontaneous actin polymerization. Here, we demonstrate that the most abundant G-actin sequestering protein thymosin-β4 (Tβ4) was involved in the regulation of subcellular localization and activity of MRTF-A. Tβ4 competed with MRTF-A for G-actin binding; thus, interfering with G-actin-MRTF-A complex formation. Tβ4 overexpression induced the MRTF-A nuclear accumulation and activation of MRTF-SRF signaling. The activation rate of MRTF-A by the Tβ4 mutant L17A, whose affinity for G-actin is very low, was lower than that by wild-type Tβ4. In contrast, the β-actin mutant 3DA, which has a lower affinity for Tβ4, more effectively suppressed MRTF-A activity than wild-type β-actin. Furthermore, ectopic Tβ4 increased the endogenous expression of SRF-dependent actin cytoskeletal genes. Thus, Tβ4 is an important MRTF regulator that controls the G-actin-MRTFs interaction. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

    Directory of Open Access Journals (Sweden)

    Elianne Egge

    Full Text Available Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.

  7. Comparing relative abundance, lengths, and habitat of temperate reef fishes using simultaneous underwater visual census, video, and trap sampling

    KAUST Repository

    Bacheler, NM

    2017-04-28

    Unbiased counts of individuals or species are often impossible given the prevalence of cryptic or mobile species. We used 77 simultaneous multi-gear deployments to make inferences about relative abundance, diversity, length composition, and habitat of the reef fish community along the southeastern US Atlantic coast. In total, 117 taxa were observed by underwater visual census (UVC), stationary video, and chevron fish traps, with more taxa being observed by UVC (100) than video (82) or traps (20). Frequency of occurrence of focal species was similar among all sampling approaches for tomtate Haemulon aurolineatum and black sea bass Centropristis striata, higher for UVC and video compared to traps for red snapper Lutjanus campechanus, vermilion snapper Rhomboplites aurorubens, and gray triggerfish Balistes capriscus, and higher for UVC compared to video or traps for gray snapper L. griseus and lionfish Pterois spp. For 6 of 7 focal species, correlations of relative abundance among gears were strongest between UVC and video, but there was substantial variability among species. The number of recorded species between UVC and video was correlated (ρ = 0.59), but relationships between traps and the other 2 methods were weaker. Lengths of fish visually estimated by UVC were similar to lengths of fish caught in traps, as were habitat characterizations from UVC and video. No gear provided a complete census for any species in our study, suggesting that analytical methods accounting for imperfect detection are necessary to make unbiased inferences about fish abundance.

  8. Mosquitoes of the rice agroecosystem of Malaysia: species composition and their abundance in relation to rice farming

    International Nuclear Information System (INIS)

    Abu Hassan Ahmad; Che Salmah Md Rawi

    2002-01-01

    Mosquito abundance in relation to rice farming was studied in the Muda and the Kerian Irrigation Schemes. Mosquito larvae were collected using dippers for several growing seasons. Adult mosquitoes were collected by using human bait and cow bait and net trap at nights. Culex, Mansonia and Anopheles were the three genera of mosquito found in the rice agroecosystem. Four species of Mansonia were found biting on human bait. Culex mosquitoes were caught biting on human and cow baits. Culex tritaeniorhynchus, C pseudovishnui, C vishnui, C gelidus and C bitaeniorhynchus were the most common Culex mosquitoes found. Anoheles sinensis and A. peditaeniatus were the most dominant panopheline mosquitoes. High abundance of larvae and adult mosquitoes were observed during ploughing, planting, and tillering stages of rice farming. (Author)

  9. Conserved regional patterns of GABA-related transcript expression in the neocortex of subjects with schizophrenia.

    Science.gov (United States)

    Hashimoto, Takanori; Bazmi, H Holly; Mirnics, Karoly; Wu, Qiang; Sampson, Allan R; Lewis, David A

    2008-04-01

    Individuals with schizophrenia exhibit disturbances in a number of cognitive, affective, sensory, and motor functions that depend on the circuitry of different cortical areas. The cognitive deficits associated with dysfunction of the dorsolateral prefrontal cortex result, at least in part, from abnormalities in GABA neurotransmission, as reflected in a specific pattern of altered expression of GABA-related genes. Consequently, the authors sought to determine whether this pattern of altered gene expression is restricted to the dorsolateral prefrontal cortex or could also contribute to the dysfunction of other cortical areas in subjects with schizophrenia. Real-time quantitative polymerase chain reaction was used to assess the levels of eight GABA-related transcripts in four cortical areas (dorsolateral prefrontal cortex, anterior cingulate cortex, and primary motor and primary visual cortices) of subjects (N=12) with schizophrenia and matched normal comparison subjects. Expression levels of seven transcripts were lower in subjects with schizophrenia, with the magnitude of reduction for each transcript comparable across the four areas. The largest reductions were detected for mRNA encoding somatostatin and parvalbumin, followed by moderate decreases in mRNA expression for the 67-kilodalton isoform of glutamic acid decarboxylase, the GABA membrane transporter GAT-1, and the alpha 1 and delta subunits of GABA(A) receptors. In contrast, the expression of calretinin mRNA did not differ between the subject groups in any of the four areas. Because the areas examined represent the major functional domains (e.g., association, limbic, motor, and sensory) of the cerebral cortex, our findings suggest that a conserved set of molecular alterations affecting GABA neurotransmission contribute to the pathophysiology of different clinical features of schizophrenia.

  10. LDL receptor-related protein 1 regulates the abundance of diverse cell-signaling proteins in the plasma membrane proteome.

    Science.gov (United States)

    Gaultier, Alban; Simon, Gabriel; Niessen, Sherry; Dix, Melissa; Takimoto, Shinako; Cravatt, Benjamin F; Gonias, Steven L

    2010-12-03

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, that are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 coimmunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not coimmunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome.

  11. Tree hole mosquito species composition and relative abundances differ between urban and adjacent forest habitats in northwestern Argentina.

    Science.gov (United States)

    Mangudo, C; Aparicio, J P; Rossi, G C; Gleiser, R M

    2018-04-01

    Water-holding tree holes are main larval habitats for many pathogen vectors, especially mosquitoes (Diptera: Culicidae). Along 3 years, the diversity and composition of mosquito species in tree holes of two neighbouring but completely different environments, a city and its adjacent forest, were compared using generalized linear mixed models, PERMANOVA, SIMPER and species association indexes. The city area (Northwest Argentina) is highly relevant epidemiologically due to the presence of Aedes aegypti L. (main dengue vector) and occurrence of dengue outbreaks; the Yungas rainforests are highly biologically diverse. In total seven mosquito species were recorded, in descending order of abundance: Ae. aegypti, Haemagogus spegazzinii Brèthes, Sabethes purpureus (Theobald), Toxorhynchites guadeloupensis Dyar and Knab, Aedes terrens Walker, Haemagogus leucocelaenus Dyar & Shannon and Sabethes petrocchiae (Shannon and Del Ponte). The seven mosquito species were recorded in both city sites and forested areas; however, their mosquito communities significantly diverged because of marked differences in the frequency and relative abundance of some species: Tx. guadeloupensis and Ae. aegypti were significantly more abundant in forest and urban areas, respectively. Positive significant associations were detected between Ae. aegypti, Hg. spegazzinii and Hg. leucocelaenus. The combined presence of Ae. aegypti, Haemagogus and Sabethes in the area also highlight a potential risk of yellow fever epidemics. Overall results show an impoverished tree hole mosquito fauna in urban environments, reflecting negative effects of urbanization on mosquito diversity.

  12. Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    Science.gov (United States)

    Steenhof, Karen; Kochert, Michael N.; Carpenter, L.B.; Lehman, Robert N.

    1999-01-01

    We studied a nesting population of Prairie Falcons (Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsend's ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 1990s, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  13. Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling.

    Science.gov (United States)

    Wang, Yubing; Guo, Huimin; Li, Haichao; Zhang, Hao; Miao, Xuexia

    2012-12-10

    Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF) are up-stream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT). We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1). We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC) of more than 2.0 (Pgenes related to BPH-induced resistance, most of them were readily induced in TN1 than in RHT by BPH feeding, for instance, 154 TF genes were up-regulated in TN1, but only 31 TF genes were up-regulated in RHT at 24 hours after BPH infestation; 2-4 times more TF genes were induced in TN1 than in RHT by BPH. At an FC threshold of >10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants

  14. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic?Anoxic Interface of the Congo Deep-Sea Fan

    OpenAIRE

    Bessette, Sandrine; Moalic, Yann; Gautey, S?bastien; Lesongeur, Fran?oise; Godfroy, Anne; Toffin, Laurent

    2017-01-01

    Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic–anoxic in...

  15. Myocardin-related transcription factors are required for cardiac development and function

    Science.gov (United States)

    Mokalled, Mayssa H.; Carroll, Kelli J.; Cenik, Bercin K.; Chen, Beibei; Liu, Ning; Olson, Eric N.; Bassel-Duby, Rhonda

    2016-01-01

    Myocardin-Related Transcription Factors A and B (MRTF-A and MRTF-B) are highly homologous proteins that function as powerful coactivators of serum response factor (SRF), a ubiquitously expressed transcription factor essential for cardiac development. The SRF/MRTF complex binds to CArG boxes found in the control regions of genes that regulate cytoskeletal dynamics and muscle contraction, among other processes. While SRF is required for heart development and function, the role of MRTFs in the developing or adult heart has not been explored. Through cardiac-specific deletion of MRTF alleles in mice, we show that either MRTF-A or MRTF-B is dispensable for cardiac development and function, whereas deletion of both MRTF-A and MRTF-B causes a spectrum of structural and functional cardiac abnormalities. Defects observed in MRTF-A/B null mice ranged from reduced cardiac contractility and adult onset heart failure to neonatal lethality accompanied by sarcomere disarray. RNA-seq analysis on neonatal hearts identified the most altered pathways in MRTF double knockout hearts as being involved in cytoskeletal organization. Together, these findings demonstrate redundant but essential roles of the MRTFs in maintenance of cardiac structure and function and as indispensible links in cardiac cytoskeletal gene regulatory networks. PMID:26386146

  16. Expression of Root-Related Transcription Factors Associated with Flooding Tolerance of Soybean (Glycine max

    Directory of Open Access Journals (Sweden)

    Babu Valliyodan

    2014-09-01

    Full Text Available Much research has been conducted on the changes in gene expression of the model plant Arabidopsis to low-oxygen stress. Flooding results in a low oxygen environment in the root zone. However, there is ample evidence that tolerance to soil flooding is more than tolerance to low oxygen alone. In this study, we investigated the physiological response and differential expression of root-related transcription factors (TFs associated with the tolerance of soybean plants to soil flooding. Differential responses of PI408105A and S99-2281 plants to ten days of soil flooding were evaluated at physiological, morphological and anatomical levels. Gene expression underlying the tolerance response was investigated using qRT-PCR of root-related TFs, known anaerobic genes, and housekeeping genes. Biomass of flood-sensitive S99-2281 roots remained unchanged during the entire 10 days of flooding. Flood-tolerant PI408105A plants exhibited recovery of root growth after 3 days of flooding. Flooding induced the development of aerenchyma and adventitious roots more rapidly in the flood-tolerant than the flood-sensitive genotype. Roots of tolerant plants also contained more ATP than roots of sensitive plants at the 7th and 10th days of flooding. Quantitative transcript analysis identified 132 genes differentially expressed between the two genotypes at one or more time points of flooding. Expression of genes related to the ethylene biosynthesis pathway and formation of adventitious roots was induced earlier and to higher levels in roots of the flood-tolerant genotype. Three potential flood-tolerance TFs which were differentially expressed between the two genotypes during the entire 10-day flooding duration were identified. This study confirmed the expression of anaerobic genes in response to soil flooding. Additionally, the differential expression of TFs associated with soil flooding tolerance was not qualitative but quantitative and temporal. Functional analyses of

  17. Expression of root-related transcription factors associated with flooding tolerance of soybean (Glycine max).

    Science.gov (United States)

    Valliyodan, Babu; Van Toai, Tara T; Alves, Jose Donizeti; de Fátima P Goulart, Patricia; Lee, Jeong Dong; Fritschi, Felix B; Rahman, Mohammed Atiqur; Islam, Rafiq; Shannon, J Grover; Nguyen, Henry T

    2014-09-29

    Much research has been conducted on the changes in gene expression of the model plant Arabidopsis to low-oxygen stress. Flooding results in a low oxygen environment in the root zone. However, there is ample evidence that tolerance to soil flooding is more than tolerance to low oxygen alone. In this study, we investigated the physiological response and differential expression of root-related transcription factors (TFs) associated with the tolerance of soybean plants to soil flooding. Differential responses of PI408105A and S99-2281 plants to ten days of soil flooding were evaluated at physiological, morphological and anatomical levels. Gene expression underlying the tolerance response was investigated using qRT-PCR of root-related TFs, known anaerobic genes, and housekeeping genes. Biomass of flood-sensitive S99-2281 roots remained unchanged during the entire 10 days of flooding. Flood-tolerant PI408105A plants exhibited recovery of root growth after 3 days of flooding. Flooding induced the development of aerenchyma and adventitious roots more rapidly in the flood-tolerant than the flood-sensitive genotype. Roots of tolerant plants also contained more ATP than roots of sensitive plants at the 7th and 10th days of flooding. Quantitative transcript analysis identified 132 genes differentially expressed between the two genotypes at one or more time points of flooding. Expression of genes related to the ethylene biosynthesis pathway and formation of adventitious roots was induced earlier and to higher levels in roots of the flood-tolerant genotype. Three potential flood-tolerance TFs which were differentially expressed between the two genotypes during the entire 10-day flooding duration were identified. This study confirmed the expression of anaerobic genes in response to soil flooding. Additionally, the differential expression of TFs associated with soil flooding tolerance was not qualitative but quantitative and temporal. Functional analyses of these genes will be

  18. Reef Sharks Exhibit Site-Fidelity and Higher Relative Abundance in Marine Reserves on the Mesoamerican Barrier Reef

    Science.gov (United States)

    Bond, Mark E.; Babcock, Elizabeth A.; Pikitch, Ellen K.; Abercrombie, Debra L.; Lamb, Norlan F.; Chapman, Demian D.

    2012-01-01

    Carcharhinid sharks can make up a large fraction of the top predators inhabiting tropical marine ecosystems and have declined in many regions due to intense fishing pressure. There is some support for the hypothesis that carcharhinid species that complete their life-cycle within coral reef ecosystems, hereafter referred to as “reef sharks”, are more abundant inside no-take marine reserves due to a reduction in fishing pressure (i.e., they benefit from marine reserves). Key predictions of this hypothesis are that (a) individual reef sharks exhibit high site-fidelity to these protected areas and (b) their relative abundance will generally be higher in these areas compared to fished reefs. To test this hypothesis for the first time in Caribbean coral reef ecosystems we combined acoustic monitoring and baited remote underwater video (BRUV) surveys to measure reef shark site-fidelity and relative abundance, respectively. We focused on the Caribbean reef shark (Carcharhinus perezi), the most common reef shark in the Western Atlantic, at Glover's Reef Marine Reserve (GRMR), Belize. Acoustically tagged sharks (N = 34) were detected throughout the year at this location and exhibited strong site-fidelity. Shark presence or absence on 200 BRUVs deployed at GRMR and three other sites (another reserve site and two fished reefs) showed that the factor “marine reserve” had a significant positive effect on reef shark presence. We rejected environmental factors or site-environment interactions as predominant drivers of this pattern. These results are consistent with the hypothesis that marine reserves can benefit reef shark populations and we suggest new hypotheses to determine the underlying mechanism(s) involved: reduced fishing mortality or enhanced prey availability. PMID:22412965

  19. Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances.

    Science.gov (United States)

    Rohde, Katja; Hau, Yvonne; Weyer, Jessica; Hochkirch, Axel

    2015-09-16

    Hybridization between species is of conservation concern as it might threaten the genetic integrity of species. Anthropogenic factors can alter hybridization dynamics by introducing new potentially hybridizing species or by diminishing barriers to hybridization. This may even affect sympatric species pairs through environmental change, which so far has received little attention. We studied hybridization prevalence and the underlying behavioral mechanisms in two sympatric grasshopper species, a rare specialist (Chorthippus montanus) and a common generalist (Chorthippus parallelus). We conducted a mate choice experiment with constant intraspecific density and varying heterospecific density, i.e. varying relative frequency of both species. Mate choice was frequency-dependent in both species with a higher risk of cross-mating with increasing heterospecific frequency, while conspecific mating increased linearly with increasing conspecific density. This illustrates that reproductive barriers could be altered by environmental change, if the relative frequency of species pairs is affected. Moreover, we performed a microsatellite analysis to detect hybridization in twelve syntopic populations (and four allotopic populations). Hybrids were detected in nearly all syntopic populations with hybridization rates reaching up to 8.9 %. Genetic diversity increased for both species when hybrids were included in the data set, but only in the common species a positive correlation between hybridization rate and genetic diversity was detected. Our study illustrates that the relative frequency of the two species strongly determines the effectiveness of reproductive barriers and that even the more choosy species (Ch. montanus) may face a higher risk of hybridization if population size decreases and its relative frequency becomes low compared to its sister species. The asymmetric mate preferences of both species may lead to quasi-unidirectional gene flow caused by unidirectional

  20. Distribution and relative abundance of anchovies (Clupeiformes-engraulididae in the Sepetiba Bay, Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Márcio de Araújo Silva

    2000-01-01

    Full Text Available Distribution and relative abundance of juvenile fish of the family Engraulididae in the Sepetiba Bay, Rio de Janeiro, Brazil was assessed to detect patterns of use of the shallows during their early life cycle. Two yearly cycle (March-1996 to February-1997 and March-1997 to February-1998 were studied by a total of 120 beach net samples at five sites, two of them located in the inner Bay and three in the outer Bay near to the sea limit. Six Engraulididae species were identified in two genera: Anchoa januaria, Anchoa marinii, Anchoa tricolor, Anchoa lyolepis, Anchoviella lepidentostole and Anchoviella brevirostris, mainly juveniles in their early life cycle. A. januaria, A. brevirostris, A. lepidentostole and A. tricolor, in decreasing order, were the top numerical abundant species, while A. tricolor and A. januaria showed the highest weight contribution, amounting approximately to 90% of the total number of fish. Spatially, A. tricolor, A. lyolepis and A. marinii distributed mainly in the outer Bay. A. januaria show higher abundance in the inner Bay, while the species of genera Anchoviella show an ample distribution, without a particular zone of higher occurrence. Seasonally, only A. januaria, A. lepidentostole and A. brevirostris presented a clear pattern of occurrence, peaking in the Autumn.A abundância relativa e distribuição espacial de juvenis de peixes da familia Engraulididae ocorrentes na Baía de Sepetiba, Rio de Janeiro, Brasil, foram estudadas visando determinar os padrões de uso da margem continental durante a fase inicial de vida. Dois ciclos anuais (Março-1996 a Fevereiro-1997 e Março-1997 a Fevereiro-1998 foram investigados através de um total de 120 amostragens de arrastos de praia, distribuídas em 5 locais de coleta na margem continental da Baía, duas delas situadas na zona mais interna e três na zona mais externa e próxima do limite com o mar. Foram identificados 6 espécies de Engraulididae, compreendendo dois g

  1. Sexual versus Asexual Reproduction: Distinct Outcomes in Relative Abundance of Parthenogenetic Mealybugs following Recent Colonization.

    Science.gov (United States)

    Tabata, Jun; Ichiki, Ryoko T; Tanaka, Hirotaka; Kageyama, Daisuke

    2016-01-01

    Asexual reproduction, including parthenogenesis in which embryos develop within a female without fertilization, is assumed to confer advantages over sexual reproduction, which includes a "cost of males." Sexual reproduction largely predominates in animals, however, indicating that this cost is outweighed by the genetic and/or ecological benefits of sexuality, including the acquisition of advantageous mutations occurring in different individuals and the elimination of deleterious mutations. But the evolution of sexual reproduction remains unclear, because we have limited examples that demonstrate the relative success of sexual lineages in the face of competition from asexual lineages in the same environment. Here we investigated a sympatric occurrence of sexual and asexual reproduction in the pineapple mealybug, Dysmicoccus brevipes. This pest invaded southwestern Japan, including Okinawa and Ishigaki Islands, in the 1930s in association with imported pineapple plants. Our recent censuses demonstrated that on Okinawa sexually reproducing individuals can coexist with and even dominate asexual individuals in the presence of habitat and resource competition, which is considered to be severe for this nearly immobile insect. Molecular phylogeny based on partial DNA sequences in the mitochondrial and nuclear genomes, as well as the endosymbiotic bacterial genome, revealed that the asexual lineage diverged from a common sexual ancestor in the relatively recent past. In contrast, only the asexual lineage exhibiting obligate apomictic thelytoky was discovered on Ishigaki. Co-existence of the two lineages cannot be explained by the results of laboratory experiments, which showed that the intrinsic rate of increase in the sexual lineage was not obviously superior to that of the asexual lineage. Differences in biotic and/or abiotic selective forces operating on the two islands might be the cause of this discrepancy. This biological system offers a unique opportunity to assess

  2. Relative Abundance of Integral Plasma Membrane Proteins in Arabidopsis Leaf and Root Tissue Determined by Metabolic Labeling and Mass Spectrometry

    Science.gov (United States)

    Bernfur, Katja; Larsson, Olaf; Larsson, Christer; Gustavsson, Niklas

    2013-01-01

    Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome. PMID:23990937

  3. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    Science.gov (United States)

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p dry season in tropical rain forest without hunting (χ2, p tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America.

  4. The distribution, relative abundance, and seasonal phenology of Ceratitis capitata, Ceratitis rosa, and Ceratitis cosyra (Diptera: Tephritidae) in South Africa.

    Science.gov (United States)

    De Villiers, Marelize; Manrakhan, Aruna; Addison, Pia; Hattingh, Vaughan

    2013-10-01

    Ceratitis capitata (Wiedemann), Ceratitis rosa Karsch, and Ceratitis cosyra (Walker) are fruit fly species (Diptera: Tephritidae) of economic importance in South Africa. These pests cause direct damage to a number of commercially produced fruit and are of phytosanitary concern. A study was conducted to determine the distribution, relative abundance, and seasonal occurrence of the three species in different climatic regions of South Africa. The relative abundance and seasonal phenology of C. capitata and C. rosa were also compared between production areas and home gardens in Stellenbosch, Western Cape. Yellow bucket traps baited with Biolure were used to trap the flies over a 2-yr period in the different sampling areas. Different fruit types were sampled in Stellenbosch to determine fruit fly infestation. C. capitata was found to have a widespread distribution in South Africa, whereas C. rosa were absent from or only present in low numbers in the drier regions. C. cosyra was restricted to the North East and East coast, following a similar pattern to the distribution of marula, Sclerocarrya birrea, an important wild host. Fruit in home gardens provided a breeding ground for C. capitata and C. rosa and a source for infestation of orchards when fruit started to mature, highlighting the need for an area-wide strategy for the control of fruit flies.

  5. Application of anti-listerial bacteriocins: monitoring enterocin expression by multiplex relative reverse transcription-PCR.

    Science.gov (United States)

    Williams, D Ross; Chanos, Panagiotis

    2012-12-01

    Listeriosis is a deadly food-borne disease, and its incidence may be limited through the biotechnological exploitation of a number of anti-listerial biocontrol agents. The most widely used of these agents are bacteriocins and the Class II enterocins are characterized by their activity against Listeria. Enterocins are primarily produced by enterococci, particularly Enterococcus faecium and many strains have been described, often encoding multiple bacteriocins. The use of these strains in food will require that they are free of virulence functions and that they exhibit a high level expression of anti-listerial enterocins in fermentation conditions. Multiplex relative RT (reverse transcription)-PCR is a technique that is useful in the discovery of advantageous expression characteristics among enterocin-producing strains. It allows the levels of individual enterocin gene expression to be monitored and determination of how expression is altered under different growth conditions.

  6. G-actin sequestering protein thymosin-β4 regulates the activity of myocardin-related transcription factor

    International Nuclear Information System (INIS)

    Morita, Tsuyoshi; Hayashi, Ken’ichiro

    2013-01-01

    Highlights: •Tβ4 competed with MRTF-A for G-actin binding. •Tβ4 activated the MRTF–SRF signaling pathway. •Tβ4 increased the endogenous expression of SRF-dependent genes. -- Abstract: Myocardin-related transcription factors (MRTFs) are robust coactivators of serum response factor (SRF). MRTFs contain three copies of the RPEL motif at their N-terminus, and they bind to monomeric globular actin (G-actin). Previous studies illustrate that G-actin binding inhibits MRTF activity by preventing the MRTFs nuclear accumulation. In the living cells, the majority of G-actin is sequestered by G-actin binding proteins that prevent spontaneous actin polymerization. Here, we demonstrate that the most abundant G-actin sequestering protein thymosin-β4 (Tβ4) was involved in the regulation of subcellular localization and activity of MRTF-A. Tβ4 competed with MRTF-A for G-actin binding; thus, interfering with G-actin–MRTF-A complex formation. Tβ4 overexpression induced the MRTF-A nuclear accumulation and activation of MRTF–SRF signaling. The activation rate of MRTF-A by the Tβ4 mutant L17A, whose affinity for G-actin is very low, was lower than that by wild-type Tβ4. In contrast, the β-actin mutant 3DA, which has a lower affinity for Tβ4, more effectively suppressed MRTF-A activity than wild-type β-actin. Furthermore, ectopic Tβ4 increased the endogenous expression of SRF-dependent actin cytoskeletal genes. Thus, Tβ4 is an important MRTF regulator that controls the G-actin–MRTFs interaction

  7. G-actin sequestering protein thymosin-β4 regulates the activity of myocardin-related transcription factor

    Energy Technology Data Exchange (ETDEWEB)

    Morita, Tsuyoshi, E-mail: tsuyo@nbiochem.med.osaka-u.ac.jp; Hayashi, Ken’ichiro

    2013-08-02

    Highlights: •Tβ4 competed with MRTF-A for G-actin binding. •Tβ4 activated the MRTF–SRF signaling pathway. •Tβ4 increased the endogenous expression of SRF-dependent genes. -- Abstract: Myocardin-related transcription factors (MRTFs) are robust coactivators of serum response factor (SRF). MRTFs contain three copies of the RPEL motif at their N-terminus, and they bind to monomeric globular actin (G-actin). Previous studies illustrate that G-actin binding inhibits MRTF activity by preventing the MRTFs nuclear accumulation. In the living cells, the majority of G-actin is sequestered by G-actin binding proteins that prevent spontaneous actin polymerization. Here, we demonstrate that the most abundant G-actin sequestering protein thymosin-β4 (Tβ4) was involved in the regulation of subcellular localization and activity of MRTF-A. Tβ4 competed with MRTF-A for G-actin binding; thus, interfering with G-actin–MRTF-A complex formation. Tβ4 overexpression induced the MRTF-A nuclear accumulation and activation of MRTF–SRF signaling. The activation rate of MRTF-A by the Tβ4 mutant L17A, whose affinity for G-actin is very low, was lower than that by wild-type Tβ4. In contrast, the β-actin mutant 3DA, which has a lower affinity for Tβ4, more effectively suppressed MRTF-A activity than wild-type β-actin. Furthermore, ectopic Tβ4 increased the endogenous expression of SRF-dependent actin cytoskeletal genes. Thus, Tβ4 is an important MRTF regulator that controls the G-actin–MRTFs interaction.

  8. Seasonal and long-term changes in relative abundance of bull sharks from a tourist shark feeding site in Fiji.

    Science.gov (United States)

    Brunnschweiler, Juerg M; Baensch, Harald

    2011-01-27

    Shark tourism has become increasingly popular, but remains controversial because of major concerns originating from the need of tour operators to use bait or chum to reliably attract sharks. We used direct underwater sampling to document changes in bull shark Carcharhinus leucas relative abundance at the Shark Reef Marine Reserve, a shark feeding site in Fiji, and the reproductive cycle of the species in Fijian waters. Between 2003 and 2009, the total number of C. leucas counted on each day ranged from 0 to 40. Whereas the number of C. leucas counted at the feeding site increased over the years, shark numbers decreased over the course of a calendar year with fewest animals counted in November. Externally visible reproductive status information indicates that the species' seasonal departure from the feeding site may be related to reproductive activity.

  9. Associations of hypoosmotic swelling test, relative sperm volume shift, aquaporin7 mRNA abundance and bull fertility estimates.

    Science.gov (United States)

    Kasimanickam, R K; Kasimanickam, V R; Arangasamy, A; Kastelic, J P

    2017-02-01

    Mammalian sperm are exposed to a natural hypoosmotic environment during male-to-female reproductive tract transition; although this activates sperm motility in vivo, excessive swelling can harm sperm structure and function. Aquaporins (AQPs) is a family of membrane-channel proteins implicated in sperm osmoregulation. The objective was to determine associations among relative sperm volume shift, hypoosmotic swelling test (HOST), sperm aquaporin (AQP) 7 mRNA abundances, and sire conception rate (SCR; fertility estimate) in Holstein bulls at a commercial artificial insemination center. Three or four sires for each full point SCR score from -4 to +4 were included. Each SCR estimate for study bulls (N = 30) was based on > 500 services (mean ± SEM) of 725 ± 13 services/sire). Sperm from a single collection day (two ejaculates) from these commercial Holstein bulls were used. Relative mRNA expression of AQP7 in sperm was determined by polymerase chain reaction. Mean relative sperm volume shift and percentage of sperm reacted in a HOST (% HOST) were determined (400 sperm per bull) after incubating in isoosmotic (300 mOsm/kg) and hypoosmotic (100 mOsm/kg) solutions for 30 min. There was no correlation between %HOST and SCR (r = 0.28 P > 0.1). However, there was a positive correlation between relative sperm volume shift and SCR (r = 0.65, P 2) fertility sire groups. In conclusion, bulls with higher SCR had significantly greater AQP7 mRNA abundance in frozen-thawed sperm. This plausibly contributed to greater regulation of sperm volume shift, which apparently conferred protection from detrimental swelling and impaired functions. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Analysis of a herpetofaunal community from an altered marshy area in Sicily; with special remarks on habitat use (niche breadth and overlap), relative abundance of lizards and snakes, and the correlation between predator abundance and tail loss in lizards

    NARCIS (Netherlands)

    Luiselli, L.; Angelici, F.M.; Di Vittorio, M.; Spinnato, A.; Politano, E.

    2005-01-01

    A field survey was conducted in a highly degraded barren environment in Sicily in order to investigate herpetofaunal community composition and structure, habitat use (niche breadth and overlap) and relative abundance of a snake predator and two species of lizard prey. The site was chosen because it

  11. Larval abundance and its relation to macrofouling settlement pattern in the coastal waters of Kalpakkam, southeastern part of India.

    Science.gov (United States)

    Sahu, Gouri; Satpathy, K K; Mohanty, A K; Biswas, Sudeepta; Achary, M Smita; Sarkar, S K

    2013-02-01

    The present work revealed that salinity, water temperature, and food availability were the most crucial factors affecting the abundance of larvae and their settlement as macrofouling community in the coastal waters of Kalpakkam. Quantitative as well as qualitative results showed that late post-monsoon (April-May) and pre-monsoon (June-September) periods were found to be suitable periods for larval growth, development, and survival to adult stages for most of the organisms. Clustering of physico-chemical and biological (including larval and adult availability) data yielded two major clusters; one formed by northeast (NE) monsoon months (October-January) and the other by post-monsoon/summer (February-May) months, whereas; pre-monsoon months (June-September) were distributed between these two clusters. Among all the major macrofouler groups, only bivalves established a successful relationship between its larval abundance and adult settlement. Principal component analysis indicated good associations of bivalve larvae with polychaete larvae and adult bivalves with adult barnacles. However, biotic relation between ascidians and bryozoans was observed both in the larval as well as adult community.

  12. NOAA ESRI Grid - predictions of relative seabird abundance in the New York offshore planning area made by the NOAA Biogeography Branch

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset represents relative seabird abundance predictions from spatial models developed for the New York offshore spatial planning area. This raster was derived...

  13. Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna

    International Nuclear Information System (INIS)

    Vandegehuchte, Michiel B.; De Coninck, Dieter; Vandenbrouck, Tine; De Coen, Wim M.; Janssen, Colin R.

    2010-01-01

    A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or down-regulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F 0 and F 1 exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative. - Zn-induced DNA hypomethylation is related to gene transcription in Daphnia magna and Zn exposure potentially induced limited temporary transgenerational effects on gene transcription.

  14. Cis-Natural Antisense Transcripts Are Mainly Co-expressed with Their Sense Transcripts and Primarily Related to Energy Metabolic Pathways during Muscle Development.

    Science.gov (United States)

    Zhao, Yunxia; Hou, Ye; Zhao, Changzhi; Liu, Fei; Luan, Yu; Jing, Lu; Li, Xinyun; Zhu, Mengjin; Zhao, Shuhong

    2016-01-01

    Cis-natural antisense transcripts (cis-NATs) are a new class of RNAs identified in various species. However, the biological functions of cis-NATs are largely unknown. In this study, we investigated the transcriptional characteristics and functions of cis-NATs in the muscle tissue of lean Landrace and indigenous fatty Lantang pigs. In total, 3,306 cis-NATs of 2,469 annotated genes were identified in the muscle tissue of pigs. More than 1,300 cis-NATs correlated with their sense genes at the transcriptional level, and approximately 80% of them were co-expressed in the two breeds. Furthermore, over 1,200 differentially expressed cis-NATs were identified during muscle development. Function annotation showed that the cis-NATs participated in muscle development mainly by co-expressing with genes involved in energy metabolic pathways, including citrate cycle (TCA cycle), glycolysis or gluconeogenesis, mitochondrial activation and so on. Moreover, these cis-NATs and their sense genes abruptly increased at the transition from the late fetal stages to the early postnatal stages and then decreased along with muscle development. In conclusion, the cis-NATs in the muscle tissue of pigs were identified and determined to be mainly co-expressed with their sense genes. The co-expressed cis-NATs and their sense gene were primarily related to energy metabolic pathways during muscle development in pigs. Our results offered novel evidence on the roles of cis-NATs during the muscle development of pigs.

  15. Loss of runt-related transcription factor 3 expression leads hepatocellular carcinoma cells to escape apoptosis

    Directory of Open Access Journals (Sweden)

    Nakamura Shinichiro

    2011-01-01

    Full Text Available Abstract Background Runt-related transcription factor 3 (RUNX3 is known as a tumor suppressor gene for gastric cancer and other cancers, this gene may be involved in the development of hepatocellular carcinoma (HCC. Methods RUNX3 expression was analyzed by immunoblot and immunohistochemistry in HCC cells and tissues, respectively. Hep3B cells, lacking endogenous RUNX3, were introduced with RUNX3 constructs. Cell proliferation was measured using the MTT assay and apoptosis was evaluated using DAPI staining. Apoptosis signaling was assessed by immunoblot analysis. Results RUNX3 protein expression was frequently inactivated in the HCC cell lines (91% and tissues (90%. RUNX3 expression inhibited 90 ± 8% of cell growth at 72 h in serum starved Hep3B cells. Forty-eight hour serum starvation-induced apoptosis and the percentage of apoptotic cells reached 31 ± 4% and 4 ± 1% in RUNX3-expressing Hep3B and control cells, respectively. Apoptotic activity was increased by Bim expression and caspase-3 and caspase-9 activation. Conclusion RUNX3 expression enhanced serum starvation-induced apoptosis in HCC cell lines. RUNX3 is deleted or weakly expressed in HCC, which leads to tumorigenesis by escaping apoptosis.

  16. Hyperosmotic stress regulates the distribution and stability of myocardin-related transcription factor, a key modulator of the cytoskeleton

    DEFF Research Database (Denmark)

    Ly, Donald L.; Waheed, Faiza; Lodyga, Monika

    2013-01-01

    Hyperosmotic stress initiates several adaptive responses, including the remodeling of the cytoskeleton. Besides maintaining structural integrity, the cytoskeleton has emerged as an important regulator of gene transcription. Myocardin-related transcription factor (MRTF), an actin-regulated coactiv......Hyperosmotic stress initiates several adaptive responses, including the remodeling of the cytoskeleton. Besides maintaining structural integrity, the cytoskeleton has emerged as an important regulator of gene transcription. Myocardin-related transcription factor (MRTF), an actin......-regulated coactivator of serum response factor, is a major link between the actin skeleton and transcriptional control. We therefore investigated whether MRTF is regulated by hyperosmotic stress. Here we show that hypertonicity induces robust, rapid, and transient translocation of MRTF from the cytosol to the nucleus...... in kidney tubular cells. We found that the hyperosmolarity-triggered MRTF translocation is mediated by the RhoA/Rho kinase (ROK) pathway. Moreover, the Rho guanine nucleotide exchange factor GEF-H1 is activated by hyperosmotic stress, and it is a key contributor to the ensuing RhoA activation and MRTF...

  17. Arabidopsis transcriptional responses differentiating closely related chemicals (herbicides) and cross-species extrapolation to Brassica

    Science.gov (United States)

    Using whole genome Affymetrix ATH1 GeneChips we characterized the transcriptional response of Arabidopsis thaliana Columbia 24 hours after treatment with five different herbicides. Four of them (chloransulam, imazapyr, primisulfuron, sulfometuron) inhibit acetolactate synthase (A...

  18. Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci.

    Science.gov (United States)

    Boldogköi, Zsolt

    2012-01-01

    The regulation of gene expression is essential for normal functioning of biological systems in every form of life. Gene expression is primarily controlled at the level of transcription, especially at the phase of initiation. Non-coding RNAs are one of the major players at every level of genetic regulation, including the control of chromatin organization, transcription, various post-transcriptional processes, and translation. In this study, the Transcriptional Interference Network (TIN) hypothesis was put forward in an attempt to explain the global expression of antisense RNAs and the overall occurrence of tandem gene clusters in the genomes of various biological systems ranging from viruses to mammalian cells. The TIN hypothesis suggests the existence of a novel layer of genetic regulation, based on the interactions between the transcriptional machineries of neighboring genes at their overlapping regions, which are assumed to play a fundamental role in coordinating gene expression within a cluster of functionally linked genes. It is claimed that the transcriptional overlaps between adjacent genes are much more widespread in genomes than is thought today. The Waterfall model of the TIN hypothesis postulates a unidirectional effect of upstream genes on the transcription of downstream genes within a cluster of tandemly arrayed genes, while the Seesaw model proposes a mutual interdependence of gene expression between the oppositely oriented genes. The TIN represents an auto-regulatory system with an exquisitely timed and highly synchronized cascade of gene expression in functionally linked genes located in close physical proximity to each other. In this study, we focused on herpesviruses. The reason for this lies in the compressed nature of viral genes, which allows a tight regulation and an easier investigation of the transcriptional interactions between genes. However, I believe that the same or similar principles can be applied to cellular organisms too.

  19. The cellular transcription factor CREB corresponds to activating transcription factor 47 (ATF-47) and forms complexes with a group of polypeptides related to ATF-43.

    Science.gov (United States)

    Hurst, H C; Masson, N; Jones, N C; Lee, K A

    1990-12-01

    Promoter elements containing the sequence motif CGTCA are important for a variety of inducible responses at the transcriptional level. Multiple cellular factors specifically bind to these elements and are encoded by a multigene family. Among these factors, polypeptides termed activating transcription factor 43 (ATF-43) and ATF-47 have been purified from HeLa cells and a factor referred to as cyclic AMP response element-binding protein (CREB) has been isolated from PC12 cells and rat brain. We demonstrated that CREB and ATF-47 are identical and that CREB and ATF-43 form protein-protein complexes. We also found that the cis requirements for stable DNA binding by ATF-43 and CREB are different. Using antibodies to ATF-43 we have identified a group of polypeptides (ATF-43) in the size range from 40 to 43 kDa. ATF-43 polypeptides are related by their reactivity with anti-ATF-43, DNA-binding specificity, complex formation with CREB, heat stability, and phosphorylation by protein kinase A. Certain cell types vary in their ATF-43 complement, suggesting that CREB activity is modulated in a cell-type-specific manner through interaction with ATF-43. ATF-43 polypeptides do not appear simply to correspond to the gene products of the ATF multigene family, suggesting that the size of the ATF family at the protein level is even larger than predicted from cDNA-cloning studies.

  20. Transcription Factor EB Expression in Early Breast Cancer Relates to Lysosomal/Autophagosomal Markers and Prognosis.

    Science.gov (United States)

    Giatromanolaki, Alexandra; Sivridis, Efthimios; Kalamida, Dimitra; Koukourakis, Michael I

    2017-06-01

    Disrupting the autophagic balance to trigger autophagic death may open new strategies for cancer therapy. Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and may play a role in cancer biology and clinical behavior. The expression of TFEB and the lysosomal cancer cell content (expression of lysosomal associated membrane protein 2a [LAMP2a] and cathepsin D) was studied in a series of 100 T1-stage breast carcinomas. Expression patterns were correlated with autophagy/hypoxia-related proteins, angiogenesis, and clinical outcome. The effect of hypoxic/acidic conditions on TFEB kinetics was studied in the MCF-7 cancer cell line. Overexpression of TFEB in cancer cell cytoplasm and the perinuclear/nuclear area was noted in 23 (23%) of 100 cases. High LAMP2a and cathepsin D expression was noted in 30 (30%) of 100 and 28 (28%) of 100 cases, respectively. TFEB expression was directly linked with LAMP2a (P factor 2-alpha (HIF-2α) (P = .01, r = 0.25) expression and inversely with progesterone receptor (P = .01, r = 0.22). High vascular density was directly linked with LAMP2a (P = .05, r = 0.18) and cathepsin D (P = .005, r = 0.28). In Kaplan-Meier survival analysis, TFEB and cathepsin D expression were related to an ominous prognosis (P = .001 and P = .03, respectively). In multivariate analysis, TFEB expression sustained its independent prognostic significance (P = .05, hazard ratio 2.1). In in vitro experiments, acidity triggered overexpression of TFEB and nuclear translocation. Intense TFEB expression and lysosomal biogenesis, evident in one fourth of early breast carcinomas, define poor prognosis. Tumor acidity is among the microenvironmental conditions that trigger TFEB overactivity. TFEB is a sound target for the development of lysosomal targeting therapies. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic–Anoxic Interface of the Congo Deep-Sea Fan

    Directory of Open Access Journals (Sweden)

    Laurent Toffin

    2017-04-01

    Full Text Available Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon. This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB communities at the oxic–anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

  2. The Mediator Complex MED15 Subunit Mediates Activation of Downstream Lipid-Related Genes by the WRINKLED1 Transcription Factor.

    Science.gov (United States)

    Kim, Mi Jung; Jang, In-Cheol; Chua, Nam-Hai

    2016-07-01

    The Mediator complex is known to be a master coordinator of transcription by RNA polymerase II, and this complex is recruited by transcription factors (TFs) to target promoters for gene activation or repression. The plant-specific TF WRINKLED1 (WRI1) activates glycolysis-related and fatty acid biosynthetic genes during embryogenesis. However, no Mediator subunit has yet been identified that mediates WRI1 transcriptional activity. Promoter-β-glucuronidase fusion experiments showed that MEDIATOR15 (MED15) is expressed in the same cells in the embryo as WRI1. We found that the Arabidopsis (Arabidopsis thaliana) MED15 subunit of the Mediator complex interacts directly with WRI1 in the nucleus. Overexpression of MED15 or WRI1 increased transcript levels of WRI1 target genes involved in glycolysis and fatty acid biosynthesis; these genes were down-regulated in wild-type or WRI1-overexpressing plants by silencing of MED15 However, overexpression of MED15 in the wri1 mutant also increased transcript levels of WRI1 target genes, suggesting that MED15 also may act with other TFs to activate downstream lipid-related genes. Chromatin immunoprecipitation assays confirmed the association of MED15 with six WRI1 target gene promoters. Additionally, silencing of MED15 resulted in reduced fatty acid content in seedlings and mature seeds, whereas MED15 overexpression increased fatty acid content in both developmental stages. Similar results were found in wri1 mutant and WRI1 overexpression lines. Together, our results indicate that the WRI1/MED15 complex transcriptionally regulates glycolysis-related and fatty acid biosynthetic genes during embryogenesis. © 2016 American Society of Plant Biologists. All Rights Reserved.

  3. Modulation of Caenorhabditis elegans transcription factor activity by HIM-8 and the related Zinc-Finger ZIM proteins.

    Science.gov (United States)

    Sun, Hongliu; Nelms, Brian L; Sleiman, Sama F; Chamberlin, Helen M; Hanna-Rose, Wendy

    2007-10-01

    The previously reported negative regulatory activity of HIM-8 on the Sox protein EGL-13 is shared by the HIM-8-related ZIM proteins. Furthermore, mutation of HIM-8 can modulate the effects of substitution mutations in the DNA-binding domains of at least four other transcription factors, suggesting broad regulatory activity by HIM-8.

  4. Novel estrogen receptor-related Transcripts in Marisa cornuarietis; a freshwater snail with reported sensitivity to estrogenic chemicals.

    Science.gov (United States)

    Bannister, Richard; Beresford, Nicola; May, Denise; Routledge, Edwin J; Jobling, Susan; Rand-Weaver, Mariann

    2007-04-01

    We have isolated novel molluskan steroid receptor transcripts orthologous to vertebrate estrogen receptors (ERs) and estrogen receptor-related receptors (ERRs) from the freshwater snail Marisa cornuarietis. Radiolabeled ligand binding analyses showed that neither recombinant receptor protein specifically bound 17beta-estradiol over the range applied (0.3-9.6 nM). These novel receptor transcripts have thus been designated mcER-like and mcERR respectively. Quantitative PCR revealed mcER-like to be expressed ubiquitously throughout a range of male and female structures studied, including neural and reproductive tissues. Highest absolute levels were seen in the male penis-sheath complex. The mcERR mRNA was also expressed ubiquitously throughout all male and female tissues analyzed here, with very low absolute transcript numbers in female accessory sex structures compared to other tissues.

  5. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.

    Science.gov (United States)

    Stecher, Bärbel; Chaffron, Samuel; Käppeli, Rina; Hapfelmeier, Siegfried; Freedrich, Susanne; Weber, Thomas C; Kirundi, Jorum; Suar, Mrutyunjay; McCoy, Kathy D; von Mering, Christian; Macpherson, Andrew J; Hardt, Wolf-Dietrich

    2010-01-01

    The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance) is poorly understood. To analyze the mechanisms of microbiota-mediated protection from Salmonella enterica induced enterocolitis, we used a mouse infection model and large scale high-throughput pyrosequencing. In contrast to conventional mice (CON), mice with a gut microbiota of low complexity (LCM) were highly susceptible to S. enterica induced colonization and enterocolitis. Colonization resistance was partially restored in LCM-animals by co-housing with conventional mice for 21 days (LCM(con21)). 16S rRNA sequence analysis comparing LCM, LCM(con21) and CON gut microbiota revealed that gut microbiota complexity increased upon conventionalization and correlated with increased resistance to S. enterica infection. Comparative microbiota analysis of mice with varying degrees of colonization resistance allowed us to identify intestinal ecosystem characteristics associated with susceptibility to S. enterica infection. Moreover, this system enabled us to gain further insights into the general principles of gut ecosystem invasion by non-pathogenic, commensal bacteria. Mice harboring high commensal E. coli densities were more susceptible to S. enterica induced gut inflammation. Similarly, mice with high titers of Lactobacilli were more efficiently colonized by a commensal Lactobacillus reuteri(RR) strain after oral inoculation. Upon examination of 16S rRNA sequence data from 9 CON mice we found that closely related phylotypes generally display significantly correlated abundances (co-occurrence), more so than distantly related phylotypes. Thus, in essence, the presence of closely related species can increase the chance of invasion of newly incoming species into the gut

  6. Investigation of the relative abundance of heavy versus light nuclei in primary cosmic rays using underground muon bundles

    International Nuclear Information System (INIS)

    Sundaralingam, N.

    1993-01-01

    We study multiple muon events (muon bundles) recorded underground at a depth of 2090 mwe. To penetrate to this depth, the muons must have energies above 0.8 TeV at the Earth's surface; the primary cosmic ray nuclei which give rise to the observed muon bundles have energies at incidence upon the upper atmosphere of 10 to 10 5 TeV. The events are detected using the Soudan 2 experiment's fine grained tracking calorimeter which is surrounded by a 14 m x10 m x 31 m proportional tube array (the ''active shield''). Muon bundles which have at least one muon traversing the calorimeter, are reconstructed using tracks in the calorimeter together with hit patterns in the proportional tube shield. All ionization pulses are required to be coincident within 3 microseconds. A goal of this study is to investigate the relative nuclear abundances in the primary cosmic radiation around the ''knee'' region (10 3 - 10 4 TeV) of the incident energy spectrum. Four models for the nuclear composition of cosmic rays are considered: The Linsley model, the Constant Mass Composition model (CMC), the Maryland model and the Proton-poor model. A Monte Carlo which incorporates one model at a time is used to simulate events which are then reconstructed using the same computer algorithms that are used for the data. Identical cuts and selections are applied to the data and to the simulated events

  7. Abundances of polycyclic aromatic hydrocarbons (PAHs) in 14 chinese and american coals and their relation to coal rank and weathering

    Science.gov (United States)

    Wang, R.; Liu, Gaisheng; Zhang, Jiahua; Chou, C.-L.; Liu, J.

    2010-01-01

    The abundances of 16 polycyclic aromatic hydrocarbons (PAHs) on the priority list of the United States Environmental Protection Agency (U.S. EPA) have been determined in 14 Chinese and American coals. The ranks of the samples range from lignite, bituminous coal, anthracite, to natural coke. Soxhlet extraction was conducted on each coal for 48 h. The extract was analyzed on a gas chromatograph-mass spectrometer (GC-MS). The results show that the total PAH content ranged from 0.31 to 57.6 ??g/g of coal (on a dry basis). It varied with coal rank and is highest in the maturity range of bituminous coal rank. High-molecular-weight (HMW) PAHs are predominant in low-rank coals, but low-molecular-weight (LMW) PAHs are predominant in high-rank coals. The low-sulfur coals have a higher PAH content than high-sulfur coals. It may be explained by an increasing connection between disulfide bonds and PAHs in high-sulfur coal. In addition, it leads us to conclude that the PAH content of coals may be related to the depositional environment. ?? 2010 American Chemical Society.

  8. Effects of Replication and Transcription on DNA Structure-Related Genetic Instability.

    Science.gov (United States)

    Wang, Guliang; Vasquez, Karen M

    2017-01-05

    Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.

  9. Container Type Influences the Relative Abundance, Body Size, and Susceptibility of Ochlerotatus triseriatus (Diptera: Culicidae) to La Crosse Virus.

    Science.gov (United States)

    Bara, Jeffrey J; Muturi, Ephantus J

    2015-05-01

    Ochlerotatus triseriatus (Say), the primary vector of La Crosse virus (LAC), develops in a variety of natural and artificial aquatic containers where it often co-occurs with larvae of other mosquito species. We conducted a field study at two woodlots (South Farms and Trelease Woods) in Urbana, IL, to examine how container type influences vector abundance, body size, and susceptibility to LAC. Mosquito pupae were collected from tree holes, plastic bins, and waste tires, and eclosing adults were identified to species morphologically. Oc. triseriatus and Ochlerotatus japonicus (Theobald) females were orally challenged with LAC and midgut infection rate, disseminated infection rate, and body titer were determined by reverse-transcriptase real-time PCR. Oc. triseriatus was the dominant species collected in tree holes while Oc. japonicus and Culex restuans (Theobald) were mostly dominant in artificial containers. Female Oc. triseriatus and Oc. japonicus collected from plastic bins were significantly larger than those collected from tree holes or waste tires. Oc. japonicus females from South Farms were also significantly larger than those from Trelease Woods. Oc. triseriatus females collected from plastic bins and waste tires were significantly more susceptible to LAC infection relative to females collected from tree holes. In addition, Oc. triseriatus females from waste tires had significantly higher LAC titer relative to Oc. triseriatus from tree holes. For each container type and study site, wing length was not correlated to infection or dissemination rates. These findings suggest that the container type in which Oc.triseriatus develop may contribute to the spatial and temporal dynamics of LAC transmission. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Lithium-induced neuroprotection in stroke involves increased miR-124 expression, reduced RE1-silencing transcription factor abundance and decreased protein deubiquitination by GSK3β inhibition-independent pathways.

    Science.gov (United States)

    Doeppner, Thorsten R; Kaltwasser, Britta; Sanchez-Mendoza, Eduardo H; Caglayan, Ahmet B; Bähr, Mathias; Hermann, Dirk M

    2017-03-01

    Lithium promotes acute poststroke neuronal survival, which includes mechanisms that are not limited to GSK3β inhibition. However, whether lithium induces long-term neuroprotection and enhanced brain remodeling is unclear. Therefore, mice were exposed to transient middle cerebral artery occlusion and lithium (1 mg/kg bolus followed by 2 mg/kg/day over up to 7 days) was intraperitoneally administered starting 0-9 h after reperfusion onset. Delivery of lithium no later than 6 h reduced infarct volume on day 2 and decreased brain edema, leukocyte infiltration, and microglial activation, as shown by histochemistry and flow cytometry. Lithium-induced neuroprotection persisted throughout the observation period of 56 days and was associated with enhanced neurological recovery. Poststroke angioneurogenesis and axonal plasticity were also enhanced by lithium. On the molecular level, lithium increased miR-124 expression, reduced RE1-silencing transcription factor abundance, and decreased protein deubiquitination in cultivated cortical neurons exposed to oxygen-glucose deprivation and in brains of mice exposed to cerebral ischemia. Notably, this effect was not mimicked by pharmacological GSK3β inhibition. This study for the first time provides efficacy data for lithium in the postacute ischemic phase, reporting a novel mechanism of action, i.e. increased miR-124 expression facilitating REST degradation by which lithium promotes postischemic neuroplasticity and angiogenesis.

  11. Relative Abundances of Candida albicans and Candida glabrata in In Vitro Coculture Biofilms Impact Biofilm Structure and Formation.

    Science.gov (United States)

    Olson, Michelle L; Jayaraman, Arul; Kao, Katy C

    2018-04-15

    Candida is a member of the normal human microbiota and often resides on mucosal surfaces such as the oral cavity or the gastrointestinal tract. In addition to their commensality, Candida species can opportunistically become pathogenic if the host microbiota is disrupted or if the host immune system becomes compromised. An important factor for Candida pathogenesis is its ability to form biofilm communities. The two most medically important species- Candida albicans and Candida glabrata -are often coisolated from infection sites, suggesting the importance of Candida coculture biofilms. In this work, we report that biofilm formation of the coculture population depends on the relative ratio of starting cell concentrations of C. albicans and C. glabrata When using a starting ratio of C. albicans to C. glabrata of 1:3, ∼6.5- and ∼2.5-fold increases in biofilm biomass were observed relative to those of a C. albicans monoculture and a C. albicans / C. glabrata ratio of 1:1, respectively. Confocal microscopy analysis revealed the heterogeneity and complex structures composed of long C. albicans hyphae and C. glabrata cell clusters in the coculture biofilms, and reverse transcription-quantitative PCR (qRT-PCR) studies showed increases in the relative expression of the HWP1 and ALS3 adhesion genes in the C. albicans / C. glabrata 1:3 biofilm compared to that in the C. albicans monoculture biofilm. Additionally, only the 1:3 C. albicans / C. glabrata biofilm demonstrated an increased resistance to the antifungal drug caspofungin. Overall, the results suggest that interspecific interactions between these two fungal pathogens increase biofilm formation and virulence-related gene expression in a coculture composition-dependent manner. IMPORTANCE Candida albicans and Candida glabrata are often coisolated during infection, and the occurrence of coisolation increases with increasing inflammation, suggesting possible synergistic interactions between the two Candida species in

  12. The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.

    Science.gov (United States)

    Soler, Marçal; Camargo, Eduardo Leal Oliveira; Carocha, Victor; Cassan-Wang, Hua; San Clemente, Hélène; Savelli, Bruno; Hefer, Charles A; Paiva, Jorge A Pinto; Myburg, Alexander A; Grima-Pettenati, Jacqueline

    2015-06-01

    The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

  13. Reorganization of the actin cytoskeleton via transcriptional regulation of cytoskeletal/focal adhesion genes by myocardin-related transcription factors (MRTFs/MAL/MKLs)

    International Nuclear Information System (INIS)

    Morita, Tsuyoshi; Mayanagi, Taira; Sobue, Kenji

    2007-01-01

    RhoA is a crucial regulator of stress fiber and focal adhesion formation through the activation of actin nucleation and polymerization. It also regulates the nuclear translocation of myocardin-related transcription factor-A and -B (MRTF-A/B, MAL or MKL 1/2), which are co-activators of serum response factor (SRF). In dominant-negative MRTF-A (DN-MRTF-A)-expressing NIH 3T3 cell lines, the expressions of several cytoskeletal/focal adhesion genes were down-regulated, and the formation of stress fiber and focal adhesion was severely diminished. MRTF-A/B-knockdown cells also exhibited such cytoskeletal defects. In reporter assays, both RhoA and MRTF-A enhanced promoter activities of these genes in a CArG-box-dependent manner, and DN-MRTF-A inhibited the RhoA-mediated activation of these promoters. In dominant-negative RhoA (RhoA-N19)-expressing NIH 3T3 cell lines, the nuclear translocation of MRTF-A/B was predominantly prevented, resulting in the reduced expression of cytoskeletal/focal adhesion proteins. Further, constitutive-active MRTF-A/B increased the expression of endogenous cytoskeletal/focal adhesion proteins, and thereby rescued the defective phenotype of stress fibers and focal adhesions in RhoA-N19 expressing cells. These results indicate that MRTF-A/B act as pivotal mediators of stress fiber and focal adhesion formation via the transcriptional regulation of a subset of cytoskeletal/focal adhesion genes

  14. Survival of Listeria monocytogenes in simulated gastrointestinal system and transcriptional profiling of stress- and adhesion-related genes

    DEFF Research Database (Denmark)

    Jiang, Lingli; Olesen, Inger; Andersen, Thomas

    2010-01-01

    -related genes after exposure to the conditions similar to those encountered in the mouth, stomach, and small intestine. None of the L. monocytogenes strains investigated could survive in the gastric juice at pH 2.5 or 3.0. Their survival increased at higher pH (3.5 and 4.0) in the gastric stress. Relative...... afterpassing through the simulated gastrointestinal tract, whereas that of the adhesion-related gene ami was downregulated. Taken together, this study revealed that L. monocytogenes strains enhanced the expression of stressrelated genes and decreased the transcription of adhesion-related gene in order...

  15. Influence of species, size and relative abundance on the outcomes of competitive interactions between brook trout and juvenile coho salmon

    Science.gov (United States)

    Thornton, Emily J; Duda, Jeff; Quinn, Thomas P.

    2016-01-01

    Resource competition between animals is influenced by a number of factors including the species, size and relative abundance of competing individuals. Stream-dwelling animals often experience variably available food resources, and some employ territorial behaviors to increase their access to food. We investigated the factors that affect dominance between resident, non-native brook trout and recolonizing juvenile coho salmon in the Elwha River, WA, USA, to see if brook trout are likely to disrupt coho salmon recolonization via interference competition. During dyadic laboratory feeding trials, we hypothesized that fish size, not species, would determine which individuals consumed the most food items, and that species would have no effect. We found that species, not size, played a significant role in dominance; coho salmon won 95% of trials, even when only 52% the length of their brook trout competitors. As the pairs of competing fish spent more time together during a trial sequence, coho salmon began to consume more food, and brook trout began to lose more, suggesting that the results of early trials influenced fish performance later. In group trials, we hypothesized that group composition and species would not influence fish foraging success. In single species groups, coho salmon consumed more than brook trout, but the ranges overlapped. Brook trout consumption remained constant through all treatments, but coho salmon consumed more food in treatments with fewer coho salmon, suggesting that coho salmon experienced more intra- than inter-specific competition and that brook trout do not pose a substantial challenge. Based on our results, we think it is unlikely that competition from brook trout will disrupt Elwha River recolonization by coho salmon.

  16. Lowland tapir (Tapirus terrestris) distribution, activity patterns and relative abundance in the Greater Madidi-Tambopata Landscape.

    Science.gov (United States)

    Wallace, Robert; Ayala, Guido; Viscarra, Maria

    2012-12-01

    Lowland tapir distribution is described in northwestern Bolivia and southeastern Peru within the Greater Madidi-Tambopata Landscape, a priority Tapir Conservation Unit, using 1255 distribution points derived from camera trapping efforts, field research and interviews with park guards from 5 national protected areas and hunters from 19 local communities. A total of 392 independent camera trapping events from 14 camera trap surveys at 11 sites demonstrated the nocturnal and crepuscular activity patterns (86%) of the lowland tapir and provide 3 indices of relative abundance for spatial and temporal comparison. Capture rates for lowland tapirs were not significantly different between camera trapping stations placed on river beaches versus those placed in the forest. Lowland tapir capture rates were significantly higher in the national protected areas of the region versus indigenous territories and unprotected portions of the landscape. Capture rates through time suggested that lowland tapir populations are recovering within the Tuichi Valley, an area currently dedicated towards ecotourism activities, following the creation (1995) and subsequent implementation (1997) of the Madidi National Park in Bolivia. Based on our distributional data and published conservative estimates of population density, we calculated that this transboundary landscape holds an overall lowland tapir population of between 14 540 and 36 351 individuals, of which at least 24.3% are under protection from national and municipal parks. As such, the Greater Madidi-Tambopata Landscape should be considered a lowland tapir population stronghold and priority conservation efforts are discussed in order to maintain this population. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

  17. Determination of the decay constants and relative abundances of delayed neutrons by noise analysis in zero-power reactors

    International Nuclear Information System (INIS)

    Diniz, Ricardo

    2005-01-01

    A reactor noise approach has been employed at the IPEN/MB-01 research reactor facility in order to determine experimentally the effective delayed neutron parameters β i and λ i in a six group model and assuming the point reactor. The method can be considered a novice one because exploits the very low frequency domain of the spectral densities. The proposed method has some advantages to other in-pile methods since it does not disturb the reactor system and consequently does not 'excite' any sort of harmonic modes. As a byproduct and a consistency check, the β eff parameter was obtained without the need of the Diven factor and the power normalization and it is in excellent agreement with independent measurements. The theory/experiment comparison shows that for the abundances the JENDL 3.3 presents the best performance while for the decay constants the revised version of ENDF/B-VI.8 shows the best agreement. The best performance for the β eff determination is obtained with JENDL3.3. In contrast, ENDF/B-VI.8 and its revised version performed at LANL overestimate β eff by as much as 4%. The β eff results of this work support totally the proposal of reducing the thermal delayed neutron number for 235 U fission as made by Sakurai and Okajima. A new observed effect related to the correlation between the fluctuations of both measurement channels is also presented and discussed. This effect can be considered as an indirect evidence for the use of the point reactor model in this work as well as a possible useful tool in the understanding of reactor dynamics. (author)

  18. ON THE RELATIVE ABUNDANCE OF LiH AND LiH+ MOLECULES IN THE EARLY UNIVERSE: NEW RESULTS FROM QUANTUM REACTIONS

    International Nuclear Information System (INIS)

    Bovino, Stefano; Tacconi, Mario; Gianturco, Franco A.; Galli, Daniele; Palla, Francesco

    2011-01-01

    The relative efficiencies of the chemical pathways that can lead to the destruction of LiH and LiH + molecules, conjectured to be present in the primordial gas and to control molecular cooling processes in the gravitational collapse of the post-recombination era, are revisited by using accurate quantum calculations for the several reactions involved. The new rates are employed to survey the behavior of the relative abundance of these molecules at redshifts of interest for early universe conditions. We find significant differences with respect to previous calculations, the present ones yielding LiH abundances higher than LiH + at all redshifts.

  19. Application of General Circulation Models to Assess the Potential Impact of Climate Change on Potential Distribution and Relative Abundance of Melanoplus sanguinipes (Fabricius (Orthoptera: Acrididae in North America

    Directory of Open Access Journals (Sweden)

    O. Olfert

    2011-01-01

    Full Text Available Climate is the dominant factor determining the distribution and abundance of most insect species. In recent years, the issue of climatic changes caused by human activities and the effects on agriculture has raised concern. General circulation model scenarios were applied to a bioclimatic model of Melanoplus sanguinipes to assess the potential impact of global warming on its distribution and relative abundance. Native to North America and widely distributed, M. sanguinipes is one of the grasshopper species of the continent most responsible for economic damage to grain, oilseed, pulse, and forage crops. Compared to predicted range and distribution under current climate conditions, model results indicated that M. sanguinipes would have increased range and relative abundance under the three general circulation model scenarios in more northern regions of North America. Conversely, model output predicted that the range of this crop pest could contract in regions where climate conditions became limiting.

  20. The Role of Estrogen Related Receptor in Modulating Estrogen Receptor Mediated Transcription in Breast Cancer Cells

    Science.gov (United States)

    2005-04-01

    tumors correlates with an unfavorable prognosis (Ariazi 2002; Lu 2001; Suzuki 2004; Vanacker 1999). The transcriptional activity of ERRa is not inhibited...SA. 101:6570-5. Needham, M ., S. Raines, J. McPheat, C. Stacey, J. Ellston, S. Hoare, and M . Parker. 2000. Differential interaction of steroid hormone...R. Graves, M . Wright, and B.M. Spiegelman. 1998. A cold- inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell. 92:829- 39

  1. Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus.

    Directory of Open Access Journals (Sweden)

    Wei Chi

    Full Text Available The natural sex reversal severely affects the sex ratio and thus decreases the productivity of the rice field eel (Monopterus albus. How to understand and manipulate this process is one of the major issues for the rice field eel stocking. So far the genomics and transcriptomics data available for this species are still scarce. Here we provide a comprehensive study of transcriptomes of brain and gonad tissue in three sex stages (female, intersex and male from the rice field eel to investigate changes in transcriptional level during the sex reversal process.Approximately 195 thousand unigenes were generated and over 44.4 thousand were functionally annotated. Comparative study between stages provided multiple differentially expressed genes in brain and gonad tissue. Overall 4668 genes were found to be of unequal abundance between gonad tissues, far more than that of the brain tissues (59 genes. These genes were enriched in several different signaling pathways. A number of 231 genes were found with different levels in gonad in each stage, with several reproduction-related genes included. A total of 19 candidate genes that could be most related to sex reversal were screened out, part of these genes' expression patterns were validated by RT-qPCR. The expression of spef2, maats1, spag6 and dmc1 were abundant in testis, but was barely detected in females, while the 17β-hsd12, zpsbp3, gal3 and foxn5 were only expressed in ovary.This study investigated the complexity of brain and gonad transcriptomes in three sex stages of the rice field eel. Integrated analysis of different gene expression and changes in signaling pathways, such as PI3K-Akt pathway, provided crucial data for further study of sex transformation mechanisms.

  2. Transcription factor Fos-Related Antigen-2 induces progressive peripheral vasculopathy in mice closely resembling human systemic sclerosis

    OpenAIRE

    Maurer, B; Busch, N; Jüngel, A; Pileckyte, M; Gay, R E; Michel, B A; Schett, G; Gay, S; Distler, J; Distler, O

    2009-01-01

    BACKGROUND: -Microvascular damage is one of the first pathological changes in systemic sclerosis. In this study, we investigated the role of Fos-related antigen-2 (Fra-2), a transcription factor of the activator protein-1 family, in the peripheral vasculopathy of systemic sclerosis and examined the underlying mechanisms. Methods and Results-Expression of Fra-2 protein was significantly increased in skin biopsies of systemic sclerosis patients compared with healthy controls, especially in endo...

  3. Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis.

    Science.gov (United States)

    Kageyama, Shinya; Takeshita, Toru; Asakawa, Mikari; Shibata, Yukie; Takeuchi, Kenji; Yamanaka, Wataru; Yamashita, Yoshihisa

    2017-01-01

    Increasing attention is being focused on evaluating the salivary microbiota as a promising method for monitoring oral health; however, its bacterial composition greatly differs from that of dental plaque microbiota, which is a dominant etiologic factor of oral diseases. This study evaluated the relative abundance of subgingival plaque-specific bacteria in the salivary microbiota and examined a relationship between the abundance and severity of periodontal condition in patients with periodontitis. Four samples (subgingival and supragingival plaques, saliva, and tongue coating) per each subject were collected from 14 patients with a broad range of severity of periodontitis before periodontal therapy. The bacterial composition was analyzed by 16S rRNA gene amplicon sequencing using Ion PGM. Of the 66 species-level operational taxonomic units (OTUs) representing the mean relative abundance of ≥ 1% in any of the four niches, 12 OTUs corresponding to known periodontal pathogens, including Porphyromonas gingivalis, were characteristically predominant in the subgingival plaque and constituted 37.3 ± 22.9% of the microbiota. The total relative abundance of these OTUs occupied only 1.6 ± 1.2% of the salivary microbiota, but significantly correlated with the percentage of diseased sites (periodontal pocket depth ≥ 4 mm; r = 0.78, P periodontal therapy, the total relative abundance of these 12 OTUs was evaluated as well as before periodontal therapy and reductions of the abundance through periodontal therapy were strongly correlated in saliva and subgingival plaque (r = 0.81, P bacteria representing the present condition of periodontal health.

  4. Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD

    International Nuclear Information System (INIS)

    Prokopec, Stephenie D.; Watson, John D.; Lee, Jamie; Pohjanvirta, Raimo; Boutros, Paul C.

    2015-01-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that produces myriad toxicities in most mammals. In rodents alone, there is a huge divergence in the toxicological response across species, as well as among different strains within a species. But there are also significant differences between males and females animals of a single strain. These differences are inconsistent across model systems: the severity of toxicity is greater in female rats than males, while male mice and guinea pigs are more sensitive than females. Because the specific events that underlie this difference remain unclear, we characterized the hepatic transcriptional response of adult male and female C57BL/6 mice to 500 μg/kg TCDD at multiple time-points. The transcriptional profile diverged significantly between the sexes. Female mice demonstrated a large number of altered transcripts as early as 6 h following treatment, suggesting a large primary response. Conversely, male animals showed the greatest TCDD-mediated response 144 h following exposure, potentially implicating significant secondary responses. Nr1i3 was statistically significantly induced at all time-points in the sensitive male animals. This mRNA encodes the constitutive androstane receptor (CAR), a transcription factor involved in the regulation of xenobiotic metabolism, lipid metabolism, cell cycle and apoptosis. Surprisingly though, changes at the protein level (aside from the positive control, CYP1A1) were modest, with only FMO3 showing clear induction, and no genes with sex-differences. Thus, while male and female mice show transcriptional differences in their response to TCDD, their association with TCDD-induced toxicities remains unclear. - Highlights: • Differences exist between the toxicity phenotypes to TCDD in male and female mice. • TCDD-mediated transcriptomic differences were identified between the sexes. • Resistant female mice displayed a large, early-onset, transcriptomic response.

  5. Survival-related profile, pathways, and transcription factors in ovarian cancer.

    Directory of Open Access Journals (Sweden)

    Anne P G Crijns

    2009-02-01

    Full Text Available BACKGROUND: Ovarian cancer has a poor prognosis due to advanced stage at presentation and either intrinsic or acquired resistance to classic cytotoxic drugs such as platinum and taxoids. Recent large clinical trials with different combinations and sequences of classic cytotoxic drugs indicate that further significant improvement in prognosis by this type of drugs is not to be expected. Currently a large number of drugs, targeting dysregulated molecular pathways in cancer cells have been developed and are introduced in the clinic. A major challenge is to identify those patients who will benefit from drugs targeting these specific dysregulated pathways.The aims of our study were (1 to develop a gene expression profile associated with overall survival in advanced stage serous ovarian cancer, (2 to assess the association of pathways and transcription factors with overall survival, and (3 to validate our identified profile and pathways/transcription factors in an independent set of ovarian cancers. METHODS AND FINDINGS: According to a randomized design, profiling of 157 advanced stage serous ovarian cancers was performed in duplicate using approximately 35,000 70-mer oligonucleotide microarrays. A continuous predictor of overall survival was built taking into account well-known issues in microarray analysis, such as multiple testing and overfitting. A functional class scoring analysis was utilized to assess pathways/transcription factors for their association with overall survival. The prognostic value of genes that constitute our overall survival profile was validated on a fully independent, publicly available dataset of 118 well-defined primary serous ovarian cancers. Furthermore, functional class scoring analysis was also performed on this independent dataset to assess the similarities with results from our own dataset. An 86-gene overall survival profile discriminated between patients with unfavorable and favorable prognosis (median survival, 19

  6. Sex-related differences in murine hepatic transcriptional and proteomic responses to TCDD

    Energy Technology Data Exchange (ETDEWEB)

    Prokopec, Stephenie D.; Watson, John D. [Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto (Canada); Lee, Jamie [Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto (Canada); Department of Pharmacology & Toxicology, University of Toronto, Toronto (Canada); Pohjanvirta, Raimo [Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio Finland (Finland); Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki (Finland); Boutros, Paul C., E-mail: Paul.Boutros@oicr.on.ca [Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto (Canada); Department of Pharmacology & Toxicology, University of Toronto, Toronto (Canada); Department of Medical Biophysics, University of Toronto, Toronto (Canada)

    2015-04-15

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that produces myriad toxicities in most mammals. In rodents alone, there is a huge divergence in the toxicological response across species, as well as among different strains within a species. But there are also significant differences between males and females animals of a single strain. These differences are inconsistent across model systems: the severity of toxicity is greater in female rats than males, while male mice and guinea pigs are more sensitive than females. Because the specific events that underlie this difference remain unclear, we characterized the hepatic transcriptional response of adult male and female C57BL/6 mice to 500 μg/kg TCDD at multiple time-points. The transcriptional profile diverged significantly between the sexes. Female mice demonstrated a large number of altered transcripts as early as 6 h following treatment, suggesting a large primary response. Conversely, male animals showed the greatest TCDD-mediated response 144 h following exposure, potentially implicating significant secondary responses. Nr1i3 was statistically significantly induced at all time-points in the sensitive male animals. This mRNA encodes the constitutive androstane receptor (CAR), a transcription factor involved in the regulation of xenobiotic metabolism, lipid metabolism, cell cycle and apoptosis. Surprisingly though, changes at the protein level (aside from the positive control, CYP1A1) were modest, with only FMO3 showing clear induction, and no genes with sex-differences. Thus, while male and female mice show transcriptional differences in their response to TCDD, their association with TCDD-induced toxicities remains unclear. - Highlights: • Differences exist between the toxicity phenotypes to TCDD in male and female mice. • TCDD-mediated transcriptomic differences were identified between the sexes. • Resistant female mice displayed a large, early-onset, transcriptomic response.

  7. Relations between fish abundances, summer temperatures, and forest harvest in a northern Minnesota stream system from 1997 to 2007

    Science.gov (United States)

    Eric Merten; Nathaniel Hemstad; Susan Eggert; Lucinda Johnson; Randall Kolka; Bruce Vondracek; Raymond. Newman

    2010-01-01

    Short-term effects of forest harvest on fish habitat have been well documented, including sediment inputs, leaf litter reductions, and stream warming. However, few studies have considered changes in local climate when examining postlogging changes in fish communities. To address this need, we examined fish abundances between 1997 and 2007 in a basin in a northern...

  8. Rock-colonizing plants: abundance of the endemic cactus Mammillaria fraileana related to rock type in the southern Sonoran Desert

    Science.gov (United States)

    Blanca R. Lopez; Yoav Bashan; Macario Bacilio; Gustavo. De la Cruz-Aguero

    2009-01-01

    Establishment, colonization, and permanence of plants affect biogenic and physical processes leading to development of soil. Rockiness, temperature, and humidity are accepted explanations to the influence and the presence of rock-dwelling plants, but the relationship between mineral and chemical composition of rocks with plant abundance is unknown in some regions. This...

  9. The cellular transcription factor CREB corresponds to activating transcription factor 47 (ATF-47) and forms complexes with a group of polypeptides related to ATF-43.

    OpenAIRE

    Hurst, H C; Masson, N; Jones, N C; Lee, K A

    1990-01-01

    Promoter elements containing the sequence motif CGTCA are important for a variety of inducible responses at the transcriptional level. Multiple cellular factors specifically bind to these elements and are encoded by a multigene family. Among these factors, polypeptides termed activating transcription factor 43 (ATF-43) and ATF-47 have been purified from HeLa cells and a factor referred to as cyclic AMP response element-binding protein (CREB) has been isolated from PC12 cells and rat brain. We...

  10. [The role of Smads and related transcription factors in the signal transduction of bone morphogenetic protein inducing bone formation].

    Science.gov (United States)

    Xu, Xiao-liang; Dai, Ke-rong; Tang, Ting-ting

    2003-09-01

    To clarify the mechanisms of the signal transduction of bone morphogenetic proteins (BMPs) inducing bone formation and to provide theoretical basis for basic and applying research of BMPs. We looked up the literature of the role of Smads and related transcription factors in the signal transduction of BMPs inducing bone formation. The signal transduction processes of BMPs included: 1. BMPs combined with type II and type I receptors; 2. the type I receptor phosphorylated Smads; and 3. Smads entered the cell nucleus, interacted with transcription factors and influenced the transcription of related proteins. Smads could be divided into receptor-regulated Smads (R-Smads: Smad1, Smad2, Smad3, Smad5, Smad8 and Smad9), common-mediator Smad (co-Smad: Smad4), and inhibitory Smads (I-Smads: Smad6 and Smad7). Smad1, Smad5, Smad8, and probable Smad9 were involved in the signal transduction of BMPs. Multiple kinases, such as focal adhesion kinase (FAK), Ras-extracellular signal-regulated kinase (ERK), phosphatidylinositol 3-kinase (PI3K), and Akt serine/threonine kinase were related to Smads signal transduction. Smad1 and Smad5 related with transcription factors included core binding factor A1 (CBFA1), smad-interacting protein 1 (SIP1), ornithine decarboxylase antizyme (OAZ), activating protein-1 (AP-1), xenopus ventralizing homeobox protein-2 (Xvent-2), sandostatin (Ski), antiproliferative proteins (Tob), and homeodomain-containing transcriptian factor-8 (Hoxc-8), et al. CBFA1 could interact with Smad1, Smad2, Smad3, and Smad5, so it was involved in TGF-beta and BMP-2 signal transduction, and played an important role in the bone formation. Cleidocranial dysplasia (CCD) was thought to be caused by heterozygous mutations in CBFA1. The CBFA1 knockout mice showed no osteogenesis and had maturational disturbance of chondrocytes. Smads and related transcription factors, especially Smad1, Smad5, Smad8 and CBFA1, play an important role in the signal transduction of BMPs inducing bone

  11. Two MYB-related transcription factors play opposite roles in sugar signaling in Arabidopsis.

    Science.gov (United States)

    Chen, Yi-Shih; Chao, Yi-Chi; Tseng, Tzu-Wei; Huang, Chun-Kai; Lo, Pei-Ching; Lu, Chung-An

    2017-02-01

    Sugar regulation of gene expression has profound effects at all stages of the plant life cycle. Although regulation at the transcriptional level is one of the most prominent mechanisms by which gene expression is regulated, only a few transcription factors have been identified and demonstrated to be involved in the regulation of sugar-regulated gene expression. OsMYBS1, an R1/2-type MYB transcription factor, has been demonstrated to be involved in sugar- and hormone-regulated α-amylase gene expression in rice. Arabidopsis contains two OsMYBS1 homologs. In the present study, we investigate MYBS1 and MYBS2 in sugar signaling in Arabidopsis. Our results indicate that MYBS1 and MYBS2 play opposite roles in regulating glucose and ABA signaling in Arabidopsis during seed germination and early seedling development. MYB proteins have been classified into four subfamilies: R2R3-MYB, R1/2-MYB, 3R-MYB, and 4R-MYB. An R1/2-type MYB transcription factor, OsMYBS1, has been demonstrated to be involved in sugar- and hormone-regulated α-amylase genes expression in rice. In this study, two genes homologous to OsMYBS1, MYBS1 and MYBS2, were investigated in Arabidopsis. Subcellular localization analysis showed that MYBS1 and MYBS2 were localized in the nucleus. Rice embryo transient expression assays indicated that both MYBS1 and MYBS2 could recognize the sugar response element, TA-box, in the promoter and induced promoter activity. mybs1 mutant exhibited hypersensitivity to glucose, whereas mybs2 seedlings were hyposensitive to it. MYBS1 and MYBS2 are involved in the control of glucose-responsive gene expression, as the mybs1 mutant displayed increased expression of a hexokinase gene (HXK1), chlorophyll a/b-binding protein gene (CAB1), ADP-glucose pyrophosphorylase gene (APL3), and chalcone synthase gene (CHS), whereas the mybs2 mutant exhibited decreased expression of these genes. mybs1 also showed an enhanced response to abscisic acid (ABA) in the seed germination and seedling

  12. Transcriptional targets shared by estrogen receptor- related receptors (ERRs) and estrogen receptor (ER) alpha, but not by ERbeta.

    Science.gov (United States)

    Vanacker, J M; Pettersson, K; Gustafsson, J A; Laudet, V

    1999-01-01

    The physiological activities of estrogens are thought to be mediated by specific nuclear receptors, ERalpha and ERbeta. However, certain tissues, such as the bone, that are highly responsive to estrogens only express a low level of these receptors. Starting from this apparent contradiction, we have evaluated the potentials of two related receptors ERRalpha and ERRbeta to intervene in estrogen signaling. ERalpha, ERRalpha and ERRbeta bind to and activate transcription through both the classical estrogen response element (ERE) and the SF-1 response element (SFRE). In contrast, ERbeta DNA-binding and transcriptional activity is restricted to the ERE. Accordingly, the osteopontin gene promoter is stimulated through SFRE sequences, by ERRalpha as well as by ERalpha, but not by ERbeta. Analysis of the cross-talk within the ER/ERR subgroup of nuclear receptors thus revealed common targets but also functional differences between the two ERs. PMID:10428965

  13. Curcumin enhances neurogenesis and cognition in aged rats: implications for transcriptional interactions related to growth and synaptic plasticity.

    Directory of Open Access Journals (Sweden)

    Suzhen Dong

    Full Text Available BACKGROUND: Curcumin has been demonstrated to have many neuroprotective properties, including improvement of cognition in humans and neurogenesis in animals, yet the mechanism of such effects remains unclear. METHODOLOGY: We assessed behavioural performance and hippocampal cell proliferation in aged rats after 6- and 12-week curcumin-fortified diets. Curcumin enhanced non-spatial and spatial memory, as well as dentate gyrate cell proliferation as compared to control diet rats. We also investigated underlying mechanistic pathways that might link curcumin treatment to increased cognition and neurogenesis via exon array analysis of cortical and hippocampal mRNA transcription. The results revealed a transcriptional network interaction of genes involved in neurotransmission, neuronal development, signal transduction, and metabolism in response to the curcumin treatment. CONCLUSIONS: The results suggest a neurogenesis- and cognition-enhancing potential of prolonged curcumin treatment in aged rats, which may be due to its diverse effects on genes related to growth and plasticity.

  14. Curcumin Enhances Neurogenesis and Cognition in Aged Rats: Implications for Transcriptional Interactions Related to Growth and Synaptic Plasticity

    Science.gov (United States)

    Mitchell, E. Siobhan; Xiu, Jin; Tiwari, Jyoti K.; Hu, Yinghe; Cao, Xiaohua; Zhao, Zheng

    2012-01-01

    Background Curcumin has been demonstrated to have many neuroprotective properties, including improvement of cognition in humans and neurogenesis in animals, yet the mechanism of such effects remains unclear. Methodology We assessed behavioural performance and hippocampal cell proliferation in aged rats after 6- and 12-week curcumin-fortified diets. Curcumin enhanced non-spatial and spatial memory, as well as dentate gyrate cell proliferation as compared to control diet rats. We also investigated underlying mechanistic pathways that might link curcumin treatment to increased cognition and neurogenesis via exon array analysis of cortical and hippocampal mRNA transcription. The results revealed a transcriptional network interaction of genes involved in neurotransmission, neuronal development, signal transduction, and metabolism in response to the curcumin treatment. Conclusions The results suggest a neurogenesis- and cognition-enhancing potential of prolonged curcumin treatment in aged rats, which may be due to its diverse effects on genes related to growth and plasticity. PMID:22359574

  15. nalyot, a mutation of the Drosophila myb-related Adf1 transcription factor, disrupts synapse formation and olfactory memory.

    Science.gov (United States)

    DeZazzo, J; Sandstrom, D; de Belle, S; Velinzon, K; Smith, P; Grady, L; DelVecchio, M; Ramaswami, M; Tully, T

    2000-07-01

    nalyot (nal) is a novel olfactory memory mutant of Drosophila, encoding Adf1, a myb-related transcription factor. Following extended training sessions, Adf1 mutants show normal early memory but defective longterm memory. Adf1 shows widespread spatiotemporal expression, yet mutant alleles reveal no discernible disruptions in gross morphology of the nervous system. Studies at the larval neuromuscular junction, however, reveal a role for Adf1 in the modulation of synaptic growth-in contrast to the role established for dCREB2 in the control of synaptic function (Davis et al., 1996). These findings suggest that Adf1 and dCREB2 regulate distinct transcriptional cascades involved in terminal stages of synapse maturation. More generally, Adf1 provides a novel link between molecular mechanisms of developmental and behavioral plasticity.

  16. The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

    Science.gov (United States)

    Bulik, Sascha; Holzhütter, Hermann-Georg; Berndt, Nikolaus

    2016-03-02

    Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis. Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects. In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes.

  17. Long-term temporal and spatial changes in the richness and relative abundance of the inshore fish community of the British North Sea Coast

    Science.gov (United States)

    Henderson, Peter A.

    2017-09-01

    Changes in temporal and spatial composition of the British inshore North Sea fish community are reviewed. Sampling from the cooling water filter screens of power stations bordering the North Sea commenced in the early 1960s. To date, a total of 112 marine fish species have been recorded, a high proportion of the total inshore fish species complement of shallow North Sea British waters. The unrecorded top predators, such as large sharks, swordfish and tuna are not regularly observed in waters fish diversity and abundance in large industrialised estuaries such as the Thames and the Firth of Forth. Linked to spawning and nursery habitat gain, smelt, Osmerus eperlangus, and bass, Dicentrarchus labrax, have greatly increased in abundance. There is no evidence for a decline in species richness since the 1970s. However, elasmobranch species number has declined while two species Raja clavata and Scyliorhinus canicula have remained abundant and one, Mustelus asterias, has increased in abundance. It is argued that overexploitation and habitat destruction remain, as they have been for the last 300 years, the most serious threats to the health of North Sea inshore fish communities. There are no clear signs that climate change is causing species loss, although it may be influencing relative species abundance as species at the southern edge of their range such as the viviparous blenny, Zoarces viviparous, have declined in the southern British North Sea. Power station water temperature records do not show a warming trend, in some estuarine locations temperature has declined with reduced thermal pollution; the temperature record cannot explain the observed major changes in fish relative abundance observed since the 1970s.

  18. Transcriptional profiling of protein expression related genes of Pichia pastoris under simulated microgravity.

    Directory of Open Access Journals (Sweden)

    Feng Qi

    Full Text Available The physiological responses and transcription profiling of Pichia pastoris GS115 to simulated microgravity (SMG were substantially changed compared with normal gravity (NG control. We previously reported that the recombinant P. pastoris grew faster under SMG than NG during methanol induction phase and the efficiencies of recombinant enzyme production and secretion were enhanced under SMG, which was considered as the consequence of changed transcriptional levels of some key genes. In this work, transcriptiome profiling of P. pastoris cultured under SMG and NG conditions at exponential and stationary phases were determined using next-generation sequencing (NGS technologies. Four categories of 141 genes function as methanol utilization, protein chaperone, RNA polymerase and protein transportation or secretion classified according to Gene Ontology (GO were chosen to be analyzed on the basis of NGS results. And 80 significantly changed genes were weighted and estimated by Cluster 3.0. It was found that most genes of methanol metabolism (85% of 20 genes and protein transportation or secretion (82.2% of 45 genes were significantly up-regulated under SMG. Furthermore the quantity and fold change of up-regulated genes in exponential phase of each category were higher than those of stationary phase. The results indicate that the up-regulated genes of methanol metabolism and protein transportation or secretion mainly contribute to enhanced production and secretion of the recombinant protein under SMG.

  19. Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2018-03-01

    Full Text Available Tanshinones are a class of bioactive components in the traditional Chinese medicine Salvia miltiorrhiza, and their biosynthesis and regulation have been widely studied. Current studies show that basic leucine zipper (bZIP proteins regulate plant secondary metabolism, growth and developmental processes. However, the bZIP transcription factors involved in tanshinone biosynthesis are unknown. Here, we conducted the first genome-wide survey of the bZIP gene family and analyzed the phylogeny, gene structure, additional conserved motifs and alternative splicing events in S. miltiorrhiza. A total of 70 SmbZIP transcription factors were identified and categorized into 11 subgroups based on their phylogenetic relationships with those in Arabidopsis. Moreover, seventeen SmbZIP genes underwent alternative splicing events. According to the transcriptomic data, the SmbZIP genes that were highly expressed in the Danshen root and periderm were selected. Based on the prediction of bZIP binding sites in the promoters and the co-expression analysis and co-induction patterns in response to Ag+ treatment via quantitative real-time polymerase chain reaction (qRT-PCR, we concluded that SmbZIP7 and SmbZIP20 potentially participate in the regulation of tanshinone biosynthesis. These results provide a foundation for further functional characterization of the candidate SmbZIP genes, which have the potential to increase tanshinone production. KEY WORDS: bZIP genes, Salvia miltiorrhiza, Phylogenetic analysis, Expression pattern analysis, Tanshinone biosynthesis

  20. Validation of aspirin response-related transcripts in patients with coronary artery disease and preliminary investigation on CMTM5 function.

    Science.gov (United States)

    Zhang, J W; Liu, T F; Chen, X H; Liang, W Y; Feng, X R; Wang, L; Fu, Sidney W; McCaffrey, Timothy A; Liu, M L

    2017-08-15

    Aspirin is widely used in the prevention of cardiovascular diseases, but the antiplatelet responses vary from one patient to another. To validate aspirin response related transcripts and illustrate their roles in predicting cardiovascular events, we have quantified the relative expression of 14 transcripts previously identified as related to high on-aspirin platelet reactivity (HAPR) in 223 patients with coronary artery disease (CAD) on regular aspirin treatment. All patients were followed up regularly for cardiovascular events (CVE). The mean age of our enrolled population was 75.80±8.57years. HAPR patients showed no significant differences in terms of co-morbidities and combined drugs. Besides, the relative expression of HLA-DQA1 was significantly lower in low on-aspirin platelet reactivity (LAPR) patients, when compared with HAPR and high normal (HN) group (p=0.028). What's more, the number of arteries involved, HAPR status and the relative expression of CLU, CMTM5 and SPARC were independent risk factors for CVE during follow up (p<0.05). In addition, overexpression of CMTM5 attenuated endothelial cells (ECs) migration and proliferation, with significantly decreased phosphorylated-Akt levels, while its inhibition promoted these processes in vitro (p<0.05).Our study provides evidence that circulating transcripts might be potential biomarkers in predicting cardiovascular events. CMTM5 might exert anti-atherosclerotic effects via suppressing migration and proliferation in the vessel wall. Nevertheless, larger-scale and long-term studies are still needed. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Identification of the G13 (cAMP-response-element-binding protein-related protein) gene product related to activating transcription factor 6 as a transcriptional activator of the mammalian unfolded protein response.

    Science.gov (United States)

    Haze, K; Okada, T; Yoshida, H; Yanagi, H; Yura, T; Negishi, M; Mori, K

    2001-04-01

    Eukaryotic cells control the levels of molecular chaperones and folding enzymes in the endoplasmic reticulum (ER) by a transcriptional induction process termed the unfolded protein response (UPR). The mammalian UPR is mediated by the cis-acting ER stress response element consisting of 19 nt (CCAATN(9)CCACG), the CCACG part of which is considered to provide specificity. We recently identified the basic leucine zipper (bZIP) protein ATF6 as a mammalian UPR-specific transcription factor; ATF6 is activated by ER stress-induced proteolysis and binds directly to CCACG. Here we report that eukaryotic cells express another bZIP protein closely related to ATF6 in both structure and function. This protein encoded by the G13 (cAMP response element binding protein-related protein) gene is constitutively synthesized as a type II transmembrane glycoprotein anchored in the ER membrane and processed into a soluble form upon ER stress as occurs with ATF6. The proteolytic processing of ATF6 and the G13 gene product is accompanied by their relocation from the ER to the nucleus; their basic regions seem to function as a nuclear localization signal. Overexpression of the soluble form of the G13 product constitutively activates the UPR, whereas overexpression of a mutant lacking the activation domain exhibits a strong dominant-negative effect. Furthermore, the soluble forms of ATF6 and the G13 gene product are unable to bind to several point mutants of the cis-acting ER stress response element in vitro that hardly respond to ER stress in vivo. We thus concluded that the two related bZIP proteins are crucial transcriptional regulators of the mammalian UPR, and propose calling the ATF6 gene product ATF6alpha and the G13 gene product ATF6beta.

  2. GALAXIES IN ΛCDM WITH HALO ABUNDANCE MATCHING: LUMINOSITY-VELOCITY RELATION, BARYONIC MASS-VELOCITY RELATION, VELOCITY FUNCTION, AND CLUSTERING

    International Nuclear Information System (INIS)

    Trujillo-Gomez, Sebastian; Klypin, Anatoly; Primack, Joel; Romanowsky, Aaron J.

    2011-01-01

    It has long been regarded as difficult if not impossible for a cosmological model to account simultaneously for the galaxy luminosity, mass, and velocity distributions. We revisit this issue using a modern compilation of observational data along with the best available large-scale cosmological simulation of dark matter (DM). We find that the standard cosmological model, used in conjunction with halo abundance matching (HAM) and simple dynamical corrections, fits—at least on average—all basic statistics of galaxies with circular velocities V circ > 80 km s –1 calculated at a radius of ∼10 kpc. Our primary observational constraint is the luminosity-velocity (LV) relation—which generalizes the Tully-Fisher and Faber-Jackson relations in allowing all types of galaxies to be included, and provides a fundamental benchmark to be reproduced by any theory of galaxy formation. We have compiled data for a variety of galaxies ranging from dwarf irregulars to giant ellipticals. The data present a clear monotonic LV relation from ∼50 km s –1 to ∼500 km s –1 , with a bend below ∼80 km s –1 and a systematic offset between late- and early-type galaxies. For comparison to theory, we employ our new ΛCDM 'Bolshoi' simulation of DM, which has unprecedented mass and force resolution over a large cosmological volume, while using an up-to-date set of cosmological parameters. We use HAM to assign rank-ordered galaxy luminosities to the DM halos, a procedure that automatically fits the empirical luminosity function and provides a predicted LV relation that can be checked against observations. The adiabatic contraction of DM halos in response to the infall of the baryons is included as an optional model ingredient. The resulting predictions for the LV relation are in excellent agreement with the available data on both early-type and late-type galaxies for the luminosity range from M r = –14 to M r = –22. We also compare our predictions for the 'cold' baryon mass (i

  3. The relative isotopic abundance (δ13C, δ15N) during composting of agricultural wastes in relation to compost quality and feedstock.

    Science.gov (United States)

    Inácio, Caio T; Magalhães, Alberto M T; Souza, Paulo O; Chalk, Phillip M; Urquiaga, Segundo

    2018-05-01

    Variations in the relative isotopic abundance of C and N (δ 13 C and δ 15 N) were measured during the composting of different agricultural wastes using bench-scale bioreactors. Different mixtures of agricultural wastes (horse bedding manure + legume residues; dairy manure + jatropha mill cake; dairy manure + sugarcane residues; dairy manure alone) were used for aerobic-thermophilic composting. No significant differences were found between the δ 13 C values of the feedstock and the final compost, except for dairy manure + sugarcane residues (from initial ratio of -13.6 ± 0.2 ‰ to final ratio of -14.4 ± 0.2 ‰). δ 15 N values increased significantly in composts of horse bedding manure + legumes residues (from initial ratio of +5.9 ± 0.1 ‰ to final ratio of +8.2 ± 0.5 ‰) and dairy manure + jatropha mill cake (from initial ratio of +9.5 ± 0.2 ‰ to final ratio of +12.8 ± 0.7 ‰) and was related to the total N loss (mass balance). δ 13 C can be used to differentiate composts from different feedstock (e.g. C 3 or C 4 sources). The quantitative relationship between N loss and δ 15 N variation should be determined.

  4. FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation.

    Directory of Open Access Journals (Sweden)

    Jennifer R Stevens

    Full Text Available Gene transcription is constrained by the nucleosomal nature of chromosomal DNA. This nucleosomal barrier is modulated by FACT, a conserved histone-binding heterodimer. FACT mediates transcription-linked nucleosome disassembly and also nucleosome reassembly in the wake of the RNA polymerase II transcription complex, and in this way maintains the repression of 'cryptic' promoters found within some genes. Here we focus on a novel mutant version of the yeast FACT subunit Spt16 that supplies essential Spt16 activities but impairs transcription-linked nucleosome reassembly in dominant fashion. This Spt16 mutant protein also has genetic effects that are recessive, which we used to show that certain Spt16 activities collaborate with histone acetylation and the activities of a Bur-kinase/Spt4-Spt5/Paf1C pathway that facilitate transcription elongation. These collaborating activities were opposed by the actions of Rpd3S, a histone deacetylase that restores a repressive chromatin environment in a transcription-linked manner. Spt16 activity paralleling that of HirC, a co-repressor of histone gene expression, was also found to be opposed by Rpd3S. Our findings suggest that Spt16, the Bur/Spt4-Spt5/Paf1C pathway, and normal histone abundance and/or stoichiometry, in mutually cooperative fashion, facilitate nucleosome disassembly during transcription elongation. The recessive nature of these effects of the mutant Spt16 protein on transcription-linked nucleosome disassembly, contrasted to its dominant negative effect on transcription-linked nucleosome reassembly, indicate that mutant FACT harbouring the mutant Spt16 protein competes poorly with normal FACT at the stage of transcription-linked nucleosome disassembly, but effectively with normal FACT for transcription-linked nucleosome reassembly. This functional difference is consistent with the idea that FACT association with the transcription elongation complex depends on nucleosome disassembly, and that the

  5. Species composition, diversity and relative abundance of amphibians in forests and non-forest habitats on Langkawi Island, Peninsular Malaysia

    Science.gov (United States)

    Nur Johana, J.; Muzzneena, A. M.; Grismer, L. L.; Norhayati, A.

    2016-11-01

    Anurans on Langkawi Island, Peninsular Malaysia exhibit variation in their habits and forms, ranging from small (SVL 150 mm), and occupy a range of habitats, such as riverine forests, agricultural fields, peat swamps, and lowland and upland dipterocarp forests. These variations provide a platform to explore species diversity, distribution, abundance, microhabitat, and other ecological parameters to understand the distribution patterns and to facilitate conservation and management of sensitive or important species and areas. The objective of this study was to evaluate the diversity and distribution of anuran species in different types of habitat on Langkawi Island. Specimens were collected based on active sampling using the Visual Encounter Survey (VES) method. We surveyed anuran species inhabiting seven types of habitat, namely agriculture (AG), coastal (CL), forest (FT), pond (PD), mangrove (MG), riparian forest (RF) and river (RV). A total of 775 individuals were sampled from all localities, representing 23 species from 12 genera and included all six families of frogs in Malaysia. FT and RF showed high values of Shannon Index, H', 2.60 and 2.38, respectively, followed by the other types of habitat, CL (1.82), RV (1.71), MG (1.56), PD (1.54), and AG (1.53). AG had the highest abundance (156 individuals) compared to other habitat types. Based on Cluster Analysis by using Jaccard coefficient (UPGMA), two groups can be clearly seen and assigned as forested species group (FT and RF) and species associating with human activity (AG, CL, PD, MG and RV). Forest species group is more diverse compared to non-forest group. Nevertheless, non-forest species are found in abundance, highlighting the relevance of these disturbed habitats in supporting the amphibians.

  6. Explaining variation in adult Anopheles indoor resting abundance: the relative effects of larval habitat proximity and insecticide-treated bed net use.

    Science.gov (United States)

    McCann, Robert S; Messina, Joseph P; MacFarlane, David W; Bayoh, M Nabie; Gimnig, John E; Giorgi, Emanuele; Walker, Edward D

    2017-07-17

    Spatial determinants of malaria risk within communities are associated with heterogeneity of exposure to vector mosquitoes. The abundance of adult malaria vectors inside people's houses, where most transmission takes place, should be associated with several factors: proximity of houses to larval habitats, structural characteristics of houses, indoor use of vector control tools containing insecticides, and human behavioural and environmental factors in and near houses. While most previous studies have assessed the association of larval habitat proximity in landscapes with relatively low densities of larval habitats, in this study these relationships were analysed in a region of rural, lowland western Kenya with high larval habitat density. 525 houses were sampled for indoor-resting mosquitoes across an 8 by 8 km study area using the pyrethrum spray catch method. A predictive model of larval habitat location in this landscape, previously verified, provided derivations of indices of larval habitat proximity to houses. Using geostatistical regression models, the association of larval habitat proximity, long-lasting insecticidal nets (LLIN) use, house structural characteristics (wall type, roof type), and peridomestic variables (cooking in the house, cattle near the house, number of people sleeping in the house) with mosquito abundance in houses was quantified. Vector abundance was low (mean, 1.1 adult Anopheles per house). Proximity of larval habitats was a strong predictor of Anopheles abundance. Houses without an LLIN had more female Anopheles gambiae s.s., Anopheles arabiensis and Anopheles funestus than houses where some people used an LLIN (rate ratios, 95% CI 0.87, 0.85-0.89; 0.84, 0.82-0.86; 0.38, 0.37-0.40) and houses where everyone used an LLIN (RR, 95% CI 0.49, 0.48-0.50; 0.39, 0.39-0.40; 0.60, 0.58-0.61). Cooking in the house also reduced Anopheles abundance across all species. The number of people sleeping in the house, presence of cattle near the house

  7. The relative abundance of dimethylsulfoniopropionate (DMSP) among other zwitterions in branching coral at Heron Island, southern Great Barrier Reef.

    Science.gov (United States)

    Swan, Hilton B; Deschaseaux, Elisabeth S M; Jones, Graham B; Eyre, Bradley D

    2017-07-01

    Dimethylsulfoniopropionate (DMSP) and eleven other target zwitterions were quantified in the branch tips of six Acropora species and Stylophora pistillata hard coral growing on the reef flat surrounding Heron Island in the southern Great Barrier Reef (GBR), Australia. Hydrophilic interaction liquid chromatography mass spectrometry (HILIC-MS) was used for sample analysis with isotope dilution MS applied to quantify DMSP. The concentration of DMSP was ten times greater in A. aspera than A. valida, with this difference being maintained throughout the spring, summer and winter seasons. In contrast, glycine betaine was present in significantly higher concentrations in these species during the summer than the winter. Exposure of branch tips of A. aspera to air and hypo-saline seawater for up to 1 h did not alter the concentrations of DMSP present in the coral when compared with control samples. DMSP was the most abundant target zwitterion in the six Acropora species examined, ranging from 44-78% of all target zwitterions in A. millepora and A. aspera, respectively. In contrast, DMSP only accounted for 7% in S. pistillata, with glycine betaine and stachydrine collectively accounting for 88% of all target zwitterions in this species. The abundance of DMSP in the six Acropora species examined points to Acropora coral being an important source for the biogeochemical cycling of sulfur throughout the GBR, since this reef-building branching coral dominates the coral cover of the GBR. Graphical Abstract HILIC-MS extracted ion chromatogram showing zwitterionic metabolites from the branching coral Acropora isopora.

  8. Primary effect of chemotherapy on the transcription profile of AIDS-related Kaposi's sarcoma

    International Nuclear Information System (INIS)

    Kuyl, Antoinette C van der; Burg, Remco van den; Zorgdrager, Fokla; Dekker, John T; Maas, Jolanda; Noesel, Carel JM van; Goudsmit, Jaap; Cornelissen, Marion

    2002-01-01

    Drugs & used in anticancer chemotherapy have severe effects upon the cellular transcription and replication machinery. From in vitro studies it has become clear that these drugs can affect specific genes, as well as have an effect upon the total transcriptome. Total mRNA from two skin lesions from a single AIDS-KS patient was analyzed with the SAGE (Serial Analysis of Gene Expression) technique to assess changes in the transcriptome induced by chemotherapy. SAGE libraries were constructed from material obtained 24 (KS-24) and 48 (KS-48) hrs after combination therapy with bleomycin, doxorubicin and vincristine. KS-24 and KS-48 were compared to SAGE libraries of untreated AIDS-KS, and to libraries generated from normal skin and from isolated CD4+ T-cells, using the programs USAGE and HTM. SAGE libraries were also compared with the SAGEmap database. In order to assess the primary response of AIDS-related Kaposi's sarcoma (AIDS-KS) to chemotherapy in vivo, we analyzed the transcriptome of AIDS-KS skin lesions from a HIV-1 seropositive patient at two time points after therapy. The mRNA profile was found to have changed dramatically within 24 hours after drug treatment. There was an almost complete absence of transcripts highly expressed in AIDS-KS, probably due to a transcription block. Analysis of KS-24 suggested that mRNA pool used in its construction originated from poly(A) binding protein (PABP) mRNP complexes, which are probably located in nuclear structures known as interchromatin granule clusters (IGCs). IGCs are known to fuse after transcription inhibition, probably affecting poly(A)+RNA distribution. Forty-eight hours after chemotherapy, mRNA isolated from the lesion was largely derived from infiltrating lymphocytes, confirming the transcriptional block in the AIDS-KS tissue. These in vivo findings indicate that the effect of anti-cancer drugs is likely to be more global than up- or downregulation of specific genes, at least in this single patient with

  9. Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

    Science.gov (United States)

    Romero, J; García-Varela, M; Laclette, J P; Espejo, R T

    2002-11-01

    To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

  10. Inhibition of transcription of abscisic acid in relation to the binding with DNA

    International Nuclear Information System (INIS)

    Basak, Sukla; Basu, P.S.; Biswas, B.B.

    1976-01-01

    Abscisic acid (ABA), a plant substance inhibits RNA synthesis in vivo and vitro. In vitro inhibition by ABA has been demonstrated in isolated RNA polymerase system from coconut endosperm chromatin. This inhibition can be partly reversible with indole acetic acid-receptor protein complex if added in the system. To find the mechanism of inhibition of transcription by ABA, it has been found that ABA (10 -4 -10 -5 M) can bind with DNA and can prevent strand separation. This binding increases the Tm value. ABA binds with DNA but not with RNA. Moreover, ABA can equally bind and prevent denaturation of calfthymus DNA and E. coli DNA. pH optimum for this binding is 8.0. The bound complex is resistant to alkali and alcohol but susceptible to acid below pH 5.0. It has further been demonstrated that free aBA at this pH is changed to another component which has tentatively been identified as lactone form of ABA. (author)

  11. Distribution, density and abundance of the western Baltic herring ( Clupea harengus ) in the Sound (ICES Subdivision 23) in relation to hydrographical features

    DEFF Research Database (Denmark)

    Nielsen, J. Rasmus; Lundgren, Bo; Jensen, T. F.

    2001-01-01

    Biomass and duration of the over-wintering period of the Rugen spring spawning herring stock (RHS) in the Sound (ICES Subdivison 23) were investigated as well as possible hydrographical factors affecting relative distribution and triggering southwards migration towards the spawning grounds. Monit....... Monitoring was performed during 27 surveys over a 6-year period (1993-1998). Abundance of 45-165 000 t in August-February, 560 000 t in March-May, and...

  12. Pou1f1, the key transcription factor related to somatic growth in tilapia (Orechromis niloticus), is regulated by two independent post-transcriptional regulation mechanisms.

    Science.gov (United States)

    Wang, Dongfang; Qin, Jingkai; Jia, Jirong; Yan, Peipei; Li, Wensheng

    2017-01-29

    This study aims to determine the post-transcriptional regulation mechanism of the transcription factor pou1f1 (pou class 1 homeobox 1), which is the key gene for pituitary development, somatic growth in vertebrates, and transcription of several hormone genes in teleost fish. MicroRNA miR-223-3p was identified as a bona fide target of pou1f; overexpression of miR-223-3p in primary pituitary cells led to the down-regulation of pou1f1 and downstream genes, and inhibition of miR-223-3p led to the up-regulation of pou1f1 in Nile tilapia dispersed primary pituitary cells. An adenylate-uridylate-rich element (AU-Rich element) was found in the 3'UTR of pou1f1 mRNA, and deletion of the AU-Rich element led to slower mRNA decay and therefore more protein output. A potential mutual relationship between miR-223-3p and the AU-rich element was also investigated, and the results demonstrated that with or without the AU-Rich element, miR-223-3p induced the up-regulation of a reporter system under serum starvation conditions, indicating that miR-223-3p and the AU-Rich element function independent of each other. This study is the first to investigate the post-transcriptional mechanism of pou1f1, which revealed that miR-223-3p down-regulated pou1f1 and downstream gene expressions, and the AU-Rich element led to rapid decay of pou1f1 mRNA. MicroRNA miR-223-3p and the AU-Rich element co-regulated the post-transcriptional expression of pou1f1 independently in Nile tilapia, demonstrating that pou1f1 is under the control of a dual post-transcription regulation mechanism. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Relative Abundance of Carsonella ruddii (Gamma Proteobacterium) in Females and Males of Cacopsylla pyricola (Hemiptera: Psyllidae) and Bactericera cockerelli (Hemiptera: Triozidae)

    Science.gov (United States)

    Cooper, W. Rodney; Garczynski, Stephen F.; Horton, David R.

    2015-01-01

    Carsonella ruddii (Gamma Proteobacterium) is an obligate bacterial endosymbiont of psyllids that produces essential amino acids that are lacking in the insect’s diet. Accurate estimations of Carsonella populations are important to studies of Carsonella-psyllid interactions and to developing ways to target Carsonella for control of psyllid pests including pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae) and potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). We used two methods, namely fluorescence in situ hybridization and quantitative polymerase chain reaction (qPCR), to estimate relative abundance of Carsonella in bacteriocytes and whole bodies of psyllids, respectively. Using these two methods, we compared Carsonella populations between female and male insects. Estimations using fluorescence in situ hybridization indicated that Carsonella was more abundant in bacteriocytes of female C. pyricola than in those of males, but Carsonella abundance in bacteriocytes did not differ between sexes of B. cockerelli. Analyses by qPCR using whole-body specimens indicated Carsonella was more abundant in females than in males of both psyllids. Neither fluorescence in situ hybridization nor qPCR indicated that Carsonella populations differed in abundance among adults of different ages (0–3 wk after adult eclosion). Using fluorescence in situ hybridization, Carsonella was observed in ovarioles of newly emerged females and formed an aggregation in the posterior end of mature oocytes. Results of our study indicate that female psyllids harbor greater populations of Carsonella than do males and that sex should be controlled for in studies which require estimations of Carsonella populations. PMID:26056318

  14. Whole-genome transcriptional analysis of Escherichia coli during heat inactivation processes related to industrial cooking.

    Science.gov (United States)

    Guernec, A; Robichaud-Rincon, P; Saucier, L

    2013-08-01

    Escherichia coli K-12 was grown to the stationary phase, for maximum physiological resistance, in brain heart infusion (BHI) broth at 37°C. Cells were then heated at 58°C or 60°C to reach a process lethality value \\[\\mathbf{\\left(}{{\\mathit{F}}^{\\mathit{o}}}_{\\mathbf{70}}^{\\mathbf{10}}\\mathbf{\\right)} \\] of 2 or 3 or to a core temperature of 71°C (control industrial cooking temperature). Growth recovery and cell membrane integrity were evaluated immediately after heating, and a global transcription analysis was performed using gene expression microarrays. Only cells heated at 58°C with F(o) = 2 were still able to grow on liquid or solid BHI broth after heat treatment. However, their transcriptome did not differ from that of bacteria heated at 58°C with F(o) = 3 (P value for the false discovery rate [P-FDR] > 0.01), where no growth recovery was observed posttreatment. Genome-wide transcriptomic data obtained at 71°C were distinct from those of the other treatments without growth recovery. Quantification of heat shock gene expression by real-time PCR revealed that dnaK and groEL mRNA levels decreased significantly above 60°C to reach levels similar to those of control cells at 37°C (P citE, glyS, oppB, and asd, whose expression was upregulated at 71°C, may be worth investigating as good biomarkers for accurately determining the efficiency of heat treatments, especially when cells are too injured to be enumerated using growth media.

  15. Two novel transcriptional regulators are essential for infection-related morphogenesis and pathogenicity of the rice blast fungus Magnaporthe oryzae.

    Directory of Open Access Journals (Sweden)

    Xia Yan

    2011-12-01

    Full Text Available The cyclic AMP-dependent protein kinase A signaling pathway plays a major role in regulating plant infection by the rice blast fungus Magnaporthe oryzae. Here, we report the identification of two novel genes, MoSOM1 and MoCDTF1, which were discovered in an insertional mutagenesis screen for non-pathogenic mutants of M. oryzae. MoSOM1 or MoCDTF1 are both necessary for development of spores and appressoria by M. oryzae and play roles in cell wall differentiation, regulating melanin pigmentation and cell surface hydrophobicity during spore formation. MoSom1 strongly interacts with MoStu1 (Mstu1, an APSES transcription factor protein, and with MoCdtf1, while also interacting more weakly with the catalytic subunit of protein kinase A (CpkA in yeast two hybrid assays. Furthermore, the expression levels of MoSOM1 and MoCDTF1 were significantly reduced in both Δmac1 and ΔcpkA mutants, consistent with regulation by the cAMP/PKA signaling pathway. MoSom1-GFP and MoCdtf1-GFP fusion proteins localized to the nucleus of fungal cells. Site-directed mutagenesis confirmed that nuclear localization signal sequences in MoSom1 and MoCdtf1 are essential for their sub-cellular localization and biological functions. Transcriptional profiling revealed major changes in gene expression associated with loss of MoSOM1 during infection-related development. We conclude that MoSom1 and MoCdtf1 functions downstream of the cAMP/PKA signaling pathway and are novel transcriptional regulators associated with cellular differentiation during plant infection by the rice blast fungus.

  16. PEA3/ETV4-related transcription factors coupled with active ERK signalling are associated with poor prognosis in gastric adenocarcinoma

    LENUS (Irish Health Repository)

    Keld, R

    2011-06-28

    Background: Transcription factors often play important roles in tumourigenesis. Members of the PEA3 subfamily of ETS-domain transcription factors fulfil such a role and have been associated with tumour metastasis in several different cancers. Moreover, the activity of the PEA3 subfamily transcription factors is potentiated by Ras-ERK pathway signalling, which is itself often deregulated in tumour cells.\\r\

  17. The use of kDNA minicircle subclass relative abundance to differentiate between Leishmania (L.) infantum and Leishmania (L.) amazonensis.

    Science.gov (United States)

    Ceccarelli, Marcello; Galluzzi, Luca; Diotallevi, Aurora; Andreoni, Francesca; Fowler, Hailie; Petersen, Christine; Vitale, Fabrizio; Magnani, Mauro

    2017-05-16

    Leishmaniasis is a neglected disease caused by many Leishmania species, belonging to subgenera Leishmania (Leishmania) and Leishmania (Viannia). Several qPCR-based molecular diagnostic approaches have been reported for detection and quantification of Leishmania species. Many of these approaches use the kinetoplast DNA (kDNA) minicircles as the target sequence. These assays had potential cross-species amplification, due to sequence similarity between Leishmania species. Previous works demonstrated discrimination between L. (Leishmania) and L. (Viannia) by SYBR green-based qPCR assays designed on kDNA, followed by melting or high-resolution melt (HRM) analysis. Importantly, these approaches cannot fully distinguish L. (L.) infantum from L. (L.) amazonensis, which can coexist in the same geographical area. DNA from 18 strains/isolates of L. (L.) infantum, L. (L.) amazonensis, L. (V.) braziliensis, L. (V.) panamensis, L. (V.) guyanensis, and 62 clinical samples from L. (L.) infantum-infected dogs were amplified by a previously developed qPCR (qPCR-ML) and subjected to HRM analysis; selected PCR products were sequenced using an ABI PRISM 310 Genetic Analyzer. Based on the obtained sequences, a new SYBR-green qPCR assay (qPCR-ama) intended to amplify a minicircle subclass more abundant in L. (L.) amazonensis was designed. The qPCR-ML followed by HRM analysis did not allow discrimination between L. (L.) amazonensis and L. (L.) infantum in 53.4% of cases. Hence, the novel SYBR green-based qPCR (qPCR-ama) has been tested. This assay achieved a detection limit of 0.1 pg of parasite DNA in samples spiked with host DNA and did not show cross amplification with Trypanosoma cruzi or host DNA. Although the qPCR-ama also amplified L. (L.) infantum strains, the C q values were dramatically increased compared to qPCR-ML. Therefore, the combined analysis of C q values from qPCR-ML and qPCR-ama allowed to distinguish L. (L.) infantum and L. (L.) amazonensis in 100% of tested samples

  18. De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids

    Science.gov (United States)

    Jayakumar, Vasanthan; Damodaran, Anand C.; Rao, Sudha Narayana; Katta, Mohan A. V. S. K.; Gopinathan, Sreeja; Sarma, Santosh Prasad; Senthilkumar, Vanitha; Niranjan, Vidya; Gopinath, Ashok; Mugasimangalam, Raja C.

    2013-01-01

    Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa. PMID:23468859

  19. Global identification of the full-length transcripts and alternative splicing related to phenolic acid biosynthetic genes in Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Zhichao eXu

    2016-02-01

    Full Text Available Salvianolic acids are among the main bioactive components in Salvia miltiorrhiza, and their biosynthesis has attracted widespread interest. However, previous studies on the biosynthesis of phenolic acids using next-generation sequencing platforms are limited with regard to the assembly of full-length transcripts. Based on hybrid-seq (next-generation and single molecular real-time sequencing of the S. miltiorrhiza root transcriptome, we experimentally identified 15 full-length transcripts and 4 alternative splicing events of enzyme-coding genes involved in the biosynthesis of rosmarinic acid. Moreover, we herein demonstrate that lithospermic acid B accumulates in the phloem and xylem of roots, in agreement with the expression patterns of the identified key genes related to rosmarinic acid biosynthesis. According to co-expression patterns, we predicted that 6 candidate cytochrome P450s and 5 candidate laccases participate in the salvianolic acid pathway. Our results provide a valuable resource for further investigation into the synthetic biology of phenolic acids in S. miltiorrhiza.

  20. The Related Transcriptional Enhancer Factor-1 Isoform, TEAD4216, Can Repress Vascular Endothelial Growth Factor Expression in Mammalian Cells

    Science.gov (United States)

    Appukuttan, Binoy; McFarland, Trevor J.; Stempel, Andrew; Kassem, Jean B.; Hartzell, Matthew; Zhang, Yi; Bond, Derek; West, Kelsey; Wilson, Reid; Stout, Andrew; Pan, Yuzhen; Ilias, Hoda; Robertson, Kathryn; Klein, Michael L.; Wilson, David; Smith, Justine R.; Stout, J. Timothy

    2012-01-01

    Increased cellular production of vascular endothelial growth factor (VEGF) is responsible for the development and progression of multiple cancers and other neovascular conditions, and therapies targeting post-translational VEGF products are used in the treatment of these diseases. Development of methods to control and modify the transcription of the VEGF gene is an alternative approach that may have therapeutic potential. We have previously shown that isoforms of the transcriptional enhancer factor 1-related (TEAD4) protein can enhance the production of VEGF. In this study we describe a new TEAD4 isoform, TEAD4216, which represses VEGF promoter activity. The TEAD4216 isoform inhibits human VEGF promoter activity and does not require the presence of the hypoxia responsive element (HRE), which is the sequence critical to hypoxia inducible factor (HIF)-mediated effects. The TEAD4216 protein is localized to the cytoplasm, whereas the enhancer isoforms are found within the nucleus. The TEAD4216 isoform can competitively repress the stimulatory activity of the TEAD4434 and TEAD4148 enhancers. Synthesis of the native VEGF165 protein and cellular proliferation is suppressed by the TEAD4216 isoform. Mutational analysis indicates that nuclear or cytoplasmic localization of any isoform determines whether it acts as an enhancer or repressor, respectively. The TEAD4216 isoform appears to inhibit VEGF production independently of the HRE required activity by HIF, suggesting that this alternatively spliced isoform of TEAD4 may provide a novel approach to treat VEGF-dependent diseases. PMID:22761647

  1. De Novo transcriptome assembly (NGS of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.

    Directory of Open Access Journals (Sweden)

    Ramasamy S Annadurai

    Full Text Available Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

  2. De Novo transcriptome assembly (NGS) of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.

    Science.gov (United States)

    Annadurai, Ramasamy S; Neethiraj, Ramprasad; Jayakumar, Vasanthan; Damodaran, Anand C; Rao, Sudha Narayana; Katta, Mohan A V S K; Gopinathan, Sreeja; Sarma, Santosh Prasad; Senthilkumar, Vanitha; Niranjan, Vidya; Gopinath, Ashok; Mugasimangalam, Raja C

    2013-01-01

    Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

  3. Transcriptional profiling of primary endometrial epithelial cells following acute HIV-1 exposure reveals gene signatures related to innate immunity.

    Science.gov (United States)

    Zahoor, Muhammad Atif; Woods, Matthew William; Dizzell, Sara; Nazli, Aisha; Mueller, Kristen M; Nguyen, Philip V; Verschoor, Chris P; Kaushic, Charu

    2018-04-01

    Genital epithelial cells (GECs) line the mucosal surface of the female genital tract (FGT) and are the first cells that interface with both commensal microbiota and sexually transmitted pathogens. Despite the protective barrier formed by GECs, the FGT is a major site of HIV-1 infection. This highlights the importance of studying the interaction of HIV-1 and GECs. Using microarray analysis, we characterized the transcriptional profile of primary endometrial GECs grown in the presence or absence of physiological levels of E2 (10 -9  mol/L) or P4 (10 -7  mol/L) following acute exposure to HIV-1 for 6 hours. Acute exposure of primary endometrial GECs to HIV-1 resulted in the expression of genes related to inflammation, plasminogen activation, adhesion and diapedesis and interferon response. Interestingly, exposure to HIV-1 in the presence of E2 and P4 resulted in differential transcriptional profiles, suggesting that the response of primary endometrial GECs to HIV-1 exposure is modulated by female sex hormones. The gene expression signature of endometrial GECs indicates that the response of these cells may be key to determining host susceptibility to HIV-1 and that sex hormones modulate these interactions. This study allows us to explore possible mechanisms that explain the hormone-mediated fluctuation of HIV-1 susceptibility in women. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Cloning and expression analysis of transcription factor RrTTG1 related to prickle development in rose (Rosa Rugosa

    Directory of Open Access Journals (Sweden)

    Feng Li-Guo

    2015-01-01

    Full Text Available A prickle is an acuminate protuberance formed by the deformation of plant trichomes together with a few cortical cells. It is a type of multicellular eglandular trichome with special morphology, which originates from the phloem but is not connected to the xylem. Rosa rugosa is an important ornamental/commercial plant and an important raw material in the food and perfume industries. However, the firm prickles on its stems are inconvenient to field management, the harvesting of flowers and garden management. The TTG1 transcription factor related to the development of prickle was isolated from R. rugosa in the present study. Its expression patterns in different tissues and varieties were analyzed. Results showed the expression level of the RrTTG1 gene was highest in the leaves, followed by the stems, but was lower in the pericarps and petals. Moreover, the higher expression level of the RrTTG1 gene in all tissues of the ‘Ciguo rose’, as compared with that of the ‘Weihai wild rose’, follows the results of field morphological observation. Therefore, the RrTTG1 transcription factor is likely to regulate the development of rose prickles. This study allows for further discussion on the molecular mechanisms of prickle formation and development in R. rugosa and provides a molecular basis for the cultivation of roses with fewer or no prickles via genetic engineering.

  5. The abundance and pollen foraging behaviour of bumble bees in relation to population size of whortleberry (Vaccinium uliginosum.

    Directory of Open Access Journals (Sweden)

    Carolin Mayer

    Full Text Available Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l. on Vaccinium uliginosum (Ericaceae in up to nine populations in Belgium ranging in size from 80 m(2 to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V.uliginosum, Sorbus aucuparia and Cytisus scoparius. We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when

  6. Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats.

    Science.gov (United States)

    Van Campenhout, Jelle; Vanreusel, Ann; Van Belleghem, Steven; Derycke, Sofie

    2015-12-03

    Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm(-2)). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5's common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi's closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible

  7. Offal dumping sites influence the relative abundance and roosting site selection of Black Kites (Milvus migrans govinda) in urban landscape: a study from Kolkata metropolis, India.

    Science.gov (United States)

    Mazumdar, Subhendu; Ghose, Dipankar; Saha, Goutam Kumar

    2017-12-14

    Although Black Kites (Milvus migrans govinda) serve as major scavenging raptor in most of the urban areas, scientific studies on this important ecosystem service provider are almost non-existent in Indian context. The present study was carried out in a metropolis in eastern India to find out the factors influencing relative abundance and roosting site selection of Black Kites. Separate generalized linear models (GLMs) were performed considering encounter rate and roosting Black Kite abundance as response variables. The study conclusively indicated that encounter rates of Black Kites were significantly influenced by the presence of garbage dumps in its vicinity. Numbers of Black Kites were also higher in the roosting sites situated closer to garbage dumps and open spaces. In addition, expected counts of Black Kites significantly increased in roosting sites situated away from buildings and water bodies. However, built-up area and tree cover around the roosting sites had no influence on the abundance of Black Kites therein. With rapid urbanization and changing offal disposal patterns, our findings would be useful to ensure continued availability of food and roosting sites of Black Kites in urban areas.

  8. Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

    Science.gov (United States)

    Liang, Yuxue; Neta, Pedatsur; Yang, Xiaoyu; Stein, Stephen E

    2018-03-01

    High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.

  9. Plant Macrofossils from the Takht Coal Mine, Minoodasht and its Dating, Relative abundance and Sørensen index in comparison with the other Florizones in Iran and Eurasia

    Directory of Open Access Journals (Sweden)

    Fatemeh Vaez Javadi

    2015-02-01

    Full Text Available Takht mine, SE Minoodasht contains well-preserved plant macrofossils belonging to 27 species allocated to 22 genera of various orders viz., Equisetales, Osmundales, Filicales, Peltaspermales, Bennettitales, Ginkgoales and Coniferales. The plant macrofossils in this area are studied for the first time. Based on the occurrence of Equisetites muensteri, Clathropteris meniscoides, Dictyophyllum exile, Anthrophyopsis crassinervis, Scytophyllum persicum, Pterophyllum bavieri, and Baiera muensteriana a Rhaetian age is suggested for this assemblage. Since, there was no differentiation between formations in geological map these flora emphasized spreading the Kalariz Formation in this area. The Minoodasht flora is correlated to the plant macrofossil assemblages of Zirab, Tazareh, Narges-Chal, Hiv, Jajarm (Alborz, Parvadeh mines (Tabas, and Darbid-Khun (Kerman Basin. Therefore, there were close floristic relationships between North and Central-East Iran (i.e. Kerman Basin and Tabas Block and two areas were palaeogeographically closely related, probably forming a uniform paleoenvironment. On the basis of relative abundances of taxa, Filicales, Bennettitales, Ginkgoales and Pinales were 42.02%, 38.11%, 7.17% and 6.51%, respectively. It is noteworthy that variety and relative abundance of the species of Filicophyta and Bennetittales were high within Iran during the Late Triassic epoch. Therefore, a warm wet climatic regime dominated. In addition, a more uniform climate in continental scale is suggested. On the basis of similarity indices and relative abundance of taxa, Iran located within Eurasia climatic belt, Euro-Sinian Region, and the Middle Asia Province of Vakhrameev’s subdivisions and south-western region of Dubroskina’s subdivisions during this epoch.

  10. Distribution, relative abundance and occupancy of selected mammals along paved road in Kubah National Park, Sarawak, Borneo

    Directory of Open Access Journals (Sweden)

    Jayasilan Mohd-Azlan

    2018-06-01

    (Tragulus kanchil showed preference at 5–100 m. This might be due to their general diet behaviour and abundance of food resources nearby the forest edge. The findings from this study need to be carefully interpreted as it is based on a small scale project, therefore may not provide information required to quantify and mitigate the negative effects of roads in protected areas. Comprehensive long-term monitoring with appropriate replications, will be required for making appropriate management recommendations for enhancing conservation within the protected areas of Sarawak.

  11. Distribution and Abundance of Human Specific Bacteroides and Relation to Traditional Indicators in an Urban Tropical Catchment

    Science.gov (United States)

    Nshimyimana, J.; Shanahan, P.; Thompson, J. R.; Ekklesia, E.; Chua Hock Chye, L.

    2012-12-01

    The Singapore government through its Public Utilities Board is interested in opening Kranji Reservoir to recreational use. However, water courses within the Kranji Reservoir catchment contain human fecal indicator bacteria above recreational water quality criteria; their sources and distribution are unknown. The primary goals of this study were to determine the distribution of fecal indicator bacteria in drainages and water bodies in the Kranji reservoir catchment area. Total coliforms, E. coli, and the DNA-based HF marker (targeting a human specific strain of Bacteroides) were quantified in 27 samples collected in January 2009 and 54 samples collected in July 2009. Correlation of HF marker cell equivalents (CE) and E. coli abundance (colony forming units (CFU) or Most Probable Number (MPN)) to different land-use categories revealed potential sources of fecal contamination to the Kranji reservoir. Notably, areas designated as farming/agricultural were associated with the highest levels of E. coli (geometric mean 30,500 CFU/100 ml) and HF marker (1.23±1.13x106 CE/100 ml ± S.D.) while in general lower HF marker and E. coli levels were observed in residential areas, undeveloped areas, and within the Kranji reservoir (i.e. Kranji Reservoir had 2 to 17 MPN/100 ml of E. coli and 103 to 105 HF marker CE/100 ml). A partial survey of potential point sources for fecal contamination within the farming area revealed a wastewater effluent stream with HF marker levels exceeding 107 CE/100ml. As observed in previous studies, total coliforms and E. coli levels were weakly (Robligate anaerobe that is not expected to grow in aerated surface waters. In contrast, numerous studies have demonstrated that total coliforms, including E. coli, are able to grow well under some tropical conditions, limiting their utility as neutral tracers of fecal contamination in tropical environments. Phylogenetic analysis of cloned HF marker sequences from Kranji reservoir and catchment samples

  12. Abundance, biting behaviour and parous rate of anopheline mosquito species in relation to malaria incidence in gold-mining areas of southern Venezuela.

    Science.gov (United States)

    Moreno, J E; Rubio-Palis, Y; Páez, E; Pérez, E; Sánchez, V

    2007-12-01

    A longitudinal entomological and epidemiological study was conducted in five localities of southern Venezuela between January 1999 and April 2000 to determine the abundance, biting behaviour and parity of anopheline mosquitoes (Diptera: Culicidae) in relation to climate variables and malaria incidence. A total of 3685 female anopheline mosquitoes, representing six species, were collected. The most abundant species were Anopheles marajoara Galvão & Damasceno (60.7%) and Anopheles darlingi Root (35.1%), which together represented 95.8% of the total anophelines collected. Abundance and species distribution varied by locality. Malaria prevalence varied from 12.5 to 21.4 cases per 1000 population. Transmission occurred throughout the year; the annual parasite index (API) for the study period was 813.0 cases per 1000 population, with a range of 71.6-2492 per 1000 population, depending on locality. Plasmodium vivax (Grassi & Feletti) (Coccidia: Plasmodiidae) accounted for 78.6% of cases, Plasmodium falciparum (Welch) for 21.4% and mixed infections (Pv+Pf) for 0.05) between mosquito abundance and rainfall. Correlations between malaria incidence by parasite species and mosquito abundance were not significant (P > 0.05). Monthly parous rates were similar for An. marajoara and An. darlingi throughout the year, with two peaks that coincided with the dry-rainy transition period and the period of less rain. Peaks in the incidence of malaria cases were observed 1 month after major peaks in biting rates of parous anophelines. Anopheles darlingi engages in biting activity throughout the night, with two minor peaks at 23.00-00.00 hours and 03.00-04.00 hours. Anopheles marajoara has a different pattern, with a biting peak at 19.00-21.00 hours and 76.6% of biting occurring before midnight. Although both vectors bite indoors and outdoors, they showed a highly significant (P < 0.01) degree of exophagic behaviour. The present study constitutes the first effort to characterize the

  13. Orion A helium abundance

    International Nuclear Information System (INIS)

    Tsivilev, A.P.; Ershov, A.A.; Smirnov, G.T.; Sorochenko, R.L.

    1986-01-01

    The 22.4-GHz (H,He)66-alpha and 36.5-GHz (H,He)56-alpha radio recombination lines have been observed at several Jaffe-Pankonin positions in the central part of the Orion A source. The measured relative abundance of ionized helium increases with distance, averaging 11.6 percent at peripheral points. The observed behavior is interpreted by a blister-type model nebula, which implies that Orion A has a true He abundance of 12 percent, is moving with a radial velocity of 5 km/sec, and is expanding. 18 references

  14. In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS

    DEFF Research Database (Denmark)

    Jensen, Sheila I; Steunou, Anne-Soisig; Bhaya, Devaki

    2011-01-01

    The relative abundance of transcripts encoding proteins involved in inorganic carbon concentrating mechanisms (CCM), detoxification of reactive oxygen species (ROS) and photosynthesis in the thermophilic cyanobacterium Synechococcus OS-B' was measured in hot spring microbial mats over two diel...

  15. [Relative abundance and microhabitat use by the frog Geobatrachus walkeri (Anura: Strabomantidae) in two habitats of Sierra Nevada de Santa Marta, Colombia].

    Science.gov (United States)

    Martínez Baños, Vera; Pacheco Florez, Vanesa; Ramírez-Pinilla, Martha P

    2011-06-01

    Geobatrachus walkeri belongs to a monotypic frog genus endemic to the San Lorenzo area, Sierra Nevada de Santa Marta, Colombia. This species has been categorized as endangered because of its small distribution area and the decline in the extent and quality of its habitat. It inhabits two forest types with different composition and structure, the native secondary forest and a pine plantation (dominated by Pinus patula). To compare the relative abundance and microhabitat use of this species in these habitat types, 30 quadrants/environment were distributed randomly. The individual number, microhabitat use and other aspects of its natural history were registered using visual encounter surveys in both sites, including non-sampled areas in the quadrants. The relative abundance of frogs was significantly different between habitats and among seasons. The highest abundance of G. walkeri relative to the total area was found in the pine plantation, being 2.3 times higher than in the natural forest. More frogs were significantly found during the rainy season; nevertheless, active individuals were also found during the dry season. Significant differences were found in the microhabitat use with respect to the forest type and season. The most frequently microhabitat used in the two forest types was the pine leaf-litter; besides, in the native forest, the microhabitat occupied more frequently presented medium and large size stones. Geobatrachus walkeri is a successful species in pine plantations, associated permanently to its leaf-litter environment where it seems to develop its entire life cycle. The clear modifications in the soils and water, derived from the introduction of the pine plantation in this area, seem not to have negatively affected the conservation and successful maintenance of this species.

  16. Trait-abundance relation in response to nutrient addition in a Tibetan alpine meadow: The importance of species trade-off in resource conservation and acquisition.

    Science.gov (United States)

    Liu, Huiying; Li, Ying; Ren, Fei; Lin, Li; Zhu, Wenyan; He, Jin-Sheng; Niu, Kechang

    2017-12-01

    In competition-dominated communities, traits promoting resource conservation and competitive ability are expected to have an important influence on species relative abundance (SRA). Yet, few studies have tested the trait-abundance relations in the line of species trade-off in resource conservation versus acquisition, indicating by multiple traits coordination. We measured SRA and key functional traits involving leaf economic spectrum (SLA, specific leaf area; LDMC, leaf dry matter content; LCC, leaf carbon concentration; LNC, leaf nitrogen concentration; LPC, leaf phosphorus concentration; Hs, mature height) for ten common species in all plots subjected to addition of nitrogen fertilizer (N), phosphorus fertilizer (P), or both of them (NP) in a Tibetan alpine meadow. We test whether SRA is positively related with traits promoting plant resource conservation, while negatively correlated with traits promoting plant growth and resource acquisition. We found that species were primarily differentiated along a trade-off axis involving traits promoting nutrient acquisition and fast growth (e.g., LPC and SLA) versus traits promoting resource conservation and competition ability (e.g., large LDMC). We further found that SRA was positively correlated with plant height, LDMC, and LCC, but negatively associated with SLA and leaf nutrient concentration irrespective of fertilization. A stronger positive height-SRA was found in NP-fertilized plots than in other plots, while negative correlations between SRA and SLA and LPC were found in N or P fertilized plots. The results indicate that species trade-off in nutrient acquisition and resource conservation was a key driver of SRA in competition-dominated communities following fertilization, with the linkage between SRA and traits depending on plant competition for specific soil nutrient and/or light availability. The results highlight the importance of competitive exclusion in plant community assembly following fertilization and

  17. Transcription profiling and identification of infection-related genes in Phytophthora cactorum.

    Science.gov (United States)

    Chen, Xiao-Ren; Huang, Shen-Xin; Zhang, Ye; Sheng, Gui-Lin; Zhang, Bo-Yue; Li, Qi-Yuan; Zhu, Feng; Xu, Jing-You

    2018-04-01

    Phytophthora cactorum, an oomycete pathogen, infects more than 200 plant species within several plant families. To gain insight into the repertoire of the infection-related genes of P. cactorum, Illumina RNA-Seq was used to perform a global transcriptome analysis of three life cycle stages of the pathogen, mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). From over 9.8 million Illumina reads for each library, 18,402, 18,569 and 19,443 distinct genes were identified for MY, ZO and GC libraries, respectively. Furthermore, the transcriptome difference among MY, ZO and GC stages was investigated. Gene ontology (GO) and KEGG pathway enrichment analyses revealed diverse biological functions and processes. Comparative analysis identified a large number of genes that are associated with specific stages and pathogenicity, including 166 effector genes. Of them, most of RXLR and NLP genes showed induction while the majority of CRN genes were down-regulated in GC, the important pre-infection stage, compared to either MY or ZO. And 14 genes encoding small cysteine-rich (SCR) secretory proteins showed differential expression during the developmental stages and in planta. Ectopic expression in the Solanaceae indicated that SCR113 and one elicitin PcINF1 can trigger cell death on Nicotiana benthamiana, tobacco (N. tabacum) and tomato (Solanum lycopersicum) leaves. Neither conserved domain nor homologues of SCR113 in other organisms can be identified. Collectively, our study provides a comprehensive examination of gene expression across three P. cactorum developmental stages and describes pathogenicity-related genes, all of which will help elucidate the pathogenicity mechanism of this destructive pathogen.

  18. Conventional oil and natural gas infrastructure increases brown-headed cowbird (Molothrus ater) relative abundance and parasitism in mixed-grass prairie.

    Science.gov (United States)

    Bernath-Plaisted, Jacy; Nenninger, Heather; Koper, Nicola

    2017-07-01

    The rapid expansion of oil and natural gas development across the Northern Great Plains has contributed to habitat fragmentation, which may facilitate brood parasitism of ground-nesting grassland songbird nests by brown-headed cowbirds ( Molothrus ater ), an obligate brood parasite, through the introduction of perches and anthropogenic edges. We tested this hypothesis by measuring brown-headed cowbird relative abundance and brood parasitism rates of Savannah sparrow ( Passerculus sandwichensis ) nests in relation to the presence of infrastructure features and proximity to potential perches and edge habitat. The presence of oil and natural gas infrastructure increased brown-headed cowbird relative abundance by a magnitude of four times, which resulted in four times greater brood parasitism rates at infrastructure sites. While the presence of infrastructure and the proximity to roads were influential in predicting brood parasitism rates, the proximity of perch sites was not. This suggests that brood parasitism associated with oil and natural gas infrastructure may result in additional pressures that reduce productivity of this declining grassland songbird.

  19. Relative importance of plant-mediated bottom-up and top-down forces on herbivore abundance on Brassica oleracea

    NARCIS (Netherlands)

    Kos, M.; Broekgaarden, C.; Kabouw, P.; Oude Lenferink, K.; Poelman, E.H.; Vet, L.E.M.; Dicke, M.; Loon, van J.J.A.

    2011-01-01

    1. Arthropod communities are structured by complex interactions between bottom-up (resource-based) and top-down (natural enemy-based) forces. Their relative importance in shaping arthropod communities, however, continues to be under debate. Bottom-up and top-down forces can be affected by

  20. Changes in transcript related to osmosis and intracellular ion homeostasis in Paulownia tomentosa under salt stress

    Directory of Open Access Journals (Sweden)

    Guoqiang eFan

    2016-03-01

    Full Text Available Paulownia tomentosa is an important economic and greening tree species that is cultivated widely, including salt environment. Our previous studies indicated its autotetraploid induced by colchicine showed better stress tolerance, but the underlying molecular mechanism related to ploidy and salt stress is still unclear. To investigate this issue, physiological measurements and transcriptome profiling of diploid and autotetraploid plants untreated and treated with NaCl were performed. Through the comparisons among four accessions, for one thing, we found different physiological changes between diploid and autotetraploid P. tomentosa; for another, and we detected many differentially expressed unigenes involved in salt stress response. These differentially expressed unigenes were assigned to several metabolic pathways, including plant hormone signal transduction, RNA transporter, protein processing in endoplasmic reticulum and plant-pathogen interaction, which constructed the complex regulatory network to maintain osmotic and intracellular ion homeostasis. Quantitative real-time polymerase chain reaction was used to confirm the expression patterns of 20 unigenes. The results establish the foundation for the genetic basis of salt tolerance in P. tomentosa, which in turn accelerates Paulownia breeding and expands available arable land.

  1. Bioinformatics Identification of Modules of Transcription Factor Binding Sites in Alzheimer's Disease-Related Genes by In Silico Promoter Analysis and Microarrays

    Directory of Open Access Journals (Sweden)

    Regina Augustin

    2011-01-01

    Full Text Available The molecular mechanisms and genetic risk factors underlying Alzheimer's disease (AD pathogenesis are only partly understood. To identify new factors, which may contribute to AD, different approaches are taken including proteomics, genetics, and functional genomics. Here, we used a bioinformatics approach and found that distinct AD-related genes share modules of transcription factor binding sites, suggesting a transcriptional coregulation. To detect additional coregulated genes, which may potentially contribute to AD, we established a new bioinformatics workflow with known multivariate methods like support vector machines, biclustering, and predicted transcription factor binding site modules by using in silico analysis and over 400 expression arrays from human and mouse. Two significant modules are composed of three transcription factor families: CTCF, SP1F, and EGRF/ZBPF, which are conserved between human and mouse APP promoter sequences. The specific combination of in silico promoter and multivariate analysis can identify regulation mechanisms of genes involved in multifactorial diseases.

  2. Novel Variants in ZNF34 and Other Brain-Expressed Transcription Factors are Shared Among Early-Onset MDD Relatives

    Science.gov (United States)

    Subaran, Ryan L.; Odgerel, Zagaa; Swaminathan, Rajeswari; Glatt, Charles E.; Weissman, Myrna M.

    2018-01-01

    There are no known genetic variants with large effects on susceptibility to major depressive disorder (MDD). Although one proposed study approach is to increase sensitivity by increasing sample sizes, another is to focus on families with multiple affected individuals to identify genes with rare or novel variants with strong effects. Choosing the family-based approach, we performed whole-exome analysis on affected individuals (n = 12) across five MDD families, each with at least five affected individuals, early onset, and prepubertal diagnoses. We identified 67 genes where novel deleterious variants were shared among affected relatives. Gene ontology analysis shows that of these 67 genes, 18 encode transcriptional regulators, eight of which are expressed in the human brain, including four KRAB-A box-containing Zn2+ finger repressors. One of these, ZNF34, has been reported as being associated with bipolar disorder and as differentially expressed in bipolar disorder patients compared to healthy controls. We found a novel variant—encoding a non-conservative P17R substitution in the conserved repressor domain of ZNF34 protein—segregating completely with MDD in all available individuals in the family in which it was discovered. Further analysis showed a common ZNF34 coding indel segregating with MDD in a separate family, possibly indicating the presence of an unobserved, linked, rare variant in that particular family. Our results indicate that genes encoding transcription factors expressed in the brain might be an important group of MDD candidate genes and that rare variants in ZNF34 might contribute to susceptibility to MDD and perhaps other affective disorders. PMID:26823146

  3. KP4 to control Ustilago tritici in wheat: Enhanced greenhouse resistance to loose smut and changes in transcript abundance of pathogen related genes in infected KP4 plants.

    Science.gov (United States)

    Quijano, Carolina Diaz; Wichmann, Fabienne; Schlaich, Thomas; Fammartino, Alessandro; Huckauf, Jana; Schmidt, Kerstin; Unger, Christoph; Broer, Inge; Sautter, Christof

    2016-09-01

    Ustilago tritici causes loose smut, which is a seed-borne fungal disease of wheat, and responsible for yield losses up to 40%. Loose smut is a threat to seed production in developing countries where small scale farmers use their own harvest as seed material. The killer protein 4 (KP4) is a virally encoded toxin from Ustilago maydis and inhibits growth of susceptible races of fungi from the Ustilaginales. Enhanced resistance in KP4 wheat to stinking smut, which is caused by Tilletia caries, had been reported earlier. We show that KP4 in genetically engineered wheat increased resistance to loose smut up to 60% compared to the non-KP4 control under greenhouse conditions. This enhanced resistance is dose and race dependent. The overexpression of the transgene kp4 and its effect on fungal growth have indirect effects on the expression of endogenous pathogen defense genes.

  4. KP4 to control Ustilago tritici in wheat: Enhanced greenhouse resistance to loose smut and changes in transcript abundance of pathogen related genes in infected KP4 plants

    Directory of Open Access Journals (Sweden)

    Carolina Diaz Quijano

    2016-09-01

    Full Text Available Ustilago tritici causes loose smut, which is a seed-borne fungal disease of wheat, and responsible for yield losses up to 40%. Loose smut is a threat to seed production in developing countries where small scale farmers use their own harvest as seed material. The killer protein 4 (KP4 is a virally encoded toxin from Ustilago maydis and inhibits growth of susceptible races of fungi from the Ustilaginales. Enhanced resistance in KP4 wheat to stinking smut, which is caused by Tilletia caries, had been reported earlier. We show that KP4 in genetically engineered wheat increased resistance to loose smut up to 60% compared to the non-KP4 control under greenhouse conditions. This enhanced resistance is dose and race dependent. The overexpression of the transgene kp4 and its effect on fungal growth have indirect effects on the expression of endogenous pathogen defense genes.

  5. Age- and Activity-Related Differences in the Abundance of Myosin Essential and Regulatory Light Chains in Human Muscle

    Directory of Open Access Journals (Sweden)

    James N. Cobley

    2016-04-01

    Full Text Available Traditional methods for phenotyping skeletal muscle (e.g., immunohistochemistry are labor-intensive and ill-suited to multixplex analysis, i.e., assays must be performed in a series. Addressing these concerns represents a largely unmet research need but more comprehensive parallel analysis of myofibrillar proteins could advance knowledge regarding age- and activity-dependent changes in human muscle. We report a label-free, semi-automated and time efficient LC-MS proteomic workflow for phenotyping the myofibrillar proteome. Application of this workflow in old and young as well as trained and untrained human skeletal muscle yielded several novel observations that were subsequently verified by multiple reaction monitoring (MRM. We report novel data demonstrating that human ageing is associated with lesser myosin light chain 1 content and greater myosin light chain 3 content, consistent with an age-related reduction in type II muscle fibers. We also disambiguate conflicting data regarding myosin regulatory light chain, revealing that age-related changes in this protein more closely reflect physical activity status than ageing per se. This finding reinforces the need to control for physical activity levels when investigating the natural process of ageing. Taken together, our data confirm and extend knowledge regarding age- and activity-related phenotypes. In addition, the MRM transitions described here provide a methodological platform that can be fine-tuned to suite multiple research needs and thus advance myofibrillar phenotyping.

  6. On the impact of helium abundance on the Cepheid period-luminosity and Wesenheit relations and the distance ladder

    Science.gov (United States)

    Carini, R.; Brocato, E.; Raimondo, G.; Marconi, M.

    2017-08-01

    This work analyses the effect of the helium content on synthetic period-luminosity relations (PLRs) and period-Wesenheit relations (PWRs) of Cepheids and the systematic uncertainties on the derived distances that a hidden population of He-enhanced Cepheids may generate. We use new stellar and pulsation models to build a homogeneous and consistent framework to derive the Cepheid features. The Cepheid populations expected in synthetic colour-magnitude diagrams of young stellar systems (from 20 to 250 Myr) are computed in several photometric bands for Y = 0.25 and 0.35, at a fixed metallicity (Z = 0.008). The PLRs appear to be very similar in the two cases, with negligible effects (few per cent) on distances, while PWRs differ somewhat, with systematic uncertainties in deriving distances as high as ˜ 7 per cent at log P Statistical effects due to the number of variables used to determine the relations contribute to a distance systematic error of the order of few percent, with values decreasing from optical to near-infrared bands. The empirical PWRs derived from multiwavelength data sets for the Large Magellanic Cloud (LMC) is in a very good agreement with our theoretical PWRs obtained with a standard He content, supporting the evidence that LMC Cepheids do not show any He effect.

  7. Stellar Oxygen Abundances

    Science.gov (United States)

    King, Jeremy

    1994-04-01

    This dissertation addresses several issues concerning stellar oxygen abundances. The 7774 {\\AA} O I triplet equivalent widths of Abia & Rebolo [1989, AJ, 347, 186] for metal-poor dwarfs are found to be systematically too high. I also argue that current effective temperatures used in halo star abundance studies may be ~150 K too low. New color-Teff relations are derived for metal-poor stars. Using the revised Teff values and improved equivalent widths for the 7774A O I triplet, the mean [O/Fe] ratio for a handful of halo stars is found to be +0.52 with no dependence on Teff or [Fe/H]. Possible cosmological implications of the hotter Teff scale are discussed along with additional evidence supporting the need for a higher temperature scale for metal-poor stars. Our Teff scale leads to a Spite Li plateau value of N(Li)=2.28 +/- 0.09. A conservative minimal primordial value of N(Li)=2.35 is inferred. If errors in the observations and models are considered, consistency with standard models of Big Bang nucleosynthesis is still achieved with this larger Li abundance. The revised Teff scale raises the observed B/Be ratio of HD 140283 from 10 to 12, making its value more comfortably consistent with the production of the observed B and Be by ordinary spallation. Our Teff values are found to be in good agreement with values predicted from both the Victoria and Yale isochrone color-Teff relations. Thus, it appears likely that no changes in globular cluster ages would result. Next, we examine the location of the break in the [O/Fe] versus [Fe/H] plane in a quantitative fashion. Analysis of a relatively homogeneous data set does not favor any unique break point in the range -1.7 /= -3), in agreement with the new results for halo dwarfs. We find that the gap in the observed [O/H] distribution, noted by Wheeler et al. [1989, ARAA, 27, 279], persists despite the addition of more O data and may betray the occurrence of a hiatus in star formation between the end of halo formation and

  8. Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

    Science.gov (United States)

    Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

    2015-01-01

    In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

  9. Space-time variation of the relative abundance of Limnoperna fortunei in deep zones of São Gonçalo Channel, Rio Grande do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Michelle Lopes

    Full Text Available This work describes the spatial-temporal variation of the relative abundance and size of Limnoperna fortunei (Dunker, 1857 collected in São Gonçalo Channel through bottom trawl with a 0.5 cm mesh, at depths between 3 and 6 m. The estimative of mean relative abundance (CPUE ranged from 2,425.3 individuals per drag (ind./drag in the spring to 21,715.0 ind./drag in the fall, with an average of 9,515.3 ind./drag throughout the year. The estimated mean density of L. fortunei for the deep region of São Gonçalo Channel ranged from 1.2 to 10.3 ind./m², and it was recorded a maximum density of 84.9 ind./m² in the fall of 2008. The method of sampling using bottom trawl enabled the capture of L. fortunei under the soft muddy bottom of the channel, in different sizes ranging from 0.4 to 3.2 cm. This shows that the structure of the L. fortunei adult population under the bottom of the São Gonçalo Channel is composed mostly of small individuals (<1.4 cm, which represent up to 74% of the population collected.

  10. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

    Science.gov (United States)

    Auerbach, Raymond K; Chen, Bin; Butte, Atul J

    2013-08-01

    Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

  11. Gender-related aspects of transmasculine people's vocal situations: insights from a qualitative content analysis of interview transcripts.

    Science.gov (United States)

    Azul, David

    2016-11-01

    Transmasculine people assigned female gender at birth but who do not identify with this classification have traditionally received little consideration in the voice literature. Existing analyses tend to be focused on evaluating speaker voice characteristics, whereas other factors that contribute to the production of vocal gender have remained underexplored. Most studies rely on researcher-centred perspectives, whereas very little is known about how transmasculine people themselves experience and make sense of their vocal situations. To explore how participants described their subjective gender positionings; which gender attributions they wished to receive from others; which gender they self-attributed to their voices; which gender attributions they had received from others; and how far participants were satisfied with the gender-related aspects of their vocal situations. Transcripts of semi-structured interviews with 14 German-speaking transmasculine people served as the original data corpus. Sections in which participants described the gender-related aspects of their vocal situations and that were relevant to the current research objectives were selected and explored using qualitative content analysis. The analysis revealed diverse accounts pertaining to the factors that contribute to the production of vocal gender for individual participants and variable levels of satisfaction with vocal gender presentation and attribution. Transmasculine people need to be regarded as a heterogeneous population and clinical practice needs to follow a client-centred, individualized approach. © 2016 Royal College of Speech and Language Therapists.

  12. Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

    Science.gov (United States)

    Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

    2016-04-01

    Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

  13. Differential regulation of HIF-1α and HIF-2α in neuroblastoma: Estrogen-related receptor alpha (ERRα) regulates HIF2A transcription and correlates to poor outcome

    International Nuclear Information System (INIS)

    Hamidian, Arash; Stedingk, Kristoffer von; Munksgaard Thorén, Matilda; Mohlin, Sofie; Påhlman, Sven

    2015-01-01

    Hypoxia-inducible factors (HIFs) are differentially regulated in tumor cells. While the current paradigm supports post-translational regulation of the HIF-α subunits, we recently showed that hypoxic HIF-2α is also transcriptionally regulated via insulin-like growth factor (IGF)-II in the childhood tumor neuroblastoma. Here, we demonstrate that transcriptional regulation of HIF-2α seems to be restricted to neural cell-derived tumors, while HIF-1α is canonically regulated at the post-translational level uniformly across different tumor forms. Enhanced expression of HIF2A mRNA at hypoxia is due to de novo transcription rather than increased mRNA stability, and chemical stabilization of the HIF-α proteins at oxygen-rich conditions unexpectedly leads to increased HIF2A transcription. The enhanced HIF2A levels do not seem to be dependent on active HIF-1. Using a transcriptome array approach, we identified members of the Peroxisome proliferator-activated receptor gamma coactivator (PGC)/Estrogen-related receptor (ERR) complex families as potential regulators of HIF2A. Knockdown or inhibition of one of the members, ERRα, leads to decreased expression of HIF2A, and high expression of the ERRα gene ESRRA correlates with poor overall and progression-free survival in a clinical neuroblastoma material consisting of 88 tumors. Thus, targeting of ERRα and pathways regulating transcriptional HIF-2α are promising therapeutic avenues in neuroblastoma. - Highlights: • Transcriptional control of HIF-2α is restricted to neural cell-derived tumors. • Enhanced transcription of HIF2A is not due to increased mRNA stability. • Chemical stabilization of the HIF-α subunits leads to increased HIF2A transcription. • ERRα regulates HIF2A mRNA expression in neuroblastoma. • High expression of ESRRA correlates to poor outcome in neuroblastoma

  14. Differential regulation of HIF-1α and HIF-2α in neuroblastoma: Estrogen-related receptor alpha (ERRα) regulates HIF2A transcription and correlates to poor outcome

    Energy Technology Data Exchange (ETDEWEB)

    Hamidian, Arash; Stedingk, Kristoffer von; Munksgaard Thorén, Matilda; Mohlin, Sofie; Påhlman, Sven, E-mail: sven.pahlman@med.lu.se

    2015-06-05

    Hypoxia-inducible factors (HIFs) are differentially regulated in tumor cells. While the current paradigm supports post-translational regulation of the HIF-α subunits, we recently showed that hypoxic HIF-2α is also transcriptionally regulated via insulin-like growth factor (IGF)-II in the childhood tumor neuroblastoma. Here, we demonstrate that transcriptional regulation of HIF-2α seems to be restricted to neural cell-derived tumors, while HIF-1α is canonically regulated at the post-translational level uniformly across different tumor forms. Enhanced expression of HIF2A mRNA at hypoxia is due to de novo transcription rather than increased mRNA stability, and chemical stabilization of the HIF-α proteins at oxygen-rich conditions unexpectedly leads to increased HIF2A transcription. The enhanced HIF2A levels do not seem to be dependent on active HIF-1. Using a transcriptome array approach, we identified members of the Peroxisome proliferator-activated receptor gamma coactivator (PGC)/Estrogen-related receptor (ERR) complex families as potential regulators of HIF2A. Knockdown or inhibition of one of the members, ERRα, leads to decreased expression of HIF2A, and high expression of the ERRα gene ESRRA correlates with poor overall and progression-free survival in a clinical neuroblastoma material consisting of 88 tumors. Thus, targeting of ERRα and pathways regulating transcriptional HIF-2α are promising therapeutic avenues in neuroblastoma. - Highlights: • Transcriptional control of HIF-2α is restricted to neural cell-derived tumors. • Enhanced transcription of HIF2A is not due to increased mRNA stability. • Chemical stabilization of the HIF-α subunits leads to increased HIF2A transcription. • ERRα regulates HIF2A mRNA expression in neuroblastoma. • High expression of ESRRA correlates to poor outcome in neuroblastoma.

  15. Relative abundance of PcP energy in explosion seismic signals from Eastern Kazakh and South Western Russia recorded at Eskdalemuir, Yellowknife and Gauribidanur arrays

    International Nuclear Information System (INIS)

    Basu, T.K.; Arora, S.K.

    1991-01-01

    In this study further evidence of relative abundance of PcP (core reflected P) energy in explosion seismic records is gathered. It is based on the analysis of temporal and spectral characteristics of P and PcP digital seismograms of twenty-three underground nuclear explosions in Eastern Kazakh and Southern Russia recorded at Eskdalemuir (EKA) and Yellowkinfe (YKA) arrays. The results are compared with those obtained earlier using Gauribidanur array (GBA) data. It is found that seismic sources in Southwestern Russia give consistently large values of the PcP identifier when both EKA and YKA data are used thus corroborating authors' earlier finding with regard to this Soviet region of typical Q-structure inferred from GBA data. As regards relative levels of PcP energy in explosion generated seismic waves, it is found to be substantially large at GBA, moderate at YKA and least at EKA. (author). 8 figs., 3 tabs

  16. Assessment of complex water pollution with heavy metals and Pyrethroid pesticides on transcript levels of metallothionein and immune related genes.

    Science.gov (United States)

    Ghazy, Haneen A; Abdel-Razek, Mohamed A S; El Nahas, Abeer F; Mahmoud, Shawky

    2017-09-01

    Alteration of immunological function of an aquatic organism can be used as an indicator for evaluating the direct effect of exposure to pollutants. The aim of this work is to assess the impact of complex water pollution with special reference to Pyrethroid pesticides and heavy metals on mRNA transcript levels of Metallothionine and some immune related genes of Nile tilapia (Oreochromas Niloticus). Residues of six heavy metals and six Pyrethroid were assessed in water as well as fish tissues at three different sites of Lake Burullus, located at Northern Egypt. Variations of water physicochemical properties associated with different levels of heavy metals at the three different sections were recorded. Tissue residues of Fe, Mn and Zn, Cu, Ni exceed water levels in contrast to elevated water level of Pb. All assessed Pyrethroids are detected in fish tissue samples with higher concentration (3-42 folds) than that found in water samples especially Cypermethrin. Significant down-regulation of expression levels of metallothionein (MT) at the three sections of the lake was observed. The expression of immune related genes (IgM) and inflammatory cytokines (TNF, IL.8 and IL.1) were affected. IgM and TNF were significantly down-regulated at eastern and western section of the lake; meanwhile the expression of IL8 is down regulated at the three sections of the lack. IL1 was significantly up-regulated at eastern and middle sections. We conclude that, variable gene expression of MT and immune-related genes at the three sections of the lack impose different response to complex water pollution in relation to variable aquatic environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

    KAUST Repository

    Kudo, Toshiaki

    2018-04-26

    Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.

  18. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

    KAUST Repository

    Kudo, Toshiaki; Kobiyama, Atsushi; Rashid, Jonaira; Reza, Shaheed; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Segawa, Satoshi; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo

    2018-01-01

    Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.

  19. Is gene transcription involved in seed dry after-ripening?

    Directory of Open Access Journals (Sweden)

    Patrice Meimoun

    Full Text Available Orthodox seeds are living organisms that survive anhydrobiosis and may display dormancy, an inability to germinate at harvest. Seed germination potential can be acquired during a prolonged period of dry storage called after-ripening. The aim of this work was to determine if gene transcription is an underlying regulatory mechanism for dormancy alleviation during after-ripening. To identify changes in gene transcription strictly associated with the acquisition of germination potential but not with storage, we used seed storage at low relative humidity that maintains dormancy as control. Transcriptome profiling was performed using DNA microarray to compare change in gene transcript abundance between dormant (D, after-ripened non-dormant (ND and after-ripened dormant seeds (control, C. Quantitative real-time polymerase chain reaction (qPCR was used to confirm gene expression. Comparison between D and ND showed the differential expression of 115 probesets at cut-off values of two-fold change (p<0.05. Comparisons between both D and C with ND in transcript abundance showed that only 13 transcripts, among 115, could be specific to dormancy alleviation. qPCR confirms the expression pattern of these transcripts but without significant variation between conditions. Here we show that sunflower seed dormancy alleviation in the dry state is not related to regulated changes in gene expression.

  20. Abundances in the Galactic bulge

    Energy Technology Data Exchange (ETDEWEB)

    Barbuy, B; Alves-Brito, A [Universidade de Sao Paulo, IAG, Rua do Matao 1226, Sao Paulo 05508-900 (Brazil); Ortolani, S; Zoccali, M [Dipartimento di Astronomia, Universita di Padova, Vicolo dell' Osservatorio 2, I-35122 Padova (Italy); Hill, V; Gomez, A [Observatoire de Paris-Meudon, 92195 Meudon Cedex (France); Melendez, J [Centro de AstrofIsica da Universidade de Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Asplund, M [Max Planck Institute for Astrophysics, Postfach 1317, 85741 Garching (Germany); Bica, E [Departamento de Astronomia, Universidade Federal do Rio Grande do Sul, CP 15051, Porto Alegre 91501-970 (Brazil); Renzini, A [Osservatorio Astronomico di Padova, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy); Minniti, D [Department of Astronomy and Astrophysics, Universidad Catolica de Chile, Casilla 306, Santiago 22 (Chile)], E-mail: barbuy@astro.iag.usp.br

    2008-12-15

    The metallicity distribution and abundance ratios of the Galactic bulge are reviewed. Issues raised by recent work of different groups, in particular the high metallicity end, the overabundance of {alpha}-elements in the bulge relative to the thick disc and the measurement of giants versus dwarfs, are discussed. Abundances in the old moderately metal-poor bulge globular clusters are described.

  1. The relative abundance of predicted genes associated with ammonia-oxidation, nitrate reduction, and biomass decomposition in mineral soil are altered by intensive timber harvest.

    Science.gov (United States)

    Mushinski, R. M.; Zhou, Y.; Gentry, T. J.; Boutton, T. W.

    2017-12-01

    Forest ecosystems in the southern United States are substantially altered by anthropogenic disturbances such as timber harvest and land conversion, with effects being observed in carbon and nutrient pools as well as biogeochemical processes. Furthermore, the desire to develop renewable energy sources in the form of biomass extraction from logging residues may result in alterations in soil community structure and function. While the impact of forest management on soil physicochemical properties of the region has been studied, its' long-term effect on soil bacterial community composition and metagenomic potential is relatively unknown, especially at deeper soil depths. This study investigates how intensive organic matter removal intensities associated with timber harvest influence decadal-scale alterations in bacterial community structure and functional potential in the upper 1-m of the soil profile, 18 years post-harvest in a Pinus taeda L. forest of eastern Texas. Amplicon sequencing of the 16S rRNA gene was used in conjunction with soil chemical analyses to evaluate treatment-induced differences in community composition and potential environmental drivers of associated change. Furthermore, functional potential was assessed by using amplicon data to make metagenomic predictions. Results indicate that increasing organic matter removal intensity leads to altered community composition and the relative abundance of dominant OTUs annotated to Burkholderia and Aciditerrimonas. The relative abundance of predicted genes associated with dissimilatory nitrate reduction and denitrification were highest in the most intensively harvested treatment while genes involved in nitrification were significantly lower in the most intensively harvested treatment. Furthermore, genes associated with glycosyltransferases were significantly reduced with increasing harvest intensity while polysaccharide lyases increased. These results imply that intensive organic matter removal may create

  2. Transcription factor fos-related antigen-2 induces progressive peripheral vasculopathy in mice closely resembling human systemic sclerosis.

    Science.gov (United States)

    Maurer, Britta; Busch, Nicole; Jüngel, Astrid; Pileckyte, Margarita; Gay, Renate E; Michel, Beat A; Schett, Georg; Gay, Steffen; Distler, Jörg; Distler, Oliver

    2009-12-08

    Microvascular damage is one of the first pathological changes in systemic sclerosis. In this study, we investigated the role of Fos-related antigen-2 (Fra-2), a transcription factor of the activator protein-1 family, in the peripheral vasculopathy of systemic sclerosis and examined the underlying mechanisms. Expression of Fra-2 protein was significantly increased in skin biopsies of systemic sclerosis patients compared with healthy controls, especially in endothelial and vascular smooth muscle cells. Fra-2 transgenic mice developed a severe loss of small blood vessels in the skin that was paralleled by progressive skin fibrosis at 12 weeks of age. The reduction in capillary density was preceded by a significant increase in apoptosis in endothelial cells at week 9 as detected by immunohistochemistry. Similarly, suppression of Fra-2 by small interfering RNA prevented human microvascular endothelial cells from staurosporine-induced apoptosis and improved both the number of tubes and the cumulative tube lengths in the tube formation assay. In addition, cell migration in the scratch assay and vascular endothelial growth factor-dependent chemotaxis in a modified Boyden chamber assay were increased after transfection of human microvascular endothelial cells with Fra-2 small interfering RNA, whereas proliferation was not affected. Fra-2 is present in human systemic sclerosis and may contribute to the development of microvasculopathy by inducing endothelial cell apoptosis and by reducing endothelial cell migration and chemotaxis. Fra-2 transgenic mice are a promising preclinical model to study the mechanisms and therapeutic approaches of the peripheral vasculopathy in systemic sclerosis.

  3. Copper oxide nanoparticles induce the transcriptional modulation of oxidative stress-related genes in Arbacia lixula embryos.

    Science.gov (United States)

    Giannetto, Alessia; Cappello, Tiziana; Oliva, Sabrina; Parrino, Vincenzo; De Marco, Giuseppe; Fasulo, Salvatore; Mauceri, Angela; Maisano, Maria

    2018-06-14

    Copper oxide nanoparticles (CuO NPs) are widely used in various industrial applications, i.e. semiconductor devices, batteries, solar energy converter, gas sensor, microelectronics, heat transfer fluids, and have been recently recognized as emerging pollutants of increasing concern for human and marine environmental health. Therefore, the toxicity of CuO NPs needs to be thoroughly understood. In this study, we evaluated the potential role of oxidative stress in CuO NP toxicity by exploring the molecular response of Arbacia lixula embryos to three CuO NP concentrations (0.7, 10, 20 ppb) by investigating the transcriptional patterns of oxidative stress-related genes (catalase and superoxide dismutase) and metallothionein, here cloned and characterized for the first time. Time- and concentration-dependent changes in gene expression were detected in A. lixula embryos exposed to CuO NPs, up to pluteus stage (72 h post-fertilization, hpf), indicating that oxidative stress is one of the toxicity mechanisms for CuO NPs. These findings provide new insights into the comprehension of the molecular mechanisms underlying copper nanoparticle toxicity in A. lixula sea urchin and give new tools for monitoring of aquatic areas, thus corroborating the suitability of this embryotoxicity assay for future evaluation of impacted sites. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Impaired transcriptional activity of Nrf2 in age-related myocardial oxidative stress is reversible by moderate exercise training.

    Directory of Open Access Journals (Sweden)

    Sellamuthu S Gounder

    Full Text Available Aging promotes accumulation of reactive oxygen/nitrogen species (ROS/RNS in cardiomyocytes, which leads to contractile dysfunction and cardiac abnormalities. These changes may contribute to increased cardiovascular disease in the elderly. Inducible antioxidant pathways are regulated by nuclear erythroid 2 p45-related factor 2 (Nrf2 through antioxidant response cis-elements (AREs and are impaired in the aging heart. Whereas acute exercise stress (AES activates Nrf2 signaling and promotes myocardial antioxidant function in young mice (~2 months, aging mouse (>23 months hearts exhibit significant oxidative stress as compared to those of the young. The purpose of this study was to investigate age-dependent regulation of Nrf2-antioxidant mechanisms and redox homeostasis in mouse hearts and the impact of exercise. Old mice were highly susceptible to oxidative stress following high endurance exercise stress (EES, but demonstrated increased adaptive redox homeostasis after moderate exercise training (MET; 10m/min, for 45 min/day for ~6 weeks. Following EES, transcription and protein levels for most of the ARE-antioxidants were increased in young mice but their induction was blunted in aging mice. In contrast, 6-weeks of chronic MET promoted nuclear levels of Nrf2 along with its target antioxidants in the aging heart to near normal levels as seen in young mice. These observations suggest that enhancing Nrf2 function and endogenous cytoprotective mechanisms by MET, may combat age-induced ROS/RNS and protect the myocardium from oxidative stress diseases.

  5. Transcriptional profiles of pilocytic astrocytoma are related to their three different locations, but not to radiological tumor features

    International Nuclear Information System (INIS)

    Zakrzewski, Krzysztof; Jarząb, Michał; Pfeifer, Aleksandra; Oczko-Wojciechowska, Małgorzata; Jarząb, Barbara; Liberski, Paweł P.; Zakrzewska, Magdalena

    2015-01-01

    Pilocytic astrocytoma is the most common type of brain tumor in the pediatric population, with a generally favorable prognosis, although recurrences or leptomeningeal dissemination are sometimes also observed. For tumors originating in the supra-or infratentorial location, a different molecular background was suggested, but plausible correlations between the transcriptional profile and radiological features and/or clinical course are still undefined. The purpose of this study was to identify gene expression profiles related to the most frequent locations of this tumor, subtypes based on various radiological features, and the clinical pattern of the disease. Eighty six children (55 males and 31 females) with histologically verified pilocytic astrocytoma were included in this study. Their age at the time of diagnosis ranged from fourteen months to seventeen years, with a mean age of seven years. There were 40 cerebellar, 23 optic tract/hypothalamic, 21 cerebral hemispheric, and two brainstem tumors. According to the radiological features presented on MRI, all cases were divided into four subtypes: cystic tumor with a non-enhancing cyst wall; cystic tumor with an enhancing cyst wall; solid tumor with central necrosis; and solid or mainly solid tumor. In 81 cases primary surgical resection was the only and curative treatment, and in five cases progression of the disease was observed. In 47 cases the analysis was done by using high density oligonucleotide microarrays (Affymetrix HG-U133 Plus 2.0) with subsequent bioinformatic analyses and confirmation of the results by independent RT-qPCR (on 39 samples). Bioinformatic analyses showed that the gene expression profile of pilocytic astrocytoma is highly dependent on the tumor location. The most prominent differences were noted for IRX2, PAX3, CXCL14, LHX2, SIX6, CNTN1 and SIX1 genes expression even within different compartments of the supratentorial region. Analysis of the genes potentially associated with radiological

  6. Physiological changes and sHSPs genes relative transcription in relation to the acquisition of seed germination during maturation of hybrid rice seed.

    Science.gov (United States)

    Zhu, Li-Wei; Cao, Dong-Dong; Hu, Qi-Juan; Guan, Ya-Jing; Hu, Wei-Min; Nawaz, Aamir; Hu, Jin

    2016-03-30

    During the production of early hybrid rice seed, the seeds dehydrated slowly and retained high moisture levels when rainy weather lasted for a couple of days, and the rice seeds easily occurred pre-harvest sprouting (PHS) along with high temperature. Therefore it is necessary to harvest the seeds before the PHS occurred. The seeds of hybrid rice (Oryza sativa L. subsp. indica) cv. Qianyou No1 that harvests from 19 to 28 days after pollination (DAP) all had high seed vigour. The seed moisture content at 10 DAP was 36.1%, and declined to 28.6% at 19 DAP; the contents of soluble sugar and total starch increased significantly with the development of seeds. The soluble protein content, the level of abscisic acid (ABA) and gibberellin (GA3 ), and ascorbate peroxidase (APX) activity continued to decrease from 10 DAP to 19 DAP. The seeds at 19 DAP had the highest peroxidase (POD) activity and lowest catalase (CAT) activity while the superoxide dismutase (SOD) activity had no significant difference among the different developing periods. The relative expressions of genes 64S Hsp18.0 and Os03g0267200 transcripts increased significantly from 10 to 19 DAP, and then decreased. However, no significant change was recorded in soluble protein, sugar and GA3 after 16 DAP, and they all significantly correlated with seed viability and vigour during the process of seed maturity. The seeds of hybrid rice Qianyou No1 had a higher viability and vigour when harvested from 19 DAP to 28 DAP, the transcription levels of 64S Hsp18.0 and Os03g0267200 increased significantly from 10 DAP to 19 DAP and the highest value was recorded at 19 DAP. The seeds could be harvested as early as 19 DAP without negative influence on seed vigour and viability. © 2015 Society of Chemical Industry.

  7. Transcriptional interference networks coordinate the expression of functionally-related genes clustered in the same genomic loci

    Directory of Open Access Journals (Sweden)

    Zsolt eBoldogkoi

    2012-07-01

    Full Text Available The regulation of gene expression is essential for normal functioning of biological systems in every form of life. Gene expression is primarily controlled at the level of transcription, especially at the phase of initiation. Non-coding RNAs are one of the major players at every level of genetic regulation, including the control of chromatin organisation, transcription, various post-transcriptional processes and translation. In this study, the Transcriptional Interference Network (TIN hypothesis was put forward in an attempt to explain the global expression of antisense RNAs and the overall occurrence of tandem gene clusters in the genomes of various biological systems ranging from viruses to mammalian cells. The TIN hypothesis suggests the existence of a novel layer of genetic regulation, based on the interactions between the transcriptional machineries of neighbouring genes at their overlapping regions, which are assumed to play a fundamental role in coordinating gene expression within a cluster of functionally-linked genes. It is claimed that the transcriptional overlaps between adjacent genes are much more widespread in genomes than is thought today. The Waterfall model of the TIN hypothesis postulates a unidirectional effect of upstream genes on the transcription of downstream genes within a cluster of tandemly-arrayed genes, while the Seesaw model proposes a mutual interdependence of gene expression between the oppositely-oriented genes. The TIN represents an auto-regulatory system with an exquisitely timed and highly synchronised cascade of gene expression in functionally-linked genes located in close physical proximity to each other. In this study, we focused on herpesviruses. The reason for this lies in the compressed nature of viral genes, which allows a tight regulation and an easier investigation of the transcriptional interactions between genes. However, I believe that the same or similar principles can be applied to cellular

  8. The Csr/Rsm system of Yersinia and related pathogens: a post-transcriptional strategy for managing virulence.

    Science.gov (United States)

    Heroven, Ann Kathrin; Böhme, Katja; Dersch, Petra

    2012-04-01

    This review emphasizes the function and regulation of the Csr regulatory system in the human enteropathogen Yersinia pseudotuberculosis and compares its features with the homologous Csr/Rsm systems of related pathogens. The Csr/Rsm systems of eubacteria form a complex regulatory network in which redundant non-translated Csr/Rsm-RNAs bind the RNA-binding protein CsrA/RsmA, thereby preventing its interaction with mRNA targets. The Csr system is controlled by the BarA/UvrY-type of two-component sensor-regulator systems. Apart from that, common or pathogen-specific regulators control the abundance of the Csr components. The coordinate control of virulence factors and infection-linked physiological traits by the Csr/Rsm systems helps the pathogens to adapt individually to rapidly changing conditions to which they are exposed during the different stages of an infection. As Csr/Rsm function is relevant for full virulence, it represents a target suitable for antimicrobial drug development.

  9. Species composition and relative abundance of sand flies of the genus Lutzomyia (Diptera: Psychodidae) at an endemic focus of visceral leishmaniasis in Colombia.

    Science.gov (United States)

    Ferro, C; Morrison, A C; Torres, M; Pardo, R; Wilson, M L; Tesh, R B

    1995-07-01

    Ecological studies on the sand fly Lutzomyia longipalpis (Lutz & Neiva) were conducted during 1990-1993 at a small rural community in Colombia where American visceral leishmaniasis is endemic. Weekly sand fly collections were made from pigpens, houses, and natural resting sites, using hand-held aspirators, sticky (oiled) paper traps, and opossum-baited Disney traps. In total, 263,094 sand flies were collected; L. longipalpis predominated (86.1%), followed by L. trinidadensis (11.0%), L. cayennensis (2.7%), and 8 other Lutzomyia species. The species composition and sex ratio of these sand flies varied among sites and by collection method. L. longipalpis were captured most efficiently by direct aspiration from animal bait. Conversely, sticky paper traps, especially inside houses and at rock resting sites, collected a greater diversity of species, but a lower relative abundance of L. longipalpis.

  10. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    OpenAIRE

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription ...

  11. SEPALLATA1/2-suppressed mature apples have low ethylene, high auxin and reduced transcription of ripening-related genes

    Science.gov (United States)

    Schaffer, Robert J.; Ireland, Hilary S.; Ross, John J.; Ling, Toby J.; David, Karine M.

    2012-01-01

    Background and aims Fruit ripening is an important developmental trait in fleshy fruits, making the fruit palatable for seed dispersers. In some fruit species, there is a strong association between auxin concentrations and fruit ripening. We investigated the relationship between auxin concentrations and the onset of ethylene-related ripening in Malus × domestica (apples) at both the hormone and transcriptome levels. Methodology Transgenic apples suppressed for the SEPALLATA1/2 (SEP1/2) class of gene (MADS8/9) that showed severely reduced ripening were compared with untransformed control apples. In each apple type, free indole-3-acetic acid (IAA) concentrations were measured during early ripening. The changes observed in auxin were assessed in light of global changes in gene expression. Principal results It was found that mature MADS8/9-suppressed apples had a higher concentration of free IAA. This was associated with increased expression of the auxin biosynthetic genes in the indole-3-acetamide pathway. Additionally, in the MADS8/9-suppressed apples, there was less expression of the GH3 auxin-conjugating enzymes. A number of genes involved in the auxin-regulated transcription (AUX/IAA and ARF classes of genes) were also observed to change in expression, suggesting a mechanism for signal transduction at the start of ripening. Conclusions The delay in ripening observed in MADS8/9-suppressed apples may be partly due to high auxin concentrations. We propose that, to achieve low auxin associated with fruit maturation, the auxin homeostasis is controlled in a two-pronged manner: (i) by the reduction in biosynthesis and (ii) by an increase in auxin conjugation. This is associated with the change in expression of auxin-signalling genes and the up-regulation of ripening-related genes. PMID:23346344

  12. Diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest in the Isthmus of Tehuantepec, Oaxaca, Mexico

    Directory of Open Access Journals (Sweden)

    Malinalli Cortés-Marcial

    2014-12-01

    Full Text Available The use of camera traps and mammal track search are complementary methods to monitoring species of which is not well documented their natural history, as in the case of medium and large mammals. To ensure its conservation and good management, it is necessary to generate information about the structure of the community and their populations. The objective of the present study was to estimate the diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest located in the Isthmus of Tehuantepec, Oaxaca, Mexico. Samplings were conducted in three month intervals, from September 2011 to May 2013. We used photographic-sampling and track search, two complementary sampling methods. For photographic-sampling, 12 camera traps were placed covering an area of 60km², while for the tracks search a monthly tour of four line-transect surveys of three kilometers length each was undertaken. We obtained a total of 344 pictures with 5 292 trap-days total sampling effort; in addition, 187 track records in a total of 144km. With both methods we registered 21 species of mammals, in 13 families and seven orders, and five species resulted in new records to the area. The diversity index of Shannon-Wiener obtained with the method of tracks was H´=2.41, while the most abundant species were Urocyon cinereoargenteus (IAR=0.23 and Pecari tajacu (IAR=0.20. By the method of trap the most abundant species were P. tajacu (IAR=2.62 and Nasua narica (IAR=1.28. In terms of patterns of activity P. tajacu, N. narica and Odocoileus virginianus were primarily diurnal species; Canis latrans and Leopardus pardalis did not show preference for any schedule in particular, and Didelphis virginiana and Dasypus novemcinctus preferred to have nocturnal activity. This information can be of help to the creation of programs of management and conservation of mammals of medium and large in the Isthmus of Tehuantepec, Oaxaca, México. Rev. Biol. Trop

  13. [Diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest in the Isthmus of Tehuantepec, Oaxaca, Mexico].

    Science.gov (United States)

    Cortés-Marcial, Malinalli; Briones-Salas, Miguel

    2014-12-01

    The use of camera traps and mammal track search are complementary methods to monitoring species of which is not well documented their natural history, as in the case of medium and large mammals. To ensure its conservation and good management, it is necessary to generate information about the structure of the community and their populations. The objective of the present study was to estimate the diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest located in the Isthmus of Tehuantepec, Oaxaca, Mexico. Samplings were conducted in three month intervals, from September 2011 to May 2013. We used photographic-sampling and track search, two complementary sampling methods. For photographic-sampling, 12 camera traps were placed covering an area of 60 km2, while for the tracks search a monthly tour of four line-transect surveys of three kilometers length each was undertaken. We obtained a total of 344 pictures with 5292 trap-days total sampling effort; in addition, 187 track records in a total of 144 km. With both methods we registered 21 species of mammals, in 13 families and seven orders, and five species resulted in new records to the area. The diversity index of Shannon-Wiener obtained with the method of tracks was H' = 2.41, while the most abundant species were Urocyon cinereoargen- teus (IAR = 0.23) and Pecari tajacu (IAR = 0.20). By the method of trap the most abundant species were P. tajacu (IAR = 2.62) and Nasua narica (IAR = 1.28). In terms of patterns of activity P. tajacu, N. narica and Odocoileus virginianus were primarily diurnal species; Canis latrans and Leopardus pardalis did not show preference for any schedule in particular, and Didelphis virginiana and Dasypus novemcinctus preferred to have nocturnal activity. This information can be of help to the creation of programs of management and conservation of mam- mals of medium and large in the Isthmus of Tehuantepec, Oaxaca, México.

  14. Dwarf Tiller1, a Wuschel-related homeobox transcription factor, is required for tiller growth in rice.

    Directory of Open Access Journals (Sweden)

    Wenfei Wang

    2014-03-01

    Full Text Available Unlike many wild grasses, domesticated rice cultivars have uniform culm height and panicle size among tillers and the main shoot, which is an important trait for grain yield. However, the genetic basis of this trait remains unknown. Here, we report that Dwarf Tiller1 (DWT1 controls the developmental uniformity of the main shoot and tillers in rice (Oryza sativa. Most dwt1 mutant plants develop main shoots with normal height and larger panicles, but dwarf tillers bearing smaller panicles compared with those of the wild type. In addition, dwt1 tillers have shorter internodes with fewer and un-elongated cells compared with the wild type, indicating that DWT1 affects cell division and cell elongation. Map-based cloning revealed that DWT1 encodes a Wuschel-related homeobox (WOX transcription factor homologous to the Arabidopsis WOX8 and WOX9. The DWT1 gene is highly expressed in young panicles, but undetectable in the internodes, suggesting that DWT1 expression is spatially or temporally separated from its effect on the internode growth. Transcriptomic analysis revealed altered expression of genes involved in cell division and cell elongation, cytokinin/gibberellin homeostasis and signaling in dwt1 shorter internodes. Moreover, the non-elongating internodes of dwt1 are insensitive to exogenous gibberellin (GA treatment, and some of the slender rice1 (slr1 dwt1 double mutant exhibits defective internodes similar to the dwt1 single mutant, suggesting that the DWT1 activity in the internode elongation is directly or indirectly associated with GA signaling. This study reveals a genetic pathway synchronizing the development of tillers and the main shoot, and a new function of WOX genes in balancing branch growth in rice.

  15. DWARF TILLER1, a WUSCHEL-Related Homeobox Transcription Factor, Is Required for Tiller Growth in Rice

    Science.gov (United States)

    Wang, Wenfei; Li, Gang; Zhao, Jun; Chu, Huangwei; Lin, Wenhui; Zhang, Dabing; Wang, Zhiyong; Liang, Wanqi

    2014-01-01

    Unlike many wild grasses, domesticated rice cultivars have uniform culm height and panicle size among tillers and the main shoot, which is an important trait for grain yield. However, the genetic basis of this trait remains unknown. Here, we report that DWARF TILLER1 (DWT1) controls the developmental uniformity of the main shoot and tillers in rice (Oryza sativa). Most dwt1 mutant plants develop main shoots with normal height and larger panicles, but dwarf tillers bearing smaller panicles compared with those of the wild type. In addition, dwt1 tillers have shorter internodes with fewer and un-elongated cells compared with the wild type, indicating that DWT1 affects cell division and cell elongation. Map-based cloning revealed that DWT1 encodes a WUSCHEL-related homeobox (WOX) transcription factor homologous to the Arabidopsis WOX8 and WOX9. The DWT1 gene is highly expressed in young panicles, but undetectable in the internodes, suggesting that DWT1 expression is spatially or temporally separated from its effect on the internode growth. Transcriptomic analysis revealed altered expression of genes involved in cell division and cell elongation, cytokinin/gibberellin homeostasis and signaling in dwt1 shorter internodes. Moreover, the non-elongating internodes of dwt1 are insensitive to exogenous gibberellin (GA) treatment, and some of the slender rice1 (slr1) dwt1 double mutant exhibits defective internodes similar to the dwt1 single mutant, suggesting that the DWT1 activity in the internode elongation is directly or indirectly associated with GA signaling. This study reveals a genetic pathway synchronizing the development of tillers and the main shoot, and a new function of WOX genes in balancing branch growth in rice. PMID:24625559

  16. Relative abundance of deformed wing virus, Varroa destructor virus 1, and their recombinants in honey bees (Apis mellifera) assessed by kmer analysis of public RNA-Seq data

    Science.gov (United States)

    Cornman, Robert S.

    2017-01-01

    Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids were observed in recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.

  17. [Construction of Corynebacterium crenatum AS 1.542 δ argR and analysis of transcriptional levels of the related genes of arginine biosynthetic pathway].

    Science.gov (United States)

    Chen, Xuelan; Tang, Li; Jiao, Haitao; Xu, Feng; Xiong, Yonghua

    2013-01-04

    ArgR, coded by the argR gene from Corynebacterium crenatum AS 1.542, acts as a negative regulator in arginine biosynthetic pathway. However, the effect of argR on transcriptional levels of the related biosynthetic genes has not been reported. Here, we constructed a deletion mutant of argR gene: C. crenatum AS 1.542 Delta argR using marker-less knockout technology, and compared the changes of transcriptional levels of the arginine biosynthetic genes between the mutant strain and the wild-type strain. We used marker-less knockout technology to construct C. crenatum AS 1.542 Delta argR and analyzed the changes of the relate genes at the transcriptional level using real-time fluorescence quantitative PCR. C. crenatum AS 1.542 Delta argR was successfully obtained and the transcriptional level of arginine biosynthetic genes in this mutant increased significantly with an average of about 162.1 folds. The arginine biosynthetic genes in C. crenatum are clearly controlled by the negative regulator ArgR. However, the deletion of this regulator does not result in a clear change in arginine production in the bacteria.

  18. Morphological variability, spatial distribution and abundance of Helicostomella species (Ciliophora: Tintinnina in relation to environmental factors (Argentine shelf; 40-55°S

    Directory of Open Access Journals (Sweden)

    Luciana F. Santoferrara

    2009-12-01

    Full Text Available For the first time a taxonomic and ecological study of species belonging to Helicostomella was performed over a mesoscale spatial distribution by examining ca. 3000 loricae collected in Argentine shelf waters during the austral autumn. Microscopic and statistical analysis revealed that the general shape and the oral diameter remained practically constant in the whole area surveyed, despite a continuous length fluctuation of ca. 300 µm, which includes the entire range present in eight previously reported species. Consequently, we consider that the genus may be represented only by H. subulata, whose strong fluctuations in length (mostly attributed to an increase in the collar length, density and biomass seem to respond to temperature, food availability and front-related processes. In Buenos Aires coastal waters associated with a quasi permanent estuarine front (40-40.5°S, mixed conditions would favour moderate abundances of long loricae, whereas in northern (42.5-45.5°S and southern (46-54.5°S Patagonian waters, high (103 ind. L-1 and low (< 5 ind. L-1 densities of short loricae seem to be a consequence of stratification and encystment, respectively. The non-occurrence of the species at 41-42°S, together with a three-fold reduction in length-related parameters between specimens from Buenos Aires and Patagonian waters, suggests a disjunct distribution.

  19. Molecular Characterization of a Leaf Senescence-Related Transcription Factor BrWRKY75 of Chinese Flowering Cabbage

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    Xiaoli Tan

    2016-09-01

    Full Text Available WRKY is a plant-specific transcription factor (TF involved in the regulation of many biological processes; however, its role in leaf senescence of leafy vegetables remains unknown. In the present work, a WRKY TF, termed BrWRKY75 was isolated from Chinese flowering cabbage [Brassica rapa L. ssp. chinensis (L. Mokino var. utilis Tsen et Lee]. Analysis of deduced amino acid sequence and the phylogenetic tree showed that BrWRKY75 has high homology with WRKY75 from Brassica oleracea and Arabidopsis thaliana, and belongs to the II c sub-group. Sub-cellular localization and transcriptional activity analysis revealed that BrWRKY75 is a nuclear protein with transcriptional repression activity, and was up-regulated during leaf senescence. Electrophoretic mobility shift assay confirmed that BrWRKY75 directly bound to the W-box (TTGAC cis-element. Collectively, these results provide a basis for further investigation of the transcriptional regulation of Chinese flowering cabbage leaf senescence.

  20. Caenorhabditis elegans DAF-16/FOXO Transcription Factor and Its Mammalian Homologs Associate with Age-Related Disease

    NARCIS (Netherlands)

    Hesp, K.; Smant, G.; Kammenga, J.E.

    2015-01-01

    The insulin/IGF-1 signaling pathway is evolutionarily conserved and its function is mediated largely by FOXO transcription factors. Reduced insulin/IGF-1 signaling leads to translocation of FOXO proteins from the cytoplasm to the nucleus where they activate a set of genes that mediate oxidative

  1. Impact of nitrogen concentration on validamycin A production and related gene transcription in fermentation of Streptomyces hygroscopicus 5008.

    Science.gov (United States)

    Wei, Zhen-Hua; Bai, Linquan; Deng, Zixin; Zhong, Jian-Jiang

    2012-09-01

    Validamycin A (VAL-A) is an important and widely used agricultural antibiotic. In this study, statistical screening designs were applied to identify significant medium variables for VAL-A production and to find their optimal levels. The optimized medium caused 70% enhancement of VAL-A production. The difference between optimized medium and original medium suggested that low nitrogen source level might attribute to the enhancement of VAL-A production. The addition of different nitrogen sources to the optimized medium inhibited VAL-A production, which confirmed the importance of nitrogen concentration for VAL-A production. Furthermore, differences in structural gene transcription and enzyme activity between the two media were assayed. The results showed that lower nitrogen level in the optimized medium could regulate VAL-A production in gene transcriptional level. Our previous study indicated that the transcription of VAL-A structural genes could be enhanced at elevated temperature. In this work, the increased fermentation temperature from 37 to 42 °C with the optimized medium enhanced VAL-A production by 39%, which testified to the importance of structural gene transcription in VAL-A production. The information is useful for further VAL-A production enhancement.

  2. Relative gene transcription and pathogenicity of enterohemorrhagic Escherichia coli after long-term adaptation to acid and salt stress

    DEFF Research Database (Denmark)

    Olesen, Inger; Jespersen, Lene

    2010-01-01

    Relative gene transcription and virulence potential, as measured by a Caco-2 adhesion assay, were investigated for three enterohemorrhagic Escherichia coli (EHEC) strains after long-term adaptation for 24 h to acid (BHI pH 5.5) and salt (BHI 4.5% (w/v) NaCl) stress. Five virulence genes (eae, lpf...... compared to EDL933 (O157:H7, raw hamburger). Long-term adaptation to salt stress significantly increased the adhesion of all three EHEC strains to Caco-2 compared to the non-stressed controls. The present study shows that long-term adaptation to food related stress factors such as acid and salt is capable...... of changing the relative transcription of important virulence and stress response genes and increasing the virulence potential as measured by adhesion to the human colonic epithelial cell line, Caco-2....

  3. Brassinosteroids-Induced Systemic Stress Tolerance was Associated with Increased Transcripts of Several Defence-Related Genes in the Phloem in Cucumis sativus.

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    Pingfang Li

    Full Text Available Brassinosteroids (BRs, a group of naturally occurring plant steroidal compounds, are essential for plant growth, development and stress tolerance. Recent studies showed that BRs could induce systemic tolerance to biotic and abiotic stresses; however, the molecular mechanisms by which BRs signals lead to responses in the whole plant are largely unknown. In this study, 24-epibrassinosteroid (EBR-induced systemic tolerance in Cucumis sativus L. cv. Jinyan No. 4 was analyzed through the assessment of symptoms of photooxidative stress by chlorophyll fluorescence imaging pulse amplitude modulation. Expression of defense/stress related genes were induced in both treated local leaves and untreated systemic leaves by local EBR application. With the suppressive subtractive hybridization (SSH library using cDNA from the phloem sap of EBR-treated plants as the tester and distilled water (DW-treated plants as the driver, 14 transcripts out of 260 clones were identified. Quantitative Real Time-Polymerase Chain Reaction (RT-qPCR validated the specific up-regulation of these transcripts. Of the differentially expressed transcripts with known functions, transcripts for the selected four cDNAs, which encode an auxin-responsive protein (IAA14, a putative ankyrin-repeat protein, an F-box protein (PP2, and a major latex, pathogenesis-related (MLP-like protein, were induced in local leaves, systemic leaves and roots after foliar application of EBR onto mature leaves. Our results demonstrated that EBR-induced systemic tolerance is accompanied with increased transcript of genes in the defense response in other organs. The potential role of phloem mRNAs as signaling components in mediating BR-regulated systemic resistance is discussed.

  4. Abundance, biomass and caloric content of Chukchi Sea bivalves and association with Pacific walrus (Odobenus rosmarus divergens) relative density and distribution in the northeastern Chukchi Sea

    Science.gov (United States)

    Young, Jordann K.; Black, Bryan A.; Clarke, Janet T.; Schonberg, Susan V.; Dunton, Kenneth H.

    2017-10-01

    The northeastern Chukchi Sea is a shallow subarctic shelf ecosystem that supports a substantial benthic infaunal community of which bivalves are a major component. We assessed the patterns in population abundance, biomass, and caloric content of ten dominant bivalve taxa in relation to the distribution of the upper trophic level consumer Pacific walrus (Odobenus rosmarus divergens). Bivalves were collected over four cruises in the northeastern Chukchi Sea (2009, 2010, 2012, 2013). Our samples were largely dominated by calorie-dense, deposit-feeding species, including Macoma spp., Ennucula tenuis, Nuculana spp. and Yoldia spp. Weight-frequency distributions were strongly right-skewed for most taxa, though some showed evidence of a bimodal distribution. Caloric densities as measured through bomb calorimetry significantly differed among taxa (ANOVA F = 32.57, df = 9, p-valueanimal wet weight was found to be a reliable predictor of whole animal caloric content. Bivalve populations and peak caloric densities were centered on and to the southeast of Hanna Shoal, which coincided with peak Pacific walrus relative density (walruses per km surveyed) from July through October. Significant differences in mean caloric values were found between areas with and without walruses present (student's t-test, t=-2.9088, df = 252.24, p-value = 0.003952), as well as between areas with low and high walrus relative densities in the pooled annual dataset and in each individual month except October (ANOVA, p-value<0.05). The high-calorie deposit feeders that dominate these bivalve communities preferentially consume food sources, such as sea ice algae, that are likely to be affected by shifting sea ice dynamics. As such, continued warming has the potential to alter bivalve communities in the northeastern Chukchi Sea, which may have profound implications for upper trophic levels.

  5. Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

    Science.gov (United States)

    Marsh, T. L.; Reich, C. I.; Whitelock, R. B.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1994-01-01

    The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.

  6. Relative abundance of 'Bacillus' spp., surfactant-associated bacterium present in a natural sea slick observed by satellite SAR imagery over the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Kathryn Lynn Howe

    2018-01-01

    Full Text Available The damping of short gravity-capillary waves (Bragg waves due to surfactant accumulation under low wind speed conditions results in the formation of natural sea slicks. These slicks are detectable visually and in synthetic aperture radar satellite imagery. Surfactants are produced by natural life processes of many marine organisms, including bacteria, phytoplankton, seaweed, and zooplankton. In this work, samples were collected in the Gulf of Mexico during a research cruise on the R/V 'F.G. Walton Smith' to evaluate the relative abundance of 'Bacillus' spp., surfactant-associated bacteria, in the sea surface microlayer compared to the subsurface water at 0.2 m depth. A method to reduce potential contamination of microlayer samples during their collection on polycarbonate filters was implemented and advanced, including increasing the number of successive samples per location and changing sample storage procedures. By using DNA analysis (real-time polymerase chain reaction to target 'Bacillus' spp., we found that in the slick areas, these surfactant-associated bacteria tended to reside mostly in subsurface waters, lending support to the concept that the surfactants they may produce move to the surface where they accumulate under calm conditions and enrich the sea surface microlayer.

  7. Permafrost response to increasing Arctic shrub abundance depends on the relative influence of shrubs on local soil cooling versus large-scale climate warming

    International Nuclear Information System (INIS)

    Lawrence, David M; Swenson, Sean C

    2011-01-01

    Deciduous shrub abundance is increasing across the Arctic in response to climatic warming. In a recent field manipulation experiment in which shrubs were removed from a plot and compared to a control plot with shrubs, Blok et al (2010 Glob. Change Biol. 16 1296–305) found that shrubs protect the ground through shading, resulting in a ∼ 9% shallower active layer thickness (ALT) under shrubs compared to grassy-tundra, which led them to argue that continued Arctic shrub expansion could mitigate future permafrost thaw. We utilize the Community Land Model (CLM4) coupled to the Community Atmosphere Model (CAM4) to evaluate this hypothesis. CLM4 simulates shallower ALT (∼− 11 cm) under shrubs, consistent with the field manipulation study. However, in an idealized pan-Arctic + 20% shrub area experiment, atmospheric heating, driven mainly by surface albedo changes related to protrusion of shrub stems above the spring snowpack, leads to soil warming and deeper ALT (∼+ 10 cm). Therefore, if climate feedbacks are considered, shrub expansion may actually increase rather than decrease permafrost vulnerability. When we account for blowing-snow redistribution from grassy-tundra to shrubs, shifts in snowpack distribution in low versus high shrub area simulations counter the climate warming impact, resulting in a grid cell mean ALT that is unchanged. These results reinforce the need to consider vegetation dynamics and blowing-snow processes in the permafrost thaw model projections.

  8. Distribuição e abundância relativa de bagres marinhos (Siluriformes, Ariidae na Baía de Sepetiba, Rio de Janeiro Distribution and relative abundance of the marine catfish (Siluriformes, Ariidae in Sepetiba Bay, Rio de Janeiro

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    Márcia Cristina Costa de Azevedo

    1998-12-01

    Full Text Available Marine catfish (Ariidae are abundant resources in otter trawl fisheries carried out at Sepetiba Bay, Rio de Janeiro (Lat. 22º54, 23º04'S; Long. 43º34 44º10'W. Relative abundance and distribution were assessed, based in 158 fishing sampling at seven sites in the Bay, between July-1993 e June-1996. Five species were recorded in the following abundance rank order: Genidens genidens (Valenciennes, 1839, Caihorops spixii (Agassiz,1829, Sciadeichthys lunisculis (Valenciennes, 1840, Nelunia barba (Lacépède, 1803, and Bagre marinus (Mitchill, 1814, the latter have been caught in only two samples. Marine catfish showed higher abundance in the inner Bay, with indication of spatial segregation. G genidens was abundant in ali sites of lhe inner Bay, C. spixii e N. barba, near to rivers mouths, andS lunisculis, being widespread in ali studied area. Sazonality was not evident, with few exceplions in some of the three annual cycles; G. genidens and S. luniscutis were more abundant in biomass in summer 1994/95 (G. genidens and 1993/94 (S. luniscutis. G. genidens e N. barba show higher abundance (CPUE and biomass between July-93 and June-95 and C. spixii e S. luniscutis between July-95 and June-96. Total association index indicates a overall positive association among ali species, with. higher Jaccard and Sorensen similarities coefficient for the pairs C. spixii/G. genidens, G. genidens/S. luniscutis, e C. spixii/S. luniscutis. Pearson linear correlation and Sperman rank indicate that G. genidens and N. barba are inversely correlated to C. spixii and S. luniscutis. Spatial segregation strategy may be explaining the coexistence of the marine catfish at Sepetiba Bay.

  9. Is Ammonification Rate in Marine Sediment Related to Plankton Composition and Abundance? A Time-series Study in Villefranche Bay (NW Mediterranean)

    Science.gov (United States)

    Fernex, François E.; Braconnot, Jean-Claude; Dallot, Serge; Boisson, Michel

    1996-09-01

    Observations were made near Cap Ferrat (Station B, about 80 m in water depth) France, in the water column and in the sediment, in order to evaluate to what extent variations in the ammonia and nitrate concentrations of the sediments are related to plankton population abundance and composition. Nitrate, nitrite, ammonia and chlorophyll awere measured several times during 1987 to 1989, at two depths (1 and 40 m). Copepods and salps in the upper 75 m of the water column were counted several times a week from 1987 to 1990. Ammonia and nitrate concentrations and ammonification rate were determined in the underlying sediments. During Spring 1987, phytoplankton biomass showed a maximum at the end of March; copepod populations increased regularly till the end of April, and salps increased from this time to the end of May. These populations were not so well developed during Spring 1988 and 1989. During the blooms, salp were mainly represented by Thalia democratica. The biomass of phytoplankton and zooplankton was low in summer. The sequence suggests that the copepod decline was related to reduced food levels after the phytoplankton decline. Salp population growth was not at the expense of phytoplankton and it can be assumed that the salp fed on other material. In 1987 and 1988, maximum organic nitrogen concentration in the bottom sediment and maximum ammonification rate directly followed the salp spring bloom. In 1987, the highest ammonification rate measured in the surficial sediment (0-2 cm) reached 0·05 μ M cm 3day -1(in June). In 1990, the rate exceeded 0·1 μM cm -3 day -1during an important salp bloom. Therefore, it seems that the sinking of salp fecal pellets plays an important part in the transfer of organic matter to the bottom, and microbial activity in the surficial sediment leads to mineralization of a great part of the organic nitrogen quickly after its deposition.

  10. Oxygen abundances in halo stars

    Science.gov (United States)

    Bessell, Michael S.; Sutherland, Ralph S.; Ruan, Kui

    1991-12-01

    The present study determines the oxygen abundance for a sample of metal-poor G dwarfs by analysis of OH lines between 3080 and 3200 A and the permitted high-excitation far-red O I triple. The oxygen abundances determined from the low-excitation OH lines are up to 0.55 dex lower than those measured from the high-excitation O I lines. The abundances for the far-red O I triplet lines agree with those rederived from Abia and Rebolo (1989), and the abundances from the OH lines in dwarfs and giants are in agreement with the rederived O abundances of Barbuy (1988) and others from the forbidden resonance O I line. Because the chi = 0.1.7 eV OH lines are formed in the same layers as the majority of Fe, Ti, and other neutral metal lines used for abundance analyses, it is argued that the OH lines and the forbidden O I line yield the true oxygen abundances relative to the metals.

  11. Relative transcription of Listeria monocytogenes virulence genes in liver pâtés with varying NaCl content

    DEFF Research Database (Denmark)

    Olesen, Inger; Thorsen, Line; Jespersen, Lene

    2010-01-01

    three liver pâtés with reduced NaCl content of which one also has been supplied with organic acids (Ca-acetate and Ca-lactate). The three strains (EGD-e: reference strain; O57: more NaCl sensitive; 6896: more NaCl tolerant) were selected out of twelve strains based on their growth in BHI broth adjusted......B for both O57 and 6896 were significantly higher when the strains were grown in BHI compared to the standard liver pâté. Reducing the NaCl content of the standard liver pâté did not change relative transcription levels of prfA, inlA, sigB or clpC (except for prfA in O57 and sigB in 6896). However......, the presence of Ca-acetate and Ca-lactate induced relative transcription of the stress response gene, clpC, for all three strains. This study demonstrates that relative microbial gene transcription can be measured in complex food matrices and points to the need for designing experimental set-ups in real food...

  12. Multiple marker abundance profiling

    DEFF Research Database (Denmark)

    Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna

    2017-01-01

    proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment...

  13. The ascorbate peroxidase APX1 is a direct target of a zinc finger transcription factor ZFP36 and a late embryogenesis abundant protein OsLEA5 interacts with ZFP36 to co-regulate OsAPX1 in seed germination in rice.

    Science.gov (United States)

    Huang, Liping; Jia, Jing; Zhao, Xixi; Zhang, MengYao; Huang, Xingxiu; E Ji; Ni, Lan; Jiang, Mingyi

    2018-01-01

    Seed germination is a vital developmental process. Abscisic acid (ABA) is an essential repressor of seed germination, while ROS (reactive oxygen species) also plays a vital role in regulating seed germination. ABA could inhibit the production of ROS in seed germination, but the mechanism of ABA reduced ROS production in seed germination was hitherto unknown. Here, by ChIP (chromatin immunoprecipitation)-seq, we found that ZFP36, a rice zinc finger transcription factor, could directly bind to the promoter of OsAPX1, coding an ascorbate peroxidase (APX) which has the most affinity for H 2 O 2 (substrate; a type of ROS), and act as a transcriptional activator of OsAPX1 promoter. Moreover, ZFP36 could interact with a late embryogenesis abundant protein OsLEA5 to co-regulate the promoter activity of OsAPX1. The seed germination is highly inhibited in ZFP36 overexpression plants under ABA treatment, while an RNA interference (RNAi) mutant of OsLEA5 rice seeds were less sensitive to ABA, and exogenous ASC (ascorbate acid) could alleviate the inhibition induced by ABA. Thus, our conclusion is that OsAPX1 is a direct target of ZFP36 and OsLEA5 could interact with ZFP36 to co-regulate ABA-inhibited seed germination by controlling the expression of OsAPX1. Copyright © 2017. Published by Elsevier Inc.

  14. Land use type significantly affects microbial gene transcription in soil.

    Science.gov (United States)

    Nacke, Heiko; Fischer, Christiane; Thürmer, Andrea; Meinicke, Peter; Daniel, Rolf

    2014-05-01

    Soil microorganisms play an essential role in sustaining biogeochemical processes and cycling of nutrients across different land use types. To gain insights into microbial gene transcription in forest and grassland soil, we isolated mRNA from 32 sampling sites. After sequencing of generated complementary DNA (cDNA), a total of 5,824,229 sequences could be further analyzed. We were able to assign nonribosomal cDNA sequences to all three domains of life. A dominance of bacterial sequences, which were affiliated to 25 different phyla, was found. Bacterial groups capable of aromatic compound degradation such as Phenylobacterium and Burkholderia were detected in significantly higher relative abundance in forest soil than in grassland soil. Accordingly, KEGG pathway categories related to degradation of aromatic ring-containing molecules (e.g., benzoate degradation) were identified in high abundance within forest soil-derived metatranscriptomic datasets. The impact of land use type forest on community composition and activity is evidently to a high degree caused by the presence of wood breakdown products. Correspondingly, bacterial groups known to be involved in lignin degradation and containing ligninolytic genes such as Burkholderia, Bradyrhizobium, and Azospirillum exhibited increased transcriptional activity in forest soil. Higher solar radiation in grassland presumably induced increased transcription of photosynthesis-related genes within this land use type. This is in accordance with high abundance of photosynthetic organisms and plant-infecting viruses in grassland.

  15. Magellanic Clouds Cepheids: Thorium Abundances

    Directory of Open Access Journals (Sweden)

    Yeuncheol Jeong

    2018-03-01

    Full Text Available The analysis of the high-resolution spectra of 31 Magellanic Clouds Cepheid variables enabled the identification of thorium lines. The abundances of thorium were found with spectrum synthesis method. The calculated thorium abundances exhibit correlations with the abundances of other chemical elements and atmospheric parameters of the program stars. These correlations are similar for both Clouds. The correlations of iron abundances of thorium, europium, neodymium, and yttrium relative to the pulsational periods are different in the Large Magellanic Cloud (LMC and the Small Magellanic Cloud (SMC, namely the correlations are negative for LMC and positive or close to zero for SMC. One of the possible explanations can be the higher activity of nucleosynthesis in SMC with respect to LMC in the recent several hundred million years.

  16. LIFE CYCLE, DISTRIBUTION AND ABUNDANCE OF CARCINONEMERTES EPIALTI, A NEMERTEAN EGG PREDATOR OF THE SHORE CRAB, HEMIGRAPSUS OREGONENSIS, IN RELATION TO HOST SIZE, REPRODUCTION AND MOLT CYCLE.

    Science.gov (United States)

    Kuris, Armand M

    1978-02-01

    1. The geographic range of Carcinonemertes epialti has been greatly extended. The worms are found from Bahia San Quintin, Baja California, Mexico, to Page's Lagoon, Vancouver Island, British Columbia, Canada. 2. New host records for C. epialti include H. oregonensis, and H. nudus. It is rare on its type host Pugettia producta. Specimens of Carcinonemertes of uncertain affinities are also found on Cancer antennarius, C. anthonyi and C. productus. 3. Carcinonemertes epialti adults are egg predators on ovigerous hosts. Growth, demography and abundance are described in relation to the embryogenic stage of the host brood at Bodega Harbor, California. 4. Nonfeeding juveniles are ensheathed on individuals of both host sexes over 8.0 mm carapace width. 5. Transmission experiments show that contact transfer of juvenile nemerteans from males to other hosts may occur. 6. The percentage of infestation and mean density peak in autumn on H. oregonensis at Bodega Harbor. 7. Ovigerous female hosts are more frequently infested with C. epialti, particularly at small host sizes, than are male or nonovigerous female hosts at Bodega Harbor. However, average worm density on ovigerous females is low. 8. Mean density of C. epialti rises through late postmolt, declines during intermolt and rebuilds to a high level in late premolt H. oregonensisfrom Bodega Harbor. 9. Large crabs have a higher percentage of infestations and mean densities per infection than do small crabs. Nemerteans are more frequently found in the sternal-abdominal furrow and less frequently in the limb axillae on large crabs. 10. A model of C. epialti transmission and site occupancy is proposed, incorporating the influence of host size, sex, reproductive state, embryogenesis, molt cycle stage and molt cycle duration of H. oregonensis at Bodega Harbor. Site availability increases with host size. At higher densities the juvenile nemerteans increasingly occupy less preferred sites. Transferral of juvenile nemerteans occurs

  17. High Relative Abundance of Biofuel Sourced Ethanol in Precipitation in the US and Brazil Determined Using Compound Specific Stable Carbon Isotopes

    Science.gov (United States)

    Shimizu, M. S.; Felix, J. D. D.; Casas, M.; Avery, G. B., Jr.; Kieber, R. J.; Mead, R. N.; Willey, J. D.; Lane, C.

    2017-12-01

    Ethanol biofuel production and consumption have increased exponentially over the last two decades to help reduce greenhouse gas emissions. Currently, 85% of global ethanol production and consumption occurs in the US and Brazil. Increasing biofuel ethanol usage in these two countries enhances emissions of uncombusted ethanol to the atmosphere contributing to poor air quality. Although measurements of ethanol in the air and the precipitation reveal elevated ethanol concentrations in densely populated cities, other sources such as natural vegetation can contribute to emission to the atmosphere. Previous modeling studies indicated up to 12% of atmospheric ethanol is from anthropogenic emissions. Only one gas phase study in southern Florida attempted to constrain the two sources through direct isotopic measurements. The current study used a stable carbon isotope method to constrain sources of ethanol in rainwater from the US and Brazil. A method was developed using solid phase microextraction (SPME) with subsequent analysis by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). Stable carbon isotope signatures (δ13C) of vehicle ethanol emission sources for both the US (-9.8‰) and Brazil (-12.7‰) represented C4 plants as feedstock (corn and sugarcane) for biofuel production. An isotope mixing model using biofuel from vehicles (C4 plants) and biogenic (C3 plants) end-members was implemented to estimate ethanol source apportionment in the rain. We found that stable carbon isotope ratio of ethanol in the rain ranged between -22.6‰ and -12.7‰. Our results suggest that the contribution of biofuel to atmospheric ethanol can be higher than previously estimated. As biofuel usage increasing globally, it is essential to determine the relative abundance of anthropogenic ethanol in other areas of the world.

  18. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein.

    Science.gov (United States)

    Bielohuby, Maximilian; Menhofer, Dominik; Kirchner, Henriette; Stoehr, Barbara J M; Müller, Timo D; Stock, Peggy; Hempel, Madlen; Stemmer, Kerstin; Pfluger, Paul T; Kienzle, Ellen; Christ, Bruno; Tschöp, Matthias H; Bidlingmaier, Martin

    2011-01-01

    Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, which only differed in the relative abundance of fat and protein (percentages of fat/protein in dry matter: LC-75/10; LC-65/20; LC-55/30). We subsequently measured body composition by nuclear magnetic resonance (NMR), analyzed blood chemistry and urine acetone content, evaluated gene expression changes of key ketogenic and gluconeogenic genes, and measured energy expenditure (EE) and locomotor activity (LA) during the first 4 days and after 3 wk on the respective diets. Compared with chow, rats fed with LC-75/10, LC-65/20, and LC-55/30 gained significantly less body weight. Reductions in body weight were mainly due to lower lean body mass and paralleled by significantly increased fat mass. Levels of β-hydroxybutyate were significantly elevated feeding LC-75/10 and LC-65/20 but decreased in parallel to reductions in dietary fat. Acetone was about 16-fold higher with LC-75/10 only (P ketosis. LC-HFDs must be high in fat, but also low in protein contents to be clearly ketogenic. Independent of the macronutrient composition, LC-HFD-induced weight loss is not due to increased EE and LA.

  19. Comparative transcriptional and translational analysis of leptospiral outer membrane protein expression in response to temperature.

    Science.gov (United States)

    Lo, Miranda; Cordwell, Stuart J; Bulach, Dieter M; Adler, Ben

    2009-12-08

    Leptospirosis is a global zoonosis affecting millions of people annually. Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. Past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. However, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. Given the abundance of post-transcriptional expression control mechanisms, this finding highlighted the importance of global protein analysis systems. To complement our previous transcription study, we evaluated differences in the proteins of the leptospiral outer membrane fraction in response to temperature upshift. Outer membrane protein-enriched fractions from Leptospira interrogans grown at 30 degrees C or overnight upshift to 37 degrees C were isolated and the relative abundance of each protein was determined by iTRAQ analysis coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2-DLC/MS-MS). We identified 1026 proteins with 99% confidence; 27 and 66 were present at elevated and reduced abundance respectively. Protein abundance changes were compared with transcriptional differences determined from the microarray studies. While there was some correlation between the microarray and iTRAQ data, a subset of genes that showed no differential expression by microarray was found to encode temperature-regulated proteins. This set of genes is of particular interest as it is likely that regulation of their expression occurs post-transcriptionally, providing an opportunity to develop hypotheses about the molecular dynamics of the outer membrane of Leptospira in response to changing environments. This is the first study to compare transcriptional and translational responses to temperature shift in L. interrogans. The results thus provide an insight into the mechanisms used by L

  20. Abundance and size changes in the calcareous nannofossil Schizosphaerella - relation to sea-level and palaeoenvironmental change across the Sinemurian to earliest Toarcian of the Paris Basin

    Science.gov (United States)

    Peti, Leonie; Thibault, Nicolas

    2017-04-01

    The nannolith Schizosphaerella spp. was predominant in Early Jurassic calcareous nannofossil assemblages. Previous studies have shown a significant drop in abundance and mean size of Schizosphaerella during the early Toarcian Oceanic Anoxic Event which has been interpreted by some authors either as a calcification crisis due to increased pCO2, or as a response to increased nutrient availability, and/or greenhouse warming. Abundance and size changes in Schizosphaerella have here been thoroughly investigated throughout the upper Sinemurian to lowermost Toarcian (Early Jurassic) of the Sancerre-Couy core (Paris Basin) based on 116 samples. Our results show a stepwise rise in abundance of Schizosphaerella in the lower part of the investigated section and a rise in abundance of coccoliths during the major transgression of the Sinemurian, confirming that Schizosphaerella was better adapted to proximal areas than coccoliths. Mixture analysis of the biometric measurements show the existence of three populations of Schizosphaerella, interpreted as different morphotypes with different ecological affinities. Proximal, cool environmental conditions of the upper Sinemurian are associated with a dominance of the large population of Schizosphaerella. A dominance of the medium population, corresponds to cool surface waters and more distal conditions. Warm episodes are systematically linked to a dominance of the small population. Therefore we propose that the size response of Schizosphaerella throughout the Early Jurassic was rather a change in abundance of different ecophenotypes or (sub-) species of Schizosphaerella, with distinct affinities to temperature and proximal/distal environmental conditions.

  1. Species richness and relative species abundance of Nymphalidae (Lepidoptera in three forests with different perturbations in the North-Central Caribbean of Costa Rica

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    Carolyn Stephen

    2014-09-01

    Full Text Available Measurements of species richness and species abundance can have important implications for regulations and conservation. This study investigated species richness and abundance of butterflies in the family Nymphalidae at undisturbed, and disturbed habitats in Tirimbina Biological Reserve and Nogal Private Reserve, Sarapiquí, Costa Rica. Traps baited with rotten banana were placed in the canopy and the understory of three habitats: within mature forest, at a river/forest border, and at a banana plantation/forest border. In total, 71 species and 487 individuals were caught and identified during May and June 2011 and May 2013. Species richness and species abundance were found to increase significantly at perturbed habitats (p<0.0001, p<0.0001, respectively. The edge effect, in which species richness and abundance increase due to greater complementary resources from different habitats, could be one possible explanation for increased species richness and abundance. Rev. Biol. Trop. 62 (3: 919-928. Epub 2014 September 01.

  2. Decline in Proliferation and Immature Neuron Markers in the Human Subependymal Zone during Aging: Relationship to EGF- and FGF-related Transcripts

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    Christin Weissleder

    2016-11-01

    Full Text Available Neuroblasts exist within the human subependymal zone (SEZ; however, it is debated to what extent neurogenesis changes during normal aging. It is also unknown how precursor proliferation may correlate with the generation of neuronal and glial cells or how expression of growth factors and receptors may change throughout the adult lifespan. We provided evidence of dividing cells in the human SEZ in conjunction with a dramatic age-related decline (n=50; 21-103 years of mRNAs indicative of proliferating cells (Ki67 and immature neurons (doublecortin. Microglia mRNA (ionized calcium-binding adapter molecule 1 increased during aging, whereas transcript levels of stem/precursor cells (glial fibrillary acidic protein delta and achaete-scute homolog 1, astrocytes (vimentin and glial fibrillary acidic protein and oligodendrocytes (oligodendrocyte lineage transcription factor 2 remained stable. Epidermal growth factor receptor (EGFR and fibroblast growth factor 2 (FGF2 mRNAs increased throughout adulthood, while transforming growth factor alpha (TGFα, EGF, Erb-B2 receptor tyrosine kinase 4 (ErbB4 and FGF receptor 1 (FGFR1 mRNAs were unchanged across adulthood. Cell proliferation mRNA positively correlated with FGFR1 transcripts. Immature neuron and oligodendrocyte expression positively correlated with TGFα and ErbB4 mRNAs, whilst astrocyte transcripts positively correlated with EGF, FGF2 and FGFR1 mRNAs. Microglia mRNA positively correlated with EGF and FGF2 expression. Our findings indicate that neurogenesis in the human SEZ continues well into adulthood, although proliferation and neuronal differentiation may decline across adulthood. We suggest that mRNA expression of EGF- and FGF-related family members do not become limited during aging and may modulate neuronal and glial fate determination in the SEZ throughout human life.

  3. Relation of Transcriptional Factors to the Expression and Activity of Cytochrome P450 and UDP-Glucuronosyltransferases 1A in Human Liver: Co-Expression Network Analysis.

    Science.gov (United States)

    Zhong, Shilong; Han, Weichao; Hou, Chuqi; Liu, Junjin; Wu, Lili; Liu, Menghua; Liang, Zhi; Lin, Haoming; Zhou, Lili; Liu, Shuwen; Tang, Lan

    2017-01-01

    Cytochrome P450 (CYPs) and UDP-glucuronosyltransferases (UGTs) play important roles in the metabolism of exogenous and endogenous compounds. The gene transcription of CYPs and UGTs can be enhanced or reduced by transcription factors (TFs). This study aims to explore novel TFs involved in the regulatory network of human hepatic UGTs/CYPs. Correlations between the transcription levels of 683 key TFs and CYPs/UGTs in three different human liver expression profiles (n = 640) were calculated first. Supervised weighted correlation network analysis (sWGCNA) was employed to define hub genes among the selected TFs. The relationship among 17 defined TFs, CYPs/UGTs expression, and activity were evaluated in 30 liver samples from Chinese patients. The positive controls (e.g., PPARA, NR1I2, NR1I3) and hub TFs (NFIA, NR3C2, and AR) in the Grey sWGCNA Module were significantly and positively associated with CYPs/UGTs expression. And the cancer- or inflammation-related TFs (TEAD4, NFKB2, and NFKB1) were negatively associated with mRNA expression of CYP2C9/CYP2E1/UGT1A9. Furthermore, the effect of NR1I2, NR1I3, AR, TEAD4, and NFKB2 on CYP450/UGT1A gene transcription translated into moderate influences on enzyme activities. To our knowledge, this is the first study to integrate Gene Expression Omnibus (GEO) datasets and supervised weighted correlation network analysis (sWGCNA) for defining TFs potentially related to CYPs/UGTs. We detected several novel TFs involved in the regulatory network of hepatic CYPs and UGTs in humans. Further validation and investigation may reveal their exact mechanism of CYPs/UGTs regulation.

  4. Dataset on differential gene expression analysis for splenic transcriptome profiling and the transcripts related to six immune pathways in grass carp

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    Guoxi Li

    2017-02-01

    Full Text Available The data presented in this paper are related to the research article entitled “Transcriptome profiling of developing spleen tissue and discovery of immune-related genes in grass carp (Ctenopharyngodon idella” (Li et al. 2016 [1]. Please refer to this article for interpretation of the data. Data provided in this submission are comprised of the expression levels of unigenes, significantly differentially expressed genes(DEGs, significant enrichment GO term and KEGG pathway of DEGs, and information of the transcripts assigned to six immune pathways.

  5. Effects of HIF-1 inhibition by chetomin on hypoxia-related transcription and radiosensitivity in HT 1080 human fibrosarcoma cells

    International Nuclear Information System (INIS)

    Staab, Adrian; Einsele, Hermann; Flentje, Michael; Vordermark, Dirk; Loeffler, Jürgen; Said, Harun M; Diehlmann, Désirée; Katzer, Astrid; Beyer, Melanie; Fleischer, Markus; Schwab, Franz; Baier, Kurt

    2007-01-01

    Hypoxia-inducible factor-1 (HIF-1) overexpression has been linked to tumor progression and poor prognosis. We investigated whether targeting of HIF-1 using chetomin, a disrupter of the interaction of HIF-1 with the transcriptional coactivator p300, influences the radiosensitivity of hypoxic HT 1080 human fibrosarcoma cells. Optimal dose of chetomin was determined by EGFP-HRE gene reporter assay in stably transfected HT 1080 cells. Cells were assayed for expression of the hypoxia-inducible genes carbonic anhydrase 9 (CA9) and vascular endothelial growth factor (VEGF) by RT-PCR and for clonogenic survival after irradiation with 2, 5 or 10 Gy, under normoxic or hypoxic (0.1% O 2 , 12 h) conditions in the presence or absence of chetomin (150 nM, 12 h, pre-treatment of 4 h). Chetomin treatment significantly reduced CA9 and VEGF mRNA expression in hypoxic cells to 44.4 ± 7.2% and 39.6 ± 16.0%, respectively, of untreated hypoxic controls. Chetomin clearly reduced the modified oxygen enhancement ratio (OER') compared to untreated cells, from 2.02 to 1.27, from 1.86 to 1.22 and from 1.49 to 1.06 at the 50%, 37% and 10% clonogenic survival levels, respectively. HIF-1 inhibition by chetomin effectively reduces hypoxia-dependent transcription and radiosensitizes hypoxic HT 1080 human fibrosarcoma cells in vitro

  6. Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors.

    Science.gov (United States)

    Yokoyama, Katsushi; Ishijima, Sanae A; Clowney, Lester; Koike, Hideaki; Aramaki, Hironori; Tanaka, Chikako; Makino, Kozo; Suzuki, Masashi

    2006-01-01

    Feast/famine regulatory proteins comprise a diverse family of transcription factors, which have been referred to in various individual identifications, including Escherichia coli leucine-responsive regulatory protein and asparagine synthase C gene product. A full length feast/famine regulatory protein consists of the N-terminal DNA-binding domain and the C-domain, which is involved in dimerization and further assembly, thereby producing, for example, a disc or a chromatin-like cylinder. Various ligands of the size of amino acids bind at the interface between feast/famine regulatory protein dimers, thereby altering their assembly forms. Also, the combination of feast/famine regulatory protein subunits forming the same assembly is altered. In this way, a small number of feast/famine regulatory proteins are able to regulate a large number of genes in response to various environmental changes. Because feast/famine regulatory proteins are shared by archaea and eubacteria, the genome-wide regulation by feast/famine regulatory proteins is traceable back to their common ancestor, being the prototype of highly differentiated transcription regulatory mechanisms found in organisms nowadays.

  7. Distribution and abundance of the Lesser electric ray Narcine brasiliensis (Olfers, 1831 (Elasmobranchii: Narcinidae in southern Brazil in relation to environmental factors

    Directory of Open Access Journals (Sweden)

    Gabriel Maciel de Souza Vianna

    2009-06-01

    Full Text Available The distribution and abundance of the lesser electric ray, Narcine brasiliensis, was assessed based on bottom-trawl survey data collected off the coast of Rio Grande do Sul, southern Brazil. Between 1980 and 1984 and in 2005, 416 bottom trawl hauls were carried out at depths of 10-100 m. Narcine brasiliensis occurred mainly in waters with bottom temperature between 20 and 25ºC. Density of the species was higher between the depths of 10 and 20 m, during the summer and autumn. The seasonal pattern of N. brasiliensis in the shallow coastal water of Rio Grande do Sul reflects a southward migration in summer. This is conditioned by the southward advance of warmer and high-salinity Tropical Water of the Brazil Current In winter, the return or northward migration is a response to seasonal cooling of the coastal waters and to the northward advance of cold Coastal Water of lower salinity. The latitudinal gradient in density of N. brasiliensis was related to the latitudinal gradient in salinity of the bottom waters. This was caused by the freshwater runoff from the Patos Lagoon establishing a physical barrier to the occurrence of the species farther south than the city of Rio Grande.A distribuição e abundância da raia elétrica Narcine brasiliensis foi analisada com base em 416 lances de arrasto de fundo realizados entre as profundidades de 10- 100 m ao longo da costa do Rio Grande do Sul, em 1980-1984 e 2005. A espécie ocorreu prioritariamente em águas com temperatura de fundo entre 20 e 25ºC. A densidade de N. brasiliensis foi maior durante o verão e outono e entre as profundidades de 10 e 20 m. O padrão sazonal de densidade da espécie nas águas costeiras rasas do Rio Grande do Sul reflete uma migração no sentido norte-sul condicionada pelo avanço das águas quentes e de alta salinidade da Água Tropical da Corrente do Brasil em direção ao sul durante o verão. A redução sazonal da temperatura da água e o avanço da Água Costeira, de

  8. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

    Science.gov (United States)

    Fabisch, Maria; Beulig, Felix; Akob, Denise M.; Küsel, Kirsten

    2013-01-01

    We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic “Ferrovum myxofaciens” was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and “Ferrovum myxofaciens” revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

  9. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

    Directory of Open Access Journals (Sweden)

    Maria eFabisch

    2013-12-01

    Full Text Available We identified and quantified abundant iron-oxidizing bacteria (FeOB at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7, to moderately acidic (R2, pH 4.4, to slightly acidic (R3, pH 6.3 in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic ‘Ferrovum myxofaciens’ was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and ‘Ferrovum myxofaciens’ revealed that approximately 72% (R2 sediment and 37% (R3 sediment of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

  10. Transcriptional regulation by competing transcription factor modules.

    Directory of Open Access Journals (Sweden)

    Rutger Hermsen

    2006-12-01

    Full Text Available Gene regulatory networks lie at the heart of cellular computation. In these networks, intracellular and extracellular signals are integrated by transcription factors, which control the expression of transcription units by binding to cis-regulatory regions on the DNA. The designs of both eukaryotic and prokaryotic cis-regulatory regions are usually highly complex. They frequently consist of both repetitive and overlapping transcription factor binding sites. To unravel the design principles of these promoter architectures, we have designed in silico prokaryotic transcriptional logic gates with predefined input-output relations using an evolutionary algorithm. The resulting cis-regulatory designs are often composed of modules that consist of tandem arrays of binding sites to which the transcription factors bind cooperatively. Moreover, these modules often overlap with each other, leading to competition between them. Our analysis thus identifies a new signal integration motif that is based upon the interplay between intramodular cooperativity and intermodular competition. We show that this signal integration mechanism drastically enhances the capacity of cis-regulatory domains to integrate signals. Our results provide a possible explanation for the complexity of promoter architectures and could be used for the rational design of synthetic gene circuits.

  11. Induction of time-dependent oxidative stress and related transcriptional effects of perfluorododecanoic acid in zebrafish liver

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yang [Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Beijing 100101 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100080 (China); Wang Jianshe; Wei Yanhong; Zhang Hongxia; Xu Muqi [Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Beijing 100101 (China); Dai Jiayin [Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Datun Road, Beijing 100101 (China)], E-mail: daijy@ioz.ac.cn

    2008-09-29

    The effects of acute perfluorododecanoic acid (PFDoA) exposure on the induction of oxidative stress and alteration of mitochondrial gene expression were studied in the livers of female zebrafish (Danio rerio). Female zebrafish were exposed to PFDoA via a single intraperitoneal injection (0, 20, 40, or 80 {mu}g PFDoA/g body weight) and were then sacrificed 48 h, 96 h, or seven days post-PFDoA administration. PFDoA-treated fish exhibited histopathological liver damage, including swollen hepatocytes, vacuolar degeneration, and nuclei pycnosis. Glutathione (GSH) content and catalase (CAT) activity decreased significantly at 48 h post-injection while superoxide dismutase (SOD) activity was initially decreased at 48 h post-injection but was then elevated by seven days post-injection. The activity of glutathione peroxidase (GPx) increased at 48 h and seven days compared to control fish, although the increased level at seven days post-injection was decreased compared to the level at 48 h post-injection. Lipid peroxidation levels were increased at seven days post-injection, while no apparent induction was observed at 48 h or 96 h post-injection. The mRNA expression of medium-chain fatty acid dehydrogenase (MCAD) was induced, while the transcriptional expression of liver fatty acid binding protein (L-FABP), peroxisome proliferating activating receptor {alpha} (PPAR{alpha}), carnitine palmitoyl-transferase I (CPT-I), uncoupling protein 2 (UCP-2), and Bcl-2 were significantly inhibited. Furthermore, the transcriptional expression of peroxisomal fatty acyl-CoA oxidase (ACOX), very long-chain acyl-CoA dehydrogenase (VLCAD), long-chain acyl-CoA dehydrogenase (LCAD) did not exhibit significant changes following PFDoA treatment. No significant changes were noted in the transcriptional expression of genes involved in mitochondrial respiratory chain and ATP synthesis, including cytochrome c oxidase subunit I (COXI), NADH dehydrogenase subunit I (NDI), and ATP synthase F0 subunit 6

  12. Induction of time-dependent oxidative stress and related transcriptional effects of perfluorododecanoic acid in zebrafish liver

    International Nuclear Information System (INIS)

    Liu Yang; Wang Jianshe; Wei Yanhong; Zhang Hongxia; Xu Muqi; Dai Jiayin

    2008-01-01

    The effects of acute perfluorododecanoic acid (PFDoA) exposure on the induction of oxidative stress and alteration of mitochondrial gene expression were studied in the livers of female zebrafish (Danio rerio). Female zebrafish were exposed to PFDoA via a single intraperitoneal injection (0, 20, 40, or 80 μg PFDoA/g body weight) and were then sacrificed 48 h, 96 h, or seven days post-PFDoA administration. PFDoA-treated fish exhibited histopathological liver damage, including swollen hepatocytes, vacuolar degeneration, and nuclei pycnosis. Glutathione (GSH) content and catalase (CAT) activity decreased significantly at 48 h post-injection while superoxide dismutase (SOD) activity was initially decreased at 48 h post-injection but was then elevated by seven days post-injection. The activity of glutathione peroxidase (GPx) increased at 48 h and seven days compared to control fish, although the increased level at seven days post-injection was decreased compared to the level at 48 h post-injection. Lipid peroxidation levels were increased at seven days post-injection, while no apparent induction was observed at 48 h or 96 h post-injection. The mRNA expression of medium-chain fatty acid dehydrogenase (MCAD) was induced, while the transcriptional expression of liver fatty acid binding protein (L-FABP), peroxisome proliferating activating receptor α (PPARα), carnitine palmitoyl-transferase I (CPT-I), uncoupling protein 2 (UCP-2), and Bcl-2 were significantly inhibited. Furthermore, the transcriptional expression of peroxisomal fatty acyl-CoA oxidase (ACOX), very long-chain acyl-CoA dehydrogenase (VLCAD), long-chain acyl-CoA dehydrogenase (LCAD) did not exhibit significant changes following PFDoA treatment. No significant changes were noted in the transcriptional expression of genes involved in mitochondrial respiratory chain and ATP synthesis, including cytochrome c oxidase subunit I (COXI), NADH dehydrogenase subunit I (NDI), and ATP synthase F0 subunit 6 (ATPo6). These

  13. Relative abundance of small mammals in nest core areas and burned wintering areas of Mexican spotted owls in the Sacramento Mountains, New Mexico

    Science.gov (United States)

    Joseph L. Ganey; Sean C. Kyle; Todd A. Rawlinson; Darrell L. Apprill; James P Ward

    2014-01-01

    Mexican Spotted Owls (Strix occidentalis lucida) are common in older forests within their range but also persist in many areas burned by wildfire and may selectively forage in these areas. One hypothesis explaining this pattern postulates that prey abundance increases in burned areas following wildfire. We observed movement to wintering areas within areas burned by...

  14. The NAD-Dependent Deacetylase Sirtuin-1 Regulates the Expression of Osteogenic Transcriptional Activator Runt-Related Transcription Factor 2 (Runx2 and Production of Matrix Metalloproteinase (MMP-13 in Chondrocytes in Osteoarthritis

    Directory of Open Access Journals (Sweden)

    Koh Terauchi

    2016-06-01

    Full Text Available Aging is one of the major pathologic factors associated with osteoarthritis (OA. Recently, numerous reports have demonstrated the impact of sirtuin-1 (Sirt1, which is the NAD-dependent deacetylase, on human aging. It has been demonstrated that Sirt1 induces osteogenic and chondrogenic differentiation of mesenchymal stem cells. However, the role of Sirt1 in the OA chondrocytes still remains unknown. We postulated that Sirt1 regulates a hypertrophic chondrocyte lineage and degeneration of articular cartilage through the activation of osteogenic transcriptional activator Runx2 and matrix metalloproteinase (MMP-13 in OA chondrocytes. To verify whether sirtuin-1 (Sirt1 regulates chondrocyte activity in OA, we studied expressions of Sirt1, Runx2 and production of MMP-13, and their associations in human OA chondrocytes. The expression of Sirt1 was ubiquitously observed in osteoarthritic chondrocytes; in contrast, Runx2 expressed in the osteophyte region in patients with OA and OA model mice. OA relating catabolic factor IL-1βincreased the expression of Runx2 in OA chondrocytes. OA chondrocytes, which were pretreated with Sirt1 inhibitor, inhibited the IL-1β-induced expression of Runx2 compared to the control. Since the Runx2 is a promotor of MMP-13 expression, Sirt1 inactivation may inhibit the Runx2 expression and the resultant down-regulation of MMP-13 production in chondrocytes. Our findings suggest thatSirt1 may regulate the expression of Runx2, which is the osteogenic transcription factor, and the production of MMP-13 from chondrocytes in OA. Since Sirt1 activity is known to be affected by several stresses, including inflammation and oxidative stress, as well as aging, SIRT may be involved in the development of OA.

  15. Tumor protein D52 expression is post-transcriptionally regulated by T-cell intercellular antigen (TIA) 1 and TIA-related protein via mRNA stability.

    Science.gov (United States)

    Motohashi, Hiromi; Mukudai, Yoshiki; Ito, Chihiro; Kato, Kosuke; Shimane, Toshikazu; Kondo, Seiji; Shirota, Tatsuo

    2017-05-04

    Although tumor protein D52 (TPD52) family proteins were first identified nearly 20 years ago, their molecular regulatory mechanisms remain unclear. Therefore, we investigated the post-transcriptional regulation of TPD52 family genes. An RNA immunoprecipitation (RIP) assay showed the potential binding ability of TPD52 family mRNAs to several RNA-binding proteins, and an RNA degradation assay revealed that TPD52 is subject to more prominent post-transcriptional regulation than are TPD53 and TPD54. We subsequently focused on the 3'-untranslated region (3'-UTR) of TPD52 as a cis -acting element in post-transcriptional gene regulation. Several deletion mutants of the 3'-UTR of TPD52 mRNA were constructed and ligated to the 3'-end of a reporter green fluorescence protein gene. An RNA degradation assay revealed that a minimal cis -acting region, located in the 78-280 region of the 5'-proximal region of the 3'-UTR, stabilized the reporter mRNA. Biotin pull-down and RIP assays revealed specific binding of the region to T-cell intracellular antigen 1 (TIA-1) and TIA-1-related protein (TIAR). Knockdown of TIA-1/TIAR decreased not only the expression, but also the stability of TPD52 mRNA; it also decreased the expression and stability of the reporter gene ligated to the 3'-end of the 78-280 fragment. Stimulation of transforming growth factor-β and epidermal growth factor decreased the binding ability of these factors, resulting in decreased mRNA stability. These results indicate that the 78-280 fragment and TIA-1/TIAR concordantly contribute to mRNA stability as a cis -acting element and trans -acting factor(s), respectively. Thus, we here report the specific interactions between these elements in the post-transcriptional regulation of the TPD52 gene. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  16. Venom-related transcripts from Bothrops jararaca tissues provide novel molecular insights into the production and evolution of snake venom.

    Science.gov (United States)

    Junqueira-de-Azevedo, Inácio L M; Bastos, Carolina Mancini Val; Ho, Paulo Lee; Luna, Milene Schmidt; Yamanouye, Norma; Casewell, Nicholas R

    2015-03-01

    Attempts to reconstruct the evolutionary history of snake toxins in the context of their co-option to the venom gland rarely account for nonvenom snake genes that are paralogous to toxins, and which therefore represent important connectors to ancestral genes. In order to reevaluate this process, we conducted a comparative transcriptomic survey on body tissues from a venomous snake. A nonredundant set of 33,000 unigenes (assembled transcripts of reference genes) was independently assembled from six organs of the medically important viperid snake Bothrops jararaca, providing a reference list of 82 full-length toxins from the venom gland and specific products from other tissues, such as pancreatic digestive enzymes. Unigenes were then screened for nontoxin transcripts paralogous to toxins revealing 1) low level coexpression of approximately 20% of toxin genes (e.g., bradykinin-potentiating peptide, C-type lectin, snake venom metalloproteinase, snake venom nerve growth factor) in body tissues, 2) the identity of the closest paralogs to toxin genes in eight classes of toxins, 3) the location and level of paralog expression, indicating that, in general, co-expression occurs in a higher number of tissues and at lower levels than observed for toxin genes, and 4) strong evidence of a toxin gene reverting back to selective expression in a body tissue. In addition, our differential gene expression analyses identify specific cellular processes that make the venom gland a highly specialized secretory tissue. Our results demonstrate that the evolution and production of venom in snakes is a complex process that can only be understood in the context of comparative data from other snake tissues, including the identification of genes paralogous to venom toxins. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Relative Abundance and Plasmodium Infection Rates of Malaria Vectors in and around Jabalpur, a Malaria Endemic Region in Madhya Pradesh State, Central India.

    Science.gov (United States)

    Singh, Neeru; Mishra, Ashok K; Chand, Sunil K; Bharti, Praveen K; Singh, Mrigendra P; Nanda, Nutan; Singh, Om P; Sodagiri, Kranti; Udhyakumar, Venkatachalam

    2015-01-01

    This study was undertaken in two Primary Health Centers (PHCs) of malaria endemic district Jabalpur in Madhya Pradesh (Central India). In this study we had investigated the relative frequencies of the different anopheline species collected within the study areas by using indoor resting catches, CDC light trap and human landing methods. Sibling species of malaria vectors were identified by cytogenetic and molecular techniques. The role of each vector and its sibling species in the transmission of the different Plasmodium species was ascertained by using sporozoite ELISA. A total of 52,857 specimens comprising of 17 anopheline species were collected by three different methods (39,964 by indoor resting collections, 1059 by human landing and 11,834 by CDC light trap). Anopheles culicifacies was most predominant species in all collections (55, 71 and 32% in indoor resting, human landing and light trap collections respectively) followed by An. subpictus and An. annularis. All five sibling species of An. culicifacies viz. species A, B, C, D and E were found while only species T and S of An. fluviatilis were collected. The overall sporozoite rate in An. culicifacies and An. fluviatilis were 0.42% (0.25% for P. falciparum and 0.17% for P. vivax) and 0.90% (0.45% for P. falciparum and 0.45% for P. vivax) respectively. An. culicifacies and An. fluviatilis were found harbouring both P. vivax variants VK-210 and VK-247, and P. falciparum. An. culicifacies sibling species C and D were incriminated as vectors during most part of the year while sibling species T of An. fluviatilis was identified as potential vector in monsoon and post monsoon season. An. culicifacies species C (59%) was the most abundant species followed by An. culicifacies D (24%), B (8.7%), E (6.7%) and A (1.5%). Among An. fluviatilis sibling species, species T was common (99%) and only few specimens of S were found. Our study provides crucial information on the prevalence of An. culicifacies and An. fluviatilis

  18. Relative Abundance and Plasmodium Infection Rates of Malaria Vectors in and around Jabalpur, a Malaria Endemic Region in Madhya Pradesh State, Central India.

    Directory of Open Access Journals (Sweden)

    Neeru Singh

    Full Text Available This study was undertaken in two Primary Health Centers (PHCs of malaria endemic district Jabalpur in Madhya Pradesh (Central India.In this study we had investigated the relative frequencies of the different anopheline species collected within the study areas by using indoor resting catches, CDC light trap and human landing methods. Sibling species of malaria vectors were identified by cytogenetic and molecular techniques. The role of each vector and its sibling species in the transmission of the different Plasmodium species was ascertained by using sporozoite ELISA.A total of 52,857 specimens comprising of 17 anopheline species were collected by three different methods (39,964 by indoor resting collections, 1059 by human landing and 11,834 by CDC light trap. Anopheles culicifacies was most predominant species in all collections (55, 71 and 32% in indoor resting, human landing and light trap collections respectively followed by An. subpictus and An. annularis. All five sibling species of An. culicifacies viz. species A, B, C, D and E were found while only species T and S of An. fluviatilis were collected. The overall sporozoite rate in An. culicifacies and An. fluviatilis were 0.42% (0.25% for P. falciparum and 0.17% for P. vivax and 0.90% (0.45% for P. falciparum and 0.45% for P. vivax respectively. An. culicifacies and An. fluviatilis were found harbouring both P. vivax variants VK-210 and VK-247, and P. falciparum. An. culicifacies sibling species C and D were incriminated as vectors during most part of the year while sibling species T of An. fluviatilis was identified as potential vector in monsoon and post monsoon season.An. culicifacies species C (59% was the most abundant species followed by An. culicifacies D (24%, B (8.7%, E (6.7% and A (1.5%. Among An. fluviatilis sibling species, species T was common (99% and only few specimens of S were found. Our study provides crucial information on the prevalence of An. culicifacies and An

  19. Relative Abundances of Calcite and Silica in Fracture Coatings as a Possible Indicator of Evaporation in a Thick Unsaturated Zone, Yucca Mountain, Nevada

    Science.gov (United States)

    Marshall, B. D.; Moscati, R. J.

    2005-12-01

    Yucca Mountain, a ridge of shallowly dipping, Miocene-age volcanic rocks in southwest Nevada, is the proposed site for a nuclear waste repository to be constructed in the 500- to 700-m-thick unsaturated zone (UZ). At the proposed repository, the 300-m-thick Topopah Spring Tuff welded unit (TSw) is overlain by approximately 30 m of nonwelded tuffs (PTn); the Tiva Canyon Tuff welded unit (TCw) overlies the PTn with a range in thickness from 0 to approximately 130 m at the site. The amount of water percolation through the UZ is low and difficult to measure directly, but local seepage into mined tunnels has been observed in the TCw. Past water seepage in the welded tuffs is recorded by widespread, thin (0.3 cm) coatings of calcite and silica on fracture surfaces and within cavities. Abundances of calcite and silica in the coatings were determined by X-ray microfluorescence mapping and subsequent multispectral image analysis of over 200 samples. The images were classified into constituent phases including opal-chalcedony-quartz (secondary silica) and calcite. In the TCw samples, the median calcite/silica ratio is 8; in the TSw samples within 35 m below the PTn, median calcite/silica falls to 2, perhaps reflecting an increase in soluble silica from the presence of glass in the nonwelded tuffs. In the deeper parts of the TSw, median calcite/silica reaches 100 and many samples contain no detectable secondary silica phase. Evaporation and changing pCO2 control precipitation of calcite from water percolating downward in the UZ, but precipitation of opal requires only evaporation. Calcite/silica ratios, therefore, can constrain the relative importance of evaporation in the UZ. Although calcite/silica values scatter widely within the TSw, reflecting the spatial variability of gas and water flow, average calcite/silica ratios increase with stratigraphic depth, indicating less evaporation at the deeper levels of the UZ. Coupled with the much smaller calcite/silica ratios

  20. Distribution and Abundance of Dungeness Crab and Crangon Shrimp and Dredging-Related Mortality of Invertebrates and Fish in Grays Harbor, Washington,

    Science.gov (United States)

    1982-01-01

    to this evidence, crabs may have been more abundant in samples taken from high salinity areas. In this respect the buoy 13 site was an anomaly ...in 1-2 hr. Continued respiration and branchial water movement by Dungeness crab caught in impacted areas of slurried sediment could cause loading of...particulate material among branchial filaments, resulting in impeded oxygen transport and physical abrasion and damage to gills. To 304 our knowledge

  1. Expression of SRY-related HMG Box Transcription Factors (Sox) 2 and 9 in Craniopharyngioma Subtypes and Surrounding Brain Tissue.

    Science.gov (United States)

    Thimsen, Vivian; John, Nora; Buchfelder, Michael; Flitsch, Jörg; Fahlbusch, Rudolf; Stefanits, Harald; Knosp, Engelbert; Losa, Marco; Buslei, Rolf; Hölsken, Annett

    2017-11-20

    Stem cells have been discovered as key players in the genesis of different neoplasms including craniopharyngioma (CP), a rare tumour entity in the sellar region. Sox2 and Sox9 are well-known stem cell markers involved in pituitary development. In this study we analysed the expression of both transcription factors using immunohistochemistry in a large cohort of 64 adamantinomatous (aCP) and 9 papillary CP (pCP) and quantitative PCR in 26 aCP and 7 pCP. Whereas immunohistochemically Sox2+ cells were verifiable in only five aCP (7.8%) and in 39.1% of the respective surrounding cerebral tissue, pCP specimens appeared always negative. In contrast, Sox9 was detectable in all tumours with a significantly higher expression in aCP compared to pCP (protein, p < 0.0001; mRNA p = 0.0484) This was also true for the respective tumour adjacent CNS where 63 aCP (98.4%) and six pCP (66.7%) showed Sox9+ cells. We further confirmed absence of Sox9 expression in nuclear β-catenin accumulating cells of aCP. Our results point to the conclusion that Sox2 and Sox9, seem to play essential roles not only in the specific formation of aCP, but also in processes involving the cerebral tumour environment, which needs to be illuminated in the future.

  2. Nitrogen abundance in Comet Halley

    International Nuclear Information System (INIS)

    Wyckoff, S.; Tegler, S.C.; Engel, L.

    1991-01-01

    Data on the nitrogen-containing compounds that observed spectroscopically in the coma of Comet Halley are summarized, and the elemental abundance of nitrogen in the Comet Halley nucleus is derived. It is found that 90 percent of elemental nitrogen is in the dust fraction of the coma, while in the gas fraction, most of the nitrogen is contained in NH3 and CN. The elemental nitrogen abundance in the ice component of the nucleus was found to be deficient by a factor of about 75, relative to the solar photosphere, indicating that the chemical partitioning of N2 into NH3 and other nitrogen compounds during the evolution of the solar nebula cannot account completely for the low abundance ratio N2/NH3 = 0.1, observed in the comet. It is suggested that the low N2/NH3 ratio in Comet Halley may be explained simply by physical fractionation and/or thermal diffusion. 88 refs

  3. The roles of Dmrt (Double sex/Male-abnormal-3 Related Transcription factor) genes in sex determination and differentiation mechanisms: Ubiquity and diversity across the animal kingdom.

    Science.gov (United States)

    Picard, Marion Anne-Lise; Cosseau, Céline; Mouahid, Gabriel; Duval, David; Grunau, Christoph; Toulza, Ève; Allienne, Jean-François; Boissier, Jérôme

    2015-07-01

    The Dmrt (Double sex/Male-abnormal-3 Related Transcription factor) genes have been intensively studied because they represent major transcription factors in the pathways governing sex determination and differentiation. These genes have been identified in animal groups ranging from cnidarians to mammals, and some of the genes functionally studied. Here, we propose to analyze (i) the presence/absence of various Dmrt gene groups in the different taxa across the animal kingdom; (ii) the relative expression levels of the Dmrt genes in each sex; (iii) the specific spatial (by organ) and temporal (by developmental stage) variations in gene expression. This review considers non-mammalian animals at all levels of study (i.e. no particular importance is given to animal models), and using all types of sexual strategy (hermaphroditic or gonochoric) and means of sex determination (i.e. genetic or environmental). To conclude this global comparison, we offer an analysis of the DM domains conserved among the different DMRT proteins, and propose a general sex-specific pattern for each member of the Dmrt gene family. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  4. Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae: a comparison with haploid males, queens and workers

    Directory of Open Access Journals (Sweden)

    Andreia A. Borges

    2011-01-01

    Full Text Available In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

  5. Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae) - A comparison with haploid males, queens and workers.

    Science.gov (United States)

    Borges, Andreia A; Humann, Fernanda C; Oliveira Campos, Lucio A; Tavares, Mara G; Hartfelder, Klaus

    2011-10-01

    In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid) on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i) gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii) in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

  6. Genetic variation in metallothionein and metal-regulatory transcription factor 1 in relation to urinary cadmium, copper, and zinc

    International Nuclear Information System (INIS)

    Adams, Scott V.; Barrick, Brian; Christopher, Emily P.; Shafer, Martin M.; Makar, Karen W.; Song, Xiaoling; Lampe, Johanna W.; Vilchis, Hugo; Ulery, April; Newcomb, Polly A.

    2015-01-01

    Background: Metallothionein (MT) proteins play critical roles in the physiological handling of both essential (Cu and Zn) and toxic (Cd) metals. MT expression is regulated by metal-regulatory transcription factor 1 (MTF1). Hence, genetic variation in the MT gene family and MTF1 might influence excretion of these metals. Methods: 321 women were recruited in Seattle, WA and Las Cruces, NM and provided demographic information, urine samples for measurement of metal concentrations by mass spectrometry and creatinine, and blood or saliva for extraction of DNA. Forty-one single nucleotide polymorphisms (SNPs) within the MTF1 gene region and the region of chromosome 16 encoding the MT gene family were selected for genotyping in addition to an ancestry informative marker panel. Linear regression was used to estimate the association of SNPs with urinary Cd, Cu, and Zn, adjusted for age, urinary creatinine, smoking history, study site, and ancestry. Results: Minor alleles of rs28366003 and rs10636 near the MT2A gene were associated with lower urinary Cd, Cu, and Zn. Minor alleles of rs8044719 and rs1599823, near MT1A and MT1B, were associated with lower urinary Cd and Zn, respectively. Minor alleles of rs4653329 in MTF1 were associated with lower urinary Cd. Conclusions: These results suggest that genetic variation in the MT gene region and MTF1 influences urinary Cd, Cu, and Zn excretion. - Highlights: • Genetic variation in metallothionein (MT) genes was assessed in two diverse populations. • Single nucleotide polymorphisms (SNPs) in MT genes were associated with mean urinary Cd, Cu and Zn. • Genetic variation may influence biomarkers of exposure, and associations of exposure with health.

  7. Genetic variation in metallothionein and metal-regulatory transcription factor 1 in relation to urinary cadmium, copper, and zinc

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Scott V., E-mail: sadams@fhcrc.org [Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 (United States); Barrick, Brian [Department of Plant and Environmental Sciences, New Mexico State University, Box 30003 MSC 3Q, Las Cruces, NM 88003 (United States); Christopher, Emily P. [Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 (United States); Shafer, Martin M. [Environmental Chemistry and Technology, Wisconsin State Laboratory of Hygiene, University of Wisconsin, 2601 Agriculture Dr., Madison, WI 53718 (United States); Makar, Karen W.; Song, Xiaoling [Public Health Science Biomarker Laboratory, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 (United States); Lampe, Johanna W. [Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 (United States); Vilchis, Hugo [Border Epidemiology and Environmental Health Center, New Mexico State University, Box 30001 MSC 3BEC, Las Cruces, NM 88003 (United States); Ulery, April [Department of Plant and Environmental Sciences, New Mexico State University, Box 30003 MSC 3Q, Las Cruces, NM 88003 (United States); Newcomb, Polly A. [Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 (United States)

    2015-12-15

    Background: Metallothionein (MT) proteins play critical roles in the physiological handling of both essential (Cu and Zn) and toxic (Cd) metals. MT expression is regulated by metal-regulatory transcription factor 1 (MTF1). Hence, genetic variation in the MT gene family and MTF1 might influence excretion of these metals. Methods: 321 women were recruited in Seattle, WA and Las Cruces, NM and provided demographic information, urine samples for measurement of metal concentrations by mass spectrometry and creatinine, and blood or saliva for extraction of DNA. Forty-one single nucleotide polymorphisms (SNPs) within the MTF1 gene region and the region of chromosome 16 encoding the MT gene family were selected for genotyping in addition to an ancestry informative marker panel. Linear regression was used to estimate the association of SNPs with urinary Cd, Cu, and Zn, adjusted for age, urinary creatinine, smoking history, study site, and ancestry. Results: Minor alleles of rs28366003 and rs10636 near the MT2A gene were associated with lower urinary Cd, Cu, and Zn. Minor alleles of rs8044719 and rs1599823, near MT1A and MT1B, were associated with lower urinary Cd and Zn, respectively. Minor alleles of rs4653329 in MTF1 were associated with lower urinary Cd. Conclusions: These results suggest that genetic variation in the MT gene region and MTF1 influences urinary Cd, Cu, and Zn excretion. - Highlights: • Genetic variation in metallothionein (MT) genes was assessed in two diverse populations. • Single nucleotide polymorphisms (SNPs) in MT genes were associated with mean urinary Cd, Cu and Zn. • Genetic variation may influence biomarkers of exposure, and associations of exposure with health.

  8. The BPA-substitute bisphenol S alters the transcription of genes related to endocrine, stress response and biotransformation pathways in the aquatic midge Chironomus riparius (Diptera, Chironomidae.

    Directory of Open Access Journals (Sweden)

    Óscar Herrero

    Full Text Available Bisphenol S (BPS is an industrial alternative to the endocrine disruptor bisphenol A (BPA, and can be found in many products labeled "BPA-free". Its use has grown in recent years, and presently it is considered a ubiquitous emerging pollutant. To date there is a lack of information on the effects of BPS on invertebrates, although they represent more than 95% of known species in the animal kingdom and are crucial for the structure and proper function of ecosystems. In this study, real-time RT-PCR was used to determine the early detrimental effects of BPS on the transcriptional rate of genes in the model species Chironomus riparius, specifically those related to the ecdysone pathway (EcR, ERR, E74, Vtg, cyp18a1 crucial for insect development and metamorphosis, stress and biotransformation mechanisms (hsp70, hsp40, cyp4g, GPx, GSTd3 that regulate adaptive responses and determine survival, and ribosome biogenesis (its2, rpL4, rpL13 which is essential for protein synthesis and homeostasis. While 24-hour exposure to 0.5, 5, 50, and 500 μg/L BPS had no effect on larval survival, almost all the studied genes were upregulated following a non-monotonic dose-response curve. Genes with the greatest increases in transcriptional activity (fold change relative to control were EcR (3.8, ERR (2, E74 (2.4, cyp18a1 (2.5, hsp70 (1.7, hsp40 (2.5, cyp4g (6.4, GPx (1.8, and GST (2.1, while others including Vtg, GAPDH, and selected ribosomal genes remained stable. We also measured the transcriptional activity of these genes 24 hours after BPS withdrawal and a general downregulation compared to controls was observed, though not significant in most cases. Our findings showed that BPS exposure altered the transcriptional profile of these genes, which may have consequences for the hormone system and several metabolic pathways. Although further research is needed to elucidate its mode of action, these results raise new concerns about the safety of BPA alternatives.

  9. The BPA-substitute bisphenol S alters the transcription of genes related to endocrine, stress response and biotransformation pathways in the aquatic midge Chironomus riparius (Diptera, Chironomidae).

    Science.gov (United States)

    Herrero, Óscar; Aquilino, Mónica; Sánchez-Argüello, Paloma; Planelló, Rosario

    2018-01-01

    Bisphenol S (BPS) is an industrial alternative to the endocrine disruptor bisphenol A (BPA), and can be found in many products labeled "BPA-free". Its use has grown in recent years, and presently it is considered a ubiquitous emerging pollutant. To date there is a lack of information on the effects of BPS on invertebrates, although they represent more than 95% of known species in the animal kingdom and are crucial for the structure and proper function of ecosystems. In this study, real-time RT-PCR was used to determine the early detrimental effects of BPS on the transcriptional rate of genes in the model species Chironomus riparius, specifically those related to the ecdysone pathway (EcR, ERR, E74, Vtg, cyp18a1) crucial for insect development and metamorphosis, stress and biotransformation mechanisms (hsp70, hsp40, cyp4g, GPx, GSTd3) that regulate adaptive responses and determine survival, and ribosome biogenesis (its2, rpL4, rpL13) which is essential for protein synthesis and homeostasis. While 24-hour exposure to 0.5, 5, 50, and 500 μg/L BPS had no effect on larval survival, almost all the studied genes were upregulated following a non-monotonic dose-response curve. Genes with the greatest increases in transcriptional activity (fold change relative to control) were EcR (3.8), ERR (2), E74 (2.4), cyp18a1 (2.5), hsp70 (1.7), hsp40 (2.5), cyp4g (6.4), GPx (1.8), and GST (2.1), while others including Vtg, GAPDH, and selected ribosomal genes remained stable. We also measured the transcriptional activity of these genes 24 hours after BPS withdrawal and a general downregulation compared to controls was observed, though not significant in most cases. Our findings showed that BPS exposure altered the transcriptional profile of these genes, which may have consequences for the hormone system and several metabolic pathways. Although further research is needed to elucidate its mode of action, these results raise new concerns about the safety of BPA alternatives.

  10. Abundances in field dwarf stars. II. Carbon and nitrogen abundances

    Energy Technology Data Exchange (ETDEWEB)

    Laird, J.B.

    1985-02-15

    Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in (Fe/H) of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to (Fe/H)roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities.

  11. Abundances in field dwarf stars. II. Carbon and nitrogen abundances

    International Nuclear Information System (INIS)

    Laird, J.B.

    1985-01-01

    Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in [Fe/H] of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to [Fe/H]roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities

  12. Thiamine content of eggs and lengths of coho salmon (Oncorhynchus kisutch) in relation to abundance of alewife (Alosa pseudoharengus) in eastern Lake ontario, 2003 to 2006

    Science.gov (United States)

    Ketola, H.G.; Rinchard, J.; O'Gorman, R.; Begnoche, L.J.; Bishop, D.L.; Greulich, A.W.

    2009-01-01

    Early mortality syndrome in fry of Great Lakes salmonines is linked to reduced levels of thiamine in eggs, which reflects maternal consumption of forage fishes such as alewife (Alosa pseudoharengus) that contain thiaminase, an enzyme that destroys thiamine. We assessed annual variations in abundance and condition of alewives and thiamine status of coho salmon (Oncorhynchus kisutch) in Lake Ontario. We analyzed total thiamine in eggs of 20 coho salmon collected annually between 2003 and 2006 at the Salmon River Hatchery on the Salmon River, New York. Alewife abundance was assessed annually in southern and eastern Lake Ontario with bottom trawls during late April and early May. Mean thiamine concentration in eggs varied annually, with those collected in 2003 (2.5 nmol/g) being significantly higher than those collected in 2004 to 2006 (1.5 to 1.7 nmol/g). Although we did not test survival of fry, if reported threshold levels of thiamine for preventing mortality of Lake Michigan coho salmon fry apply, then many or most Lake Ontario coho salmon produced fry were likely to incur thiamine-deficiency mortality, especially during years 2004 to 2006. Comparison to indices of annual abundance of alewife in Lake Ontario with thiamine concentration in coho salmon eggs failed to show any significant correlations (P > 0.05). However, total length of female spawning coho salmon was positively correlated (P < 0.05) with increasing condition and estimated energy content of adult alewives in the previous spring. These results suggest that growth of coho salmon in Lake Ontario was first limited by energy intake, whereas the amount of thiamine provided by alewives was sufficient for growth (in length) but not for producing thiamine-adequate eggs.

  13. Twilight of Abundance

    Science.gov (United States)

    Archibald, David

    2014-03-01

    Baby boomers enjoyed the most benign period in human history: fifty years of relative peace, cheap energy, plentiful grain supply, and a warming climate due to the highest solar activity for 8,000 years. The party is over - prepare for the twilight of abundance. David Archibald reveals the grim future the world faces on its current trajectory: massive fuel shortages, the bloodiest warfare in human history, a global starvation crisis, and a rapidly cooling planet. Archibald combines pioneering science with keen economic knowledge to predict the global disasters that could destroy civilization as we know it - disasters that are waiting just around the corner. But there's good news, too: We can have a good future if we prepare for it. Advanced, civilized countries can have a permanently high standard of living if they choose to invest in the technologies that will get them there. Archibald, a climate scientist as well as an inventor and a financial specialist, explains which scientific breakthroughs can save civilization in the coming crisis - if we can cut through the special interest opposition to these innovations and allow free markets to flourish.

  14. No substantial changes in estrogen receptor and estrogen-related receptor orthologue gene transcription in Marisa cornuarietis exposed to estrogenic chemicals.

    Science.gov (United States)

    Bannister, Richard; Beresford, Nicola; Granger, David W; Pounds, Nadine A; Rand-Weaver, Mariann; White, Roger; Jobling, Susan; Routledge, Edwin J

    2013-09-15

    Estrogen receptor orthologues in molluscs may be targets for endocrine disruptors, although mechanistic evidence is lacking. Molluscs are reported to be highly susceptible to effects caused by very low concentrations of environmental estrogens which, if substantiated, would have a major impact on the risk assessment of many chemicals. The present paper describes the most thorough evaluation to-date of the susceptibility of Marisa cornuarietis ER and ERR gene transcription to modulation by vertebrate estrogens in vivo and in vitro. We investigated the effects of estradiol-17β and 4-tert-Octylphenol exposure on in vivo estrogen receptor (ER) and estrogen-related receptor (ERR) gene transcription in the reproductive and neural tissues of the gastropod snail M. cornuarietis over a 12-week period. There was no significant effect (p>0.05) of treatment on gene transcription levels between exposed and non-exposed snails. Absence of a direct interaction of estradiol-17β and 4-tert-Octylphenol with mollusc ER and ERR protein was also supported by in vitro studies in transfected HEK-293 cells. Additional in vitro studies with a selection of other potential ligands (including methyl-testosterone, 17α-ethinylestradiol, 4-hydroxytamoxifen, diethylstilbestrol, cyproterone acetate and ICI182780) showed no interaction when tested using this assay. In repeated in vitro tests, however, genistein (with mcER-like) and bisphenol-A (with mcERR) increased reporter gene expression at high concentrations only (>10(-6)M for Gen and >10(-5)M for BPA, respectively). Like vertebrate estrogen receptors, the mollusc ER protein bound to the consensus vertebrate estrogen-response element (ERE). Together, these data provide no substantial evidence that mcER-like and mcERR activation and transcript levels in tissues are modulated by the vertebrate estrogen estradiol-17β or 4-tert-Octylphenol in vivo, or that other ligands of vertebrate ERs and ERRs (with the possible exception of genistein and

  15. No substantial changes in estrogen receptor and estrogen-related receptor orthologue gene transcription in Marisa cornuarietis exposed to estrogenic chemicals☆☆☆

    Science.gov (United States)

    Bannister, Richard; Beresford, Nicola; Granger, David W.; Pounds, Nadine A.; Rand-Weaver, Mariann; White, Roger; Jobling, Susan; Routledge, Edwin J.

    2013-01-01

    Estrogen receptor orthologues in molluscs may be targets for endocrine disruptors, although mechanistic evidence is lacking. Molluscs are reported to be highly susceptible to effects caused by very low concentrations of environmental estrogens which, if substantiated, would have a major impact on the risk assessment of many chemicals. The present paper describes the most thorough evaluation to-date of the susceptibility of Marisa cornuarietis ER and ERR gene transcription to modulation by vertebrate estrogens in vivo and in vitro. We investigated the effects of estradiol-17β and 4-tert-Octylphenol exposure on in vivo estrogen receptor (ER) and estrogen-related receptor (ERR) gene transcription in the reproductive and neural tissues of the gastropod snail M. cornuarietis over a 12-week period. There was no significant effect (p > 0.05) of treatment on gene transcription levels between exposed and non-exposed snails. Absence of a direct interaction of estradiol-17β and 4-tert-Octylphenol with mollusc ER and ERR protein was also supported by in vitro studies in transfected HEK-293 cells. Additional in vitro studies with a selection of other potential ligands (including methyl-testosterone, 17α-ethinylestradiol, 4-hydroxytamoxifen, diethylstilbestrol, cyproterone acetate and ICI182780) showed no interaction when tested using this assay. In repeated in vitro tests, however, genistein (with mcER-like) and bisphenol-A (with mcERR) increased reporter gene expression at high concentrations only (>10−6 M for Gen and >10−5 M for BPA, respectively). Like vertebrate estrogen receptors, the mollusc ER protein bound to the consensus vertebrate estrogen-response element (ERE). Together, these data provide no substantial evidence that mcER-like and mcERR activation and transcript levels in tissues are modulated by the vertebrate estrogen estradiol-17β or 4-tert-Octylphenol in vivo, or that other ligands of vertebrate ERs and ERRs (with the possible exception of

  16. AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals.

    Science.gov (United States)

    Fagard, M; Boutet, S; Morel, J B; Bellini, C; Vaucheret, H

    2000-10-10

    Introduction of transgene DNA may lead to specific degradation of RNAs that are homologous to the transgene transcribed sequence through phenomena named post-transcriptional gene silencing (PTGS) in plants, quelling in fungi, and RNA interference (RNAi) in animals. It was shown previously that PTGS, quelling, and RNAi require a set of related proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the isolation of Arabidopsis mutants impaired in PTGS which are affected at the Argonaute1 (AGO1) locus. AGO1 is similar to QDE-2 required for quelling and RDE-1 required for RNAi. Sequencing of ago1 mutants revealed one amino acid essential for PTGS that is also present in QDE-2 and RDE-1 in a highly conserved motif. Taken together, these results confirm the hypothesis that these processes derive from a common ancestral mechanism that controls expression of invading nucleic acid molecules at the post-transcriptional level. As opposed to rde-1 and qde-2 mutants, which are viable, ago1 mutants display several developmental abnormalities, including sterility. These results raise the possibility that PTGS, or at least some of its elements, could participate in the regulation of gene expression during development in plants.

  17. Relative distribution and abundance of fishes and crayfish in 2010 and 2014 prior to saltcedar (Tamarix ssp.) removal in the Amargosa River Canyon, southeastern California

    Science.gov (United States)

    Hereford, Mark E.

    2016-07-22

    The Amargosa River Canyon, located in the Mojave Desert of southeastern California, contains the longest perennial reach of the Amargosa River. Because of its diverse flora and fauna, it has been designated as an Area of Critical Environmental Concern and a Wild and Scenic River by the Bureau of Land Management. A survey of fishes conducted in summer 2010 indicated that endemic Amargosa River pupfish (Cyprinodon nevadensis amargosae) and speckled dace (Rhinichthys osculus spp.) were abundant and occurred throughout the Amargosa River Canyon. The 2010 survey reported non-native red swamp crayfish (Procambarus clarkii) and western mosquitofish (Gambusia affinis) captures were significantly higher, whereas pupfish captures were lower, in areas dominated by non-native saltcedar (Tamarix ssp.). Based on the 2010 survey, it was hypothesized that the invasion of saltcedar could result in a decrease in native species. In an effort to maintain and enhance native fish populations, the Bureau of Land Management removed saltcedar from a 1,550 meter reach of stream on the Amargosa River in autumn 2014 and autumn 2015. Prior to the removal of saltcedar, a survey of fishes and crayfish using baited minnow traps was conducted in the treatment reach to serve as a baseline for future comparisons with post-saltcedar removal surveys. During the 2014 survey, 1,073 pupfish and 960 speckled dace were captured within the treatment reach. Catch per unit effort of pupfish and speckled dace in the treatment reach was less in 2014 than in 2010, although differences could be owing to seasonal variation in capture probability. Non-native mosquitofish catch per unit effort decreased from 2010 to 2014; however, the catch per unit effort of crayfish increased from 2010 to 2014. Future monitoring efforts of this reach should be conducted at the same time period to account for potential seasonal fluctuations of abundance and distribution of fishes and crayfish. A more robust study design that

  18. OXYGEN ABUNDANCES IN CEPHEIDS

    International Nuclear Information System (INIS)

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V.

    2013-01-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  19. Habitat use and relative abundance of the Spotted Paca Cuniculus paca (Linnaeus, 1766 (Rodentia: Cuniculidae and the Red-rumped Agouti Dasyprocta leporina (Linnaeus, 1758 (Rodentia: Dasyproctidae in Guatopo National Park, Venezuela

    Directory of Open Access Journals (Sweden)

    Elinor Jax

    2015-01-01

    Full Text Available The Spotted Paca Cuniculus paca and the Red-rumped Agouti Dasyprocta leporina are affected by habitat loss and hunting.  In Venezuela, their conservation status is unknown, even within protected areas.  The objective of this study was to estimate the relative abundance, activity patterns, habitat use, and effect of human activities on these species in Venezuela.  To achieve this, 26 camera-trap stations (20.8km2 were established in Guatopo National Park between February and April 2011, characterization of the habitat was undertaken and occupancy models were created.  The relative abundance of the Spotted Paca was 1.62 captures/100trap-nights, with a fully nocturnal activity pattern.  The relative abundance of the Red-rumped Agouti was 2.32 captures/100trap-nights, with a pronounced diurnal activity pattern. The occupation probability of the Red-rumped Agouti (0.61 SE 0.02 was higher than that of the Spotted Paca (0.27 SE 0.02. Spotted Pacas were mainly found in areas with mature forest and high tree density, whereas the  Red-rumped Agoutis were most frequently found in valleys with little disturbed forest.  A positive correlation was found between illegal hunting activities and areas occupied by the Spotted Paca.  It is important to strengthen the park control measurements to reduce illegal hunting of Spotted Pacas.

  20. Accumulation of defence-related transcripts and cloning of a chitinase mRNA from pea leaves (Pisum sativum L.) inoculated with Ascochyta pisi Lib

    DEFF Research Database (Denmark)

    Vad, Knud; de Neergaard, Eigil; Madriz-Ordeñana, Kenneth

    1993-01-01

    The race specific resistance of pea to Ascochyta pisi Lib. was shown to be exhibited as a hypersensitive response associated with the production of polyphenolic substances in epidermal and mesophyll cells. The levels of transcripts representing a pathogenesis-related (PR) protein (chitinase......) and an enzyme of phytoalexin biosynthesis (chalcone synthase) were shown to accumulate more rapidly during the hypersensitive response than during lesion development in the compatible interaction. A full-length (1143 bp) cDNA sequence of a pea chitinase (EC 3.2.1.14) (coding for an approx. 34 500 Da protein......) was deduced by combining the overlapping sequences of three clones obtained following PCR amplification of cDNA prepared from mRNA isolated 24 h after inoculation of pea leaves with Ascochyta pisi. The combined sequences were identified as a class I chitinase corresponding to the basic A1-chitinase enzyme...

  1. Diversity, composition and abundance of macroinvertebrates ...

    African Journals Online (AJOL)

    user

    these genera were found at all sampling stations as shown in Table 2. Out of the orders sampled, Hemiptera, Pulmonata and. Coleoptera had the highest number of genera with 5, 4 and 4, respectively. In terms of relative abundance, dipterans and Pulmonata were the most abundant while. Hydracarina (water mites) were ...

  2. Increased expression of interleukin-6 (IL-6) gene transcript in relation to IL-6 promoter hypomethylation in gingival tissue from patients with chronic periodontitis.

    Science.gov (United States)

    Kobayashi, Tetsuo; Ishida, Kohei; Yoshie, Hiromasa

    2016-09-01

    DNA methylation of the cytokine genes may play a role in the pathogenesis of periodontitis. The aim of this study is to evaluate whether the alteration of interleukin-6 (IL-6) gene promoter methylation in the gingival tissue (GT) and peripheral blood (PB) is unique to chronic periodontitis (CP). DNA isolated from the GT and PB of 25 patients with (CP) and 20 healthy controls (H) was modified with sodium bisulfite and analyzed for IL-6 promoter methylation with direct sequencing. The levels of IL-6 mRNA and serum IL-6 protein were evaluated by a quantitative reverse transcription polymerase chain reaction and an enzyme-linked immunosorbent assay. The CP group showed that the overall methylation rates of IL-6 promoter that contained 19 cytosine-guanine dinucleotide (CpG) motifs were significantly decreased in GT in comparison to PB (p<0.001), which was significantly negatively correlated with the probing depth (p=0.003). The GT and PB of the H group displayed similar overall methylation rates. No significant difference was observed in the methylation rates at each CpG in GT in comparison to the PB in both groups. The levels of IL-6 mRNA in the GT and PB and serum IL-6 of the two groups were comparable. The ratio of IL-6 mRNA in the GT relative to the PB was significantly higher in the CP group than in the H group (p=0.03). The increased expression of IL-6 gene transcription may be related to IL-6 promoter hypomethylation in the GT from CP patients. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress.

    Science.gov (United States)

    Hu, Longxing; Li, Huiying; Chen, Liang; Lou, Yanhong; Amombo, Erick; Fu, Jinmin

    2015-08-04

    Soil salinity is one of the most significant abiotic stresses affecting plant shoots and roots growth. The adjustment of root architecture to spatio-temporal heterogeneity in salinity is particularly critical for plant growth and survival. Bermudagrass (Cynodon dactylon) is a widely used turf and forage perennial grass with a high degree of salinity tolerance. Salinity appears to stimulate the growth of roots and decrease their mortality in tolerant bermudagrass. To estimate a broad spectrum of genes related to root elongation affected by salt stress and the molecular mechanisms that control the positive response of root architecture to salinity, we analyzed the transcriptome of bermudagrass root tips in response to salinity. RNA-sequencing was performed in root tips of two bermudagrass genotypes contrasting in salt tolerance. A total of 237,850,130 high quality clean reads were generated and 250,359 transcripts were assembled with an average length of 1115 bp. Totally, 103,324 unigenes obtained with 53,765 unigenes (52 %) successfully annotated in databases. Bioinformatics analysis indicated that major transcription factor (TF) families linked to stress responses and growth regulation (MYB, bHLH, WRKY) were differentially expressed in root tips of bermudagrass under salinity. In addition, genes related to cell wall loosening and stiffening (xyloglucan endotransglucosylase/hydrolases, peroxidases) were identified. RNA-seq analysis identified candidate genes encoding TFs involved in the regulation of lignin synthesis, reactive oxygen species (ROS) homeostasis controlled by peroxidases, and the regulation of phytohormone signaling that promote cell wall loosening and therefore root growth under salinity.

  4. Heme oxygenase up-regulation under ultraviolet-B radiation is not epigenetically restricted and involves specific stress-related transcriptions factors

    Directory of Open Access Journals (Sweden)

    Diego Santa-Cruz

    2017-08-01

    Full Text Available Heme oxygenase-1 (HO-1 plays a protective role against oxidative stress in plants. The mechanisms regulating its expression, however, remain unclear. Here we studied the methylation state of a GC rich HO-1 promoter region and the expression of several stress-related transcription factors (TFs in soybean plants subjected to ultraviolet-B (UV-B radiation. Genomic DNA and total RNA were isolated from leaves of plants irradiated with 7.5 and 15 kJ m-2 UV-B. A 304 bp HO-1 promoter region was amplified by PCR from sodium bisulfite-treated DNA, cloned into pGEMT plasmid vector and evaluated by DNA sequencing. Bisulfite sequencing analysis showed similar HO-1 promoter methylation levels in control and UV-B-treated plants (C: 3.4±1.3%; 7.5: 2.6±0.5%; 15: 3.1±1.1%. Interestingly, HO-1 promoter was strongly unmethylated in control plants. Quantitative RT-PCR analysis of TFs showed that GmMYB177, GmMYBJ6, GmWRKY21, GmNAC11, GmNAC20 and GmGT2A but not GmWRK13 and GmDREB were induced by UV-B radiation. The expression of several TFs was also enhanced by hemin, a potent and specific HO inducer, inferring that they may mediate HO-1 up-regulation. These results suggest that soybean HO-1 gene expression is not epigenetically regulated. Moreover, the low level of HO-1 promoter methylation suggests that this antioxidant enzyme can rapidly respond to environmental stress. Finally, this study has identified some stress-related TFs involved in HO-1 up-regulation under UV-B radiation. Keywords: Heme oxygenase, DNA methylation, Transcription factors, Ultraviolet-B radiation, Glycine max

  5. Molecular effect of fenofibrate on PBMC gene transcription related to lipid metabolism in patients with metabolic syndrome.

    Science.gov (United States)

    Moreno-Indias, I; Tinahones, F J; Clemente-Postigo, M; Castellano-Castillo, D; Fernández-García, J C; Macias-Gonzalez, M; Queipo-Ortuño, M I; Cardona, F

    2017-06-01

    Both fasting and postprandial hypertriglyceridaemia are considered independent risk factors for atherosclerosis. Treatment of hypertriglyceridaemia is based on fibrates, which activate the peroxisome proliferator-activated receptor alpha (PPARα). However, the metabolic pathways that activate or inhibit fibrates, and how the postprandial triglyceride levels are modified, have not yet been fully described. Accordingly, the aim of this study was to determine the feasibility of peripheral blood mononuclear cells (PBMC) to study the effects of fenofibrate in patients with the metabolic syndrome. A fat overload was given to 50 patients before and after treatment with fenofibrate for 3 months. Anthropometric and biochemical variables as well as gene expression in PBMC were analysed. After treatment with fenofibrate, we observed a decrease in both baseline and postprandial (3 h after the fat overload) levels of serum triglycerides, cholesterol and uric acid and an increase in HDL cholesterol and apolipoprotein AI levels. After treatment, there was also a rise in PPARα and RXRα expression and changes in genes regulated by PPARα, both baseline and postprandial. Furthermore, in vitro experiments showed that a PPARα agonist changed the expression of genes related with lipid metabolism. Treatment with fenofibrate reduced fasting and postprandial serum triglyceride levels, possibly through a mechanism related with an increase in the expression of RXRα and PPARα, by activating the pathways involved in the uptake and degradation of triglycerides and increasing the synthesis of apolipoprotein. These results suggest that PBMC may be useful for the easy study of fenofibrate actions. © 2017 John Wiley & Sons Ltd.

  6. Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments

    Directory of Open Access Journals (Sweden)

    François eThomas

    2014-06-01

    Full Text Available Salt marshes are highly productive ecosystems hosting an intense sulfur (S cycle, yet little is known about S-oxidizing microorganisms in these ecosystems. Here, we studied the diversity and transcriptional activity of S-oxidizers in salt marsh sediments colonized by the plant Spartina alterniflora, and assessed variations with sediment depth and small-scale compartments within the rhizosphere. We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB. Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT-qPCR assays. We identified a diverse assemblage of S-oxidizers, with Chromatiales and Thiotrichales being dominant. The detection of transcripts from S-oxidizers was mostly confined to the upper 5 cm sediments, following the expected distribution of root biomass. A common pool of species dominated by Gammaproteobacteria transcribed S-oxidation genes across roots, rhizosphere, and surrounding sediment compartments, with rdsrAB transcripts prevailing over soxB. However, the root environment fine-tuned the abundance and transcriptional activity of the S-oxidizing community. In particular, the global transcription of soxB was higher on the roots compared to mix and rhizosphere samples. Furthermore, the contribution of Epsilonproteobacteria-related S-oxidizers tended to increase on Spartina roots compared to surrounding sediments. These data shed light on the under-studied oxidative part of the sulfur cycle in salt marsh sediments and indicate small-scale heterogeneities are important factors shaping abundance and potential activity of S-oxidizers in the rhizosphere.

  7. A study on the abundance of quartz in thermal coals of India and its relation to abrasion index: Development of predictive model for abrasion

    Energy Technology Data Exchange (ETDEWEB)

    Bandopadhyay, A.K. [Central Institute of Mining and Fuel Research Digwadih Campus, P.O.-FRI, Dhanbad-828108, Jharkhand (India)

    2010-10-01

    The quartz content of each of the 61 thermal coals used in power stations in India has been determined using Fourier Transform Infra-Red (FTIR) Spectroscopy. It has been observed that quartz is abundant in the thermal coals and its proportion varies from 5 to 20% by wt. The abrasion index (AI), a measure of abrasion caused by coals, has been determined for each coal according to the procedure laid down in Indian Standard IS: 9949-1986. The data generated on abrasion together with ash and quartz percentages of the coals studied have been subjected to regression and correlation analysis. Positive correlations have been found between AI and quartz content and between AI and ash yield, but the correlation between AI and ash (A) and quartz (Q) percentages has been observed to be the most significant (R{sup 2} = 0.86). The linear regression model AI = 1.00A + 1.35Q thus developed has the ability to predict AI of the thermal coals within {+-} 10 mg/kg at 95.5% confidence level. Results of application of the model to predicting abrasion of a limited number of foreign coals with different origins have been found to be encouraging. Integration of other variables like the size and the shape of the abrading particles along with other physical properties of coal, like the bulk density and the grindability, with the model, in addition to the variables already considered, has been suggested for improved prediction. (author)

  8. Summer Distribution, Relative Abundance and Encounter Rates of Cetaceans in the Mediterranean Waters off Southern Italy (Western Ionian Sea and Southern Tyrrhenian Sea

    Directory of Open Access Journals (Sweden)

    R. SANTORO

    2015-07-01

    Full Text Available In summer 2010 and summer 2011, weekly cetacean surveys were undertaken in “passing mode”, using ferries as platform of opportunity, along the “fixed line transect” between Catania and Civitavecchia (Southern Italy. Of the 20 species of cetaceans confirmed for the Mediterranean sea, 8 were sighted within the survey period: 7 species represented by Mediterranean subpopulations (Balaenoptera physalus, Physeter macrocephalus, Stenella coeruleoalba, Delphinus delphis, Grampus griseus, Tursiops truncatus and Ziphius cavirostris and one considered visitor (Steno bredanensis. We had a total of 220 sightings during the 2010 and a total of 240 sightings in the 2011. The most frequent species was S. coeruleoalba. By the comparison of the data from the two sampling seasons, a significant increase of D. delphis sightings and a decrease of sightings of B. physalus and P. macrocephalus was observed from 2010 to 2011. While all the other species were observed in both sampling seasons, Z. cavirostris and Steno bredanensis were observed only during 2011. The presence of mixed groups of odontocetes was documented too: we sighted groups composed by S. coeruleoalba and D. delphis, by S. coeruleoalba and T. truncatus, and by S. coeruleoalba and G. griseus. The results of this research add useful information on cetacean species in a very poorly known area and highlight the need to standardize large scale and long term monitoring programs in order to detect variation in presence, abundance and distribution of cetaceans populations and understand the effect of anthropogenic factors.

  9. Nitrogen content, 15N natural abundance and biomass of the two pleurocarpous mosses Pleurozium schreberi (Brid.) Mitt. and Scleropodium purum (Hedw.) Limpr. in relation to atmospheric nitrogen deposition

    International Nuclear Information System (INIS)

    Solga, A.; Burkhardt, J.; Zechmeister, H.G.; Frahm, J.-P.

    2005-01-01

    The suitability of the two pleurocarpous mosses Pleurozium schreberi and Scleropodium purum for assessing spatial variation in nitrogen deposition was investigated. Sampling was carried out at eight sites in the western part of Germany with bulk deposition rates ranging between 6.5 and 18.5 kg N ha -1 yr -1 . In addition to the effect of deposition on the nitrogen content of the two species, its influence on 15 N natural abundance (δ 15 N values) and on productivity was examined. Annual increases of the mosses were used for all analyses. Significant relationships between bulk N deposition and nitrogen content were obtained for both species; δ 15 N-values reflected the ratio of NH 4 -N to NO 3 -N in deposition. A negative effect of nitrogen input on productivity, i.e. decreasing biomass per area with increasing N deposition due to a reduction of stem density, was particularly evident with P. schreberi. Monitoring of N deposition by means of mosses is considered an important supplement to existing monitoring programs. It makes possible an improved spatial resolution, and thus those areas that receive high loads of nitrogen are more easily discernible. - Mosses are useful as monitors of nitrogen deposition

  10. Constitutive Transcription and Stable RNA Accumulation in Plastids during the Conversion of Chloroplasts to Chromoplasts in Ripening Tomato Fruits 1

    Science.gov (United States)

    Marano, María Rosa; Carrillo, Néstor

    1992-01-01

    The size distribution of plastid transcripts during chromoplast differentiation in ripening tomato (Lycopersicon esculentum L.) fruits was determined using northern blot analysis. Hybridization of total cellular RNA from leaves and fruits with several tobacco chloroplast DNA probes showed distinct transcript patterns in chloroplasts and chromoplasts. We also compared transcriptional rates by probing immobilized DNA fragments of small size (representing about 85% of the plastid genome) with run-on transcripts from tomato plastids. The relative rates of transcription of the various DNA regions were very similar in chloro- and chromoplasts. Parallel determination of the steady-state levels of plastid RNA showed no strict correlation between synthesis rate and RNA accumulation. Differences in the relative abundance of transcripts between chloro- and chromoplasts were not very pronounced and were limited to a small number of genes. The results indicate that the conversion of chloroplasts to chromoplasts at the onset of tomato fruit ripening proceeds with no important variations in the relative transcription rates and with only moderate changes in the relative stability of plastid-encoded transcripts. Images Figure 1 Figure 4 PMID:16653091

  11. Deletion of the transcriptional coactivator PGC1α in skeletal muscles is associated with reduced expression of genes related to oxidative muscle function

    International Nuclear Information System (INIS)

    Hatazawa, Yukino; Minami, Kimiko; Yoshimura, Ryoji; Onishi, Takumi; Manio, Mark Christian; Inoue, Kazuo; Sawada, Naoki; Suzuki, Osamu; Miura, Shinji; Kamei, Yasutomi

    2016-01-01

    The expression of the transcriptional coactivator PGC1α is increased in skeletal muscles during exercise. Previously, we showed that increased PGC1α leads to prolonged exercise performance (the duration for which running can be continued) and, at the same time, increases the expression of branched-chain amino acid (BCAA) metabolism-related enzymes and genes that are involved in supplying substrates for the TCA cycle. We recently created mice with PGC1α knockout specifically in the skeletal muscles (PGC1α KO mice), which show decreased mitochondrial content. In this study, global gene expression (microarray) analysis was performed in the skeletal muscles of PGC1α KO mice compared with that of wild-type control mice. As a result, decreased expression of genes involved in the TCA cycle, oxidative phosphorylation, and BCAA metabolism were observed. Compared with previously obtained microarray data on PGC1α-overexpressing transgenic mice, each gene showed the completely opposite direction of expression change. Bioinformatic analysis of the promoter region of genes with decreased expression in PGC1α KO mice predicted the involvement of several transcription factors, including a nuclear receptor, ERR, in their regulation. As PGC1α KO microarray data in this study show opposing findings to the PGC1α transgenic data, a loss-of-function experiment, as well as a gain-of-function experiment, revealed PGC1α’s function in the oxidative energy metabolism of skeletal muscles. - Highlights: • Microarray analysis was performed in the skeletal muscle of PGC1α KO mice. • Expression of genes in the oxidative energy metabolism was decreased. • Bioinformatic analysis of promoter region of the genes predicted involvement of ERR. • PGC1α KO microarray data in this study show the mirror image of transgenic data.

  12. The related transcriptional enhancer factor-1 isoform, TEAD4(216, can repress vascular endothelial growth factor expression in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Binoy Appukuttan

    Full Text Available Increased cellular production of vascular endothelial growth factor (VEGF is responsible for the development and progression of multiple cancers and other neovascular conditions, and therapies targeting post-translational VEGF products are used in the treatment of these diseases. Development of methods to control and modify the transcription of the VEGF gene is an alternative approach that may have therapeutic potential. We have previously shown that isoforms of the transcriptional enhancer factor 1-related (TEAD4 protein can enhance the production of VEGF. In this study we describe a new TEAD4 isoform, TEAD4(216, which represses VEGF promoter activity. The TEAD4(216 isoform inhibits human VEGF promoter activity and does not require the presence of the hypoxia responsive element (HRE, which is the sequence critical to hypoxia inducible factor (HIF-mediated effects. The TEAD4(216 protein is localized to the cytoplasm, whereas the enhancer isoforms are found within the nucleus. The TEAD4(216 isoform can competitively repress the stimulatory activity of the TEAD4(434 and TEAD4(148 enhancers. Synthesis of the native VEGF(165 protein and cellular proliferation is suppressed by the TEAD4(216 isoform. Mutational analysis indicates that nuclear or cytoplasmic localization of any isoform determines whether it acts as an enhancer or repressor, respectively. The TEAD4(216 isoform appears to inhibit VEGF production independently of the HRE required activity by HIF, suggesting that this alternatively spliced isoform of TEAD4 may provide a novel approach to treat VEGF-dependent diseases.

  13. Immunohistochemical expression of Ets-related gene-transcriptional factor in adenocarcinoma prostate and its correlation with Gleason score

    Directory of Open Access Journals (Sweden)

    Rahul Mannan

    2016-01-01

    Full Text Available Background: Prostate carcinoma is the second leading cause of cancer-related deaths in males worldwide. The burden is expected to grow 1.7 million new cases and 499,000 new deaths by 2030. In developing countries such as India, prostate carcinoma will show an increase by 140% in the next few years. Although the diagnosis of prostate carcinoma can usually be made on histological features, now a days many immunohistochemical (IHC markers are used to distinguish it from benign mimickers as well as in predicting prognosis and treatment. Out of these markers, Ets-related gene (ERG product is a proto-oncogene which participates in chromosomal translocations and is frequently over expressed in prostate carcinoma which harbors ERG-transmembrane protease, serine 2 fusion. Materials and Methods: Fifty cases of carcinoma prostate diagnosed in needle biopsies and prostatic chips, in the Department of Pathology of a tertiary care teaching hospital in Punjab, India, were included in the present study. The slides were observed under the light microscope, and Gleason scoring was done using the 2005 International Society of Urological Pathology modified Gleason system. IHC study for ERG expression was done on all the cases, for which anti-ERG monoclonal rabbit clone antibody EP111 (Dako, Denmark was used. Lymphocytes and endothelial cells were taken as in built positive controls for staining. The intensity of ERG positivity was scored as no staining (0, weak staining (+1, moderate staining (+2 and intense staining (+3. The H score was then calculated by multiplying the intensity of the stain with the percentage (0-100 of the cells showing that staining intensity. The H-score has a range of 0-300. The relationship between IHC expression and clinico-pathological parameters was compared and analyzed using Chi-square test. P < 0.05 was considered statistically significant. Results: Majority of patients included in the study were in the age group of 61-80 (84% of the

  14. Immunohistochemical expression of Ets-related gene-transcriptional factor in adenocarcinoma prostate and its correlation with Gleason score.

    Science.gov (United States)

    Mannan, Rahul; Bhasin, Tejinder Singh; Manjari, Mridu; Singh, Gagandeep; Bhatia, Puneet Kaur; Sharma, Sonam

    2016-01-01

    Prostate carcinoma is the second leading cause of cancer-related deaths in males worldwide. The burden is expected to grow 1.7 million new cases and 499,000 new deaths by 2030. In developing countries such as India, prostate carcinoma will show an increase by 140% in the next few years. Although the diagnosis of prostate carcinoma can usually be made on histological features, now a days many immunohistochemical (IHC) markers are used to distinguish it from benign mimickers as well as in predicting prognosis and treatment. Out of these markers, Ets-related gene (ERG product) is a proto-oncogene which participates in chromosomal translocations and is frequently over expressed in prostate carcinoma which harbors ERG-transmembrane protease, serine 2 fusion. Fifty cases of carcinoma prostate diagnosed in needle biopsies and prostatic chips, in the Department of Pathology of a tertiary care teaching hospital in Punjab, India, were included in the present study. The slides were observed under the light microscope, and Gleason scoring was done using the 2005 International Society of Urological Pathology modified Gleason system. IHC study for ERG expression was done on all the cases, for which anti-ERG monoclonal rabbit clone antibody EP111 (Dako, Denmark) was used. Lymphocytes and endothelial cells were taken as in built positive controls for staining. The intensity of ERG positivity was scored as no staining (0), weak staining (+1), moderate staining (+2) and intense staining (+3). The H score was then calculated by multiplying the intensity of the stain with the percentage (0-100) of the cells showing that staining intensity. The H-score has a range of 0-300. The relationship between IHC expression and clinico-pathological parameters was compared and analyzed using Chi-square test. P < 0.05 was considered statistically significant. Majority of patients included in the study were in the age group of 61-80 (84% of the total). When ERG expression was studied with age

  15. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

    Science.gov (United States)

    Ben-Yehezkel, Tuval; Atar, Shimshi; Zur, Hadas; Diament, Alon; Goz, Eli; Marx, Tzipy; Cohen, Rafael; Dana, Alexandra; Feldman, Anna; Shapiro, Ehud; Tuller, Tamir

    2015-01-01

    Deducing generic causal relations between RNA transcript features and protein expression profiles from endogenous gene expression data remains a major unsolved problem in biology. The analysis of gene expression from heterologous genes contributes significantly to solving this problem, but has been heavily biased toward the study of the effect of 5′ transcript regions and to prokaryotes. Here, we employ a synthetic biology driven approach that systematically differentiates the effect of different regions of the transcript on gene expression up to 240 nucleotides into the ORF. This enabled us to discover new causal effects between features in previously unexplored regions of transcripts, and gene expression in natural regimes. We rationally designed, constructed, and analyzed 383 gene variants of the viral HRSVgp04 gene ORF, with multiple synonymous mutations at key positions along the transcript in the eukaryote S. cerevisiae. Our results show that a few silent mutations at the 5′UTR can have a dramatic effect of up to 15 fold change on protein levels, and that even synonymous mutations in positions more than 120 nucleotides downstream from the ORF 5′end can modulate protein levels up to 160%–300%. We demonstrate that the correlation between protein levels and folding energy increases with the significance of the level of selection of the latter in endogenous genes, reinforcing the notion that selection for folding strength in different parts of the ORF is related to translation regulation. Our measured protein abundance correlates notably(correlation up to r = 0.62 (p=0.0013)) with mean relative codon decoding times, based on ribosomal densities (Ribo-Seq) in endogenous genes, supporting the conjecture that translation elongation and adaptation to the tRNA pool can modify protein levels in a causal/direct manner. This report provides an improved understanding of transcript evolution, design principles of gene expression regulation, and suggests simple

  16. Picroside II Attenuates Airway Inflammation by Downregulating the Transcription Factor GATA3 and Th2-Related Cytokines in a Mouse Model of HDM-Induced Allergic Asthma.

    Directory of Open Access Journals (Sweden)

    Jin Choi

    Full Text Available Picroside II isolated from Pseudolysimachion rotundum var. subintegrum has been used as traditional medicine to treat inflammatory diseases. In this study, we assessed whether picroside II has inhibitory effects on airway inflammation in a mouse model of house dust mite (HDM-induced asthma. In the HDM-induced asthmatic model, picroside II significantly reduced inflammatory cell counts in the bronchoalveolar lavage fluid (BALF, the levels of total immunoglobulin (Ig E and HDM-specific IgE and IgG1 in serum, airway inflammation, and mucus hypersecretion in the lung tissues. ELISA analysis showed that picroside II down-regulated the levels of Th2-related cytokines (including IL-4, IL-5, and IL-13 and asthma-related mediators, but it up-regulated Th1-related cytokine, IFNγ in BALF. Picroside II also inhibited the expression of Th2 type cytokine genes and the transcription factor GATA3 in the lung tissues of HDM-induced mice. Finally, we demonstrated that picroside II significantly decreased the expression of GATA3 and Th2 cytokines in developing Th2 cells, consistent with in vivo results. Taken together, these results indicate that picroside II has protective effects on allergic asthma by reducing GATA3 expression and Th2 cytokine bias.

  17. Abundance estimation and conservation biology

    Science.gov (United States)

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention

  18. Abundance estimation and Conservation Biology

    Directory of Open Access Journals (Sweden)

    Nichols, J. D.

    2004-06-01

    Full Text Available Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001. The initial capture–recapture models developed for partially (Darroch, 1959 and completely (Jolly, 1965; Seber, 1965 open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992, and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993. However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001. The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004 is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004 emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004 also suggest that

  19. Relação entre fator de condição relativo (Kn e abundância de ectoparasitos de brânquias, em duas espécies de ciclídeos da bacia do rio Paraná, Brasil = Relation between the relative condition factor (Kn and the abundance of gill ectoparasites in two species of cichlids from the Paraná river basin, Brazil

    Directory of Open Access Journals (Sweden)

    Fábio Hideki Yamada

    2008-04-01

    Full Text Available Foram analisados 33 espécimes de Satanoperca pappaterra, capturados entre março de 2004 e junho de 2005, na planície de inundação do alto rio Paraná e 33 espécimes de Crenicichla niederleinii, capturados entre novembro de 2005 e novembro de 2006, no reservatório de Itaipu. Ambos estavam parasitados por monogenéticos, pertencentes ao gênero Sciadicleithrum e por metacercárias de Ascocotyle sp. O fator de condição relativo (Kn não diferiu significativamente entre indivíduos parasitados e não-parasitados das duas espécies de hospedeiros. Apenas Sciadicleithrum sp.1 parasito de S. pappaterra apresentou correlação positiva e significativa entre o fator de condição relativo (Kn e a abundância de parasitismo. Por outro lado, Ascocotyle sp. de ambos os hospedeiros e Sciadicleithrum sp.2parasito de C. niederleinii não apresentaram correlações entre o Kn e a abundância de parasitismo.The study analyzed 33 specimens of Satanoperca pappaterra, captured from the Upper Paraná River floodplain between March 2004 and June of 2005, and 33 specimens of Crenicichla niederleinii captured from the Itaipu Reservoir between November 2005 and November 2006. Both were parasitized by monogeneans pertaining to the genus Sciadicleithrum and by metacercariae of Ascocotyle sp. The relative condition factor (Kn did not differ significantly between parasitized and unparasitized individuals from the two host species. Only Sciadicleithrum sp.1, parasite of S. pappaterra, presented positive and significant correlation between the relative condition factor (Kn and the abundance of parasitism. On the other hand, Ascocotyle sp. in both hosts and Sciadicleithrum sp.2 parasite of C. niederleiniidid not present correlations between the Kn and the abundance of parasitism.

  20. Plant Macrofossils from the Takht Coal Mine, Minoodasht and its Dating, Relative abundance and Sørensen index in comparison with the other Florizones in Iran and Eurasia

    Directory of Open Access Journals (Sweden)

    Akbar Parvacideh

    2015-01-01

    Full Text Available Takht mine, SE Minoodasht contains well-preserved plant macrofossils belonging to 27 species allocated to 22 genera of various orders viz., Equisetales, Osmundales, Filicales, Peltaspermales, Bennettitales, Ginkgoales and Coniferales. The plant macrofossils in this area are studied for the first time. Based on the occurrence of Equisetites muensteri, Clathropteris meniscoides, Dictyophyllum exile, Anthrophyopsis crassinervis, Scytophyllum persicum, Pterophyllum bavieri, and Baiera muensteriana a Rhaetian age is suggested for this assemblage. Since, there was no differentiation between formations in geological map these flora emphasized spreading the Kalariz Formation in this area. The Minoodasht flora is correlated to the plant macrofossil assemblages of Zirab, Tazareh, Narges-Chal, Hiv, Jajarm (Alborz, Parvadeh mines (Tabas, and Darbid-Khun (Kerman Basin. Therefore, there were close floristic relationships between North and Central-East Iran (i.e. Kerman Basin and Tabas Block and two areas were palaeogeographically closely related, probably forming a uniform paleoenvironment. On the basis of relative abundances of taxa, Filicales, Bennettitales, Ginkgoales and Pinales were 42.02%, 38.11%, 7.17% and 6.51%, respectively. It is noteworthy that variety and relative abundance of the species of Filicophyta and Bennetittales were high within Iran during the Late Triassic epoch. Therefore, a warm wet climatic regime dominated. In addition, a more uniform climate in continental scale is suggested. On the basis of similarity indices and relative abundance of taxa, Iran located within Eurasia climatic belt, Euro-Sinian Region, and the Middle Asia Province of Vakhrameev’s subdivisions and south-western region of Dubroskina’s subdivisions during this epoch.

  1. STUDY ON OCEANGRAFHIC AND WEATHER CONDITIONS RELATED TO THE ABUNDANCE OF SMALL PELAGIC FISHERY IN NATUNA SEA USING REMOTE SENSING DATA

    Directory of Open Access Journals (Sweden)

    Teguh Prayogo

    2012-11-01

    Full Text Available Indonesian waters have abundance of natural resources; the potential of small pelagic fish in Natuna Sea and SouthChina Sea have not been optimized yet explores. Unfortunately, it was caused by lacking in the data of environmentalconditions that have been changed and the information of appropriate fishing ground. Hence, dynamical oceanographicinformation and weather condition is necessary to optimize small pelagic fish exploitation.Research location in Natuna Sea and its surrounding with geographical position is 08°N–03°S; 103°–111°E. Theoceanographic condition representative by monthly SST, Chl-a, SSH that derived from satellite data and Dipole ModeIndex for 2002-2007 from FRCGC website. Monthly wind data is variable for weather condition. Small pelagic fishabundance representative by annual fish production (2002-2005 and monthly Catch Per Unit Effort (CPUE ofGoldstripe sardinella, Bigeye scad and Indian scad (2006. It was data collected from Directorate General of CaptureFisheries (Ministry of Marine Affairs and Fisheries and daily fishing operation (2007 used to calculate match-up ratiothat was collected from Pemangkat fishing port in West Kalimantan. Research process consists of image processing,descriptive correlation analysis and GIS analysis to predict fishing ground map and match-up ratio calculation.Result of this research is the annual fish catch production of Bigeye scad and Indian scad (2002-2005 is tend toincrease and the monthly CPUE of both species is high during SE Monsoon (May-Sep that is condition contrarily in NWMonsoon (Nov-Apr. Meanwhile, the annual fish catch production of Goldstripe sardinella production is tend to decreasefrom 2002-2005, it has CPUE is high in early SE Monsoon (May. During the SE Monsoon (May-Sep when DM Index ispositive (+ the Indian scad and Bigeye scad production is high, for Goldstripe sardinella the fish production is highwhen DM Index is positive (+ in May. The accuracy of prediction map of

  2. Abundance variations in solar active regions

    Science.gov (United States)

    Strong, K. T.; Lemen, J. R.; Linford, G. A.

    1991-01-01

    The diversity in the published values of coronal abundances is unsettling, especially as the range of results seems to be beyond the quoted uncertainties. Measurements of the relative abundance of iron and neon derived from soft X-ray spectra of active regions are presented. From a data base of over 200 spectra taken by the Solar Maximum Mission Flat Crystal Spectrometer, it is found that the relative abundance can vary by as much as a factor of about 7 and can change on timescales of less than 1 h.

  3. Non-constant relative atomic masses due to varying isotopic abundance of polynuclidic elements and their effect on the accuracy of analytical results

    International Nuclear Information System (INIS)

    Gerstenberger, H.

    1981-01-01

    Alterations of actual relative atomic masses occur in natural samples by natural isotope ratio shifts of polynuclidic elements. Therefore, using nuclear properties for gaining a measuring signal, isotopic shifts of certain elements may lead to significant measuring errors

  4. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  5. SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism.

    Directory of Open Access Journals (Sweden)

    Nicolas M Bertagnolli

    Full Text Available To search for evolutionary forces that might act upon transcript length, we use the singular value decomposition (SVD to identify the length distribution functions of sets and subsets of human and yeast transcripts from profiles of mRNA abundance levels across gel electrophoresis migration distances that were previously measured by DNA microarrays. We show that the SVD identifies the transcript length distribution functions as "asymmetric generalized coherent states" from the DNA microarray data and with no a-priori assumptions. Comparing subsets of human and yeast transcripts of the same gene ontology annotations, we find that in both disparate eukaryotes, transcripts involved in protein synthesis or mitochondrial metabolism are significantly shorter than typical, and in particular, significantly shorter than those involved in glucose metabolism. Comparing the subsets of human transcripts that are overexpressed in glioblastoma multiforme (GBM or normal brain tissue samples from The Cancer Genome Atlas, we find that GBM maintains normal brain overexpression of significantly short transcripts, enriched in transcripts that are involved in protein synthesis or mitochondrial metabolism, but suppresses normal overexpression of significantly longer transcripts, enriched in transcripts that are involved in glucose metabolism and brain activity. These global relations among transcript length, cellular metabolism and tumor development suggest a previously unrecognized physical mode for tumor and normal cells to differentially regulate metabolism in a transcript length-dependent manner. The identified distribution functions support a previous hypothesis from mathematical modeling of evolutionary forces that act upon transcript length in the manner of the restoring force of the harmonic oscillator.

  6. Discovery of novel transcripts of the human tissue kallikrein (KLK1) and kallikrein-related peptidase 2 (KLK2) in human cancer cells, exploiting Next-Generation Sequencing technology.

    Science.gov (United States)

    Adamopoulos, Panagiotis G; Kontos, Christos K; Scorilas, Andreas

    2018-03-31

    Tissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional properties. Several KLK transcripts have been found aberrantly expressed in numerous human malignancies, confirming their prognostic or/and diagnostic values. However, the process of alternative splicing can now be studied in-depth due to the development of Next-Generation Sequencing (NGS). In the present study, we used NGS to discover novel transcripts of the KLK1 and KLK2 genes, after nested touchdown PCR. Bioinformatics analysis and PCR experiments revealed a total of eleven novel KLK transcripts (two KLK1 and nine KLK2 transcripts). In addition, the expression profiles of each novel transcript were investigated with nested PCR experiments using variant-specific primers. Since KLKs are implicated in human malignancies, qualifying as potential biomarkers, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer. Copyright © 2018. Published by Elsevier Inc.

  7. Stellar pulsation and the abundance of helium

    International Nuclear Information System (INIS)

    Schmidt, E.G.

    1978-01-01

    It has been suggested that the appearance of nonvariable stars within the Cepheid strip could be explained by a range in the helium abundance of Population I stars. In order to study this possibility, spectra were obtained of the main-sequence B stars in the galactic cluster NGC 129, which contains a nonvariable Cepheid-strip star, and M25, which contains a relatively hot Cepheid. Unfortunately, several of the stars in these clusters turn out to be helium-weak stars. In NGC 129 two stars which appear normal give a normal abundance, while in M25 all of the observed stars have abnormally low abundances. The significance of the low abundance in M25 is not clear. The abundance in NGC 129 is not low enough to support the above suggestion. 4 figures, 2 tables

  8. Ammonia abundances in comets

    Science.gov (United States)

    Wyckoff, S.; Tegler, S.; Engel, L.

    The emission band strengths of the NH2 bands of Comets Halley, Hartley-Good, Thiele, and Borrelly were measured to determine the NH2 column densities for the comets. Production rates obtained using the Haser and vectorial models are in agreement within the observational errors, suggesting that a simple two-step decay model may be used to approximate the NH2 distribution in a comet's coma. Ammonia-to-water abundance ratios from 0.01 to 0.4 percent were found for the four comets. The ratio in Comet Halley is found to be Q(NH3)/Q(H2O) = 0.002 + or - 0.001. No significant difference in the ammonia abundance was found before or after perihelion in Comet Halley.

  9. Compilation of solar abundance data

    International Nuclear Information System (INIS)

    Hauge, Oe.; Engvold, O.

    1977-01-01

    Interest in the previous compilations of solar abundance data by the same authors (ITA--31 and ITA--39) has led to this third, revised edition. Solar abundance data of 67 elements are tabulated and in addition upper limits for the abundances of 5 elements are listed. References are made to 167 papers. A recommended abundance value is given for each element. (JIW)

  10. Abundances in galaxies

    International Nuclear Information System (INIS)

    Pagel, B.E.J.

    1991-01-01

    Standard (or mildly inhomogeneous) Big Bang nucleosynthesis theory is well confirmed by abundance measurements of light elements up to 7 Li and the resulting upper limit to the number of neutrino families confirmed in accelerator experiments. Extreme inhomogeneous models with a closure density in form of baryons seem to be ruled out and there is no evidence for a cosmic 'floor' to 9 Be or heavier elements predicted in some versions of those models. Galaxies show a correlation between luminous mass and abundance of carbon and heavier elements, usually attributed to escape of hot gas from shallow potential wells. Uncertainties include the role of dark matter and biparametric behaviour of ellipticals. Spirals have radial gradients which may arise from a variety of causes. In our own Galaxy one can distinguish three stellar populations - disk, halo and bulge - characterised by differing metallicity distribution functions. Differential abundance effects are found among different elements in stars as a function of metallicity and presumably age, notably in the ratio of oxygen and α-particle elements to iron. These may eventually be exploitable to set a time scale for the formation of the halo, bulge and disk. (orig.)

  11. Nuclear stability and transcriptional directionality separate functionally distinct RNA species

    DEFF Research Database (Denmark)

    Andersson, Robin; Refsing Andersen, Peter; Valen, Eivind

    2014-01-01

    Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. Although recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protei...

  12. Expression profile of doublesex/male abnormal-3-related transcription factor-1 during gonadal sex change in the protogynous wrasse, Halichoeres trimaculatus.

    Science.gov (United States)

    Nozu, Ryo; Horiguchi, Ryo; Kobayashi, Yasuhisa; Nakamura, Masaru

    2015-11-01

    Sex change in fish involves a dramatic transformation of gonadal tissue and a switch in gametogenesis. Doublesex/male abnormal-3-related transcription factor-1 (DMRT1), encoded by the DMRT1 gene, is involved in testicular differentiation in a wide range of vertebrates as well as in sexual differentiation and gonadal sex change. In the present study, we investigated changes in the expression of dmrt1 during artificial gonadal sex change in the three-spot wrasse, Halichoeres trimaculatus, by real-time quantitative PCR and immunolocalization, using an anti-wrasse-Dmrt1 antibody that we prepared. We found that dmrt1 expression was predominantly observed in the testes, and that Dmrt1 was expressed in Sertoli cells of testes and a few granulosa cells surrounding vitellogenic oocytes of the ovary. Additionally, the upregulation of dmrt1 expression was consistent with an increase in spermatogenic cyst quantity rather than proliferation of presumptive spermatogonia, suggesting that dmrt1 is involved in the progression of spermatogenesis during sex change. Changes in the localization of Dmrt1 during gonadal sex change further implied that Sertoli cells originate from somatic cells adjacent to gonial germ cells during testicular formation in the three-spot wrasse. © 2015 Wiley Periodicals, Inc.

  13. Increased Energy Expenditure, Ucp1 Expression, and Resistance to Diet-induced Obesity in Mice Lacking Nuclear Factor-Erythroid-2-related Transcription Factor-2 (Nrf2).

    Science.gov (United States)

    Schneider, Kevin; Valdez, Joshua; Nguyen, Janice; Vawter, Marquis; Galke, Brandi; Kurtz, Theodore W; Chan, Jefferson Y

    2016-04-01

    The NRF2 (also known as NFE2L2) transcription factor is a critical regulator of genes involved in defense against oxidative stress. Previous studies suggest thatNrf2plays a role in adipogenesisin vitro, and deletion of theNrf2gene protects against diet-induced obesity in mice. Here, we demonstrate that resistance to diet-induced obesity inNrf2(-/-)mice is associated with a 20-30% increase in energy expenditure. Analysis of bioenergetics revealed thatNrf2(-/-)white adipose tissues exhibit greater oxygen consumption. White adipose tissue showed a >2-fold increase inUcp1gene expression. Oxygen consumption is also increased nearly 2.5-fold inNrf2-deficient fibroblasts. Oxidative stress induced by glucose oxidase resulted in increasedUcp1expression. Conversely, antioxidant chemicals (such asN-acetylcysteine and Mn(III)tetrakis(4-benzoic acid)porphyrin chloride) and SB203580 (a known suppressor ofUcp1expression) decreasedUcp1and oxygen consumption inNrf2-deficient fibroblasts. These findings suggest that increasing oxidative stress by limitingNrf2function in white adipocytes may be a novel means to modulate energy balance as a treatment of obesity and related clinical disorders. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Differential transcript induction of parsley pathogenesis-related proteins and of a small heat shock protein by ozone and heat shock

    International Nuclear Information System (INIS)

    Eckey-Kaltenbach, H.; Kiefer, E.; Grosskopf, E.; Ernst, D.; Sandermann, H. Jr

    1997-01-01

    Parsley (Petroselinum (crispum L.) is known to respond to pathogen attack by the synthesis of furanocoumarins and to UV irradiation by the synthesis of flavone glycosides whereas ozone treatment results in the induction of both pathways. A cDNA library from parsley plants was differentially screened using labelled reverse-transcribed poly(A)+ RNA isolated from ozone-treated parsley plants. This resulted in the isolation of 13 independent cDNA clones representing ozone-induced genes and of 11 cDNA clones representing ozone-repressed genes. DNA sequencing of several clones resulted in the identification of pathogenesis-related protein 1-3 (PR1-3), of a new member of PR1 cDNAs (PRI-4) and of a small heat shock protein (sHSP). Northern blot analyses showed a transient induction of the three mRNA species after ozone fumigation. In contrast, heat shock treatment of parsley plants resulted in an increase of sHSP mRNA whereas no increase for transcripts of PR1-3 and PR1-4 could be observed. This is the first characterized sHSP cDNA clone for plants induced by heat shock, as well as by oxidative stress caused by ozone. (author)

  15. Alteration of runt-related transcription factor 3 gene expression and biologic behavior of esophageal carcinoma TE-1 cells after 5-azacytidine intervention.

    Science.gov (United States)

    Wang, Shuai; Liu, Hong; Akhtar, Javed; Chen, Hua-Xia; Wang, Zhou

    2013-01-01

    5-Azacytidine (5-azaC) was originally identified as an anticancer drug (NSC102876) which can cause hypomethylation of tumor suppressor genes. To assess its effects on runt-related transcription factor 3 (RUNX3), expression levels and the promoter methylation status of the RUNX3 gene were assessed. We also investigated alteration of biologic behavior of esophageal carcinoma TE-1 cells. MTT assays showed 5-azaC inhibited the proliferation of TE-1 cells in a time and dose-dependent way. Although other genes could be demethylated after 5-azaC intervention, we focused on RUNX3 gene in this study. The expression level of RUNX3 mRNA increased significantly in TE-1 cells after treatment with 5-azaC at hypotoxic levels. RT-PCR showed 5-azaC at 50 μM had the highest RUNX3-induction activity. Methylation-specific PCR indicated that 5-azaC induced RUNX3 expression through demethylation. Migration and invasion of TE-1 cells were inhibited by 5-azaC, along with growth of Eca109 xenografts in nude mice. In conclusion, we demonstrate that the RUNX3 gene can be reactivated by the demethylation reagent 5-azaC, which inhibits the proliferation, migration and invasion of esophageal carcinoma TE-1 cells.

  16. Glycogen synthase kinase 3 regulates expression of nuclear factor-erythroid-2 related transcription factor-1 (Nrf1) and inhibits pro-survival function of Nrf1

    Energy Technology Data Exchange (ETDEWEB)

    Biswas, Madhurima; Kwong, Erick K.; Park, Eujean; Nagra, Parminder; Chan, Jefferson Y., E-mail: jchan@uci.edu

    2013-08-01

    Nuclear factor E2-related factor-1 (Nrf1) is a basic leucine zipper transcription factor that is known to regulate antioxidant and cytoprotective gene expression. It was recently shown that Nrf1 is regulated by SCF–Fbw7 ubiquitin ligase. However our knowledge of upstream signals that targets Nrf1 for degradation by the UPS is not known. We report here that Nrf1 expression is negatively regulated by glycogen synthase kinase 3 (GSK3) in Fbw7-dependent manner. We show that GSK3 interacts with Nrf1 and phosphorylates the Cdc4 phosphodegron domain (CPD) in Nrf1. Mutation of serine residue in the CPD of Nrf1 to alanine (S350A), blocks Nrf1 from phosphorylation by GSK3, and stabilizes Nrf1. Knockdown of Nrf1 and expression of a constitutively active form of GSK3 results in increased apoptosis in neuronal cells in response to ER stress, while expression of the GSK3 phosphorylation resistant S350A–Nrf1 attenuates apoptotic cell death. Together these data suggest that GSK3 regulates Nrf1 expression and cell survival function in response to stress activation. Highlights: • The effect of GSK3 on Nrf1 expression was examined. • GSK3 destabilizes Nrf1 protein via Fbw7 ubiquitin ligase. • GSK3 binds and phosphorylates Nrf1. • Protection from stress-induced apoptosis by Nrf1 is inhibited by GSK3.

  17. A module of human peripheral blood mononuclear cell transcriptional network containing primitive and differentiation markers is related to specific cardiovascular health variables.

    Directory of Open Access Journals (Sweden)

    Leni Moldovan

    Full Text Available Peripheral blood mononuclear cells (PBMCs, including rare circulating stem and progenitor cells (CSPCs, have important yet poorly understood roles in the maintenance and repair of blood vessels and perfused organs. Our hypothesis was that the identities and functions of CSPCs in cardiovascular health could be ascertained by analyzing the patterns of their co-expressed markers in unselected PBMC samples. Because gene microarrays had failed to detect many stem cell-associated genes, we performed quantitative real-time PCR to measure the expression of 45 primitive and tissue differentiation markers in PBMCs from healthy and hypertensive human subjects. We compared these expression levels to the subjects' demographic and cardiovascular risk factors, including vascular stiffness. The tested marker genes were expressed in all of samples and organized in hierarchical transcriptional network modules, constructed by a bottom-up approach. An index of gene expression in one of these modules (metagene, defined as the average standardized relative copy numbers of 15 pluripotency and cardiovascular differentiation markers, was negatively correlated (all p<0.03 with age (R2 = -0.23, vascular stiffness (R2 = -0.24, and central aortic pressure (R2 = -0.19 and positively correlated with body mass index (R2 = 0.72, in women. The co-expression of three neovascular markers was validated at the single-cell level using mRNA in situ hybridization and immunocytochemistry. The overall gene expression in this cardiovascular module was reduced by 72±22% in the patients compared with controls. However, the compactness of both modules was increased in the patients' samples, which was reflected in reduced dispersion of their nodes' degrees of connectivity, suggesting a more primitive character of the patients' CSPCs. In conclusion, our results show that the relationship between CSPCs and vascular function is encoded in modules of the PBMCs transcriptional

  18. ß-catenin, a transcription factor activated by canonical Wnt signaling, is expressed in sensory neurons of calves latently infected with bovine herpesvirus 1

    Science.gov (United States)

    Like many a-herpesvirinae subfamily members, bovine herpes virus 1 (BoHV-1) expresses an abundant transcript in latently infected sensory neurons: the latency-related (LR) RNA. LR-RNA encodes a protein (ORF2) that inhibits apoptosis, interacts with Notch family members, interferes with Notch mediate...

  19. Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

    Science.gov (United States)

    Stewart, Frank J.; Dalsgaard, Tage; Young, Curtis R.; Thamdrup, Bo; Revsbech, Niels Peter; Ulloa, Osvaldo; Canfield, Don E.; DeLong, Edward F.

    2012-01-01

    Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the

  20. High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR.

    Science.gov (United States)

    Blazejak, Anna; Schippers, Axel

    2010-05-01

    Sequences of members of the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi are frequently found in 16S rRNA gene clone libraries obtained from marine sediments. Using a newly designed quantitative, real-time PCR assay, these bacterial groups were jointly quantified in samples from near-surface and deeply buried marine sediments from the Peru margin, the Black Sea, and a forearc basin off the island of Sumatra. In near-surface sediments, sequences of the JS-1 as well as Anaerolineae- and Caldilineae-related Bacteria were quantified with significantly lower 16S rRNA gene copy numbers than the sequences of total Bacteria. In contrast, in deeply buried sediments below approximately 1 m depth, similar quantities of the 16S rRNA gene copies of these specific groups and Bacteria were found. This finding indicates that JS-1 and Anaerolineae- and Caldilineae-related Bacteria might dominate the bacterial community in deeply buried marine sediments and thus seem to play an important ecological role in the deep biosphere.

  1. Space-time variation of the relative abundance of Limnoperna fortunei in deep zones of São Gonçalo Channel, Rio Grande do Sul, Brazil Variação espaço-temporal da abundância relativa de Limnoperna fortunei em zonas profundas do canal São Gonçalo, Rio Grande do Sul, Brasil

    Directory of Open Access Journals (Sweden)

    Michelle Lopes

    2012-12-01

    Full Text Available This work describes the spatial-temporal variation of the relative abundance and size of Limnoperna fortunei (Dunker, 1857 collected in São Gonçalo Channel through bottom trawl with a 0.5 cm mesh, at depths between 3 and 6 m. The estimative of mean relative abundance (CPUE ranged from 2,425.3 individuals per drag (ind./drag in the spring to 21,715.0 ind./drag in the fall, with an average of 9,515.3 ind./drag throughout the year. The estimated mean density of L. fortunei for the deep region of São Gonçalo Channel ranged from 1.2 to 10.3 ind./m², and it was recorded a maximum density of 84.9 ind./m² in the fall of 2008. The method of sampling using bottom trawl enabled the capture of L. fortunei under the soft muddy bottom of the channel, in different sizes ranging from 0.4 to 3.2 cm. This shows that the structure of the L. fortunei adult population under the bottom of the São Gonçalo Channel is composed mostly of small individuals (Este trabalho descreve a variação espaço-temporal da abundância relativa e tamanho de Limnoperna fortunei (Dunker, 1857 coletados no Canal São Gonçalo através de rede de arrasto de fundo com malha 0,5 cm, em profundidades entre 3 e 6 m. As estimativas de abundância relativa média (CPUE variaram de 2.425,3 ind./arrasto, na primavera a 21.715,0 ind./arrasto no outono, com média de 9.515,3 ind./ arrasto ao longo do ano. A densidade média estimada para L. fortunei para a região profunda do Canal São Gonçalo variou de 1,2 a 10,3 ind./m², sendo registrada uma densidade máxima de 84,9 ind./m² no outono de 2008. O método de coleta com arrasto de fundo possibilitou a captura de L. fortunei sob o fundo mole lodoso do canal, em tamanhos variando de 0,4 a 3,2 cm, revelando que a estrutura da população adulta de L. fortunei sob fundo do Canal São Gonçalo é composta, em sua maioria, por indivíduos pequenos (<1,4 cm, os quais representam até 74% da população coletada.

  2. Space-time variation of the relative abundance of Limnoperna fortunei in deep zones of São Gonçalo Channel, Rio Grande do Sul, Brazil Variação espaço-temporal da abundância relativa de Limnoperna fortunei em zonas profundas do canal São Gonçalo, Rio Grande do Sul, Brasil

    Directory of Open Access Journals (Sweden)

    Michelle Lopes

    2012-01-01

    Full Text Available This work describes the spatial-temporal variation of the relative abundance and size of Limnoperna fortunei (Dunker, 1857 collected in São Gonçalo Channel through bottom trawl with a 0.5 cm mesh, at depths between 3 and 6 m. The estimative of mean relative abundance (CPUE ranged from 2,425.3 individuals per drag (ind./drag in the spring to 21,715.0 ind./drag in the fall, with an average of 9,515.3 ind./drag throughout the year. The estimated mean density of L. fortunei for the deep region of São Gonçalo Channel ranged from 1.2 to 10.3 ind./m², and it was recorded a maximum density of 84.9 ind./m² in the fall of 2008. The method of sampling using bottom trawl enabled the capture of L. fortunei under the soft muddy bottom of the channel, in different sizes ranging from 0.4 to 3.2 cm. This shows that the structure of the L. fortunei adult population under the bottom of the São Gonçalo Channel is composed mostly of small individuals (Este trabalho descreve a variação espaço-temporal da abundância relativa e tamanho de Limnoperna fortunei (Dunker, 1857 coletados no Canal São Gonçalo através de rede de arrasto de fundo com malha 0,5 cm, em profundidades entre 3 e 6 m. As estimativas de abundância relativa média (CPUE variaram de 2.425,3 ind./arrasto, na primavera a 21.715,0 ind./arrasto no outono, com média de 9.515,3 ind./ arrasto ao longo do ano. A densidade média estimada para L. fortunei para a região profunda do Canal São Gonçalo variou de 1,2 a 10,3 ind./m², sendo registrada uma densidade máxima de 84,9 ind./m² no outono de 2008. O método de coleta com arrasto de fundo possibilitou a captura de L. fortunei sob o fundo mole lodoso do canal, em tamanhos variando de 0,4 a 3,2 cm, revelando que a estrutura da população adulta de L. fortunei sob fundo do Canal São Gonçalo é composta, em sua maioria, por indivíduos pequenos (<1,4 cm, os quais representam até 74% da população coletada.

  3. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

    Directory of Open Access Journals (Sweden)

    Settles Matthew L

    2009-05-01

    -antisense transcript pairs, analysis of the gene ontology terms showed a significant over-representation of transcripts involved in energy production. These included several representations of ATP synthase, photosystem proteins and RUBISCO, which indicated that photosynthesis is likely to be regulated by antisense transcripts. Conclusion This study demonstrated the novel use of an adapted labeling protocol and a 3'IVT GeneChip array for large-scale identification of antisense transcription in wheat. The results show that antisense transcription is relatively abundant in wheat, and may affect the expression of valuable agronomic phenotypes. Future work should select potentially interesting transcript pairs for further functional characterization to determine biological activity.

  4. Fetal life malnutrition was not reflected in the relative abundances of adiponectin and leptin mRNAs in adipose tissue in male mink kits at 9.5 weeks of age

    DEFF Research Database (Denmark)

    Matthiesen, Connie Frank; Tauson, Anne-Helene

    2016-01-01

    Background: Malnutrition in fetal life and during suckling have in some animal studies resulted in adaptive changes related to the fat and glucose metabolism, which in the long term might predispose the offspring for metabolic disorders such as obesity later in life. The objective was to study...... the effect of fetal life malnutrition in male mink on the gene expression of leptin and adiponectin in different adipose tissue sites. Results: Thirty-two male mink, strict carnivore species, exposed to low (FL) or adequate (FA) protein provision the last 16.3 ± 1.8 days of fetal life and randomly assigned.......5 weeks of age. Relative abundances of leptin and adiponectin mRNAs were different between adipose tissue sites and were significantly higher in subcutaneous than in perirenal and mesenteric tissues. Conclusion:Fetal life protein malnutrition in male mink, did not result in adaptive changes in the gene...

  5. Relative abundance of Delta(5)-sterols in plasma membrane lipids of root-tip cells correlates with aluminum tolerance of rice.

    Science.gov (United States)

    Khan, M Shahadat Hossain; Tawaraya, Keitarou; Sekimoto, Hiroshi; Koyama, Hiroyuki; Kobayashi, Yuriko; Murayama, Tetsuya; Chuba, Masaru; Kambayashi, Mihoko; Shiono, Yoshihito; Uemura, Matsuo; Ishikawa, Satoru; Wagatsuma, Tadao

    2009-01-01

    We investigated variations in aluminum (Al) tolerance among rice plants, using ancestor cultivars from the family line of the Al-tolerant and widely cultivated Japonica cultivar, Sasanishiki. The cultivar Rikuu-20 was Al sensitive, whereas a closely related cultivar that is a descendant of Rikuu-20, Rikuu-132, was Al tolerant. These two cultivars were compared to determine mechanisms underlying variations in Al tolerance. The sensitive cultivar Rikuu-20 showed increased permeability of the plasma membrane (PM) and greater Al uptake within 1 h of Al treatment. This could not be explained by organic acid release. Lipid composition of the PM differed between these cultivars, and may account for the difference in Al tolerance. The tolerant cultivar Rikuu-132 had a lower ratio of phospholipids to Delta(5)-sterols than the sensitive cultivar Rikuu-20, suggesting that the PM of Rikuu-132 is less negatively charged and less permeabilized than that of Rikuu-20. We used inhibitors of Delta(5)-sterol synthesis to alter the ratio of phospholipids to Delta(5)-sterols in both cultivars. These inhibitors reduced Al tolerance in Rikuu-132 and its Al-tolerant ancestor cultivars Kamenoo and Kyoku. In addition, Rikuu-132 showed a similar level of Al sensitivity when the ratio of phospholipids to Delta(5)-sterols was increased to match that of Rikuu-20 after treatment with uniconazole-P, an inhibitor of obtusifoliol-14alpha-demethylase. These results indicate that PM lipid composition is a factor underlying variations in Al tolerance among rice cultivars.

  6. Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

    Science.gov (United States)

    Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

    2003-06-06

    Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

  7. Anomalous behavior of tellurium abundances

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, B L

    1984-01-01

    The cosmic abundance of Te is larger than for any element with atomic number greater than 40, but it is one of the least abundant elements in the earth's lithosphere and it is one of the five elements never reported in sea water. On the other hand, it is the fourth most abundant element in the human body (after Fe, Zn and Rb), and is unusually abundant in human food. It is shown that the high abundance in human food combined with the low abundance in soil requires that it be picked up by plant roots very much more efficiently than any other trace element.

  8. Composition and abundance of tree regeneration

    Science.gov (United States)

    Todd F. Hutchinson; Elaine Kennedy Sutherland; Charles T. Scott

    2003-01-01

    The composition and abundance of tree seedlings and saplings in the four study areas in southern Ohio were related to soil moisture via a GIS-derived integrated moisture index and to soil texture and fertility. For seedlings, the total abundance of small stems (less than 30 cm tall) was significantly greater on xeric plots (81,987/ha) than on intermediate (54,531/ha)...

  9. Comparative transcriptional and translational analysis of leptospiral outer membrane protein expression in response to temperature.

    Directory of Open Access Journals (Sweden)

    Miranda Lo

    Full Text Available BACKGROUND: Leptospirosis is a global zoonosis affecting millions of people annually. Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. Past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. However, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. Given the abundance of post-transcriptional expression control mechanisms, this finding highlighted the importance of global protein analysis systems. METHODOLOGY/PRINCIPAL FINDINGS: To complement our previous transcription study, we evaluated differences in the proteins of the leptospiral outer membrane fraction in response to temperature upshift. Outer membrane protein-enriched fractions from Leptospira interrogans grown at 30 degrees C or overnight upshift to 37 degrees C were isolated and the relative abundance of each protein was determined by iTRAQ analysis coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2-DLC/MS-MS. We identified 1026 proteins with 99% confidence; 27 and 66 were present at elevated and reduced abundance respectively. Protein abundance changes were compared with transcriptional differences determined from the microarray studies. While there was some correlation between the microarray and iTRAQ data, a subset of genes that showed no differential expression by microarray was found to encode temperature-regulated proteins. This set of genes is of particular interest as it is likely that regulation of their expression occurs post-transcriptionally, providing an opportunity to develop hypotheses about the molecular dynamics of the outer membrane of Leptospira in response to changing environments. CONCLUSIONS/SIGNIFICANCE: This is the first study to compare transcriptional and translational responses to temperature

  10. Interannual variation of rare earth element abundances in corals from northern coast of the South China Sea and its relation with sea-level change and human activities

    Science.gov (United States)

    Liu, Yajing; Peng, Z.; Wei, G.; Chen, T.; Sun, W.; He, J.; Liu, Gaisheng; Chou, C.-L.; Shen, C.-C.

    2011-01-01

    Here we present interannual rare earth element (REE) records spanning the last two decades of the 20th century in two living Porites corals, collected from Longwan Bay, close to the estuarine zones off Wanquan River of Hainan Island and Hong Kong off the Pearl River Delta of Guangdong Province in the northern South China Sea. The results show that both coral REE contents (0.5-40 ng g-1 in Longwan Bay and 2-250 ng g-1 in Hong Kong for La-Lu) are characterized with a declining trend, which are significantly negative correlated with regional sea-level rise (9.4 mm a-1 from 1981 to 1996 in Longwan Bay, 13.7 mm a-1 from 1991 to 2001 in Hong Kong). The REE features are proposed to be resulted from seawater intrusion into the estuaries in response to contemporary sea-level rise. However, the tendency for the coral Er/Nd time series at Hong Kong site is absent and there is no significant relation between Er/Nd and total REEs as found for the coral at Longwan Bay site. The observations are likely attributed to changes of the water discharge and sediment load of Pearl River, which have been significantly affected by intense human activities, such as the construction of dams/reservoirs and riverbed sediment mining, in past decades. The riverine sediment load/discharge ratio of the Pearl River decreased sharply with a rate of 0.02 kg m-3 a-1, which could make significant contribution to the declining trend of coral REE. We propose that coastal corals in Longwan Bay and similar unexplored sites with little influences of river discharge and anthropogenic disruption are ideal candidates to investigate the influence of sea-level change on seawater/coral REE. ?? 2010 Elsevier Ltd.

  11. Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling.

    Science.gov (United States)

    Sun, Feifei; Zhang, Xiaoli; Zhang, Qianqian; Liu, Fanghua; Zhang, Jianping; Gong, Jun

    2015-10-01

    Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem. Copyright © 2015

  12. Changes in transcription of cytokinin metabolism and signalling genes in grape (Vitis vinifera L.) berries are associated with the ripening-related increase in isopentenyladenine.

    Science.gov (United States)

    Böttcher, Christine; Burbidge, Crista A; Boss, Paul K; Davies, Christopher

    2015-09-16

    Cytokinins are known to play an important role in fruit set and early fruit growth, but their involvement in later stages of fruit development is less well understood. Recent reports of greatly increased cytokinin concentrations in the flesh of ripening kiwifruit (Actinidia deliciosa (A. Chev.) C.F. Liang & A.R. Ferguson) and grapes (Vitis vinifera L.) have suggested that these hormones are implicated in the control of ripening-related processes. A similar pattern of isopentenyladenine (iP) accumulation was observed in the ripening fruit of several grapevine cultivars, strawberry (Fragaria ananassa Duch.) and tomato (Solanum lycopersicum Mill.), suggesting a common, ripening-related role for this cytokinin. Significant differences in maximal iP concentrations between grapevine cultivars and between fruit species might reflect varying degrees of relevance or functional adaptations of this hormone in the ripening process. Grapevine orthologues of five Arabidopsis (Arabidopsis thaliana L.) gene families involved in cytokinin metabolism and signalling were identified and analysed for their expression in developing grape berries and a range of other grapevine tissues. Members of each gene family were characterised by distinct expression profiles during berry development and in different grapevine organs, suggesting a complex regulation of cellular cytokinin activities throughout the plant. The post-veraison-specific expression of a set of biosynthesis, activation, perception and signalling genes together with a lack of expression of degradation-related genes during the ripening phase were indicative of a local control of berry iP concentrations leading to the observed accumulation of iP in ripening grapes. The transcriptional analysis of grapevine genes involved in cytokinin production, degradation and response has provided a possible explanation for the ripening-associated accumulation of iP in grapes and other fruit. The pre- and post-veraison-specific expression of

  13. Characterization of relative abundance of lactic acid bacteria species in French organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods.

    Science.gov (United States)

    Michel, Elisa; Monfort, Clarisse; Deffrasnes, Marion; Guezenec, Stéphane; Lhomme, Emilie; Barret, Matthieu; Sicard, Delphine; Dousset, Xavier; Onno, Bernard

    2016-12-19

    In order to contribute to the description of sourdough LAB composition, MiSeq sequencing and qPCR methods were performed in association with cultural methods. A panel of 16 French organic bakers and farmer-bakers were selected for this work. The lactic acid bacteria (LAB) diversity of their organic sourdoughs was investigated quantitatively and qualitatively combining (i) Lactobacillus sanfranciscensis-specific qPCR, (ii) global sequencing with MiSeq Illumina technology and (iii) molecular isolates identification. In addition, LAB and yeast enumeration, pH, Total Titratable Acidity, organic acids and bread specific volume were analyzed. Microbial and physico-chemical data were statistically treated by Principal Component Analysis (PCA) and Hierarchical Ascendant Classification (HAC). Total yeast counts were 6 log 10 to 7.6 log 10 CFU/g while LAB counts varied from 7.2 log 10 to 9.6 log 10 CFU/g. Values obtained by L. sanfranciscensis-specific qPCR were estimated between 7.2 and 10.3 log 10 CFU/g, except for one sample at 4.4 log 10 CFU/g. HAC and PCA clustered the sixteen sourdoughs into three classes described by their variables but without links to bakers' practices. L. sanfranciscensis was the dominant species in 13 of the 16 sourdoughs analyzed by Next Generation Sequencing (NGS), by the culture dependent method this species was dominant only in only 10 samples. Based on isolates identification, LAB diversity was higher for 7 sourdoughs with the recovery of L. curvatus, L. brevis, L. heilongjiangensis, L. xiangfangensis, L. koreensis, L. pontis, Weissella sp. and Pediococcus pentosaceus, as the most representative species. L. koreensis, L. heilongjiangensis and L. xiangfangensis were identified in traditional Asian food and here for the first time as dominant in organic sourdough. This study highlighted that L. sanfranciscensis was not the major species in 6/16 sourdough samples and that a relatively high LAB diversity can be observed in French organic

  14. Growth arrest-specific transcript 5 associated snoRNA levels are related to p53 expression and DNA damage in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Jonathan Krell

    Full Text Available The growth arrest-specific transcript 5 gene (GAS5 encodes a long noncoding RNA (lncRNA and hosts a number of small nucleolar RNAs (snoRNAs that have recently been implicated in multiple cellular processes and cancer. Here, we investigate the relationship between DNA damage, p53, and the GAS5 snoRNAs to gain further insight into the potential role of this locus in cell survival and oncogenesis both in vivo and in vitro.We used quantitative techniques to analyse the effect of DNA damage on GAS5 snoRNA expression and to assess the relationship between p53 and the GAS5 snoRNAs in cancer cell lines and in normal, pre-malignant, and malignant human colorectal tissue and used biological techniques to suggest potential roles for these snoRNAs in the DNA damage response.GAS5-derived snoRNA expression was induced by DNA damage in a p53-dependent manner in colorectal cancer cell lines and their levels were not affected by DICER. Furthermore, p53 levels strongly correlated with GAS5-derived snoRNA expression in colorectal tissue.In aggregate, these data suggest that the GAS5-derived snoRNAs are under control of p53 and that they have an important role in mediating the p53 response to DNA damage, which may not relate to their function in the ribosome. We suggest that these snoRNAs are not processed by DICER to form smaller snoRNA-derived RNAs with microRNA (miRNA-like functions, but their precise role requires further evaluation. Furthermore, since GAS5 host snoRNAs are often used as endogenous controls in qPCR quantifications we show that their use as housekeeping genes in DNA damage experiments can lead to inaccurate results.

  15. Activated nuclear transcription factor κB in patients with myocarditis and dilated cardiomyopathy-relation to inflammation and cardiac function

    International Nuclear Information System (INIS)

    Alter, Peter; Rupp, Heinz; Maisch, Bernhard

    2006-01-01

    Objectives and background: Myocarditis is caused by various agents and autoimmune processes. It is unknown whether viral genome persistence represents inactive remnants of previous infections or whether it is attributed to ongoing adverse processes. The latter also applies to the course of autoimmune myocarditis. One principal candidate for an adverse remodeling is nuclear factor-κB (NFκB). Methods: A total of 93 patients with suspected myocarditis/cardiomyopathy was examined. Hemodynamics were assessed by echocardiography as well as right and left heart catheterization. Endomyocardial biopsies were taken from the left ventricle. Biopsies were examined by immunohistochemistry and PCR for viral genomes. Selective immunostaining of activated NFκB was performed. Results: NFκB was increased in patients with myocarditis when compared with controls (11.1 ± 7.1% vs. 5.0 ± 5.3%, P 2 = 0.72, P 2 = 0.43, P < 0.02). Increased activated NFκB was found in adenovirus persistence when compared with controls (P = 0.001). Only a trend of increased NFκB activation was seen in cytomegalovirus persistence. Parvovirus B19 persistence did not affect NFκB activation. Conclusions: Increased activation of NFκB is related to inflammatory processes in myocarditis. Since activated NFκB correlates with left ventricular function, it could be assumed that NFκB activation occurs at early stages of inflammation. Potentially, NFκB could inhibit loss of cardiomyocytes by apoptosis and protect from cardiac dilation. Since NFκB is a crucial key transcription factor of inflammation, its prognostic and future therapeutic relevance should be addressed

  16. Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

    Science.gov (United States)

    Chen, Huei-Mei; Rosebrock, Adam P; Khan, Sohail R; Futcher, Bruce; Leatherwood, Janet K

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

  17. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    Science.gov (United States)

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression. PMID:22238674

  18. Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

    Directory of Open Access Journals (Sweden)

    Huei-Mei Chen

    Full Text Available In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

  19. Abundance, Excess, Waste

    Directory of Open Access Journals (Sweden)

    Rox De Luca

    2016-02-01

    Her recent work focuses on the concepts of abundance, excess and waste. These concerns translate directly into vibrant and colourful garlands that she constructs from discarded plastics collected on Bondi Beach where she lives. The process of collecting is fastidious, as is the process of sorting and grading the plastics by colour and size. This initial gathering and sorting process is followed by threading the components onto strings of wire. When completed, these assemblages stand in stark contrast to the ease of disposability associated with the materials that arrive on the shoreline as evidence of our collective human neglect and destruction of the environment around us. The contrast is heightened by the fact that the constructed garlands embody the paradoxical beauty of our plastic waste byproducts, while also evoking the ways by which those byproducts similarly accumulate in randomly assorted patterns across the oceans and beaches of the planet.

  20. Sensitive detection of viral transcripts in human tumor transcriptomes.

    Directory of Open Access Journals (Sweden)

    Sven-Eric Schelhorn

    Full Text Available In excess of 12% of human cancer incidents have a viral cofactor. Epidemiological studies of idiopathic human cancers indicate that additional tumor viruses remain to be discovered. Recent advances in sequencing technology have enabled systematic screenings of human tumor transcriptomes for viral transcripts. However, technical problems such as low abundances of viral transcripts in large volumes of sequencing data, viral sequence divergence, and homology between viral and human factors significantly confound identification of tumor viruses. We have developed a novel computational approach for detecting viral transcripts in human cancers that takes the aforementioned confounding factors into account and is applicable to a wide variety of viruses and tumors. We apply the approach to conducting the first systematic search for viruses in neuroblastoma, the most common cancer in infancy. The diverse clinical progression of this disease as well as related epidemiological and virological findings are highly suggestive of a pathogenic cofactor. However, a viral etiology of neuroblastoma is currently contested. We mapped 14 transcriptomes of neuroblastoma as well as positive and negative controls to the human and all known viral genomes in order to detect both known and unknown viruses. Analysis of controls, comparisons with related methods, and statistical estimates demonstrate the high sensitivity of our approach. Detailed investigation of putative viral transcripts within neuroblastoma samples did not provide evidence for the existence of any known human viruses. Likewise, de-novo assembly and analysis of chimeric transcripts did not result in expression signatures associated with novel human pathogens. While confounding factors such as sample dilution or viral clearance in progressed tumors may mask viral cofactors in the data, in principle, this is rendered less likely by the high sensitivity of our approach and the number of biological replicates

  1. Contribution of the drought tolerance-related Stress-responsive NAC1 transcription factor to resistance of barley to Ramularia leaf spot

    OpenAIRE

    MCGRANN, GRAHAM R D; STEED, ANDREW; BURT, CHRISTOPHER; GODDARD, RACHEL; LACHAUX, CLEA; BANSAL, ANURADHA; CORBITT, MARGARET; GORNIAK, KALINA; NICHOLSON, PAUL; BROWN, JAMES K M

    2014-01-01

    NAC proteins are plant transcription factors that are involved in tolerance to abiotic and biotic stresses, as well as in many developmental processes. Stress-responsive NAC1 (SNAC1) transcription factor is involved in drought tolerance in barley and rice, but has not been shown previously to have a role in disease resistance. Transgenic over-expression of HvSNAC1 in barley cv. Golden Promise reduced the severity of Ramularia leaf spot (RLS), caused by the fungus Ramularia collo-cygni, but ha...

  2. species composition, relative abundance and distribution

    African Journals Online (AJOL)

    Preferred Customer

    College of Natural Sciences, Addis Ababa University, 2011. ISSN: 0379– ... distribution at Entoto Natural Park and escarpment was carried out during July 2009 - March 2010. The study ..... University Press, Princeton and Oxford, 496 pp. 20.

  3. Gene Expression and Metabolite Profiling of Developing Highbush Blueberry Fruit Indicates Transcriptional Regulation of Flavonoid Metabolism and Activation of Abscisic Acid Metabolism1[W][OA

    Science.gov (United States)

    Zifkin, Michael; Jin, Alena; Ozga, Jocelyn A.; Zaharia, L. Irina; Schernthaner, Johann P.; Gesell, Andreas; Abrams, Suzanne R.; Kennedy, James A.; Constabel, C. Peter

    2012-01-01

    Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative real-time reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3′-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid-3′5′-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation

  4. Abundance, composition and distribution of simple sequence ...

    Indian Academy of Sciences (India)

    δ∗(W-29, W-70) = 1.25; δ∗(W-93, W-70 = 0.75)) even though they originate from different geographical regions. We can, therefore, infer that the WSSV sequences are closely related by ancestry. Table 3. Dinucleotide relative abundance in the ...

  5. De novo transcriptome sequence assembly and identification of AP2/ERF transcription factor related to abiotic stress in parsley (Petroselinum crispum.

    Directory of Open Access Journals (Sweden)

    Meng-Yao Li

    Full Text Available Parsley is an important biennial Apiaceae species that is widely cultivated as herb, spice, and vegetable. Previous studies on parsley principally focused on its physiological and biochemical properties, including phenolic compound and volatile oil contents. However, little is known about the molecular and genetic properties of parsley. In this study, 23,686,707 high-quality reads were obtained and assembled into 81,852 transcripts and 50,161 unigenes for the first time. Functional annotation showed that 30,516 unigenes had sequence similarity to known genes. In addition, 3,244 putative simple sequence repeats were detected in curly parsley. Finally, 1,569 of the identified unigenes belonged to 58 transcription factor families. Various abiotic stresses have a strong detrimental effect on the yield and quality of parsley. AP2/ERF transcription factors have important functions in plant development, hormonal regulation, and abiotic response. A total of 88 putative AP2/ERF factors were identified from the transcriptome sequence of parsley. Seven AP2/ERF transcription factors were selected in this study to analyze the expression profiles of parsley under different abiotic stresses. Our data provide a potentially valuable resource that can be used for intensive parsley research.

  6. De novo transcriptome sequence assembly and identification of AP2/ERF transcription factor related to abiotic stress in parsley (Petroselinum crispum).

    Science.gov (United States)

    Li, Meng-Yao; Tan, Hua-Wei; Wang, Feng; Jiang, Qian; Xu, Zhi-Sheng; Tian, Chang; Xiong, Ai-Sheng

    2014-01-01

    Parsley is an important biennial Apiaceae species that is widely cultivated as herb, spice, and vegetable. Previous studies on parsley principally focused on its physiological and biochemical properties, including phenolic compound and volatile oil contents. However, little is known about the molecular and genetic properties of parsley. In this study, 23,686,707 high-quality reads were obtained and assembled into 81,852 transcripts and 50,161 unigenes for the first time. Functional annotation showed that 30,516 unigenes had sequence similarity to known genes. In addition, 3,244 putative simple sequence repeats were detected in curly parsley. Finally, 1,569 of the identified unigenes belonged to 58 transcription factor families. Various abiotic stresses have a strong detrimental effect on the yield and quality of parsley. AP2/ERF transcription factors have important functions in plant development, hormonal regulation, and abiotic response. A total of 88 putative AP2/ERF factors were identified from the transcriptome sequence of parsley. Seven AP2/ERF transcription factors were selected in this study to analyze the expression profiles of parsley under different abiotic stresses. Our data provide a potentially valuable resource that can be used for intensive parsley research.

  7. Subdwarf ultraviolet excesses and metal abundances

    International Nuclear Information System (INIS)

    Carney, B.W.

    1979-01-01

    The relation between stellar ultraviolet excesses and abundances is reexamined with the aid of new data, and an investigation is made of the accuracy of previous abundance analyses. A high-resolution echellogram of the subdwarf HD 201891 is analyzed to illustrate some of the problems. Generally, the earliest and latest analytical techniques yield consistent results for dwarfs. New UBV data yield normalized ultraviolet excesses, delta (U-B)/sub 0.6/, which are compared to abundances to produce a graphical relation that may be used to estimate [Fe/H] to +- 0.2 dex, given UBV colors accurate to +- 0.01 mag. The relation suggests a possible discontinuity between the halo and old-disk stars

  8. bZIP transcription factor SmJLB1 regulates autophagy-related genes Smatg8 and Smatg4 and is required for fruiting-body development and vegetative growth in Sordaria macrospora.

    Science.gov (United States)

    Voigt, Oliver; Herzog, Britta; Jakobshagen, Antonia; Pöggeler, Stefanie

    2013-12-01

    Autophagy is a precisely controlled degradation process in eukaryotic cells, during which the bulk of the cytoplasm is engulfed by a double membrane vesicle, the autophagosome. Fusion of the autophagosome with the vacuole leads to breakdown of its contents, such as proteins and organelles, and the recycling of nutrients. Earlier studies of autophagic genes of the core autophagic machinery in the filamentous ascomycete Sordaria macrospora elucidated the impact of autophagy on fungal viability, vegetative growth and fruiting-body development. To gain further knowledge about the regulation of autophagy in S. macrospora, we analyzed the function of the bZIP transcription factor SmJLB1, a homolog of the Podospora anserina basic zipper-type transcription factor induced during incompatibility 4 (IDI-4) and the Aspergillus nidulans transcription factor jun-like bZIP A (JlbA). Generation of the homokaryotic deletion mutant demonstrated S. macrospora Smjlb1 is associated with autophagy-dependent processes. Deletion of Smjlb1 abolished fruiting-body formation and impaired vegetative growth. SmJLB1 is localized to the cytoplasm and to nuclei. Quantitative real-time PCR experiments revealed an upregulated expression of autophagy-related genes Smatg8 and Smatg4 in the Smjlb1 deletion mutant, suggesting a transcriptional repression function of SmJLB1. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Transcription of Byzantine Chant - Problems, Possibilities, Formats

    DEFF Research Database (Denmark)

    Troelsgård, Christian

    2007-01-01

    Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes.......Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes....

  10. Contribution of the drought tolerance-related Stress-responsive NAC1 transcription factor to resistance of barley to Ramularia leaf spot

    Science.gov (United States)

    MCGRANN, GRAHAM R D; STEED, ANDREW; BURT, CHRISTOPHER; GODDARD, RACHEL; LACHAUX, CLEA; BANSAL, ANURADHA; CORBITT, MARGARET; GORNIAK, KALINA; NICHOLSON, PAUL; BROWN, JAMES K M

    2015-01-01

    NAC proteins are plant transcription factors that are involved in tolerance to abiotic and biotic stresses, as well as in many developmental processes. Stress-responsive NAC1 (SNAC1) transcription factor is involved in drought tolerance in barley and rice, but has not been shown previously to have a role in disease resistance. Transgenic over-expression of HvSNAC1 in barley cv. Golden Promise reduced the severity of Ramularia leaf spot (RLS), caused by the fungus Ramularia collo-cygni, but had no effect on disease symptoms caused by Fusarium culmorum, Oculimacula yallundae (eyespot), Blumeria graminis f. sp. hordei (powdery mildew) or Magnaporthe oryzae (blast). The HvSNAC1 transcript was w