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Sample records for global expression response

  1. Global gene expression response to telomerase in bovine adrenocortical cells

    SciTech Connect

    Perrault, Steven D.; Hornsby, Peter J.; Betts, Dean H. . E-mail: bettsd@uoguelph.ca

    2005-09-30

    The infinite proliferative capability of most immortalized cells is dependent upon the presence of the enzyme telomerase and its ability to maintain telomere length and structure. However, telomerase may be involved in a greater system than telomere length regulation, as recent evidence has shown it capable of increasing wound healing in vivo, and improving cellular proliferation rate and survival from apoptosis in vitro. Here, we describe the global gene expression response to ectopic telomerase expression in an in vitro bovine adrenocortical cell model. Telomerase-immortalized cells showed an increased ability for proliferation and survival in minimal essential medium above cells transgenic for GFP. cDNA microarray analyses revealed an altered cell state indicative of increased adrenocortical cell proliferation regulated by the IGF2 pathway and alterations in members of the TGF-B family. As well, we identified alterations in genes associated with development and wound healing that support a model that high telomerase expression induces a highly adaptable, progenitor-like state.

  2. Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.).

    PubMed

    Christianson, Jed A; Llewellyn, Danny J; Dennis, Elizabeth S; Wilson, Iain W

    2010-01-01

    Waterlogging stress causes yield reduction in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging caused significant reductions in stem elongation, shoot mass, root mass and leaf number, and altered the expression of 1,012 genes (4% of genes assayed) in root tissue as early as 4 h after flooding. Many of these genes were associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global gene expression in leaf tissues, significantly changing the expression of 1,305 genes (5% of genes assayed) after 24 h of flooding. Genes affected were associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism The implications of these results for the development of waterlogging-tolerant cotton are discussed.

  3. Gene expression profiling--Opening the black box of plant ecosystem responses to global change

    SciTech Connect

    Leakey, A.D.B.; Ainsworth, E.A.; Bernard, S.M.; Markelz, R.J.C.; Ort, D.R.; Placella, S.A.P.; Rogers, A.; Smith, M.D.; Sudderth, E.A.; Weston, D.J.; Wullschleger, S.D.; Yuan, S.

    2009-11-01

    The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Since the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and non-model species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.

  4. The global gene expression response of Escherichia coli to L-phenylalanine.

    PubMed

    Polen, T; Krämer, M; Bongaerts, J; Wubbolts, M; Wendisch, V F

    2005-02-09

    We investigated the global gene expression changes of Escherichia coli due to the presence of different concentrations of phenylalanine or shikimate in the growth medium. The response to 0.5 g l(-1) phenylalanine primarily reflected a perturbed aromatic amino acid metabolism, in particular due to TyrR-mediated regulation. The addition of 5g l(-1) phenylalanine reduced the growth rate by half and elicited a great number of likely indirect effects on genes regulated in response to changed pH, nitrogen or carbon availability. Consistent with the observed gene expression changes, supplementation with shikimate, tyrosine and tryptophan relieved growth inhibition by phenylalanine. In contrast to the wild-type, a tyrR disruption strain showed increased expression of pckA and of tktB in the presence of phenylalanine, but its growth was not affected by phenylalanine at the concentrations tested. The absence of growth inhibition by phenylalanine suggested that at high phenylalanine concentrations TyrR-defective strains might perform better in phenylalanine production.

  5. Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa.

    PubMed

    Dong, Xiangshu; Yi, Hankuil; Lee, Jeongyeo; Nou, Ill-Sup; Han, Ching-Tack; Hur, Yoonkang

    2015-01-01

    Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5- 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included 'response to heat', 'response to reactive oxygen species (ROS)', 'response to temperature stimulus', 'response to abiotic stimulus', and 'MAPKKK cascade'. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as HsfB2A (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853), protein kinases, and phosphatases. Among heat stress (HS) marker genes in Arabidopsis, only exportin 1A (XPO1A) (Bra008580, Bra006382) can be applied to B. rapa for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. CYP707A3 (Bra025083, Bra021965), which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including DREB2A (Bra005852), were involved in HS tolerance in both lines, Bra024224 (MYB41) and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data could also provide a

  6. Microarray Analysis of Global Gene Expression of V. vinifera in Response to Xylella fastidiosa Infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously, we analyzed gene expression profiles of Pierce’s Disease (PD) resistant and susceptible genotypes of V. arizonica hybrids in response to infection by X. fastidiosa (Xf). Here we report the gene expression profile of the PD susceptible European grapevine (V. vinifera) in response to Xf...

  7. The Global Response Regulator RegR Controls Expression of Denitrification Genes in Bradyrhizobium japonicum

    PubMed Central

    Torres, Maria J.; Argandoña, Montserrat; Vargas, Carmen; Bedmar, Eulogio J.; Fischer, Hans-Martin; Mesa, Socorro; Delgado, María J.

    2014-01-01

    Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544) or cy2 (bll2388), and genes involved in nitric oxide detoxification (blr2806-09) and copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130, which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5′end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS. PMID:24949739

  8. The global response regulator RegR controls expression of denitrification genes in Bradyrhizobium japonicum.

    PubMed

    Torres, Maria J; Argandoña, Montserrat; Vargas, Carmen; Bedmar, Eulogio J; Fischer, Hans-Martin; Mesa, Socorro; Delgado, María J

    2014-01-01

    Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544) or cy2 (bll2388), and genes involved in nitric oxide detoxification (blr2806-09) and copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130, which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5'end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS.

  9. Global Analysis of Posttranscriptional Gene Expression in Response to Sodium Arsenite

    PubMed Central

    Qiu, Lian-Qun; Abey, Sarah; Harris, Shawn; Shah, Ruchir; Gerrish, Kevin E.

    2014-01-01

    Background: Inorganic arsenic species are potent environmental toxins and causes of numerous health problems. Most studies have assumed that arsenic-induced changes in mRNA levels result from effects on gene transcription. Objectives: We evaluated the prevalence of changes in mRNA stability in response to sodium arsenite in human fibroblasts. Methods: We used microarray analyses to determine changes in steady-state mRNA levels and mRNA decay rates following 24-hr exposure to noncytotoxic concentrations of sodium arsenite, and we confirmed some of these changes using real-time reverse-transcription polymerase chain reaction (RT-PCR). Results: In arsenite-exposed cells, 186 probe set–identified transcripts were significantly increased and 167 were significantly decreased. When decay rates were analyzed after actinomycin D treatment, only 4,992 (9.1%) of probe set–identified transcripts decayed by > 25% after 4 hr. Of these, 70 were among the 353 whose steady-state levels were altered by arsenite, and of these, only 4 exhibited significantly different decay rates between arsenite and control treatment. Real-time RT-PCR confirmed a major, significant arsenite-induced stabilization of the mRNA encoding δ aminolevulinate synthase 1 (ALAS1), the rate-limiting enzyme in heme biosynthesis. This change presumably accounted for at least part of the 2.7-fold increase in steady-state ALAS1 mRNA levels seen after arsenite treatment. This could reflect decreases in cellular heme caused by the massive induction by arsenite of heme oxygenase mRNA (HMOX1; 68-fold increase), the rate-limiting enzyme in heme catabolism. Conclusions: We conclude that arsenite modification of mRNA stability is relatively uncommon, but in some instances can result in significant changes in gene expression. Citation: Qiu LQ, Abey S, Harris S, Shah R, Gerrish KE, Blackshear PJ. 2015. Global analysis of posttranscriptional gene expression in response to sodium arsenite. Environ Health Perspect 123:324

  10. Global identification and expression analysis of stress-responsive genes of the Argonaute family in apple.

    PubMed

    Xu, Ruirui; Liu, Caiyun; Li, Ning; Zhang, Shizhong

    2016-12-01

    Argonaute (AGO) proteins, which are found in yeast, animals, and plants, are the core molecules of the RNA-induced silencing complex. These proteins play important roles in plant growth, development, and responses to biotic stresses. The complete analysis and classification of the AGO gene family have been recently reported in different plants. Nevertheless, systematic analysis and expression profiling of these genes have not been performed in apple (Malus domestica). Approximately 15 AGO genes were identified in the apple genome. The phylogenetic tree, chromosome location, conserved protein motifs, gene structure, and expression of the AGO gene family in apple were analyzed for gene prediction. All AGO genes were phylogenetically clustered into four groups (i.e., AGO1, AGO4, MEL1/AGO5, and ZIPPY/AGO7) with the AGO genes of Arabidopsis. These groups of the AGO gene family were statistically analyzed and compared among 31 plant species. The predicted apple AGO genes are distributed across nine chromosomes at different densities and include three segment duplications. Expression studies indicated that 15 AGO genes exhibit different expression patterns in at least one of the tissues tested. Additionally, analysis of gene expression levels indicated that the genes are mostly involved in responses to NaCl, PEG, heat, and low-temperature stresses. Hence, several candidate AGO genes are involved in different aspects of physiological and developmental processes and may play an important role in abiotic stress responses in apple. To the best of our knowledge, this study is the first to report a comprehensive analysis of the apple AGO gene family. Our results provide useful information to understand the classification and putative functions of these proteins, especially for gene members that may play important roles in abiotic stress responses in M. hupehensis.

  11. Global Gene Expression Analysis to Unambiguously Identify Host Gene Responses Characteristic of Exposure to Biothreat Agents

    DTIC Science & Technology

    2004-12-01

    Cell Intercellular Adhesion Molecule 1 3383 CD8 Antigen 925 alpha Polypeptide (pCD4 antigen) 920 T Cell Surface Lymphocyte-sp Protein tyr kinase...expression in human peripheral blood mononuclear cells (PBMC) in response to 15 pathogens at different time points in vitro (3-5 replicates). This provided...for “invaders”. During this reconnaissance role, when these cells find a pathogen they react to neutralize it, creating a record (unique to each

  12. Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response

    PubMed Central

    2012-01-01

    Background Spore germination of the yeast Saccharomyces cerevisiae is a multi-step developmental path on which dormant spores re-enter the mitotic cell cycle and resume vegetative growth. Upon addition of a fermentable carbon source and nutrients, the outer layers of the protective spore wall are locally degraded, the tightly packed spore gains volume and an elongated shape, and eventually the germinating spore re-enters the cell cycle. The regulatory pathways driving this process are still largely unknown. Here we characterize the global gene expression profiles of germinating spores and identify potential transcriptional regulators of this process with the aim to increase our understanding of the mechanisms that control the transition from cellular dormancy to proliferation. Results Employing detailed gene expression time course data we have analysed the reprogramming of dormant spores during the transition to proliferation stimulated by a rich growth medium or pure glucose. Exit from dormancy results in rapid and global changes consisting of different sequential gene expression subprograms. The regulated genes reflect the transition towards glucose metabolism, the resumption of growth and the release of stress, similar to cells exiting a stationary growth phase. High resolution time course analysis during the onset of germination allowed us to identify a transient up-regulation of genes involved in protein folding and transport. We also identified a network of transcription factors that may be regulating the global response. While the expression outputs following stimulation by rich glucose medium or by glucose alone are qualitatively similar, the response to rich medium is stronger. Moreover, spores sense and react to amino acid starvation within the first 30 min after germination initiation, and this response can be linked to specific transcription factors. Conclusions Resumption of growth in germinating spores is characterized by a highly synchronized

  13. Global Gene Expression Responses to Low- or High-Dose Radiation in a Human Three-Dimensional Tissue Model

    PubMed Central

    Mezentsev, Alexandre; Amundson, Sally A.

    2011-01-01

    Accumulating data suggest that the biological responses to high and low doses of radiation are qualitatively different, necessitating the direct study of low-dose responses to better understand potential risks. Most such studies have used two-dimensional culture systems, which may not fully represent responses in three-dimensional tissues. To gain insight into low-dose responses in tissue, we have profiled global gene expression in EPI-200, a three-dimensional tissue model that imitates the structure and function of human epidermis, at 4, 16 and 24 h after exposure to high (2.5 Gy) and low (0.1 Gy) doses of low-LET protons. The most significant gene ontology groups among genes altered in expression were consistent with effects observed at the tissue level, where the low dose was associated with recovery and tissue repair, while the high dose resulted in loss of structural integrity and terminal differentiation. Network analysis of the significantly responding genes suggested that TP53 dominated the response to 2.5 Gy, while HNF4A, a novel transcription factor not previously associated with radiation response, was most prominent in the low-dose response. HNF4A protein levels and phosphorylation were found to increase in tissues and cells after low- but not high-dose irradiation. PMID:21486161

  14. Modeling notch signaling in normal and neoplastic hematopoiesis: global gene expression profiling in response to activated notch expression.

    PubMed

    Ganapati, Uma; Tan, Hongying Tina; Lynch, Maureen; Dolezal, Milana; de Vos, Sven; Gasson, Judith C

    2007-08-01

    In normal hematopoiesis, proliferation is tightly linked to differentiation in ways that involve cell-cell interaction with stromal elements in the bone marrow stem cell niche. Numerous in vitro and in vivo studies strongly support a role for Notch signaling in the regulation of stem cell renewal and hematopoiesis. Not surprisingly, mutations in the Notch gene have been linked to a number of types of malignancies. To better define the function of Notch in both normal and neoplastic hematopoiesis, a tetracycline-inducible system regulating expression of a ligand-independent, constitutively active form of Notch1 was introduced into murine E14Tg2a embryonic stem cells. During coculture, OP9 stromal cells induce the embryonic stem cells to differentiate first to hemangioblasts and subsequently to hematopoietic stem cells. Our studies indicate that activation of Notch signaling in flk+ hemangioblasts dramatically reduces their survival and proliferative capacity and lowers the levels of hematopoietic stem cell markers CD34 and c-Kit and the myeloid marker CD11b. Global gene expression profiling of day 8 hematopoietic progenitors in the absence and presence of activated Notch yield candidate genes required for normal hematopoietic differentiation, as well as putative downstream targets of oncogenic forms of Notch including the noncanonical Wnts Wnt4 and 5A. Disclosure of potential conflicts of interest is found at the end of this article.

  15. Global protein expression profile response of planktonic Aeromonas hydrophila exposed to chlortetracycline.

    PubMed

    Li, Wanxin; Yao, Zujie; Zhang, Xiangyu; Huang, Fang; Lin, Wenxiong; Lin, Xiangmin

    2017-04-01

    The antibiotics resistance phenomena of Aeromonas hydrophila has become serious economic and public health problems for the world aquaculture industry and human health care. In this study, to investigate the instinct antibiotics adaptive mechanism of this pathogen, iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) based quantitative proteomics technologies were performed to compare the differential expression of A. hydrophila in planktonic status in response to chlortetracycline (CTC) stress and then identified total 1552 proteins including 285 altered proteins with 90 increasing and 195 decreasing abundance proteins. The following bioinformatics analysis showed that many metabolic metabolism pathways such as carbon metabolism, pyruvate metabolism, and glycolysis/gluconeogenesis were trend to down-regulated whereas β-Lactam resistance, RNA degradation, and amino acids biosynthesis processes were more likely to increase in CTC stress. The related pyruvate metabolism and β-Lactam resistance processes in mRNA level were further measured using the q-PCR method. Thus, an understanding of the behaviors of A. hydrophila in response to CTC would be helpful to reveal the antibiotics adaptive mechanism and for the development of novel antibiotics therapy.

  16. Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA methylation and histone acetylation are important for controlling gene expression in all eukaryotes. Microarray analysis revealed an altered gene expression profile after treatment with the DNA methylation inhibitor 5-aza-2’ deoxyctidine (5-AC), which included the upregulation of many transposab...

  17. Global gene expression changes in type 1 diabetes: insights into autoimmune response in the target organ and in the periphery.

    PubMed

    Planas, Raquel; Pujol-Borrell, Ricardo; Vives-Pi, Marta

    2010-10-30

    Type 1 diabetes (T1D) is an autoimmune disease caused by the selective destruction of the insulin-producing β cells. Research into the pathogenesis of T1D has been hindered by the lack of detection of the autoimmune process during the asymptomatic period and by the inaccessibility to the target tissue. Therefore current understanding of the immunological phenomena that take place in the pancreas of the patients is very limited and much of the current knowledge on T1D has been obtained using animal models. Microarray technology and bioinformatics allow the comparison of the gene expression profile - transcriptome - in normal and pathological conditions, creating a global picture of altered processes. Microarray experiments have defined new transcriptional alterations associated with several autoimmune diseases, and are focused on the identification of specific biomarkers. In this review we summarize current data on gene expression profiles in T1D from an immunological point of view. Reported transcriptome studies have been performed in T1D patients and Non-Obese Diabetic mouse models analyzing peripheral blood, lymphoid organs and pancreas/islets. In the periphery, the distinctive profiles are inflammatory pathways inducible by IL-1β and IFNs that can help in the identification of new biomarkers. In the target organ, a remarkable finding is the overexpression of inflammatory and innate immune response genes and the active autoimmune response at longstanding stages, contrary to the pre-existing concept of acute autoimmune process in T1D.

  18. Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves.

    PubMed

    Wu, Ting; Wang, Yi; Zheng, Yi; Fei, Zhangjun; Dandekar, Abhaya M; Xu, Kenong; Han, Zhenhai; Cheng, Lailiang

    2015-09-01

    Sorbitol is a major product of photosynthesis in apple (Malus domestica) that is involved in carbohydrate metabolism and stress tolerance. However, little is known about how the global transcript levels in apple leaves respond to decreased sorbitol synthesis. In this study we used RNA sequencing (RNA-seq) profiling to characterize the transcriptome of leaves from transgenic lines of the apple cultivar 'Greensleeves' exhibiting suppressed expression of aldose-6-phosphate reductase (A6PR) to gain insights into sorbitol function and the consequences of decreased sorbitol synthesis on gene expression. We observed that, although the leaves of the low sorbitol transgenic lines accumulate higher levels of various primary metabolites, only very limited changes were found in the levels of transcripts associated with primary metabolism. We suggest that this is indicative of post-transcriptional and/or post-translational regulation of primary metabolite accumulation and central carbon metabolism. However, we identified significantly enriched gene ontology terms belonging to the 'stress related process' category in the antisense lines (P-value < 0.05). These include genes involved in the synthesis/degradation of abscisic acid, salicylic acid and jasmonic acid, nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes and ATP-binding cassette (ABC) transporter genes. This suggests that sorbitol plays a role in the responses of apple trees to abiotic and biotic stresses.

  19. Copper stress induces a global stress response in Staphylococcus aureus and represses sae and agr expression and biofilm formation.

    PubMed

    Baker, Jonathan; Sitthisak, Sutthirat; Sengupta, Mrittika; Johnson, Miranda; Jayaswal, R K; Morrissey, Julie A

    2010-01-01

    Copper is an important cofactor for many enzymes; however, high levels of copper are toxic. Therefore, bacteria must ensure there is sufficient copper for use as a cofactor but, more importantly, must limit free intracellular levels to prevent toxicity. In this study, we have used DNA microarray to identify Staphylococcus aureus copper-responsive genes. Transcriptional profiling of S. aureus SH1000 grown in excess copper identified a number of genes which fall into four groups, suggesting that S. aureus has four main mechanisms for adapting to high levels of environmental copper, as follows: (i) induction of direct copper homeostasis mechanisms; (ii) increased oxidative stress resistance; (iii) expression of the misfolded protein response; and (iv) repression of a number of transporters and global regulators such as Agr and Sae. Our experimental data confirm that resistance to oxidative stress and particularly to H2O2 scavenging is an important S. aureus copper resistance mechanism. Our previous studies have demonstrated that Eap and Emp proteins, which are positively regulated by Agr and Sae, are required for biofilm formation under low-iron growth conditions. Our transcriptional analysis has confirmed that sae, agr, and eap are repressed under high-copper conditions and that biofilm formation is indeed repressed under high-copper conditions. Therefore, our results may provide an explanation for how copper films can prevent biofilm formation on catheters.

  20. Temporal regulation of global gene expression and cellular morphology in Xenopus kidney cells in response to clinorotation

    NASA Astrophysics Data System (ADS)

    Kitamoto, Junko; Fukui, Akimasa; Asashima, Makoto

    Here, we report changes gene expression and morphology of the renal epithelial cell line, A6, which was derived from Xenopus laevis adult kidney that had been induced by long-term culturing with a three-dimensional clinostat. An oligo microarray analysis on the A6 cells showed that mRNA levels for 52 out of 8091 genes were significantly altered in response to clinorotation. On day 5, there was no dramatic change in expression level, but by day 8 and day 10, either upregulation or downregulation of gene expression became evident. By day 15, the expression levels of 18 out of 52 genes had returned to the original levels, while the remaining 34 genes maintained the altered levels of expression. Quantitative analyses of gene expression by real-time PCR confirmed that changes in the mRNA levels of selected genes were found only under clinorotation and not under hypergravity (7 g) or ground control. Morphological changes including loss of dome-like structures and disorganization of both E-cadherin adherence junctions and cortical actin were also observed after 10 days of culturing with clinorotation. These results revealed that the expression of selected genes was altered specifically in A6 cells cultured under clinorotation.

  1. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    PubMed

    Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

    2014-01-01

    Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  2. Negative energy balance alters global gene expression and immune responses in the uterus of postpartum dairy cows.

    PubMed

    Wathes, D Claire; Cheng, Zhangrui; Chowdhury, Waliul; Fenwick, Mark A; Fitzpatrick, Richard; Morris, Dermot G; Patton, Joe; Murphy, John J

    2009-09-09

    Most dairy cows suffer uterine microbial contamination postpartum. Persistent endometritis often develops, associated with reduced fertility. We used a model of differential feeding and milking regimes to produce cows in differing negative energy balance status in early lactation (mild or severe, MNEB or SNEB). Blood hematology was assessed preslaughter at 2 wk postpartum. RNA expression in endometrial samples was compared using bovine Affymetrix arrays. Data were mapped using Ingenuity Pathway Analysis. Circulating concentrations of IGF-I remained lower in the SNEB group, whereas blood nonesterified fatty acid and beta-hydroxybutyrate concentrations were raised. White blood cell count and lymphocyte number were reduced in SNEB cows. Array analysis of endometrial samples identified 274 differentially expressed probes representing 197 recognized genes between the energy balance groups. The main canonical pathways affected related to immunological and inflammatory disease and connective tissue disorders. Inflammatory response genes with major upregulation in SNEB cows included matrix metalloproteinases, chemokines, cytokines, and calgranulins. Expression of several interferon-inducible genes including ISG20, IFIH1, MX1, and MX2 were also significantly increased in the SNEB cows. These results provide evidence that cows in SNEB were still undergoing an active uterine inflammatory response 2 wk postpartum, whereas MNEB cows had more fully recovered from their energy deficit, with their endometrium reaching a more advanced stage of repair. SNEB may therefore prevent cows from mounting an effective immune response to the microbial challenge experienced after calving, prolonging the time required for uterine recovery and compromising subsequent fertility.

  3. New Insights on Drought Stress Response by Global Investigation of Gene Expression Changes in Sheepgrass (Leymus chinensis)

    PubMed Central

    Zhao, Pincang; Liu, Panpan; Yuan, Guangxiao; Jia, Junting; Li, Xiaoxia; Qi, Dongmei; Chen, Shuangyan; Ma, Tian; Liu, Gongshe; Cheng, Liqin

    2016-01-01

    Water is a critical environmental factor that restricts the geographic distribution of plants. Sheepgrass [Leymus chinensis, (Trin.) Tzvel] is an important forage grass in the Eurasia Steppe and a close germplasm for wheat and barley. This native grass adapts well to adverse environments such as cold, salinity, alkalinity and drought, and it can survive when the soil moisture may be less than 6% in dry seasons. However, little is known about how sheepgrass tolerates water stress at the molecular level. Here, drought stress experiment and RNA-sequencing (RNA-seq) was performed in three pools of RNA samples (control, drought stress, and rewatering). We found that sheepgrass seedlings could still survive when the soil water content (SWC) was reduced to 14.09%. Differentially expressed genes (DEGs) analysis showed that 7320 genes exhibited significant responses to drought stress. Of these DEGs, 2671 presented opposite expression trends before and after rewatering. Furthermore, ~680 putative sheepgrass-specific water responsive genes were revealed that can be studied deeply. Gene ontology (GO) annotation revealed that stress-associated genes were activated extensively by drought treatment. Interestingly, cold stress-related genes were up-regulated greatly after drought stress. The DEGs of MAPK and calcium signal pathways, plant hormone ABA, jasmonate, ethylene, brassinosteroid signal pathways, cold response CBF pathway participated coordinatively in sheepgrass drought stress response. In addition, we identified 288 putative transcription factors (TFs) involved in drought response, among them, the WRKY, NAC, AP2/ERF, bHLH, bZIP, and MYB families were enriched, and might play crucial and significant roles in drought stress response of sheepgrass. Our research provided new and valuable information for understanding the mechanism of drought tolerance in sheepgrass. Moreover, the identification of genes involved in drought response can facilitate the genetic improvement of

  4. Characterization of the Humoral Immune Response during Staphylococcus aureus Bacteremia and Global Gene Expression by Staphylococcus aureus in Human Blood

    PubMed Central

    den Reijer, Paul Martijn; Lemmens-den Toom, Nicole; Kant, Samantha; Snijders, Susan V.; Boelens, Hélène; Tavakol, Mehri; Verkaik, Nelianne J.; van Belkum, Alex; Verbrugh, Henri A.; van Wamel, Willem J. B.

    2013-01-01

    Attempts to develop an efficient anti-staphylococcal vaccine in humans have so far been unsuccessful. Therefore, more knowledge of the antigens that are expressed by Staphylococcus aureus in human blood and induce an immune response in patients is required. In this study we further characterize the serial levels of IgG and IgA antibodies against 56 staphylococcal antigens in multiple serum samples of 21 patients with a S. aureus bacteremia, compare peak IgG levels between patients and 30 non-infected controls, and analyze the expression of 3626 genes by two genetically distinct isolates in human blood. The serum antibody levels were measured using a bead-based flow cytometry technique (xMAP®, Luminex corporation). Gene expression levels were analyzed using a microarray (BµG@s microarray). The initial levels and time taken to reach peak IgG and IgA antibody levels were heterogeneous in bacteremia patients. The antigen SA0688 was associated with the highest median initial-to-peak antibody fold-increase for IgG (5.05-fold) and the second highest increase for IgA (2.07-fold). Peak IgG levels against 27 antigens, including the antigen SA0688, were significantly elevated in bacteremia patients versus controls (P≤0.05). Expression of diverse genes, including SA0688, was ubiquitously high in both isolates at all time points during incubation in blood. However, only a limited number of genes were specifically up- or downregulated in both isolates when cultured in blood, compared to the start of incubation in blood or during incubation in BHI broth. In conclusion, most staphylococcal antigens tested in this study, including many known virulence factors, do not induce uniform increases in the antibody levels in bacteremia patients. In addition, the expression of these antigens by S. aureus is not significantly altered by incubation in human blood over time. One immunogenic and ubiquitously expressed antigen is the putative iron-regulated ABC transporter SA0688. PMID

  5. Analysis of global gene expression profile of rice in response to methylglyoxal indicates its possible role as a stress signal molecule

    PubMed Central

    Kaur, Charanpreet; Kushwaha, Hemant R.; Mustafiz, Ananda; Pareek, Ashwani; Sopory, Sudhir K.; Singla-Pareek, Sneh L.

    2015-01-01

    Methylglyoxal (MG) is a toxic metabolite produced primarily as a byproduct of glycolysis. Being a potent glycating agent, it can readily bind macromolecules like DNA, RNA, or proteins, modulating their expression and activity. In plants, despite the known inhibitory effects of MG on growth and development, still limited information is available about the molecular mechanisms and response pathways elicited upon elevation in MG levels. To gain insight into the molecular basis of MG response, we have investigated changes in global gene expression profiles in rice upon exposure to exogenous MG using GeneChip microarrays. Initially, growth of rice seedlings was monitored in response to increasing MG concentrations which could retard plant growth in a dose-dependent manner. Upon exposure to 10 mM concentration of MG, a total of 1685 probe sets were up- or down-regulated by more than 1.5-fold in shoot tissues within 16 h. These were classified into 10 functional categories. The genes involved in signal transduction such as, protein kinases and transcription factors, were significantly over-represented in the perturbed transcriptome, of which several are known to be involved in abiotic and biotic stress response indicating a cross-talk between MG-responsive and stress-responsive signal transduction pathways. Through in silico studies, we could predict 7–8 bp long conserved motif as a possible MG-responsive element (MGRE) in the 1 kb upstream region of genes that were more than 10-fold up- or down-regulated in the analysis. Since several perturbations were found in signaling cascades in response to MG, we hereby suggest that it plays an important role in signal transduction probably acting as a stress signal molecule. PMID:26388885

  6. Antimicrobial resistance: a global response.

    PubMed Central

    Smith, Richard D.; Coast, Joanna

    2002-01-01

    Resistance to antimicrobial therapies reduces the effectiveness of these drugs, leading to increased morbidity, mortality, and health care expenditure. Because globalization increases the vulnerability of any country to diseases occurring in other countries, resistance presents a major threat to global public health, and no country acting on its own can adequately protect the health of its population against it. International collective action is therefore essential. Nevertheless, responsibility for health remains predominantly national. Consequently, there is a potentially significant disparity between the problems and solutions related to antimicrobial resistance and the institutions and mechanisms that are available to deal with them. This paper considers the capacity of national and international institutions and mechanisms to generate a collective response to antimicrobial resistance. Strategies for containing resistance are outlined, with particular reference to globally coordinated activities of countries. The adequacy of national and international responses to resistance is assessed, and the actions that international bodies could take to solve difficulties associated with present responses are highlighted. Approaches are suggested for securing international collective action for the containment of antimicrobial resistance. PMID:11953791

  7. Co-expression of Skp and FkpA chaperones improves cell viability and alters the global expression of stress response genes during scFvD1.3 production

    PubMed Central

    2010-01-01

    Background The overexpression of scFv antibody fragments in the periplasmic space of Escherichia coli frequently results in extensive protein misfolding and loss of cell viability. Although protein folding factors such as Skp and FkpA are often exploited to restore the solubility and functionality of recombinant protein products, their exact impact on cellular metabolism during periplasmic antibody fragment expression is not clearly understood. In this study, we expressed the scFvD1.3 antibody fragment in E. coli BL21 and evaluated the overall physiological and global gene expression changes upon Skp or FkpA co-expression. Results The periplasmic expression of scFvD1.3 led to a rapid accumulation of insoluble scFvD1.3 proteins and a decrease in cell viability. The co-expression of Skp and FkpA improved scFvD1.3 solubility and cell viability in a dosage-dependent manner. Through mutagenesis experiments, it was found that only the chaperone activity of FkpA, not the peptidyl-prolyl isomerase (PPIase) activity, is required for the improvement in cell viability. Global gene expression analysis of the scFvD1.3 cells over the chaperone-expressing cells showed a clear up-regulation of genes involved in heat-shock and misfolded protein stress responses. These included genes of the major HSP70 DnaK chaperone family and key proteases belonging to the Clp and Lon protease systems. Other metabolic gene expression trends include: (1) the differential regulation of several energy metabolic genes, (2) down-regulation of the central metabolic TCA cycle and transport genes, and (3) up-regulation of ribosomal genes. Conclusions The simultaneous activation of multiple stress related and other metabolic genes may constitute the stress response to protein misfolding in the scFvD1.3 cells. These gene expression information could prove to be valuable for the selection and construction of reporter contructs to monitor the misfolded protein stress response during antibody fragment

  8. Expression of the alaE gene is positively regulated by the global regulator Lrp in response to intracellular accumulation of l-alanine in Escherichia coli.

    PubMed

    Ihara, Kohei; Sato, Kazuki; Hori, Hatsuhiro; Makino, Yumiko; Shigenobu, Shuji; Ando, Tasuke; Isogai, Emiko; Yoneyama, Hiroshi

    2017-04-01

    The alaE gene in Escherichia coli encodes an l-alanine exporter that catalyzes the active export of l-alanine using proton electrochemical potential. In our previous study, alaE expression was shown to increase in the presence of l-alanyl-l-alanine (Ala-Ala). In this study, the global regulator leucine-responsive regulatory protein (Lrp) was identified as an activator of the alaE gene. A promoter less β-galactosidase gene was fused to an alaE upstream region (240 nucleotides). Cells that were lacZ-deficient and harbored this reporter plasmid showed significant induction of β-galactosidase activity (approximately 17-fold) in the presence of 6 mM l-alanine, l-leucine, and Ala-Ala. However, a reporter plasmid possessing a smaller alaE upstream region (180 nucleotides) yielded transformants with strikingly low enzyme activity under the same conditions. In contrast, lrp-deficient cells showed almost no β-galactosidase induction, indicating that Lrp positively regulates alaE expression. We next performed an electrophoretic mobility shift assay (EMSA) and a DNase I footprinting assay using purified hexahistidine-tagged Lrp (Lrp-His). Consequently, we found that Lrp-His binds to the alaE upstream region spanning nucleotide -161 to -83 with a physiologically relevant affinity (apparent KD, 288.7 ± 83.8 nM). Furthermore, the binding affinity of Lrp-His toward its cis-element was increased by l-alanine and l-leucine, but not by Ala-Ala and d-alanine. Based on these results, we concluded that the gene expression of the alaE is regulated by Lrp in response to intracellular levels of l-alanine, which eventually leads to intracellular homeostasis of l-alanine concentrations.

  9. Culturally Responsive: Art Education in a Global Era

    ERIC Educational Resources Information Center

    Lai, Alice

    2012-01-01

    Facing the era of globalization, culturally responsive art teachers must recognize that students' home culture, including local artistic expression, is inevitably influenced by global forces. They should strive to engage with students systems and issues of globalization and its impact on their community culture and art. In this article, the author…

  10. Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break.

    PubMed

    Lindgren, Emma; Hägg, Sara; Giordano, Fosco; Björkegren, Johan; Ström, Lena

    2014-01-01

    Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.

  11. Emerging diseases: the global express.

    PubMed

    Brown, C

    2010-01-01

    The expansion of global trade has ensured that the global economy continues to improve and that political liberalization promotes changes toward democracy and enhanced world peace. However, the inherent risks due to pathogens moving from one country to another within this global trade have expanded accordingly as well. International guidelines for safe trade, promulgated by the World Trade Organization, and interpreted by the World Health Organization, the Food and Agriculture Organization, and the World Organization for Animal Health, have undergone fast-paced changes in an effort to stay current with rapidly evolving emerging disease concerns. But serious gaps remain, and the threat of pathogens moving to new areas or emerging in new ways is considerable.

  12. The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation

    PubMed Central

    Drecktrah, Dan; Lybecker, Meghan; Popitsch, Niko; Rescheneder, Philipp; Hall, Laura S.; Samuels, D. Scott

    2015-01-01

    As the Lyme disease bacterium Borrelia burgdorferi traverses its enzootic cycle, alternating between a tick vector and a vertebrate host, the spirochete must adapt and persist in the tick midgut under prolonged nutrient stress between blood meals. In this study, we examined the role of the stringent response in tick persistence and in regulation of gene expression during nutrient limitation. Nutritionally starving B. burgdorferi in vitro increased the levels of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively referred to as (p)ppGpp, products of the bifunctional synthetase/hydrolase RelBbu (RelA/SpoT homolog). Conversely, returning B. burgdorferi to a nutrient-rich medium decreased (p)ppGpp levels. B. burgdorferi survival in ticks between the larval and nymph blood meals, and during starvation in vitro, was dependent on RelBbu. Furthermore, normal morphological conversion from a flat-wave shape to a condensed round body (RB) form during starvation was dependent on RelBbu; relBbu mutants more frequently formed RBs, but their membranes were compromised. By differential RNA sequencing analyses, we found that RelBbu regulates an extensive transcriptome, both dependent and independent of nutrient stress. The RelBbu regulon includes the glp operon, which is important for glycerol utilization and persistence in the tick, virulence factors and the late phage operon of the 32-kb circular plasmid (cp32) family. In summary, our data suggest that RelBbu globally modulates transcription in response to nutrient stress by increasing (p)ppGpp levels to facilitate B. burgdorferi persistence in the tick. PMID:26371761

  13. The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.

    PubMed

    Drecktrah, Dan; Lybecker, Meghan; Popitsch, Niko; Rescheneder, Philipp; Hall, Laura S; Samuels, D Scott

    2015-09-01

    As the Lyme disease bacterium Borrelia burgdorferi traverses its enzootic cycle, alternating between a tick vector and a vertebrate host, the spirochete must adapt and persist in the tick midgut under prolonged nutrient stress between blood meals. In this study, we examined the role of the stringent response in tick persistence and in regulation of gene expression during nutrient limitation. Nutritionally starving B. burgdorferi in vitro increased the levels of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively referred to as (p)ppGpp, products of the bifunctional synthetase/hydrolase RelBbu (RelA/SpoT homolog). Conversely, returning B. burgdorferi to a nutrient-rich medium decreased (p)ppGpp levels. B. burgdorferi survival in ticks between the larval and nymph blood meals, and during starvation in vitro, was dependent on RelBbu. Furthermore, normal morphological conversion from a flat-wave shape to a condensed round body (RB) form during starvation was dependent on RelBbu; relBbu mutants more frequently formed RBs, but their membranes were compromised. By differential RNA sequencing analyses, we found that RelBbu regulates an extensive transcriptome, both dependent and independent of nutrient stress. The RelBbu regulon includes the glp operon, which is important for glycerol utilization and persistence in the tick, virulence factors and the late phage operon of the 32-kb circular plasmid (cp32) family. In summary, our data suggest that RelBbu globally modulates transcription in response to nutrient stress by increasing (p)ppGpp levels to facilitate B. burgdorferi persistence in the tick.

  14. Characterization of Changes in Global Genes Expression in the Distal Colon of Loperamide-Induced Constipation SD Rats in Response to the Laxative Effects of Liriope platyphylla

    PubMed Central

    Kim, Ji Eun; Park, So Hae; Kwak, Moon Hwa; Go, Jun; Koh, Eun Kyoung; Song, Sung Hwa; Sung, Ji Eun; Lee, Hee Seob; Hong, Jin Tae; Hwang, Dae Youn

    2015-01-01

    To characterize the changes in global gene expression in the distal colon of constipated SD rats in response to the laxative effects of aqueous extracts of Liriope platyphylla (AEtLP), including isoflavone, saponin, oligosaccharide, succinic acid and hydroxyproline, the total RNA extracted from the distal colon of AEtLP-treated constipation rats was hybridized to oligonucleotide microarrays. The AEtLP treated rats showed an increase in the number of stools, mucosa thickness, flat luminal surface thickness, mucin secretion, and crypt number. Overall, compared to the controls, 581 genes were up-regulated and 216 genes were down-regulated by the constipation induced by loperamide in the constipated rats. After the AEtLP treatment, 67 genes were up-regulated and 421 genes were down-regulated. Among the transcripts up-regulated by constipation, 89 were significantly down-regulated and 22 were recovered to the normal levels by the AEtLP treatment. The major genes in the down-regulated categories included Slc9a5, klk10, Fgf15, and Alpi, whereas the major genes in the recovered categories were Cyp2b2, Ace, G6pc, and Setbp1. On the other hand, after the AEtLP treatment, ten of these genes down-regulated by constipation were up-regulated significantly and five were recovered to the normal levels. The major genes in the up-regulated categories included Serpina3n, Lcn2 and Slc5a8, whereas the major genes in the recovered categories were Tmem45a, Rerg and Rgc32. These results indicate that several gene functional groups and individual genes as constipation biomarkers respond to an AEtLP treatment in constipated model rats. PMID:26151867

  15. The global response regulator ExpA controls virulence gene expression through RsmA-mediated and RsmA-independent pathways in Pectobacterium wasabiae SCC3193.

    PubMed

    Broberg, M; Lee, G W; Nykyri, J; Lee, Y H; Pirhonen, M; Palva, E T

    2014-03-01

    ExpA (GacA) is a global response regulator that controls the expression of major virulence genes, such as those encoding plant cell wall-degrading enzymes (PCWDEs) in the model soft rot phytopathogen Pectobacterium wasabiae SCC3193. Several studies with pectobacteria as well as related phytopathogenic gammaproteobacteria, such as Dickeya and Pseudomonas, suggest that the control of virulence by ExpA and its homologues is executed partly by modulating the activity of RsmA, an RNA-binding posttranscriptional regulator. To elucidate the extent of the overlap between the ExpA and RsmA regulons in P. wasabiae, we characterized both regulons by microarray analysis. To do this, we compared the transcriptomes of the wild-type strain, an expA mutant, an rsmA mutant, and an expA rsmA double mutant. The microarray data for selected virulence-related genes were confirmed through quantitative reverse transcription (qRT-PCR). Subsequently, assays were performed to link the observed transcriptome differences to changes in bacterial phenotypes such as growth, motility, PCWDE production, and virulence in planta. An extensive overlap between the ExpA and RsmA regulons was observed, suggesting that a substantial portion of ExpA regulation appears to be mediated through RsmA. However, a number of genes involved in the electron transport chain and oligogalacturonide metabolism, among other processes, were identified as being regulated by ExpA independently of RsmA. These results suggest that ExpA may only partially impact fitness and virulence via RsmA.

  16. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

    PubMed Central

    Zhou, Junli; Wang, Xiangfeng; Jiao, Yuling; Qin, Yonghua; Liu, Xigang; He, Kun; Chen, Chen; Ma, Ligeng; Wang, Jian; Xiong, Lizhong; Zhang, Qifa; Fan, Liumin

    2007-01-01

    To elucidate genome-level responses to drought and high-salinity stress in rice, a 70mer oligomer microarray covering 36,926 unique genes or gene models was used to profile genome expression changes in rice shoot, flag leaf and panicle under drought or high-salinity conditions. While patterns of gene expression in response to drought or high-salinity stress within a particular organ type showed significant overlap, comparison of expression profiles among different organs showed largely organ-specific patterns of regulation. Moreover, both stresses appear to alter the expression patterns of a significant number of genes involved in transcription and cell signaling in a largely organ-specific manner. The promoter regions of genes induced by both stresses or induced by one stress in more than one organ types possess relative enrichment of two cis-elements (ABRE core and DRE core) known to be associated with water stress. An initial computational analysis indicated that novel promoter motifs are present in the promoters of genes involved in rehydration after drought. This analysis suggested that rice might possess a mechanism that actively detects rehydration and facilitates rapid recovery. Overall, our data supports a notion that organ-specific gene regulation in response to the two abiotic stresses may primarily be mediated by organ-specific transcription responses. Electronic supplementary material The online version of this article (doi:10.1007/s11103-006-9111-1) contains supplementary material, which is available to authorized users. PMID:17225073

  17. Global Analysis of Arabidopsis Gene Expression Uncovers a Complex Array of Changes Impacting Pathogen Response and Cell Cycle during Geminivirus Infection1[W][OA

    PubMed Central

    Ascencio-Ibáñez, José Trinidad; Sozzani, Rosangela; Lee, Tae-Jin; Chu, Tzu-Ming; Wolfinger, Russell D.; Cella, Rino; Hanley-Bowdoin, Linda

    2008-01-01

    Geminiviruses are small DNA viruses that use plant replication machinery to amplify their genomes. Microarray analysis of the Arabidopsis (Arabidopsis thaliana) transcriptome in response to cabbage leaf curl virus (CaLCuV) infection uncovered 5,365 genes (false discovery rate <0.005) differentially expressed in infected rosette leaves at 12 d postinoculation. Data mining revealed that CaLCuV triggers a pathogen response via the salicylic acid pathway and induces expression of genes involved in programmed cell death, genotoxic stress, and DNA repair. CaLCuV also altered expression of cell cycle-associated genes, preferentially activating genes expressed during S and G2 and inhibiting genes active in G1 and M. A limited set of core cell cycle genes associated with cell cycle reentry, late G1, S, and early G2 had increased RNA levels, while core cell cycle genes linked to early G1 and late G2 had reduced transcripts. Fluorescence-activated cell sorting of nuclei from infected leaves revealed a depletion of the 4C population and an increase in 8C, 16C, and 32C nuclei. Infectivity studies of transgenic Arabidopsis showed that overexpression of CYCD3;1 or E2FB, both of which promote the mitotic cell cycle, strongly impaired CaLCuV infection. In contrast, overexpression of E2FA or E2FC, which can facilitate the endocycle, had no apparent effect. These results showed that geminiviruses and RNA viruses interface with the host pathogen response via a common mechanism, and that geminiviruses modulate plant cell cycle status by differentially impacting the CYCD/retinoblastoma-related protein/E2F regulatory network and facilitating progression into the endocycle. PMID:18650403

  18. Global Expression Studies of Yersinia Pestis Pathogenicity

    SciTech Connect

    Garcia, E; Motin, V; Brubaker, R; Fitch, P

    2002-10-15

    The aim of these studies continues to be the investigation into the molecular mechanisms that underlie the virulence process in Yersinia pestis. In particular, the focus of this work centers on the identification of novel genes and pathways responsible for the pathogenic properties of this organism. In spite of more than four decades of intense investigation in this field, the dilemma as to what makes Y. pestis such a virulent and lethal pathogen remains unanswered. The method being employed makes use microarray technology (DNA chip) that enables the examination of the global activities of the whole complement of genes in this pathogen. Two primary resources available to the investigators (one directly obtained from a separate CBNP-funded project) make these studies possible: (1) Whole genome comparisons of the genes in Y. pestis and its near neighbors with attenuated or non pathogenic characteristics, and (2) the ability to duplicate in vitro, conditions that mimic the infection process of this pathogen. This year we have extended our studies from the original work of characterizing the global transcriptional regulation in Y. pestis triggered during temperature transition from 26 C to 37 C (roughly conditions found in the flea vector and the mammalian host, respectively) to studies of regulation encountered during shift between growth from conditions of neutral pH to acidic pH (the latter conditions, those mimic the environment found inside macrophages, a likely environment found by these cells during infection.). For this work, DNA arrays containing some 5,000 genes (the entire genome of Y. pestis plus those genes found uniquely in the enteropathogen, and near neighbor, Y. pseudotuberculosis) are used to monitor the simultaneous expression levels of each gene of known and unknown function in Y. pestis. Those genes that are up-regulate under the experimental conditions represent genes potentially involved in the pathogenic process. The ultimate role in

  19. Global warming: Economic policy responses

    SciTech Connect

    Dornbusch, R.; Poterba, J.M.

    1991-01-01

    This volume contains the proceedings of a conference that brought together economic experts from Europe, the US, Latin America, and Japan to evaluate key issues in the policy debate in global warming. The following issues are at the center of debates on alternative policies to address global warming: scientific evidence on the magnitude of global warming and the extent to which it is due to human activities; availability of economic tools to control the anthropogenic emissions of greenhouse gases, and how vigorously should they be applied; and political economy considerations which influence the design of an international program for controlling greenhouse gases. Many perspectives are offered on the approaches to remedying environmental problems that are currently being pursued in Europe and the Pacific Rim. Deforestation in the Amazon is discussed, as well as ways to slow it. Public finance assessments are presented of both the domestic and international policy issues raised by plans to levy a tax on the carbon emissions from various fossil fuels. Nine chapters have been processed separately for inclusion in the appropriate data bases.

  20. Social responsibility of nursing: a global perspective.

    PubMed

    Tyer-Viola, Lynda; Nicholas, Patrice K; Corless, Inge B; Barry, Donna M; Hoyt, Pamela; Fitzpatrick, Joyce J; Davis, Sheila M

    2009-05-01

    This study addresses social responsibility in the discipline of nursing and implications for global health. The concept of social responsibility is explicated and its relevance for nursing is examined, grounded in the American Nurses Association Code of Ethics and the International Council of Nurses Code of Ethics. Social justice, human rights, nurse migration, and approaches to nursing education are discussed within the framework of nursing's social responsibility. Strategies for addressing nursing workforce issues and education within a framework of social responsibility are explored.

  1. Medical responsibility and global environmental change.

    PubMed

    McCally, M; Cassel, C K

    1990-09-15

    Global environmental change threatens the habitability of the planet and the health of its inhabitants. Toxic pollution of air and water, acid rain, destruction of stratospheric ozone, waste, species extinction and, potentially, global warming are produced by the growing numbers and activities of human beings. Progression of these environmental changes could lead to unprecedented human suffering. Physicians can treat persons experiencing the consequences of environmental change but cannot individually prevent the cause of their suffering. Physicians have information and expertise about environmental change that can contribute to its slowing or prevention. Work to prevent global environmental change is consistent with the social responsibility of physicians and other health professionals.

  2. Global Response to Local Ionospheric Mass Ejection

    NASA Technical Reports Server (NTRS)

    Moore, T. E.; Fok, M.-C.; Delcourt, D. C.; Slinker, S. P.; Fedder, J. A.

    2010-01-01

    We revisit a reported "Ionospheric Mass Ejection" using prior event observations to guide a global simulation of local ionospheric outflows, global magnetospheric circulation, and plasma sheet pressurization, and comparing our results with the observed global response. Our simulation framework is based on test particle motions in the Lyon-Fedder-Mobarry (LFM) global circulation model electromagnetic fields. The inner magnetosphere is simulated with the Comprehensive Ring Current Model (CRCM) of Fok and Wolf, driven by the transpolar potential developed by the LFM magnetosphere, and includes an embedded plasmaspheric simulation. Global circulation is stimulated using the observed solar wind conditions for the period 24-25 Sept 1998. This period begins with the arrival of a Coronal Mass Ejection, initially with northward, but later with southward interplanetary magnetic field. Test particles are launched from the ionosphere with fluxes specified by local empirical relationships of outflow to electrodynamic and particle precipitation imposed by the MIlD simulation. Particles are tracked until they are lost from the system downstream or into the atmosphere, using the full equations of motion. Results are compared with the observed ring current and a simulation of polar and auroral wind outflows driven globally by solar wind dynamic pressure. We find good quantitative agreement with the observed ring current, and reasonable qualitative agreement with earlier simulation results, suggesting that the solar wind driven global simulation generates realistic energy dissipation in the ionosphere and that the Strangeway relations provide a realistic local outflow description.

  3. Circadian Control of Global Gene Expression Patterns

    PubMed Central

    Doherty, Colleen J.; Kay, Steve A.

    2014-01-01

    An internal time-keeping mechanism has been observed in almost every organism studied from archaea to humans. This circadian clock provides a competitive advantage in fitness and survival (18, 30, 95, 129, 137). Researchers have uncovered the molecular composition of this internal clock by combining enzymology, molecular biology, genetics, and modeling approaches. However, understanding the mechanistic link between the clock and output responses has been elusive. In three model organisms, Arabidopsis thaliana, Drosophila melanogaster, and Mus musculus, whole-genome expression arrays have enabled researchers to investigate how maintaining a time-keeping mechanism connects to an adaptive advantage. Here, we review the impacts transcriptomics have had on our understanding of the clock and how this molecular clock connects with system-level circadian responses. We explore the discoveries made possible by high-throughput RNA assays, the network approaches used to investigate these large transcript datasets, and potential future directions. PMID:20809800

  4. Global expression pattern comparison between low phosphorus insensitive 4 and WT Arabidopsis reveals an important role of reactive oxygen species and jasmonic acid in the root tip response to phosphate starvation.

    PubMed

    Chacón-López, Alejandra; Ibarra-Laclette, Enrique; Sánchez-Calderón, Lenin; Gutiérrez-Alanis, Dolores; Herrera-Estrella, Luis

    2011-03-01

    Plants are exposed to several biotic and abiotic stresses. A common environmental stress that plants have to face both in natural and agricultural ecosystems that impacts both its growth and development is low phosphate (Pi) availability. There has been an important progress in the knowledge of the molecular mechanisms by which plants cope with Pi deficiency. However, the mechanisms that mediate alterations in the architecture of the Arabidopsis root system responses to Pi starvation are still largely unknown. One of the most conspicuous developmental effects of low Pi on the Arabidopsis root system is the inhibition of primary root growth that is accompanied by loss of root meristematic activity. To identify signalling pathways potentially involved in the Arabidpsis root meristem response to Pi-deprivation, here we report the global gene expression analysis of the root tip of wild type and low phosphorus insensitive4 (lpi4) mutant grown under Pi limiting conditions. Differential gene expression analysis and physiological experiments show that changes in the redox status, probably mediated by jasmonic acid and ethylene, play an important role in the primary root meristem exhaustion process triggered by Pi-starvation.

  5. Global genetic variations predict brain response to faces.

    PubMed

    Dickie, Erin W; Tahmasebi, Amir; French, Leon; Kovacevic, Natasa; Banaschewski, Tobias; Barker, Gareth J; Bokde, Arun; Büchel, Christian; Conrod, Patricia; Flor, Herta; Garavan, Hugh; Gallinat, Juergen; Gowland, Penny; Heinz, Andreas; Ittermann, Bernd; Lawrence, Claire; Mann, Karl; Martinot, Jean-Luc; Nees, Frauke; Nichols, Thomas; Lathrop, Mark; Loth, Eva; Pausova, Zdenka; Rietschel, Marcela; Smolka, Michal N; Ströhle, Andreas; Toro, Roberto; Schumann, Gunter; Paus, Tomáš

    2014-08-01

    Face expressions are a rich source of social signals. Here we estimated the proportion of phenotypic variance in the brain response to facial expressions explained by common genetic variance captured by ∼ 500,000 single nucleotide polymorphisms. Using genomic-relationship-matrix restricted maximum likelihood (GREML), we related this global genetic variance to that in the brain response to facial expressions, as assessed with functional magnetic resonance imaging (fMRI) in a community-based sample of adolescents (n = 1,620). Brain response to facial expressions was measured in 25 regions constituting a face network, as defined previously. In 9 out of these 25 regions, common genetic variance explained a significant proportion of phenotypic variance (40-50%) in their response to ambiguous facial expressions; this was not the case for angry facial expressions. Across the network, the strength of the genotype-phenotype relationship varied as a function of the inter-individual variability in the number of functional connections possessed by a given region (R(2) = 0.38, p<0.001). Furthermore, this variability showed an inverted U relationship with both the number of observed connections (R2 = 0.48, p<0.001) and the magnitude of brain response (R(2) = 0.32, p<0.001). Thus, a significant proportion of the brain response to facial expressions is predicted by common genetic variance in a subset of regions constituting the face network. These regions show the highest inter-individual variability in the number of connections with other network nodes, suggesting that the genetic model captures variations across the adolescent brains in co-opting these regions into the face network.

  6. Global Genetic Variations Predict Brain Response to Faces

    PubMed Central

    Dickie, Erin W.; Tahmasebi, Amir; French, Leon; Kovacevic, Natasa; Banaschewski, Tobias; Barker, Gareth J.; Bokde, Arun; Büchel, Christian; Conrod, Patricia; Flor, Herta; Garavan, Hugh; Gallinat, Juergen; Gowland, Penny; Heinz, Andreas; Ittermann, Bernd; Lawrence, Claire; Mann, Karl; Martinot, Jean-Luc; Nees, Frauke; Nichols, Thomas; Lathrop, Mark; Loth, Eva; Pausova, Zdenka; Rietschel, Marcela; Smolka, Michal N.; Ströhle, Andreas; Toro, Roberto; Schumann, Gunter; Paus, Tomáš

    2014-01-01

    Face expressions are a rich source of social signals. Here we estimated the proportion of phenotypic variance in the brain response to facial expressions explained by common genetic variance captured by ∼500,000 single nucleotide polymorphisms. Using genomic-relationship-matrix restricted maximum likelihood (GREML), we related this global genetic variance to that in the brain response to facial expressions, as assessed with functional magnetic resonance imaging (fMRI) in a community-based sample of adolescents (n = 1,620). Brain response to facial expressions was measured in 25 regions constituting a face network, as defined previously. In 9 out of these 25 regions, common genetic variance explained a significant proportion of phenotypic variance (40–50%) in their response to ambiguous facial expressions; this was not the case for angry facial expressions. Across the network, the strength of the genotype-phenotype relationship varied as a function of the inter-individual variability in the number of functional connections possessed by a given region (R2 = 0.38, p<0.001). Furthermore, this variability showed an inverted U relationship with both the number of observed connections (R2 = 0.48, p<0.001) and the magnitude of brain response (R2 = 0.32, p<0.001). Thus, a significant proportion of the brain response to facial expressions is predicted by common genetic variance in a subset of regions constituting the face network. These regions show the highest inter-individual variability in the number of connections with other network nodes, suggesting that the genetic model captures variations across the adolescent brains in co-opting these regions into the face network. PMID:25122193

  7. The responsible subject in the global age.

    PubMed

    Pulcini, Elena

    2010-09-01

    The first thesis of this article is that the concept of responsibility takes on an unprecedented meaning in the twentieth century resulting from the emergence of a new dimension of the other: to be responsible comes to mean not just to account for oneself in relation to the other, but also to take the other into account, to take care of the other-what I call responsibility towards (the other). The main reason for this change consists in the emergence of global risks and the necessity, as underlined by Hans Jonas, to be responsible for the destiny of the world and future generations. The problem, as explored in the article's second thesis, is that this implies the existence of a subject who is capable of responsibility. Jonas's insights on this point are insufficient, since he only recognizes duty as the fundament for his ethics of responsibility and thus neglects the problem of motivation. This is a particularly crucial problem today as we are witnessing the presence of a pathological subject, characterized by a split in his faculties (between doing and imagining, knowing and feeling). To underline this fact, this article makes use of Günther Anders's reflections, which provide a psycho-anthropological analysis of the subject, showing his pathologies and the necessity, from a moral perspective, to overcome his scission. Finally, this author suggests, as the article's third thesis, that this overcoming is the necessary fundament for the perception of risk, which in turn reinstates the subject's perception of his own vulnerability. Responsibility thus finds a motivation, which is neither altruistic nor duty-centred, in the awareness of our own vulnerability and the bond with the destiny of humankind as a whole.

  8. The global outbreak alert and response network.

    PubMed

    Mackenzie, John S; Drury, Patrick; Arthur, Ray R; Ryan, Michael J; Grein, Thomas; Slattery, Raphael; Suri, Sameera; Domingo, Christine Tiffany; Bejtullahu, Armand

    2014-01-01

    The Global Outbreak Alert and Response Network (GOARN) was established in 2000 as a network of technical institutions, research institutes, universities, international health organisations and technical networks willing to contribute and participate in internationally coordinated responses to infectious disease outbreaks. It reflected a recognition of the need to strengthen and coordinate rapid mobilisation of experts in responding to international outbreaks and to overcome the sometimes chaotic and fragmented operations characterising previous responses. The network partners agreed that the World Health Organization would coordinate the network and provide a secretariat, which would also function as the operational support team. The network has evolved to comprise 153 institutions/technical partners and 37 additional networks, the latter encompassing a further 355 members and has been directly involved in 137 missions to 79 countries, territories or areas. Future challenges will include supporting countries to achieve the capacity to detect and respond to outbreaks of international concern, as required by the International Health Regulations (2005). GOARN's increasing regional focus and expanding geographic composition will be central to meeting these challenges. The paper summarises some of network's achievements over the past 13 years and presents some of the future challenges.

  9. The Global Outbreak Alert and Response Network

    PubMed Central

    Mackenzie, John S.; Drury, Patrick; Arthur, Ray R.; Ryan, Michael J.; Grein, Thomas; Slattery, Raphael; Suri, Sameera; Domingo, Christine Tiffany; Bejtullahu, Armand

    2014-01-01

    The Global Outbreak Alert and Response Network (GOARN) was established in 2000 as a network of technical institutions, research institutes, universities, international health organisations and technical networks willing to contribute and participate in internationally coordinated responses to infectious disease outbreaks. It reflected a recognition of the need to strengthen and coordinate rapid mobilisation of experts in responding to international outbreaks and to overcome the sometimes chaotic and fragmented operations characterising previous responses. The network partners agreed that the World Health Organization would coordinate the network and provide a secretariat, which would also function as the operational support team. The network has evolved to comprise 153 institutions/technical partners and 37 additional networks, the latter encompassing a further 355 members and has been directly involved in 137 missions to 79 countries, territories or areas. Future challenges will include supporting countries to achieve the capacity to detect and respond to outbreaks of international concern, as required by the International Health Regulations (2005). GOARN's increasing regional focus and expanding geographic composition will be central to meeting these challenges. The paper summarises some of network's achievements over the past 13 years and presents some of the future challenges. PMID:25186571

  10. Title: Freshwater phytoplankton responses to global warming.

    PubMed

    Wagner, Heiko; Fanesi, Andrea; Wilhelm, Christian

    2016-09-20

    Global warming alters species composition and function of freshwater ecosystems. However, the impact of temperature on primary productivity is not sufficiently understood and water quality models need to be improved in order to assess the quantitative and qualitative changes of aquatic communities. On the basis of experimental data, we demonstrate that the commonly used photosynthetic and water chemistry parameters alone are not sufficient for modeling phytoplankton growth under changing temperature regimes. We present some new aspects of the acclimation process with respect to temperature and how contrasting responses may be explained by a more complete physiological knowledge of the energy flow from photons to new biomass. We further suggest including additional bio-markers/traits for algal growth such as carbon allocation patterns to increase the explanatory power of such models. Although carbon allocation patterns are promising and functional cellular traits for growth prediction under different nutrient and light conditions, their predictive power still waits to be tested with respect to temperature. A great challenge for the near future will be the prediction of primary production efficiencies under the global change scenario using a uniform model for phytoplankton assemblages.

  11. [Response of bryophytes to global change and its bioindicatortation].

    PubMed

    Wu, Yuhuan; Gao, Chien; Cheng, Guodong; Yu, Xinghua; Cao, Tong

    2002-07-01

    Bryophytes are sensitive to atmosphere components concentration and global climate change resulted from relatively simple structures. Bryophyte is an ideal kind of biological indicator of global changes, environmental pollution, nutrient condition, forest integrity and ecosystem health. In order to use bryophytes as indicators to environmental and global changes, further studies on response and adaptation of bryophytes to the global changes are needed.

  12. Global Gene Expression Analysis for the Assessment of Nanobiomaterials.

    PubMed

    Hanagata, Nobutaka

    2015-01-01

    Using global gene expression analysis, the effects of biomaterials and nanomaterials can be analyzed at the genetic level. Even though information obtained from global gene expression analysis can be useful for the evaluation and design of biomaterials and nanomaterials, its use for these purposes is not widespread. This is due to the difficulties involved in data analysis. Because the expression data of about 20,000 genes can be obtained at once with global gene expression analysis, the data must be analyzed using bioinformatics. A method of bioinformatic analysis called gene ontology can estimate the kinds of changes on cell functions caused by genes whose expression level is changed by biomaterials and nanomaterials. Also, by applying a statistical analysis technique called hierarchical clustering to global gene expression data between a variety of biomaterials, the effects of the properties of materials on cell functions can be estimated. In this chapter, these theories of analysis and examples of applications to nanomaterials and biomaterials are described. Furthermore, global microRNA analysis, a method that has gained attention in recent years, and its application to nanomaterials are introduced.

  13. A Global Drought Observatory for Emergency Response

    NASA Astrophysics Data System (ADS)

    Vogt, Jürgen; de Jager, Alfred; Carrão, Hugo; Magni, Diego; Mazzeschi, Marco; Barbosa, Paulo

    2016-04-01

    Droughts are occurring on all continents and across all climates. While in developed countries they cause significant economic and environmental damages, in less developed countries they may cause major humanitarian catastrophes. The magnitude of the problem and the expected increase in drought frequency, extent and severity in many, often highly vulnerable regions of the world demand a change from the current reactive, crisis-management approach towards a more pro-active, risk management approach. Such approach needs adequate and timely information from global to local scales as well as adequate drought management plans. Drought information systems are important for continuous monitoring and forecasting of the situation in order to provide timely information on developing drought events and their potential impacts. Against this background, the Joint Research Centre (JRC) is developing a Global Drought Observatory (GDO) for the European Commission's humanitarian services, providing up-to-date information on droughts world-wide and their potential impacts. Drought monitoring is achieved by a combination of meteorological and biophysical indicators, while the societal vulnerability to droughts is assessed through the targeted analysis of a series of social, economic and infrastructural indicators. The combination of the information on the occurrence and severity of a drought, on the assets at risk and on the societal vulnerability in the drought affected areas results in a likelihood of impact, which is expressed by a Likelihood of Drought Impact (LDI) indicator. The location, extent and magnitude of the LDI is then further analyzed against the number of people and land use/land cover types affected in order to provide the decision bodies with information on the potential humanitarian and economic bearings in the affected countries or regions. All information is presented through web-mapping interfaces based on OGC standards and customized reports can be drawn by the

  14. Global circuit response to seasonal variations in global surface air temperature

    NASA Technical Reports Server (NTRS)

    Williams, Earle R.

    1994-01-01

    Comparisons are made between the seasonal behavior of the global electrical circuit and the surface air temperature for the Tropics and for the globe. Positive correlations between global circuit parameters and temperature are identified on both semiannual and annual timescales. Lightning is the global circuit quantity found most responsive to temperature, with a sensitivity of the order of 10% per 1 C. These findings lend further validity to the use of global circuit measurements as a diagnostic for global change.

  15. Fungal symbionts alter plant responses to global change.

    PubMed

    Kivlin, Stephanie N; Emery, Sarah M; Rudgers, Jennifer A

    2013-07-01

    While direct plant responses to global change have been well characterized, indirect plant responses to global change, via altered species interactions, have received less attention. Here, we examined how plants associated with four classes of fungal symbionts (class I leaf endophytes [EF], arbuscular mycorrhizal fungi [AMF], ectomycorrhizal fungi [ECM], and dark septate endophytes [DSE]) responded to four global change factors (enriched CO2, drought, N deposition, and warming). We performed a meta-analysis of 434 studies spanning 174 publications to search for generalizable trends in responses of plant-fungal symbioses to future environments. Specifically, we addressed the following questions: (1) Can fungal symbionts ameliorate responses of plants to global change? (2) Do fungal symbiont groups differ in the degree to which they modify plant response to global change? (3) Do particular global change factors affect plant-fungal symbioses more than others? In all global change scenarios, except elevated CO2, fungal symbionts significantly altered plant responses to global change. In most cases, fungal symbionts increased plant biomass in response to global change. However, increased N deposition reduced the benefits of symbiosis. Of the global change factors we considered, drought and N deposition resulted in the strongest fungal mediation of plant responses. Our analysis highlighted gaps in current knowledge for responses of particular fungal groups and revealed the importance of considering not only the nonadditive effects of multiple global change factors, but also the interactive effects of multiple fungal symbioses. Our results show that considering plant-fungal symbioses is critical to predicting ecosystem response to global change.

  16. Global Climate Responses to Anthropogenic Groundwater Exploitation

    NASA Astrophysics Data System (ADS)

    Zeng, Y.; Xie, Z.

    2015-12-01

    In this study, a groundwater exploitation scheme is incorporated into the earth system model, Community Earth System Model 1.2.0 (CESM1.2.0), which is called CESM1.2_GW, and the climatic responses to anthropogenic groundwater withdrawal are then investigated on global scale. The scheme models anthropogenic groundwater exploitation and consumption, which are then divided into agricultural irrigation, industrial use and domestic use. A group of 41-year ensemble groundwater exploitation simulations with six different initial conditions, and a group of ensemble control simulations without exploitation are conducted using the developed model CESM1.2_GW with water supplies and demands estimated. The results reveal that the groundwater exploitation and water consumption cause drying effects on soil moisture in deep layers and wetting effects in upper layers, along with a rapidly declining groundwater table in Central US, Haihe River Basin in China and Northern India and Pakistan where groundwater extraction are most severe in the world. The atmosphere also responds to anthropogenic groundwater exploitation. Cooling effects on lower troposphere appear in large areas of North China Plain and of Northern India and Pakistan. Increased precipitation occurs in Haihe River Basin due to increased evapotranspiration from irrigation. Decreased precipitation occurs in Northern India because water vapor here is taken away by monsoon anomalies induced by anthropogenic alteration of groundwater. The local reducing effects of anthropogenic groundwater exploitation on total terrestrial water storage evinces that water resource is unsustainable with the current high exploitation rate. Therefore, a balance between slow groundwater withdrawal and rapid human economic development must be achieved to maintain a sustainable water resource, especially in over-exploitation regions such as Central US, Northern China, India and Pakistan.

  17. The Processing of Emotional Expressions as Discrete and Global Categories.

    ERIC Educational Resources Information Center

    Kestenbaum, Roberta

    This study explored the use of analytic and holistic modes of processing in the recognition of emotional expressions as discrete and global categories. Five- and seven-year-olds and adults were presented with a series of slides that showed different parts of faces depicting either happiness, surprise, fear, or anger. Slides ranged from single…

  18. Response to Skeptics of Global Warming.

    NASA Astrophysics Data System (ADS)

    Kellogg, William W.

    1991-04-01

    The majority of the scientific community involved in climate research is convinced of the reality of a current and future global warming due to the greenhouse effect, a change that must be largely caused by human activities. However, a minority of scientists is still skeptical of the notion that mankind is significantly influencing the climate of the earth, and it therefore argues against taking certain measures to avert this alleged global warming. In recent years the media have given considerable coverage to the statements of these skeptics. Reasons for their statements range from a simple argument that we do not understand the earth's climate system well enough to predict the future, to more complex arguments involving negative feed-backs and changes of solar activity. They question whether the global temperature increase in this century of up to 0.6 K is primarily a result of worldwide burning of fossil fuels. The purpose of this article is to show that the statements of this skeptical school of thought need to be critically analyzed (and in some cases refuted) in the light of current understanding of the planetary system that determines our climate. There is also another school of thought that agrees about the reality of present and future global warming, and claims that this will be beneficial for most of mankind and that it should be encouraged. The policy implications of the latter view are in many respects similar to those of the group that are not convinced that a significant global warming will occur. Both schools of thought argue against taking immediate steps to slow the climate change.

  19. Resourceful earth: a response to global 2000

    SciTech Connect

    Simon, J.L.; Kahn, H.

    1984-01-01

    Dismayed by the negativism of the Carter Administration's report Global 2000 and suspicious of the political uses being made of it, Professor Simon of the University of Maryland and the late Herman Kahn, with support from the Heritage Foundation, put together these studies by experts to correct what they think are fundamental errors. They call their rather optimistic statements about the future of population, food, water, resources, climate and other things unconditional predictions in the absence of an unforeseeable catastrophe - their underlying assumption being that people will do the right things to adjust constructively to change.

  20. A Global Language for the Global Village? A Response to Mary Snell-Hornby.

    ERIC Educational Resources Information Center

    Anderman, Gunilla

    1999-01-01

    This response to an article on the effect of recent developments (particularly globalization and advances in technology) on the production and perception of language discusses the role of English as a global language and issues surrounding translation. Suggests that stereotyping resulting from non-nuanced and unsubtle transfer of information might…

  1. Globally increased ultraconserved noncoding RNA expression in pancreatic adenocarcinoma

    PubMed Central

    Lee, Eun Joo; Gusev, Yuriy; Allard, David; Sutaria, Dhruvitkumar S.; Badawi, Mohamed; Elgamal, Ola A.; Lerner, Megan R.; Brackett, Daniel J.; Calin, George A.; Schmittgen, Thomas D.

    2016-01-01

    Transcribed ultraconserved regions (T-UCRs) are a class of non-coding RNAs with 100% sequence conservation among human, rat and mouse genomes. T-UCRs are differentially expressed in several cancers, however their expression in pancreatic adenocarcinoma (PDAC) has not been studied. We used a qPCR array to profile all 481 T-UCRs in pancreatic cancer specimens, pancreatic cancer cell lines, during experimental pancreatic desmoplasia and in the pancreases of P48Cre/wt; KrasLSL-G12D/wt mice. Fourteen, 57 and 29% of the detectable T-UCRs were differentially expressed in the cell lines, human tumors and transgenic mouse pancreases, respectively. The vast majority of the differentially expressed T-UCRs had increased expression in the cancer. T-UCRs were monitored using an in vitro model of the desmoplastic reaction. Twenty-five % of the expressed T-UCRs were increased in the HPDE cells cultured on PANC-1 cellular matrix. UC.190, UC.233 and UC.270 were increased in all three human data sets. siRNA knockdown of each of these three T-UCRs reduced the proliferation of MIA PaCa-2 cells up to 60%. The expression pattern among many T-UCRs in the human and mouse pancreases closely correlated with one another, suggesting that groups of T-UCRs are co-activated in PDAC. Successful knockout of the transcription factor EGR1 in PANC-1 cells caused a reduction in the expression of a subset of T-UCRs suggesting that EGR1 may control T-UCR expression in PDAC. We report a global increase in expression of T-UCRs in both human and mouse PDAC. Commonalties in their expression pattern suggest a similar mechanism of transcriptional upregulation for T-UCRs in PDAC. PMID:27363020

  2. Ecological response to global climatic change

    USGS Publications Warehouse

    Malanson, G.P.; Butler, D.R.; Walsh, S. J.; Janelle, Donald G.; Warf, Barney; Hansen, Kathy

    2004-01-01

    Climate change and ecological change go hand in hand. Because we value our ecological environment, any change has the potential to be a problem. Geographers have been drawn to this challenge, and have been successful in addressing it, because the primary ecological response to climate changes in the past — the waxing and waning of the great ice sheets over the past 2 million years – was the changing geographic range of the biota. Plants and animals changed their location. Geographers have been deeply involved in documenting the changing biota of the past, and today we are called upon to help assess the possible responses to ongoing and future climatic change and, thus, their impacts. Assessing the potential responses is important for policy makers to judge the outcomes of action or inaction and also sets the stage for preparation for and mitigation of change.

  3. Global barotropic response to a tropical forcing

    NASA Technical Reports Server (NTRS)

    Zhang, Yuxia; Mcguirk, James P.

    1993-01-01

    Zonally varying flow has been used to initialize numerical models and has been shown to play an important role in strong localized responses both in extratropics and the tropics. In this study, a climatological 200 mb January mean is used as a steady basic state of a barotropical model which consists of shallow water equations and a mass source centered at 4 deg S/120 deg E to simulate convective heating over Indonesia region. In the experiment, tropical responses appear not only over the western Pacific, where the forcing is located, but also over the eastern Pacific where the response is related to the zonally varying basic state. The westward propagating equatorial Rossby waves excited by the forcing interact with waves out of and into the tropics and the positive and negative phase of the Rossby waves result in blocking circulation over North America and tropical plumes over equatorial eastern Pacific, respectively.

  4. Marine ecosystem responses to Cenozoic global change.

    PubMed

    Norris, R D; Turner, S Kirtland; Hull, P M; Ridgwell, A

    2013-08-02

    The future impacts of anthropogenic global change on marine ecosystems are highly uncertain, but insights can be gained from past intervals of high atmospheric carbon dioxide partial pressure. The long-term geological record reveals an early Cenozoic warm climate that supported smaller polar ecosystems, few coral-algal reefs, expanded shallow-water platforms, longer food chains with less energy for top predators, and a less oxygenated ocean than today. The closest analogs for our likely future are climate transients, 10,000 to 200,000 years in duration, that occurred during the long early Cenozoic interval of elevated warmth. Although the future ocean will begin to resemble the past greenhouse world, it will retain elements of the present "icehouse" world long into the future. Changing temperatures and ocean acidification, together with rising sea level and shifts in ocean productivity, will keep marine ecosystems in a state of continuous change for 100,000 years.

  5. Differential global gene expression in red and white skeletal muscle

    NASA Technical Reports Server (NTRS)

    Campbell, W. G.; Gordon, S. E.; Carlson, C. J.; Pattison, J. S.; Hamilton, M. T.; Booth, F. W.

    2001-01-01

    The differences in gene expression among the fiber types of skeletal muscle have long fascinated scientists, but for the most part, previous experiments have only reported differences of one or two genes at a time. The evolving technology of global mRNA expression analysis was employed to determine the potential differential expression of approximately 3,000 mRNAs between the white quad (white muscle) and the red soleus muscle (mixed red muscle) of female ICR mice (30-35 g). Microarray analysis identified 49 mRNA sequences that were differentially expressed between white and mixed red skeletal muscle, including newly identified differential expressions between muscle types. For example, the current findings increase the number of known, differentially expressed mRNAs for transcription factors/coregulators by nine and signaling proteins by three. The expanding knowledge of the diversity of mRNA expression between white and mixed red muscle suggests that there could be quite a complex regulation of phenotype between muscles of different fiber types.

  6. Global analysis of the immune response

    NASA Astrophysics Data System (ADS)

    Ribeiro, Leonardo C.; Dickman, Ronald; Bernardes, Américo T.

    2008-10-01

    The immune system may be seen as a complex system, characterized using tools developed in the study of such systems, for example, surface roughness and its associated Hurst exponent. We analyze densitometric (Panama blot) profiles of immune reactivity, to classify individuals into groups with similar roughness statistics. We focus on a population of individuals living in a region in which malaria endemic, as well as a control group from a disease-free region. Our analysis groups individuals according to the presence, or absence, of malaria symptoms and number of malaria manifestations. Applied to the Panama blot data, our method proves more effective at discriminating between groups than principal-components analysis or super-paramagnetic clustering. Our findings provide evidence that some phenomena observed in the immune system can be only understood from a global point of view. We observe similar tendencies between experimental immune profiles and those of artificial profiles, obtained from an immune network model. The statistical entropy of the experimental profiles is found to exhibit variations similar to those observed in the Hurst exponent.

  7. Global transcriptome response in Lactobacillus sakei during growth on ribose

    PubMed Central

    2011-01-01

    Background Lactobacillus sakei is valuable in the fermentation of meat products and exhibits properties that allow for better preservation of meat and fish. On these substrates, glucose and ribose are the main carbon sources available for growth. We used a whole-genome microarray based on the genome sequence of L. sakei strain 23K to investigate the global transcriptome response of three L. sakei strains when grown on ribose compared with glucose. Results The function of the common regulated genes was mostly related to carbohydrate metabolism and transport. Decreased transcription of genes encoding enzymes involved in glucose metabolism and the L-lactate dehydrogenase was observed, but most of the genes showing differential expression were up-regulated. Especially transcription of genes directly involved in ribose catabolism, the phosphoketolase pathway, and in alternative fates of pyruvate increased. Interestingly, the methylglyoxal synthase gene, which encodes an enzyme unique for L. sakei among lactobacilli, was up-regulated. Ribose catabolism seems closely linked with catabolism of nucleosides. The deoxyribonucleoside synthesis operon transcriptional regulator gene was strongly up-regulated, as well as two gene clusters involved in nucleoside catabolism. One of the clusters included a ribokinase gene. Moreover, hprK encoding the HPr kinase/phosphatase, which plays a major role in the regulation of carbon metabolism and sugar transport, was up-regulated, as were genes encoding the general PTS enzyme I and the mannose-specific enzyme II complex (EIIman). Putative catabolite-responsive element (cre) sites were found in proximity to the promoter of several genes and operons affected by the change of carbon source. This could indicate regulation by a catabolite control protein A (CcpA)-mediated carbon catabolite repression (CCR) mechanism, possibly with the EIIman being indirectly involved. Conclusions Our data shows that the ribose uptake and catabolic machinery in

  8. Conceptualizing psychological processes in response to globalization: Components, antecedents, and consequences of global orientations.

    PubMed

    Chen, Sylvia Xiaohua; Lam, Ben C P; Hui, Bryant P H; Ng, Jacky C K; Mak, Winnie W S; Guan, Yanjun; Buchtel, Emma E; Tang, Willie C S; Lau, Victor C Y

    2016-02-01

    The influences of globalization have permeated various aspects of life in contemporary society, from technical innovations, economic development, and lifestyles, to communication patterns. The present research proposed a construct termed global orientation to denote individual differences in the psychological processes of acculturating to the globalizing world. It encompasses multicultural acquisition as a proactive response and ethnic protection as a defensive response to globalization. Ten studies examined the applicability of global orientations among majority and minority groups, including immigrants and sojourners, in multicultural and relatively monocultural contexts, and across Eastern and Western cultures. Multicultural acquisition is positively correlated with both independent and interdependent self-construals, bilingual proficiency and usage, and dual cultural identifications. Multicultural acquisition is promotion-focused, while ethnic protection is prevention-focused and related to acculturative stress. Global orientations affect individuating and modest behavior over and above multicultural ideology, predict overlap with outgroups over and above political orientation, and predict psychological adaptation, sociocultural competence, tolerance, and attitudes toward ethnocultural groups over and above acculturation expectations/strategies. Global orientations also predict English and Chinese oral presentation performance in multilevel analyses and the frequency and pleasantness of intercultural contact in cross-lagged panel models. We discuss how the psychological study of global orientations contributes to theory and research on acculturation, cultural identity, and intergroup relations.

  9. Regulation of global gene expression and cell proliferation by APP

    PubMed Central

    Wu, Yili; Zhang, Si; Xu, Qin; Zou, Haiyan; Zhou, Weihui; Cai, Fang; Li, Tingyu; Song, Weihong

    2016-01-01

    Down syndrome (DS), caused by trisomy of chromosome 21, is one of the most common genetic disorders. Patients with DS display growth retardation and inevitably develop characteristic Alzheimer’s disease (AD) neuropathology, including neurofibrillary tangles and neuritic plaques. The expression of amyloid precursor protein (APP) is increased in both DS and AD patients. To reveal the function of APP and elucidate the pathogenic role of increased APP expression in DS and AD, we performed gene expression profiling using microarray method in human cells overexpressing APP. A set of genes are significantly altered, which are involved in cell cycle, cell proliferation and p53 signaling. We found that overexpression of APP inhibits cell proliferation. Furthermore, we confirmed that the downregulation of two validated genes, PSMA5 and PSMB7, inhibits cell proliferation, suggesting that the downregulation of PSMA5 and PSMB7 is involved in APP-induced cell proliferation impairment. Taken together, this study suggests that APP regulates global gene expression and increased APP expression inhibits cell proliferation. Our study provides a novel insight that APP overexpression may contribute to the growth impairment in DS patients and promote AD pathogenesis by inhibiting cell proliferation including neural stem cell proliferation and neurogenesis. PMID:26936520

  10. Regulation of global gene expression and cell proliferation by APP.

    PubMed

    Wu, Yili; Zhang, Si; Xu, Qin; Zou, Haiyan; Zhou, Weihui; Cai, Fang; Li, Tingyu; Song, Weihong

    2016-03-03

    Down syndrome (DS), caused by trisomy of chromosome 21, is one of the most common genetic disorders. Patients with DS display growth retardation and inevitably develop characteristic Alzheimer's disease (AD) neuropathology, including neurofibrillary tangles and neuritic plaques. The expression of amyloid precursor protein (APP) is increased in both DS and AD patients. To reveal the function of APP and elucidate the pathogenic role of increased APP expression in DS and AD, we performed gene expression profiling using microarray method in human cells overexpressing APP. A set of genes are significantly altered, which are involved in cell cycle, cell proliferation and p53 signaling. We found that overexpression of APP inhibits cell proliferation. Furthermore, we confirmed that the downregulation of two validated genes, PSMA5 and PSMB7, inhibits cell proliferation, suggesting that the downregulation of PSMA5 and PSMB7 is involved in APP-induced cell proliferation impairment. Taken together, this study suggests that APP regulates global gene expression and increased APP expression inhibits cell proliferation. Our study provides a novel insight that APP overexpression may contribute to the growth impairment in DS patients and promote AD pathogenesis by inhibiting cell proliferation including neural stem cell proliferation and neurogenesis.

  11. Evolutionary responses to global change: lessons from invasive species.

    PubMed

    Moran, Emily V; Alexander, Jake M

    2014-05-01

    Biologists have recently devoted increasing attention to the role of rapid evolution in species' responses to environmental change. However, it is still unclear what evolutionary responses should be expected, at what rates, and whether evolution will save populations at risk of extinction. The potential of biological invasions to provide useful insights has barely been realised, despite the close analogies to species responding to global change, particularly climate change; in both cases, populations encounter novel climatic and biotic selection pressures, with expected evolutionary responses occurring over similar timescales. However, the analogy is not perfect, and invasive species are perhaps best used as an upper bound on expected change. In this article, we review what invasive species can and cannot teach us about likely evolutionary responses to global change and the constraints on those responses. We also discuss the limitations of invasive species as a model and outline directions for future research.

  12. Globalisation of tobacco industry influence and new global responses

    PubMed Central

    Yach, D.; Bettcher, D.

    2000-01-01

    The globalisation of tobacco marketing, trade, research, and industry influence represents a major threat to public health worldwide. Drawing upon tobacco industry strategy documents prepared over several decades, this paper will demonstrate how the tobacco industry operates as a global force, regarding the world as its operating market by planning, developing, and marketing its products on a global scale. The industry has used a wide range of methods to buy influence and power, and penetrate markets across the world. It has an annual turnover of almost US$400 billion. In contrast, until recently tobacco control lacked global leadership and strategic direction and had been severely underfunded. As part of moving towards a more sustainable form of globalisation, a global enabling environment linked to local actions should focus on the following strategies: global information management; development of nationally and locally grounded action; global regulation, legal instruments, and foreign policy; and establishment of strong partnerships with purpose. As the vector of the tobacco epidemic, the tobacco industry's actions fall far outside of the boundaries of global corporate responsibility. Therefore, global and local actions should not provide the tobacco industry with the two things that it needs to ensure its long term profitability: respectability and predictability.


Keywords: globalisation of tobacco marketing PMID:10841858

  13. Globalisation of tobacco industry influence and new global responses.

    PubMed

    Yach, D; Bettcher, D

    2000-06-01

    The globalisation of tobacco marketing, trade, research, and industry influence represents a major threat to public health worldwide. Drawing upon tobacco industry strategy documents prepared over several decades, this paper will demonstrate how the tobacco industry operates as a global force, regarding the world as its operating market by planning, developing, and marketing its products on a global scale. The industry has used a wide range of methods to buy influence and power, and penetrate markets across the world. It has an annual turnover of almost US$400 billion. In contrast, until recently tobacco control lacked global leadership and strategic direction and had been severely underfunded. As part of moving towards a more sustainable form of globalisation, a global enabling environment linked to local actions should focus on the following strategies: global information management; development of nationally and locally grounded action; global regulation, legal instruments, and foreign policy; and establishment of strong partnerships with purpose. As the vector of the tobacco epidemic, the tobacco industry's actions fall far outside of the boundaries of global corporate responsibility. Therefore, global and local actions should not provide the tobacco industry with the two things that it needs to ensure its long term profitability: respectability and predictability.

  14. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough.

    SciTech Connect

    Arkin, A. P.; Wall, J. D.; Hazen, T. C.; He, Z.; Zhou, J.; Huang, K. H.; Gaucher, Sara P.; He, Q.; Hadi, Masood Z.; Chhabra, Swapnil R.; Alm, Eric J.; Singh, A. K.

    2005-08-01

    Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z {ge} 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 C from a growth temperature of 37 C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors {sigma}{sup 32} and {sigma}{sup 54}. While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976

  15. Ezrin Inhibition Up-regulates Stress Response Gene Expression.

    PubMed

    Çelik, Haydar; Bulut, Gülay; Han, Jenny; Graham, Garrett T; Minas, Tsion Z; Conn, Erin J; Hong, Sung-Hyeok; Pauly, Gary T; Hayran, Mutlu; Li, Xin; Özdemirli, Metin; Ayhan, Ayşe; Rudek, Michelle A; Toretsky, Jeffrey A; Üren, Aykut

    2016-06-17

    Ezrin is a member of the ERM (ezrin/radixin/moesin) family of proteins that links cortical cytoskeleton to the plasma membrane. High expression of ezrin correlates with poor prognosis and metastasis in osteosarcoma. In this study, to uncover specific cellular responses evoked by ezrin inhibition that can be used as a specific pharmacodynamic marker(s), we profiled global gene expression in osteosarcoma cells after treatment with small molecule ezrin inhibitors, NSC305787 and NSC668394. We identified and validated several up-regulated integrated stress response genes including PTGS2, ATF3, DDIT3, DDIT4, TRIB3, and ATF4 as novel ezrin-regulated transcripts. Analysis of transcriptional response in skin and peripheral blood mononuclear cells from NSC305787-treated mice compared with a control group revealed that, among those genes, the stress gene DDIT4/REDD1 may be used as a surrogate pharmacodynamic marker of ezrin inhibitor compound activity. In addition, we validated the anti-metastatic effects of NSC305787 in reducing the incidence of lung metastasis in a genetically engineered mouse model of osteosarcoma and evaluated the pharmacokinetics of NSC305787 and NSC668394 in mice. In conclusion, our findings suggest that cytoplasmic ezrin, previously considered a dormant and inactive protein, has important functions in regulating gene expression that may result in down-regulation of stress response genes.

  16. Global-Local Precedence in the Perception of Facial Age and Emotional Expression by Children with Autism and Other Developmental Disabilities

    ERIC Educational Resources Information Center

    Gross, Thomas F.

    2005-01-01

    Global information processing and perception of facial age and emotional expression was studied in children with autism, language disorders, mental retardation, and a clinical control group. Children were given a global-local task and asked to recognize age and emotion in human and canine faces. Children with autism made fewer global responses and…

  17. Population-expression models of immune response

    NASA Astrophysics Data System (ADS)

    Stromberg, Sean P.; Antia, Rustom; Nemenman, Ilya

    2013-06-01

    The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenotype to an effector phenotype which controls the pathogen, and subsequently to a memory phenotype that is maintained and responsible for long-term protection. The expansion and the differentiation have been considered largely independently. Changes in cell populations are typically described using ecologically based ordinary differential equation models. In contrast, differentiation of single cells is studied within systems biology and is frequently modeled by considering changes in gene and protein expression in individual cells. Recent advances in experimental systems biology make available for the first time data to allow the coupling of population and high dimensional expression data of immune cells during infections. Here we describe and develop population-expression models which integrate these two processes into systems biology on the multicellular level. When translated into mathematical equations, these models result in non-conservative, non-local advection-diffusion equations. We describe situations where the population-expression approach can make correct inference from data while previous modeling approaches based on common simplifying assumptions would fail. We also explore how model reduction techniques can be used to build population-expression models, minimizing the complexity of the model while keeping the essential features of the system. While we consider problems in immunology in this paper, we expect population-expression models to be more broadly applicable.

  18. Adults' responsiveness to children's facial expressions.

    PubMed

    Aradhye, Chinmay; Vonk, Jennifer; Arida, Danielle

    2015-07-01

    We investigated the effect of young children's (hereafter children's) facial expressions on adult responsiveness. In Study 1, 131 undergraduate students from a midsized university in the midwestern United States rated children's images and videos with smiling, crying, or neutral expressions on cuteness, likelihood to adopt, and participants' experienced distress. Looking times at images and videos along with perception of cuteness, likelihood to adopt, and experienced distress using 10-point Likert scales were measured. Videos of smiling children were rated as cuter and more likely to be adopted and were viewed for longer times compared with videos of crying children, which evoked more distress. In Study 2, we recorded responses from 101 of the same participants in an online survey measuring gender role identity, empathy, and perspective taking. Higher levels of femininity (as measured by Bem's Sex Role Inventory) predicted higher "likely to adopt" ratings for crying images. These findings indicate that adult perception of children and motivation to nurture are affected by both children's facial expressions and adult characteristics and build on existing literature to demonstrate that children may use expressions to manipulate the motivations of even non-kin adults to direct attention toward and perhaps nurture young children.

  19. Global Metabolic Responses to Salt Stress in Fifteen Species

    PubMed Central

    Pollak, Georg R.; Kuehne, Andreas; Sauer, Uwe

    2016-01-01

    Cells constantly adapt to unpredictably changing extracellular solute concentrations. A cornerstone of the cellular osmotic stress response is the metabolic supply of energy and building blocks to mount appropriate defenses. Yet, the extent to which osmotic stress impinges on the metabolic network remains largely unknown. Moreover, it is mostly unclear which, if any, of the metabolic responses to osmotic stress are conserved among diverse organisms or confined to particular groups of species. Here we investigate the global metabolic responses of twelve bacteria, two yeasts and two human cell lines exposed to sustained hyperosmotic salt stress by measuring semiquantitative levels of hundreds of cellular metabolites using nontargeted metabolomics. Beyond the accumulation of osmoprotectants, we observed significant changes of numerous metabolites in all species. Global metabolic responses were predominantly species-specific, yet individual metabolites were characteristically affected depending on species’ taxonomy, natural habitat, envelope structure or salt tolerance. Exploiting the breadth of our dataset, the correlation of individual metabolite response magnitudes across all species implicated lower glycolysis, tricarboxylic acid cycle, branched-chain amino acid metabolism and heme biosynthesis to be generally important for salt tolerance. Thus, our findings place the global metabolic salt stress response into a phylogenetic context and provide insights into the cellular phenotype associated with salt tolerance. PMID:26848578

  20. Global Analysis of Protein Expression of Inner Ear Hair Cells.

    PubMed

    Hickox, Ann E; Wong, Ann C Y; Pak, Kwang; Strojny, Chelsee; Ramirez, Miguel; Yates, John R; Ryan, Allen F; Savas, Jeffrey N

    2017-02-01

    The mammalian inner ear (IE) subserves auditory and vestibular sensations via highly specialized cells and proteins. Sensory receptor hair cells (HCs) are necessary for transducing mechanical inputs and stimulating sensory neurons by using a host of known and as yet unknown protein machinery. To understand the protein composition of these unique postmitotic cells, in which irreversible protein degradation or damage can lead to impaired hearing and balance, we analyzed IE samples by tandem mass spectrometry to generate an unbiased, shotgun-proteomics view of protein identities and abundances. By using Pou4f3/eGFP-transgenic mice in which HCs express GFP driven by Pou4f3, we FACS purified a population of HCs to analyze and compare the HC proteome with other IE subproteomes from sensory epithelia and whole IE. We show that the mammalian HC proteome comprises hundreds of uniquely or highly expressed proteins. Our global proteomic analysis of purified HCs extends the existing HC transcriptome, revealing previously undetected gene products and isoform-specific protein expression. Comparison of our proteomic data with mouse and human databases of genetic auditory/vestibular impairments confirms the critical role of the HC proteome for normal IE function, providing a cell-specific pool of candidates for novel, important HC genes. Several proteins identified exclusively in HCs by proteomics and verified by immunohistochemistry map to human genetic deafness loci, potentially representing new deafness genes.

  1. Global Citizenship Incorporated: Competing Responsibilities in the Education of Global Citizens

    ERIC Educational Resources Information Center

    Hartung, Catherine

    2017-01-01

    Interest in the education of young people to be 'responsible global citizens' has grown exponentially since the turn of the century, led by increasingly diverse networks of sectors, including government, community, business and philanthropy. These networks now have a significant influence on education policy and practice, indicative of wider…

  2. Spaceflight Alters Bacterial Gene Expression and Virulence and Reveals Role for Global Regulator Hfq

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Ott, C. M.; zuBentrup, K. Honer; Ramamurthy R.; Quick, L.; Porwollik, S.; Cheng, P.; McClellan, M.; Tsaprailis, G.; Radabaugh, T.; Hunt, A.; Fernandez, D.; Richter, E.; Shah, M.; Kilcoyne, M.; Joshi, L.; Nelman-Gonzalez, M.; Hing, S.; Parra, M.; Dumaras, P.; Norwood, K.; Nickerson, C. A.; Bober, R.; Devich, J.; Ruggles, A.

    2007-01-01

    A comprehensive analysis of both the molecular genetic and phenotypic responses of any organism to the spaceflight environment has never been accomplished due to significant technological and logistical hurdles. Moreover, the effects of spaceflight on microbial pathogenicity and associated infectious disease risks have not been studied. The bacterial pathogen Salmonella typhimurium was grown aboard Space Shuttle mission STS-115 and compared to identical ground control cultures. Global microarray and proteomic analyses revealed 167 transcripts and 73 proteins changed expression with the conserved RNA-binding protein Hfq identified as a likely global regulator involved in the response to this environment. Hfq involvement was confirmed with a ground based microgravity culture model. Spaceflight samples exhibited enhanced virulence in a murine infection model and extracellular matrix accumulation consistent with a biofilm. Strategies to target Hfq and related regulators could potentially decrease infectious disease risks during spaceflight missions and provide novel therapeutic options on Earth.

  3. Environmental variation and population responses to global change.

    PubMed

    Lawson, Callum R; Vindenes, Yngvild; Bailey, Liam; van de Pol, Martijn

    2015-07-01

    Species' responses to environmental changes such as global warming are affected not only by trends in mean conditions, but also by natural and human-induced environmental fluctuations. Methods are needed to predict how such environmental variation affects ecological and evolutionary processes, in order to design effective strategies to conserve biodiversity under global change. Here, we review recent theoretical and empirical studies to assess: (1) how populations respond to changes in environmental variance, and (2) how environmental variance affects population responses to changes in mean conditions. Contrary to frequent claims, empirical studies show that increases in environmental variance can increase as well as decrease long-term population growth rates. Moreover, environmental variance can alter and even reverse the effects of changes in the mean environment, such that even if environmental variance remains constant, omitting it from population models compromises their ability to predict species' responses to changes in mean conditions. Drawing on theory relating these effects of environmental variance to the curvatures of population growth responses to the environment, we outline how species' traits such as phylogenetic history and body mass could be used to predict their responses to global change under future environmental variability.

  4. Global Earth Response to Loading by Ocean Tide Models

    NASA Technical Reports Server (NTRS)

    Estes, R. H.; Strayer, J. M.

    1979-01-01

    Mathematical and programming techniques to numerically calculate Earth response to global semidiurnal and diurnal ocean tide models were developed. Global vertical crustal deformations were evaluated for M sub 2, S sub 2, N sub 2, K sub 2, K sub 1, O sub 1, and P sub 1 ocean tide loading, while horizontal deformations were evaluated for the M sub 2 tidal load. Tidal gravity calculations were performed for M sub 2 tidal loads, and strain tensor elements were evaluated for M sub 2 loads. The M sub 2 solution used for the ocean tide included the effects of self-gravitation and crustal loading.

  5. Global Patterns in Leaf Respiration and its Temperature Response

    NASA Astrophysics Data System (ADS)

    Heskel, M.; Atkin, O. K.; O'Sullivan, O. S.; Reich, P. B.; Tjoelker, M. G.; Weerasinghe, L. K.; Penillard, A.; Egerton, J. J. G.; Creek, D.; Bloomfield, K. J.; Xiang, J.; Sinca, F.; Stangl, Z.; Martinez-de la Torre, A.; Griffin, K. L.; Huntingford, C.; Hurry, V.; Meir, P.; Turnbull, M.

    2015-12-01

    Leaf respiration (R) represents a massive flux of carbon to the atmosphere. Currently, neither physiological models nor terrestrial biosphere models are able to disentangle sources of variation in leaf R among different plant species and contrasting environments. Similarly, such models do not adequately describe the short-term temperature (T) response of R, which can lead to inaccurate representation of leaf R in simulation models of regional and global terrestrial carbon cyling. Even minor differences in the underlying basal rate of leaf R and/or shape of the T-response curve can significantly impact estimates of carbon released and stored in ecosystems. Given this, we recently assembled and analyzed two new global databases (arctic-to-tropics) of leaf R and its short-term T-dependence. The results highlight variation in basal leaf R among species and across global gradients in T and aridity, with leaf R at a standard T (e.g. 25°C) being greatest in plants growing in the cold, dry Arctic and lowest in the warm, moist tropics. Arctic plants also exhibit higher rates of leaf R at a given photosynthetic capacity or leaf N concentration than their tropical counterparts. The results also point to convergence in the short-term temperature response of respiration across biomes and plant functional types. The applicability and significance of the short-term T-response of R for simulation models of plant and ecosystem carbon fluxes will be discussed.

  6. Global regulation of gene expression in Escherichia coli.

    PubMed Central

    Chuang, S E; Daniels, D L; Blattner, F R

    1993-01-01

    Global transcription responses of Escherichia coli to various stimuli or genetic defects were studied by measuring mRNA levels in about 400 segments of the genome. Measuring mRNA levels was done by analyzing hybridization to DNA dot blots made with overlapping lambda clones spanning the genome of E. coli K-12. Conditions examined included isopropyl-beta-D-thiogalactopyranoside (IPTG) induction, heat shock, osmotic shock, starvation for various nutrients, entrance of cells into the stationary phase of growth, anaerobic growth in a tube, growth in the gnotobiotic mouse gut, and effects of pleiotropic mutations rpoH, himA, topA, and crp. Most mapped genes known to be regulated by a particular situation were successfully detected. In addition, many chromosomal regions containing no previously known regulated genes were discovered that responded to various stimuli. This new method for studying globally regulated genetic systems in E. coli combines detection, cloning, and physical mapping of a battery of coregulated genes in one step. Images PMID:8458845

  7. Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change

    PubMed Central

    Tsuchiya, Masa; Giuliani, Alessandro; Hashimoto, Midori; Erenpreisa, Jekaterina; Yoshikawa, Kenichi

    2016-01-01

    Background A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. Principal Findings Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels. The novel findings are as follows: i) Mechanism of cell-fate changes: A sandpile-type critical transition self-organizes overall expression into a few transcription response domains (critical states). A cell-fate change occurs by means of a dissipative pulse-like global perturbation in self-organization through the erasure of initial-state critical behaviors (criticality). Most notably, the reprogramming of early embryo cells destroys the zygote SOC control to initiate self-organization in the new embryonal genome, which passes through a stochastic overall expression pattern. ii) Mechanism of perturbation of SOC controls: Global perturbations in self-organization involve the temporal regulation of critical states. Quantitative evaluation of this perturbation in terminal cell fates reveals that dynamic interactions between critical states determine the critical-state coherent regulation. The occurrence of a temporal change in criticality perturbs this between-states interaction, which directly affects the entire genomic system. Surprisingly, a sub-critical state, corresponding to an ensemble of genes that shows only marginal changes in expression and consequently are considered to be devoid of any interest, plays an essential role in generating a global perturbation in self-organization directed toward the cell-fate change

  8. Will surface winds weaken in response to global warming?

    NASA Astrophysics Data System (ADS)

    Ma, Jian; Foltz, Gregory R.; Soden, Brian J.; Huang, Gang; He, Jie; Dong, Changming

    2016-12-01

    The surface Walker and tropical tropospheric circulations have been inferred to slow down from historical observations and model projections, yet analysis of large-scale surface wind predictions is lacking. Satellite measurements of surface wind speed indicate strengthening trends averaged over the global and tropical oceans that are supported by precipitation and evaporation changes. Here we use corrected anemometer-based observations to show that the surface wind speed has not decreased in the averaged tropical oceans, despite its reduction in the region of the Walker circulation. Historical simulations and future projections for climate change also suggest a near-zero wind speed trend averaged in space, regardless of the Walker cell change. In the tropics, the sea surface temperature pattern effect acts against the large-scale circulation slow-down. For higher latitudes, the surface winds shift poleward along with the eddy-driven mid-latitude westerlies, resulting in a very small contribution to the global change in surface wind speed. Despite its importance for surface wind speed change, the influence of the SST pattern change on global-mean rainfall is insignificant since it cannot substantially alter the global energy balance. As a result, the precipitation response to global warming remains ‘muted’ relative to atmospheric moisture increase. Our results therefore show consistency between projections and observations of surface winds and precipitation.

  9. Global Gene Expression Profiling in Lung Tissues of Rat Exposed to Lunar Dust Particles

    NASA Technical Reports Server (NTRS)

    Yeshitla, Samrawit A.; Lam, Chiu-Wing; Kidane, Yared H.; Feiveson, Alan H.; Ploutz-Snyder, Robert; Wu, Honglu; James, John T.; Meyers, Valerie E.; Zhang, Ye

    2014-01-01

    The Moon's surface is covered by a layer of fine, potential reactive dust. Lunar dust contain about 1-2% respirable very fine dust (less than 3 micrometers). The habitable area of any lunar landing vehicle and outpost would inevitably be contaminated with lunar dust that could pose a health risk. The purpose of the study is to analyze the dynamics of global gene expression changes in lung tissues of rats exposed to lunar dust particles. F344 rats were exposed for 4 weeks (6h/d; 5d/wk) in nose-only inhalation chambers to concentrations of 0 (control air), 2.1, 6.8, 21, and 61 mg/m3 of lunar dust. Animals were euthanized at 1 day and 13 weeks after the last inhalation exposure. After being lavaged, lung tissue from each animal was collected and total RNA was isolated. Four samples of each dose group were analyzed using Agilent Rat GE v3 microarray to profile global gene expression of 44K transcripts. After background subtraction, normalization, and log transformation, t tests were used to compare the mean expression levels of each exposed group to the control group. Correction for multiple testing was made using the method of Benjamini, Krieger, and Yekuteli (1) to control the false discovery rate. Genes with significant changes of at least 1.75 fold were identified as genes of interest. Both low and high doses of lunar dust caused dramatic, dose-dependent global gene expression changes in the lung tissues. However, the responses of lung tissue to low dose lunar dust are distinguished from those of high doses, especially those associated with 61mg/m3 dust exposure. The data were further integrated into the Ingenuity system to analyze the gene ontology (GO), pathway distribution and putative upstream regulators and gene targets. Multiple pathways, functions, and upstream regulators have been identified in response to lunar dust induced damage in the lung tissue.

  10. The responsibility of healthcare institutions to protect global health security.

    PubMed

    Wilson, Kumanan; McDougall, Christopher; Forster, Alan

    2009-01-01

    New public threats that can rapidly cross borders are continuing to challenge global health securityand will require unprecedented levels of co-operation. At the international level, the response to this challenge led to the approval of revised International Health Regulations (IHR). This unanimously approved document outlines how countries are to prepare for and respond to public health emergencies of international concern in a manner that does not unnecessarily impact on travel and trade.

  11. Global change and biodiversity loss: Some impediments to response

    NASA Technical Reports Server (NTRS)

    Borza, Karen; Jamieson, Dale

    1991-01-01

    Discussed here are the effects of anthropogenic global climate change on biodiversity. The focus is on human responses to the problem. Greenhouse warming-induced climate change may shift agricultural growing belts, reduce forests of the Northern Hemisphere and drive many species to extinction, among other effects. If these changes occur together with the mass extinctions already occurring, we may suffer a profound loss of biological diversity.

  12. Quantifying global soil carbon losses in response to warming.

    PubMed

    Crowther, T W; Todd-Brown, K E O; Rowe, C W; Wieder, W R; Carey, J C; Machmuller, M B; Snoek, B L; Fang, S; Zhou, G; Allison, S D; Blair, J M; Bridgham, S D; Burton, A J; Carrillo, Y; Reich, P B; Clark, J S; Classen, A T; Dijkstra, F A; Elberling, B; Emmett, B A; Estiarte, M; Frey, S D; Guo, J; Harte, J; Jiang, L; Johnson, B R; Kröel-Dulay, G; Larsen, K S; Laudon, H; Lavallee, J M; Luo, Y; Lupascu, M; Ma, L N; Marhan, S; Michelsen, A; Mohan, J; Niu, S; Pendall, E; Peñuelas, J; Pfeifer-Meister, L; Poll, C; Reinsch, S; Reynolds, L L; Schmidt, I K; Sistla, S; Sokol, N W; Templer, P H; Treseder, K K; Welker, J M; Bradford, M A

    2016-11-30

    The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.

  13. Quantifying global soil carbon losses in response to warming

    NASA Astrophysics Data System (ADS)

    Crowther, T. W.; Todd-Brown, K. E. O.; Rowe, C. W.; Wieder, W. R.; Carey, J. C.; Machmuller, M. B.; Snoek, B. L.; Fang, S.; Zhou, G.; Allison, S. D.; Blair, J. M.; Bridgham, S. D.; Burton, A. J.; Carrillo, Y.; Reich, P. B.; Clark, J. S.; Classen, A. T.; Dijkstra, F. A.; Elberling, B.; Emmett, B. A.; Estiarte, M.; Frey, S. D.; Guo, J.; Harte, J.; Jiang, L.; Johnson, B. R.; Kröel-Dulay, G.; Larsen, K. S.; Laudon, H.; Lavallee, J. M.; Luo, Y.; Lupascu, M.; Ma, L. N.; Marhan, S.; Michelsen, A.; Mohan, J.; Niu, S.; Pendall, E.; Peñuelas, J.; Pfeifer-Meister, L.; Poll, C.; Reinsch, S.; Reynolds, L. L.; Schmidt, I. K.; Sistla, S.; Sokol, N. W.; Templer, P. H.; Treseder, K. K.; Welker, J. M.; Bradford, M. A.

    2016-12-01

    The majority of the Earth’s terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.

  14. The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts

    PubMed Central

    Lindholm, Maléne E; Giacomello, Stefania; Werne Solnestam, Beata; Kjellqvist, Sanela

    2016-01-01

    Regularly performed endurance training has many beneficial effects on health and skeletal muscle function, and can be used to prevent and treat common diseases e.g. cardiovascular disease, type II diabetes and obesity. The molecular adaptation mechanisms regulating these effects are incompletely understood. To date, global transcriptome changes in skeletal muscles have been studied at the gene level only. Therefore, global isoform expression changes following exercise training in humans are unknown. Also, the effects of repeated interventions on transcriptional memory or training response have not been studied before. In this study, 23 individuals trained one leg for three months. Nine months later, 12 of the same subjects trained both legs in a second training period. Skeletal muscle biopsies were obtained from both legs before and after both training periods. RNA sequencing analysis of all 119 skeletal muscle biopsies showed that training altered the expression of 3,404 gene isoforms, mainly associated with oxidative ATP production. Fifty-four genes had isoforms that changed in opposite directions. Training altered expression of 34 novel transcripts, all with protein-coding potential. After nine months of detraining, no training-induced transcriptome differences were detected between the previously trained and untrained legs. Although there were several differences in the physiological and transcriptional responses to repeated training, no coherent evidence of an endurance training induced transcriptional skeletal muscle memory was found. This human lifestyle intervention induced differential expression of thousands of isoforms and several transcripts from unannotated regions of the genome. It is likely that the observed isoform expression changes reflect adaptational mechanisms and processes that provide the functional and health benefits of regular physical activity. PMID:27657503

  15. Changes in aridity in response to the global warming hiatus

    NASA Astrophysics Data System (ADS)

    Guan, Xiaodan; Huang, Jianping; Guo, Ruixia

    2017-02-01

    The global warming slowdown or warming hiatus, began around the year 2000 and has persisted for nearly 15 years. Most studies have focused on the interpretation of the hiatus in temperature. In this study, changes in a global aridity index (AI) were analyzed by using a newly developed dynamical adjustment method that can successfully identify and separate dynamically induced and radiatively forced aridity changes in the raw data. The AI and Palmer Drought Severity Index produced a wetting zone over the mid-to-high latitudes of the Northern Hemisphere in recent decades. The dynamical adjustment analysis suggested that this wetting zone occurred in response to the global warming hiatus. The dynamically induced AI (DAI) played a major role in the AI changes during the hiatus period, and its relationships with the North Atlantic Oscillation (NAO), Pacific Decadal Oscillation (PDO), and Atlantic Multi-decadal Oscillation (AMO) also indicated that different phases of the NAO, PDO, and AMO contributed to different performances of the DAI over the Northern Hemisphere. Although the aridity wetting over the mid-to-high latitudes may relieve long-term drying in certain regions, the hiatus is temporary, and so is the relief. Accelerated global warming will return when the NAO, PDO, and AMO revert to their opposite phases in the future, and the wetting zone is likely to disappear.

  16. Mentoring health researchers globally: Diverse experiences, programmes, challenges and responses

    PubMed Central

    Cole, Donald C.; Johnson, Nancy; Mejia, Raul; McCullough, Hazel; Turcotte-Tremblay, Anne-Marie; Barnoya, Joaquin; Falabella Luco, (María) Soledad

    2016-01-01

    ABSTRACT Mentoring experiences and programmes are becoming increasingly recognised as important by those engaged in capacity strengthening in global health research. Using a primarily qualitative study design, we studied three experiences of mentorship and eight mentorship programmes for early career global health researchers based in high-income and low- and middle-income countries. For the latter, we drew upon programme materials, existing unpublished data and more formal mixed-method evaluations, supplemented by individual email questionnaire responses. Research team members wrote stories, and the team assembled and analysed them for key themes. Across the diverse experiences and programmes, key emergent themes included: great mentors inspire others in an inter-generational cascade, mentorship is transformative in personal and professional development and involves reciprocity, and finding the right balance in mentoring relationships and programmes includes responding creatively to failure. Among the challenges encountered were: struggling for more level playing fields for new health researchers globally, changing mindsets in institutions that do not have a culture of mentorship and building collaboration not competition. Mentoring networks spanning institutions and countries using multiple virtual and face-to-face methods are a potential avenue for fostering organisational cultures supporting quality mentorship in global health research. PMID:26234691

  17. Mentoring health researchers globally: Diverse experiences, programmes, challenges and responses.

    PubMed

    Cole, Donald C; Johnson, Nancy; Mejia, Raul; McCullough, Hazel; Turcotte-Tremblay, Anne-Marie; Barnoya, Joaquin; Falabella Luco, María Soledad

    2016-10-01

    Mentoring experiences and programmes are becoming increasingly recognised as important by those engaged in capacity strengthening in global health research. Using a primarily qualitative study design, we studied three experiences of mentorship and eight mentorship programmes for early career global health researchers based in high-income and low- and middle-income countries. For the latter, we drew upon programme materials, existing unpublished data and more formal mixed-method evaluations, supplemented by individual email questionnaire responses. Research team members wrote stories, and the team assembled and analysed them for key themes. Across the diverse experiences and programmes, key emergent themes included: great mentors inspire others in an inter-generational cascade, mentorship is transformative in personal and professional development and involves reciprocity, and finding the right balance in mentoring relationships and programmes includes responding creatively to failure. Among the challenges encountered were: struggling for more level playing fields for new health researchers globally, changing mindsets in institutions that do not have a culture of mentorship and building collaboration not competition. Mentoring networks spanning institutions and countries using multiple virtual and face-to-face methods are a potential avenue for fostering organisational cultures supporting quality mentorship in global health research.

  18. The acid adaptive tolerance response in Campylobacter jejuni induces a global response, as suggested by proteomics and microarrays

    PubMed Central

    Varsaki, Athanasia; Murphy, Caroline; Barczynska, Alicja; Jordan, Kieran; Carroll, Cyril

    2015-01-01

    Campylobacter jejuni CI 120 is a natural isolate obtained during poultry processing and has the ability to induce an acid tolerance response (ATR) to acid + aerobic conditions in early stationary phase. Other strains tested they did not induce an ATR or they induced it in exponential phase. Campylobacter spp. do not contain the genes that encode the global stationary phase stress response mechanism. Therefore, the aim of this study was to identify genes that are involved in the C. jejuni CI 120 early stationary phase ATR, as it seems to be expressing a novel mechanism of stress tolerance. Two-dimensional gel electrophoresis was used to examine the expression profile of cytosolic proteins during the C. jejuni CI 120 adaptation to acid + aerobic stress and microarrays to determine the genes that participate in the ATR. The results indicate induction of a global response that activated a number of stress responses, including several genes encoding surface components and genes involved with iron uptake. The findings of this study provide new insights into stress tolerance of C. jejuni, contribute to a better knowledge of the physiology of this bacterium and highlight the diversity among different strains. PMID:26221965

  19. The acid adaptive tolerance response in Campylobacter jejuni induces a global response, as suggested by proteomics and microarrays.

    PubMed

    Varsaki, Athanasia; Murphy, Caroline; Barczynska, Alicja; Jordan, Kieran; Carroll, Cyril

    2015-11-01

    Campylobacter jejuni CI 120 is a natural isolate obtained during poultry processing and has the ability to induce an acid tolerance response (ATR) to acid + aerobic conditions in early stationary phase. Other strains tested they did not induce an ATR or they induced it in exponential phase. Campylobacter spp. do not contain the genes that encode the global stationary phase stress response mechanism. Therefore, the aim of this study was to identify genes that are involved in the C. jejuni CI 120 early stationary phase ATR, as it seems to be expressing a novel mechanism of stress tolerance. Two-dimensional gel electrophoresis was used to examine the expression profile of cytosolic proteins during the C. jejuni CI 120 adaptation to acid + aerobic stress and microarrays to determine the genes that participate in the ATR. The results indicate induction of a global response that activated a number of stress responses, including several genes encoding surface components and genes involved with iron uptake. The findings of this study provide new insights into stress tolerance of C. jejuni, contribute to a better knowledge of the physiology of this bacterium and highlight the diversity among different strains.

  20. Global Loss of Bmal1 Expression Alters Adipose Tissue Hormones, Gene Expression and Glucose Metabolism

    PubMed Central

    Kennaway, David John; Varcoe, Tamara Jayne; Voultsios, Athena; Boden, Michael James

    2013-01-01

    The close relationship between circadian rhythm disruption and poor metabolic status is becoming increasingly evident, but role of adipokines is poorly understood. Here we investigated adipocyte function and the metabolic status of mice with a global loss of the core clock gene Bmal1 fed either a normal or a high fat diet (22% by weight). Bmal1 null mice aged 2 months were killed across 24 hours and plasma adiponectin and leptin, and adipose tissue expression of Adipoq, Lep, Retn and Nampt mRNA measured. Glucose, insulin and pyruvate tolerance tests were conducted and the expression of liver glycolytic and gluconeogenic enzyme mRNA determined. Bmal1 null mice displayed a pattern of increased plasma adiponectin and plasma leptin concentrations on both control and high fat diets. Bmal1 null male and female mice displayed increased adiposity (1.8 fold and 2.3 fold respectively) on the normal diet, but the high fat diet did not exaggerate these differences. Despite normal glucose and insulin tolerance, Bmal1 null mice had increased production of glucose from pyruvate, implying increased liver gluconeogenesis. The Bmal1 null mice had arrhythmic clock gene expression in epigonadal fat and liver, and loss of rhythmic transcription of a range of metabolic genes. Furthermore, the expression of epigonadal fat Adipoq, Retn, Nampt, AdipoR1 and AdipoR2 and liver Pfkfb3 mRNA were down-regulated. These results show for the first time that global loss of Bmal1, and the consequent arrhythmicity, results in compensatory changes in adipokines involved in the cellular control of glucose metabolism. PMID:23750248

  1. Voluntourism and global health: preparing dental students for responsible engagement in international programs.

    PubMed

    Seymour, Brittany; Benzian, Habib; Kalenderian, Elsbeth

    2013-10-01

    Harvard School of Dental Medicine (HSDM) estimates that nearly 25 percent of its predoctoral dental students have expressed an interest in global health, including traveling abroad to conduct research or to volunteer in a project. This article addresses the important differences between "voluntourism" (combined volunteering and tourism) and responsible engagement in global health, reports on a pilot workshop at HSDM to promote responsible volunteering, and provides a recommendation on how to address these issues in the context of a dental curriculum. The pilot Workshop for Ethical Volunteering in Global Health was designed as a discussion-based, interactive program that included lectures, small-group activities, and personal reflection. The aim of the workshop was to provide students with a systematic approach to ethical volunteering, critically reflecting on their motivation and attitudes related to conventional models of volunteering and facilitating alignment with principles of global health. Students participated in an anonymous written survey at the start and the close of the workshop. After the workshop, survey results demonstrated a significant increase in understanding the value of applying principles of global health when volunteering in order to avoid negative and unintended impacts on communities. All of the students reported that the workshop influenced the way they view volunteering in dentistry.

  2. Global N2 fixation and its response to global climate change and increasing CO2 level

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Houlton, B. Z.; Field, C. B.; Vitousek, P. M.

    2007-12-01

    Biological nitrogen fixation is the largest nitrogen input to many natural terrestrial ecosystems, particularly tropical ecosystems, thereby influencing primary production, CO2 uptake, and responses to climate change. However, our understanding of biological nitrogen fixation is still very limited, and the dominant plant family capable of fixing N2 symbiotically, the Leguminasae, exhibits considerable geographic variation in the terrestrial biosphere. Based on the principles of resource optimization, we developed a new model to constrain our understanding of the geographic distribution of N fixation globally. Our model treats N fixation according to the C cost of fixing N, coupled with the N cost associated with acquiring P from the soil for plant growth. The model was used to estimate the rate of global symbiotic N2 fixation and the response of symbiotic N2 fixers to changes in climate and rising atmospheric CO2. We shall discuss global N limitation of terrestrial carbon uptake and its implications for climate-carbon cycle feedbacks from present to year 2100.

  3. [Forest litter decomposition and its responses to global climate change].

    PubMed

    Yang, Wan-Qin; Deng, Ren-Ju; Zhang, Jian

    2007-12-01

    Litter decomposition is one of the important processes in forest ecosystem, which is controlled by both biotic and abiotic factors such as climate, litter quality, and soil organisms. Up to now, numerous studies have been made on the dynamics of aboveground litter in different forest ecosystems, nutrient release during its decomposition, and effects of biotic and abiotic factors on the decomposition, but less information has been reported on the decomposition of belowground forest litter. Recently, the responses of forest litter decomposition to global climate change characterized by elevated atmospheric CO2 concentration and temperature have got worldwide concern, but there remains uncertainty in research results. In the further study, more attention should be paid on the contribution of forest litter decomposition to soil organic carbon sequestration, the physical, chemical and biological processes of below- and above-ground litter decomposition, the responses of forest litter decomposition to the ecological factors (e.g. seasonal freeze-thaw cycle and drying-rewetting cycle) and their interactions, and the mechanisms of litter (especially belowground litter) decomposition responses to global climate change.

  4. Global temperature responses to current emissions from the transport sectors

    PubMed Central

    Berntsen, Terje; Fuglestvedt, Jan

    2008-01-01

    Transport affects climate directly and indirectly through mechanisms that cause both warming and cooling of climate, and the effects operate on very different timescales. We calculate climate responses in terms of global mean temperature and find large differences between the transport sectors with respect to the size and mix of short- and long-lived effects, and even the sign of the temperature response. For year 2000 emissions, road transport has the largest effect on global mean temperature. After 20 and 100 years the response in net temperature is 7 and 6 times higher, respectively, than for aviation. Aviation and shipping have strong but quite uncertain short-lived warming and cooling effects, respectively, that dominate during the first decades after the emissions. For shipping the net cooling during the first 4 decades is due to emissions of SO2 and NOx. On a longer timescale, the current emissions from shipping cause net warming due to the persistence of the CO2 perturbation. If emissions stay constant at 2000 levels, the warming effect from road transport will continue to increase and will be almost 4 times larger than that of aviation by the end of the century. PMID:19047640

  5. Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells

    PubMed Central

    Deshpande, Nandan P.; Wilkins, Marc R.; Castaño-Rodríguez, Natalia; Bainbridge, Emily; Sodhi, Nidhi; Riordan, Stephen M.; Mitchell, Hazel M.; Kaakoush, Nadeem O.

    2016-01-01

    The epithelial response to the opportunistic pathogen Campylobacter concisus is poorly characterised. Here, we assessed the intestinal epithelial responses to two C. concisus strains with different virulence characteristics in Caco-2 cells using RNAseq, and validated a subset of the response using qPCR arrays. C. concisus strains induced distinct response patterns from intestinal epithelial cells, with the toxigenic strain inducing a significantly more amplified response. A range of cellular functions were significantly regulated in a strain-specific manner, including epithelial-to-mesenchymal transition (NOTCH and Hedgehog), cytoskeletal remodeling, tight junctions, inflammatory responses and autophagy. Pattern recognition receptors were regulated, including TLR3 and IFI16, suggesting that nucleic acid sensing was important for epithelial recognition of C. concisus. C. concisus zonula occludens toxin (ZOT) was expressed and purified, and the epithelial response to the toxin was analysed using RNAseq. ZOT upregulated PAR2 expression, as well as processes related to tight junctions and cytoskeletal remodeling. C. concisus ZOT also induced upregulation of TLR3, pro-inflammatory cytokines IL6, IL8 and chemokine CXCL16, as well as the executioner caspase CASP7. Here, we characterise distinct global epithelial responses to C. concisus strains, and the virulence factor ZOT, and provide novel information on mechanisms by which this bacterium may affect the host. PMID:27677841

  6. Terrestrial ecosystem responses to global change: A research strategy

    SciTech Connect

    1998-09-01

    Uncertainty about the magnitude of global change effects on terrestrial ecosystems and consequent feedbacks to the atmosphere impedes sound policy planning at regional, national, and global scales. A strategy to reduce these uncertainties must include a substantial increase in funding for large-scale ecosystem experiments and a careful prioritization of research efforts. Prioritization criteria should be based on the magnitude of potential changes in environmental properties of concern to society, including productivity; biodiversity; the storage and cycling of carbon, water, and nutrients; and sensitivity of specific ecosystems to environmental change. A research strategy is proposed that builds on existing knowledge of ecosystem responses to global change by (1) expanding the spatial and temporal scale of experimental ecosystem manipulations to include processes known to occur at large scales and over long time periods; (2) quantifying poorly understood linkages among processes through the use of experiments that manipulate multiple interacting environmental factors over a broader range of relevant conditions than did past experiments; and (3) prioritizing ecosystems for major experimental manipulations on the basis of potential positive and negative impacts on ecosystem properties and processes of intrinsic and/or utilitarian value to humans and on feedbacks of terrestrial ecosystems to the atmosphere.

  7. Circuitry linking the Csr and stringent response global regulatory systems.

    PubMed

    Edwards, Adrianne N; Patterson-Fortin, Laura M; Vakulskas, Christopher A; Mercante, Jeffrey W; Potrykus, Katarzyna; Vinella, Daniel; Camacho, Martha I; Fields, Joshua A; Thompson, Stuart A; Georgellis, Dimitris; Cashel, Michael; Babitzke, Paul; Romeo, Tony

    2011-06-01

    CsrA protein regulates important cellular processes by binding to target mRNAs and altering their translation and/or stability. In Escherichia coli, CsrA binds to sRNAs, CsrB and CsrC, which sequester CsrA and antagonize its activity. Here, mRNAs for relA, spoT and dksA of the stringent response system were found among 721 different transcripts that copurified with CsrA. Many of the transcripts that copurified with CsrA were previously determined to respond to ppGpp and/or DksA. We examined multiple regulatory interactions between the Csr and stringent response systems. Most importantly, DksA and ppGpp robustly activated csrB/C transcription (10-fold), while they modestly activated csrA expression. We propose that CsrA-mediated regulation is relieved during the stringent response. Gel shift assays confirmed high affinity binding of CsrA to relA mRNA leader and weaker interactions with dksA and spoT. Reporter fusions, qRT-PCR and immunoblotting showed that CsrA repressed relA expression, and (p)ppGpp accumulation during stringent response was enhanced in a csrA mutant. CsrA had modest to negligible effects on dksA and spoT expression. Transcription of dksA was negatively autoregulated via a feedback loop that tended to mask CsrA effects. We propose that the Csr system fine-tunes the stringent response and discuss biological implications of the composite circuitry.

  8. Circuitry Linking the Csr and Stringent Response Global Regulatory Systems

    PubMed Central

    Edwards, Adrianne N.; Patterson-Fortin, Laura M.; Vakulskas, Christopher A.; Mercante, Jeffrey W.; Potrykus, Katarzyna; Vinella, Daniel; Camacho, Martha I.; Fields, Joshua A.; Thompson, Stuart A.; Georgellis, Dimitris; Cashel, Michael; Babitzke, Paul; Romeo, Tony

    2011-01-01

    Summary CsrA protein regulates important cellular processes by binding to target mRNAs and altering their translation and/or stability. In Escherichia coli, CsrA binds to sRNAs, CsrB and CsrC, which sequester CsrA and antagonize its activity. Here, mRNAs for relA, spoT and dksA of the stringent response system were found among 721 different transcripts that copurified with CsrA. Many of the transcripts that copurified with CsrA were previously determined to respond to ppGpp and/or DksA. We examined multiple regulatory interactions between the Csr and stringent response systems. Most importantly, DksA and ppGpp robustly activated csrB/C transcription (10-fold), while they modestly activated csrA expression. We propose that CsrA-mediated regulation is relieved during the stringent response. Gel shift assays confirmed high affinity binding of CsrA to relA mRNA leader and weaker interactions with dksA and spoT. Reporter fusions, qRT-PCR, and immunoblotting showed that CsrA repressed relA expression, and (p)ppGpp accumulation during stringent response was enhanced in a csrA mutant. CsrA had modest to negligible effects on dksA and spoT expression. Transcription of dksA was negatively autoregulated via a feedback loop that tended to mask CsrA effects. We propose that the Csr system fine-tunes the stringent response and discuss biological implications of the composite circuitry. PMID:21488981

  9. Exceptional epidemics: AIDS still deserves a global response

    PubMed Central

    2009-01-01

    There has been a renewed debate over whether AIDS deserves an exceptional response. We argue that as AIDS is having differentiated impacts depending on the scale of the epidemic, and population groups impacted, and so responses must be tailored accordingly. AIDS is exceptional, but not everywhere. Exceptionalism developed as a Western reaction to a once poorly understood epidemic, but remains relevant in the current multi-dimensional global response. The attack on AIDS exceptionalism has arisen because of the amount of funding targeted to the disease and the belief that AIDS activists prioritize it above other health issues. The strongest detractors of exceptionalism claim that the AIDS response has undermined health systems in developing countries. We agree that in countries with low prevalence, AIDS should be normalised and treated as a public health issue--but responses must forcefully address human rights and tackle the stigma and discrimination faced by marginalized groups. Similarly, AIDS should be normalized in countries with mid-level prevalence, except when life-long treatment is dependent on outside resources--as is the case with most African countries--because treatment dependency creates unique sustainability challenges. AIDS always requires an exceptional response in countries with high prevalence (over 10 percent). In these settings there is substantial morbidity, filling hospitals and increasing care burdens; and increased mortality, which most visibly reduces life expectancy. The idea that exceptionalism is somehow wrong is an oversimplification. The AIDS response can not be mounted in isolation; it is part of the development agenda. It must be based on human rights principles, and it must aim to improve health and well-being of societies as a whole. PMID:19912658

  10. Global Magnetospheric Response to an Interplanetary Shock: THEMIS Observations

    NASA Technical Reports Server (NTRS)

    Zhang, Hui; Sibeck, David G.; Zong, Q.-G.; McFadden, James P.; Larson, Davin; Glassmeier, K.-H.; Angelopoulos, V.

    2011-01-01

    We investigate the global response of geospace plasma environment to an interplanetary shock at approx. 0224 UT on May 28, 2008 from multiple THEMIS spacecraft observations in the magnetosheath (THEMIS B and C) and the mid-afternoon (THEMIS A) and dusk magnetosphere (THEMIS D and E). The interaction of the transmitted interplanetary shock with the magnetosphere has global effects. Consequently, it can affect geospace plasma significantly. After interacting with the bow shock, the interplanetary shock transmitted a fast shock and a discontinuity which propagated through the magnetosheath toward the Earth at speeds of 300 km/s and 137 km/s respectively. THEMIS A observations indicate that the plasmaspheric plume changed significantly by the interplanetary shock impact. The plasmaspheric plume density increased rapidly from 10 to 100/ cubic cm in 4 min and the ion distribution changed from isotropic to strongly anisotropic distribution. Electromagnetic ion cyclotron (EMIC) waves observed by THEMIS A are most likely excited by the anisotropic ion distributions caused by the interplanetary shock impact. To our best knowledge, this is the first direct observation of the plasmaspheric plume response to an interplanetary shock's impact. THEMIS A, but not D or E, observed a plasmaspheric plume in the dayside magnetosphere. Multiple spacecraft observations indicate that the dawn-side edge of the plasmaspheric plume was located between THEMIS A and D (or E).

  11. Response Styles in the Assessment of Anger Expression

    ERIC Educational Resources Information Center

    Gollwitzer, Mario; Eid, Michael; Jurgensen, Ralph

    2005-01-01

    This study demonstrates how mixture distribution item response models can be used to detect different response styles in the clinical assessment of anger expression. Analyses of 3 subscales of the State-Trait Anger Expression Inventory in a clinical sample of 4,497 patients revealed that there are different response styles that manifest themselves…

  12. Impact of Neutron Exposure on Global Gene Expression in a Human Peripheral Blood Model.

    PubMed

    Broustas, Constantinos G; Xu, Yanping; Harken, Andrew D; Chowdhury, Mashkura; Garty, Guy; Amundson, Sally A

    2017-04-01

    The detonation of an improvised nuclear device would produce prompt radiation consisting of both photons (gamma rays) and neutrons. While much effort in recent years has gone into the development of radiation biodosimetry methods suitable for mass triage, the possible effect of neutrons on the endpoints studied has remained largely uninvestigated. We have used a novel neutron irradiator with an energy spectrum based on that 1-1.5 km from the epicenter of the Hiroshima blast to begin examining the effect of neutrons on global gene expression, and the impact this may have on the development of gene expression signatures for radiation biodosimetry. We have exposed peripheral blood from healthy human donors to 0.1, 0.3, 0.5 or 1 Gy of neutrons ex vivo using our neutron irradiator, and compared the transcriptomic response 24 h later to that resulting from sham exposure or exposure to 0.1, 0.3, 0.5, 1, 2 or 4 Gy of photons (X rays). We identified 125 genes that responded significantly to both radiation qualities as a function of dose, with the magnitude of response to neutrons generally being greater than that seen after X-ray exposure. Gene ontology analysis suggested broad involvement of the p53 signaling pathway and general DNA damage response functions across all doses of both radiation qualities. Regulation of immune response and chromatin-related functions were implicated only following the highest doses of neutrons, suggesting a physiological impact of greater DNA damage. We also identified several genes that seem to respond primarily as a function of dose, with less effect of radiation quality. We confirmed this pattern of response by quantitative real-time RT-PCR for BAX, TNFRSF10B, ITLN2 and AEN and suggest that gene expression may provide a means to differentiate between total dose and a neutron component.

  13. Global transcriptome analysis of the heat shock response ofshewanella oneidensis

    SciTech Connect

    Gao, Haichun; Wang, Sarah; Liu, Xueduan; Yan, Tinfeng; Wu, Liyou; Alm, Eric; Arkin, Adam P.; Thompson, Dorothea K.; Zhou, Jizhong

    2004-04-30

    Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. However, the genetic basis and regulatory mechanisms underlying the ability of S. oneidensis to survive and adapt to various environmentally relevant stresses is poorly understood. To define this organism's molecular response to elevated growth temperatures, temporal gene expression profiles were examined in cells subjected to heat stress using whole-genome DNA microarrays for S. oneidensis MR-1. Approximately 15 percent (711) of the predicted S. oneidensis genes represented on the microarray were significantly up- or down-regulated (P < 0.05) over a 25-min period following shift to the heat shock temperature (42 C). As expected, the majority of S. oneidensis genes exhibiting homology to known chaperones and heat shock proteins (Hsps) were highly and transiently induced. In addition, a number of predicted genes encoding enzymes in glycolys is and the pentose cycle, [NiFe] dehydrogenase, serine proteases, transcriptional regulators (MerR, LysR, and TetR families), histidine kinases, and hypothetical proteins were induced in response to heat stress. Genes encoding membrane proteins were differentially expressed, suggesting that cells possibly alter their membrane composition or structure in response to variations in growth temperature. A substantial number of the genes encoding ribosomal proteins displayed down-regulated co-expression patterns in response to heat stress, as did genes encoding prophage and flagellar proteins. Finally, based on computational comparative analysis of the upstream promoter regions of S.oneidensis heat-inducible genes, a putative regulatory motif, showing high conservation to the Escherichia coli sigma 32-binding consensus sequence, was identified.

  14. Plant responses to soil heterogeneity and global environmental change.

    PubMed

    García-Palacios, Pablo; Maestre, Fernando T; Bardgett, Richard D; de Kroon, Hans

    2012-11-01

    Recent evidence suggests that soil nutrient heterogeneity, a ubiquitous feature of terrestrial ecosystems, modulates plant responses to ongoing global change (GC). However, we know little about the overall trends of such responses, the GC drivers involved, and the plant attributes affected.We synthesized literature to answer the question: Does soil heterogeneity significantly affect plant responses to main GC drivers, such as elevated atmospheric carbon dioxide concentration (CO2), nitrogen (N) enrichment and changes in rainfall regime?Overall, most studies have addressed short-term effects of N enrichment on the performance of model plant communities using experiments conducted under controlled conditions. The role of soil heterogeneity as a modulator of plant responses to elevated CO2 may depend on the plasticity in nutrient uptake patterns. Soil heterogeneity does interact with N enrichment to determine plant growth and nutrient status, but the outcome of this interaction has been found to be both synergistic and inhibitory. The very few studies published on interactive effects of soil heterogeneity and changes in rainfall regime prevented us from identifying any general pattern.We identify the long-term consequences of soil heterogeneity on plant community dynamics in the field, and the ecosystem level responses of the soil heterogeneity × GC driver interaction, as the main knowledge gaps in this area of research.In order to fill these gaps and take soil heterogeneity and GC research a step forward, we propose the following research guidelines: 1) combining morphological and physiological plant responses to soil heterogeneity with field observations of community composition and predictions from simulation models; and 2) incorporating soil heterogeneity into a trait-based response-effect framework, where plant resource-use traits are used as both response variables to this heterogeneity and GC, and predictors of ecosystem functioning.Synthesis. There is enough

  15. Plant responses to soil heterogeneity and global environmental change

    PubMed Central

    García-Palacios, Pablo; Maestre, Fernando T.; Bardgett, Richard D.; de Kroon, Hans

    2015-01-01

    Summary Recent evidence suggests that soil nutrient heterogeneity, a ubiquitous feature of terrestrial ecosystems, modulates plant responses to ongoing global change (GC). However, we know little about the overall trends of such responses, the GC drivers involved, and the plant attributes affected. We synthesized literature to answer the question: Does soil heterogeneity significantly affect plant responses to main GC drivers, such as elevated atmospheric carbon dioxide concentration (CO2), nitrogen (N) enrichment and changes in rainfall regime? Overall, most studies have addressed short-term effects of N enrichment on the performance of model plant communities using experiments conducted under controlled conditions. The role of soil heterogeneity as a modulator of plant responses to elevated CO2 may depend on the plasticity in nutrient uptake patterns. Soil heterogeneity does interact with N enrichment to determine plant growth and nutrient status, but the outcome of this interaction has been found to be both synergistic and inhibitory. The very few studies published on interactive effects of soil heterogeneity and changes in rainfall regime prevented us from identifying any general pattern. We identify the long-term consequences of soil heterogeneity on plant community dynamics in the field, and the ecosystem level responses of the soil heterogeneity × GC driver interaction, as the main knowledge gaps in this area of research. In order to fill these gaps and take soil heterogeneity and GC research a step forward, we propose the following research guidelines: 1) combining morphological and physiological plant responses to soil heterogeneity with field observations of community composition and predictions from simulation models; and 2) incorporating soil heterogeneity into a trait-based response-effect framework, where plant resource-use traits are used as both response variables to this heterogeneity and GC, and predictors of ecosystem functioning. Synthesis

  16. Response of seafloor ecosystems to abrupt global climate change.

    PubMed

    Moffitt, Sarah E; Hill, Tessa M; Roopnarine, Peter D; Kennett, James P

    2015-04-14

    Anthropogenic climate change is predicted to decrease oceanic oxygen (O2) concentrations, with potentially significant effects on marine ecosystems. Geologically recent episodes of abrupt climatic warming provide opportunities to assess the effects of changing oxygenation on marine communities. Thus far, this knowledge has been largely restricted to investigations using Foraminifera, with little being known about ecosystem-scale responses to abrupt, climate-forced deoxygenation. We here present high-resolution records based on the first comprehensive quantitative analysis, to our knowledge, of changes in marine metazoans (Mollusca, Echinodermata, Arthropoda, and Annelida; >5,400 fossils and trace fossils) in response to the global warming associated with the last glacial to interglacial episode. The molluscan archive is dominated by extremophile taxa, including those containing endosymbiotic sulfur-oxidizing bacteria (Lucinoma aequizonatum) and those that graze on filamentous sulfur-oxidizing benthic bacterial mats (Alia permodesta). This record, from 16,100 to 3,400 y ago, demonstrates that seafloor invertebrate communities are subject to major turnover in response to relatively minor inferred changes in oxygenation (>1.5 to <0.5 mL⋅L(-1) [O2]) associated with abrupt (<100 y) warming of the eastern Pacific. The biotic turnover and recovery events within the record expand known rates of marine biological recovery by an order of magnitude, from <100 to >1,000 y, and illustrate the crucial role of climate and oceanographic change in driving long-term successional changes in ocean ecosystems.

  17. Response of seafloor ecosystems to abrupt global climate change

    PubMed Central

    Moffitt, Sarah E.; Hill, Tessa M.; Roopnarine, Peter D.; Kennett, James P.

    2015-01-01

    Anthropogenic climate change is predicted to decrease oceanic oxygen (O2) concentrations, with potentially significant effects on marine ecosystems. Geologically recent episodes of abrupt climatic warming provide opportunities to assess the effects of changing oxygenation on marine communities. Thus far, this knowledge has been largely restricted to investigations using Foraminifera, with little being known about ecosystem-scale responses to abrupt, climate-forced deoxygenation. We here present high-resolution records based on the first comprehensive quantitative analysis, to our knowledge, of changes in marine metazoans (Mollusca, Echinodermata, Arthropoda, and Annelida; >5,400 fossils and trace fossils) in response to the global warming associated with the last glacial to interglacial episode. The molluscan archive is dominated by extremophile taxa, including those containing endosymbiotic sulfur-oxidizing bacteria (Lucinoma aequizonatum) and those that graze on filamentous sulfur-oxidizing benthic bacterial mats (Alia permodesta). This record, from 16,100 to 3,400 y ago, demonstrates that seafloor invertebrate communities are subject to major turnover in response to relatively minor inferred changes in oxygenation (>1.5 to <0.5 mL⋅L−1 [O2]) associated with abrupt (<100 y) warming of the eastern Pacific. The biotic turnover and recovery events within the record expand known rates of marine biological recovery by an order of magnitude, from <100 to >1,000 y, and illustrate the crucial role of climate and oceanographic change in driving long-term successional changes in ocean ecosystems. PMID:25825727

  18. Response of seafloor ecosystems to abrupt global climate change

    NASA Astrophysics Data System (ADS)

    Moffitt, Sarah E.; Hill, Tessa M.; Roopnarine, Peter D.; Kennett, James P.

    2015-04-01

    Anthropogenic climate change is predicted to decrease oceanic oxygen (O2) concentrations, with potentially significant effects on marine ecosystems. Geologically recent episodes of abrupt climatic warming provide opportunities to assess the effects of changing oxygenation on marine communities. Thus far, this knowledge has been largely restricted to investigations using Foraminifera, with little being known about ecosystem-scale responses to abrupt, climate-forced deoxygenation. We here present high-resolution records based on the first comprehensive quantitative analysis, to our knowledge, of changes in marine metazoans (Mollusca, Echinodermata, Arthropoda, and Annelida; >5,400 fossils and trace fossils) in response to the global warming associated with the last glacial to interglacial episode. The molluscan archive is dominated by extremophile taxa, including those containing endosymbiotic sulfur-oxidizing bacteria (Lucinoma aequizonatum) and those that graze on filamentous sulfur-oxidizing benthic bacterial mats (Alia permodesta). This record, from 16,100 to 3,400 y ago, demonstrates that seafloor invertebrate communities are subject to major turnover in response to relatively minor inferred changes in oxygenation (>1.5 to <0.5 mLṡL-1 [O2]) associated with abrupt (<100 y) warming of the eastern Pacific. The biotic turnover and recovery events within the record expand known rates of marine biological recovery by an order of magnitude, from <100 to >1,000 y, and illustrate the crucial role of climate and oceanographic change in driving long-term successional changes in ocean ecosystems.

  19. Global climate change and planktic foraminiferal response in the Maastrichtian

    NASA Astrophysics Data System (ADS)

    Abramovich, Sigal; Yovel-Corem, Shlomit; Almogi-Labin, Ahuva; Benjamini, Chaim

    2010-04-01

    The lengthy warm, stable climate of the Cretaceous terminated in the Campanian with a cooling trend, interrupted in the early and latest Maastrichtian by two events of global warming, at ˜70-68 Ma and at 65.78-65.57 Ma. These climatic oscillations had a profound effect on pelagic ecosystems, especially on planktic foraminiferal populations. Here we compare biotic responses in the tropical-subtropical (Tethyan) open ocean and mesotrophic (Zin Valley, Israel) and oligotrophic (Tunisia) slopes, which correlate directly with global warming and cooling. The two warming events coincide with blooms of Guembelitria, an extreme opportunist genus best known as the main survivor of the Cretaceous-Paleogene (K-Pg) catastrophe. In the Maastrichtian, Guembelitria bloomed in the uppermost surface water above shelf and slope environments but failed to reach the open ocean as it did at K-Pg. The coldest interval of the late Maastrichtian (˜68-65.78 Ma) is marked by an acme of the otherwise rare species Gansserina gansseri, a deep-dwelling keeled globotruncanid. The G. gansseri acme event can be traced from the deep ocean even onto the Tethyan slope, marking copious production and circulation of cold intermediate water. This acme is abruptly terminated by extinction of the species, a dramatic reversal attributed to a short-term global warming episode. This extinction corresponds precisely with the second bloom of Guembelitria that began ˜300 kyr prior to the K-Pg event. The antithetical relationship between blooming of Guembelitria and the G. gansseri acme reflects planktic foraminiferal sensitivity to warm-cool-warm-cool climatic oscillations marking the end of the Cretaceous.

  20. Global chromatin fibre compaction in response to DNA damage

    SciTech Connect

    Hamilton, Charlotte; Hayward, Richard L.; Gilbert, Nick

    2011-11-04

    Highlights: Black-Right-Pointing-Pointer Robust KAP1 phosphorylation in response to DNA damage in HCT116 cells. Black-Right-Pointing-Pointer DNA repair foci are found in soluble chromatin. Black-Right-Pointing-Pointer Biophysical analysis reveals global chromatin fibre compaction after DNA damage. Black-Right-Pointing-Pointer DNA damage is accompanied by rapid linker histone dephosphorylation. -- Abstract: DNA is protected by packaging it into higher order chromatin fibres, but this can impede nuclear processes like DNA repair. Despite considerable research into the factors required for signalling and repairing DNA damage, it is unclear if there are concomitant changes in global chromatin fibre structure. In human cells DNA double strand break (DSB) formation triggers a signalling cascade resulting in H2AX phosphorylation ({gamma}H2AX), the rapid recruitment of chromatin associated proteins and the subsequent repair of damaged sites. KAP1 is a transcriptional corepressor and in HCT116 cells we found that after DSB formation by chemicals or ionising radiation there was a wave of, predominantly ATM dependent, KAP1 phosphorylation. Both KAP1 and phosphorylated KAP1 were readily extracted from cells indicating they do not have a structural role and {gamma}H2AX was extracted in soluble chromatin indicating that sites of damage are not attached to an underlying structural matrix. After DSB formation we did not find a concomitant change in the sensitivity of chromatin fibres to micrococcal nuclease digestion. Therefore to directly investigate higher order chromatin fibre structures we used a biophysical sedimentation technique based on sucrose gradient centrifugation to compare the conformation of chromatin fibres isolated from cells before and after DNA DSB formation. After damage we found global chromatin fibre compaction, accompanied by rapid linker histone dephosphorylation, consistent with fibres being more regularly folded or fibre deformation being stabilized by

  1. Department of Defense Global Emerging Infections Surveillance and Response System Indian Ocean tsunami response.

    PubMed

    Chretien, Jean-Paul; Glass, Jonathan S; Coldren, Rodney C; Noah, Donald L; Hyer, Randall N; Gaydos, Joel C; Malone, Joseph L

    2006-10-01

    The Department of Defense (DoD) Global Emerging Infections Surveillance and Response System (DoD-GEIS) identifies and addresses DoD vulnerabilities to emerging infections through a global network of partners. Following the Indian Ocean tsunami of December 26, 2004, DoD-GEIS facilitated the DoD medical response and coordination with the Centers for Disease Control and Prevention and the World Health Organization. DoD-GEIS partners in Southeast Asia (U.S. Naval Medical Research Unit 2, Jakarta, Indonesia; and Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand) rapidly conducted health assessments and established surveillance for communicable diseases that threatened survivors. Preexisting collaboration with the Centers for Disease Control and Prevention, the World Health Organization, and host countries was critical for the DoD-GEIS tsunami response.

  2. Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression

    PubMed Central

    Richter, Karin; Wirta, Valtteri; Dahl, Lina; Bruce, Sara; Lundeberg, Joakim; Carlsson, Leif; Williams, Cecilia

    2006-01-01

    Background Expression of the LIM-homeobox gene Lhx2 in murine hematopoietic cells allows for the generation of hematopoietic stem cell (HSC)-like cell lines. To address the molecular basis of Lhx2 function, we generated HSC-like cell lines where Lhx2 expression is regulated by a tet-on system and hence dependent on the presence of doxycyclin (dox). These cell lines efficiently down-regulate Lhx2 expression upon dox withdrawal leading to a rapid differentiation into various myeloid cell types. Results Global gene expression of these cell lines cultured in dox was compared to different time points after dox withdrawal using microarray technology. We identified 267 differentially expressed genes. The majority of the genes overlapping with HSC-specific databases were those down-regulated after turning off Lhx2 expression and a majority of the genes overlapping with those defined as late progenitor-specific genes were the up-regulated genes, suggesting that these cell lines represent a relevant model system for normal HSCs also at the level of global gene expression. Moreover, in situ hybridisations of several genes down-regulated after dox withdrawal showed overlapping expression patterns with Lhx2 in various tissues during embryonic development. Conclusion Global gene expression analysis of HSC-like cell lines with inducible Lhx2 expression has identified genes putatively linked to self-renewal / differentiation of HSCs, and function of Lhx2 in organ development and stem / progenitor cells of non-hematopoietic origin. PMID:16600034

  3. Sparse feature selection methods identify unexpected global cellular response to strontium-containing materials.

    PubMed

    Autefage, Hélène; Gentleman, Eileen; Littmann, Elena; Hedegaard, Martin A B; Von Erlach, Thomas; O'Donnell, Matthew; Burden, Frank R; Winkler, David A; Stevens, Molly M

    2015-04-07

    Despite the increasing sophistication of biomaterials design and functional characterization studies, little is known regarding cells' global response to biomaterials. Here, we combined nontargeted holistic biological and physical science techniques to evaluate how simple strontium ion incorporation within the well-described biomaterial 45S5 bioactive glass (BG) influences the global response of human mesenchymal stem cells. Our objective analyses of whole gene-expression profiles, confirmed by standard molecular biology techniques, revealed that strontium-substituted BG up-regulated the isoprenoid pathway, suggesting an influence on both sterol metabolite synthesis and protein prenylation processes. This up-regulation was accompanied by increases in cellular and membrane cholesterol and lipid raft contents as determined by Raman spectroscopy mapping and total internal reflection fluorescence microscopy analyses and by an increase in cellular content of phosphorylated myosin II light chain. Our unexpected findings of this strong metabolic pathway regulation as a response to biomaterial composition highlight the benefits of discovery-driven nonreductionist approaches to gain a deeper understanding of global cell-material interactions and suggest alternative research routes for evaluating biomaterials to improve their design.

  4. US Military contributions to the global response to pandemic chikungunya.

    PubMed

    Hoke, Charles H; Pace-Templeton, Judy; Pittman, Phillip; Malinoski, Frank J; Gibbs, Paul; Ulderich, Tracy; Mathers, Michelle; Fogtman, Beverly; Glass, Pamela; Vaughn, David W

    2012-10-19

    Chikungunya virus, transmitted by mosquitoes to man, causes an acute illness characterized by fever, rash and striking joint symptoms. US Military investigators developed, manufactured at The Salk Institute-Government Services Division (TSI-GSD), and tested the live, attenuated Chikungunya Vaccine TSI-GSD-218. The manufacturing facility stopped production in 1994. The Chikungunya Vaccine TSI-GSD-218 development effort was terminated in 1998, and materials were archived. In 2005, an alarming outbreak of chikungunya disease began in Africa and spread to islands in the Indian Ocean and throughout much of Asia. Abrupt epidemics with high attack rates and serious, even fatal, complications were reported, and travelers carried the virus to Europe and the Americas. In response to urgent requests, the US Military offered assistance by providing non-exclusive access to the previously stored vaccine production seed materials, bulk vaccine, regulatory documentation, and reports of previous clinical trials. Five companies requested technology transfers. This experience provides lessons about epidemiological unpredictability, preparedness, vaccine manufacturing, the potential global importance of vaccine seed materials and the advisability of a global strategic plan. Consideration should be given to banking of vaccine production seeds, cell substrates, and manufacturing instructions. In view of the manufacturability, attenuation, and immunogenicity of Chikungunya Vaccine TSI-GSD-218, authorities may wish to consider this product as a possible candidate itself, as a comparator vaccine to improve upon, as a seed for inactivated vaccine, or as a source of virus or antigen for neutralization assays or immunoassays.

  5. A Global Framework for Monitoring Phenological Responses to Climate Change

    SciTech Connect

    White, Michael A; Hoffman, Forrest M; Hargrove, William Walter; Nemani, Ramakrishna R

    2005-01-01

    Remote sensing of vegetation phenology is an important method with which to monitor terrestrial responses to climate change, but most approaches include signals from multiple forcings, such as mixed phenological signals from multiple biomes, urbanization, political changes, shifts in agricultural practices, and disturbances. Consequently, it is difficult to extract a clear signal from the usually assumed forcing: climate change. Here, using global 8 km 1982 to 1999 Normalized Difference Vegetation Index (NDVI) data and an eight-element monthly climatology, we identified pixels whose wavelet power spectrum was consistently dominated by annual cycles and then created phenologically and climatically self-similar clusters, which we term phenoregions. We then ranked and screened each phenoregion as a function of landcover homogeneity and consistency, evidence of human impacts, and political diversity. Remaining phenoregions represented areas with a minimized probability of non-climatic forcings and form elemental units for long-term phenological monitoring.

  6. Global response of M-I coulping revealed by AMPERE

    NASA Astrophysics Data System (ADS)

    Waters, C. L.; Anderson, B. J.; Korth, H.

    2014-12-01

    The Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) provides one of the few in-situ datasets that allows studies of global properties of magnetosphere-ionosphere (M-I) interactions. The characterisation of the Birkeland currents, sensed by the Iridium constellation of satellites for both hemispheres simultaneously, is possible particularly for storm-time events. Other data sets (e.g. HF radar) that provide large spatial coverage may also be combined with AMPERE data in order to understand hemisphere differences in power input. In this presentation, we focus on the ability of AMPERE data to provide details of M-I coupling in both hemispheres simultaneously. The presentation will be illustrated using examples showing comparisons from north and south hemisphere Birkeland current configurations and Poynting flux.

  7. Global transcriptomic analysis of the response of Corynebacterium glutamicum to ferulic acid.

    PubMed

    Chen, Can; Pan, Junfeng; Yang, Xiaobing; Xiao, He; Zhang, Yaoling; Si, Meiru; Shen, Xihui; Wang, Yao

    2017-03-01

    Corynebacterium glutamicum can survive by using ferulic acid as the sole carbon source. In this study, we assessed the response of C. glutamicum to ferulic acid stress by means of a global transcriptional response analysis. The transcriptional data showed that several genes involved in degradation of ferulic acid were affected. Moreover, several genes related to the stress response; protein protection or degradation and DNA repair; replication, transcription and translation; and the cell envelope were differentially expressed. Deletion of the katA or sigE gene in C. glutamicum resulted in a decrease in cell viability under ferulic acid stress. These insights will facilitate further engineering of model industrial strains, with enhanced tolerance to ferulic acid to enable easy production of biofuels from lignocellulose.

  8. Global Expression Studies of Schizophrenic Brain: A Meta-Analysis Study Linking Neurological Immune System with Psychological Disorders.

    PubMed

    Karim, Sajjad; Kamal, Mohammad A; Iqbal, Zafar; Ansari, Shakeel A; Rasool, Mahmood; Al-Qahtani, Mohammed H; Damanhouri, Gazi; Mirza, Zeenat

    2016-01-01

    Schizophrenia, a psychological disorder with enormous societal impact, is a result of abnormalities in gene expression and dysregulation of the immune response in the brain. Few studies have been conducted to understand its etiology, however, the exact molecular mechanism largely remains unknown, though some poorly understood theories abound. Present meta-study links the role of central nervous system, immunological system and psychological disorders by using global expression approach and pathway analysis. We retrieved genome-wide mRNA expression data and clinico-pathological information from five independent studies of schizophrenic patients from Gene Expression Omnibus database. We continued further with three studies having common platform. Our result showed a total of 527 differentially expressed genes of which 314 are up regulated and 213 are down regulated. After adjusting the sources of variation, we carried out pathway and gene ontology analysis, and observed alteration of 14-3-3-mediated signaling, γ-aminobutyric acid receptor signaling, role of nuclear factor of activated T-cells in regulation of the immune response, G beta gamma signaling, dopamine- and cyclic AMP-regulated phosphoprotein of relative molecular mass 32,000 feedback in cAMP signaling, complement system, axonal guidance signaling, dendritic cell maturation, cAMP response element-binding protein signaling in neurons and interleukin-1 signaling pathways and networks. Conclusively, our global gene expression pathway and gene set enrichment analysis studies suggest disruption of many common pathways and processes, which links schizophrenia to immune and central nervous system. Present meta-study links the role of central nervous system, immunological system and psychological disorders by using global expression approach and pathway analysis.

  9. The Influence of the Global Gene Expression Shift on Downstream Analyses.

    PubMed

    Xu, Qifeng; Zhang, Xuegong

    2016-01-01

    The assumption that total abundance of RNAs in a cell is roughly the same in different cells is underlying most studies based on gene expression analyses. But experiments have shown that changes in the expression of some master regulators such as c-MYC can cause global shift in the expression of almost all genes in some cell types like cancers. Such shift will violate this assumption and can cause wrong or biased conclusions for standard data analysis practices, such as detection of differentially expressed (DE) genes and molecular classification of tumors based on gene expression. Most existing gene expression data were generated without considering this possibility, and are therefore at the risk of having produced unreliable results if such global shift effect exists in the data. To evaluate this risk, we conducted a systematic study on the possible influence of the global gene expression shift effect on differential expression analysis and on molecular classification analysis. We collected data with known global shift effect and also generated data to simulate different situations of the effect based on a wide collection of real gene expression data, and conducted comparative studies on representative existing methods. We observed that some DE analysis methods are more tolerant to the global shift while others are very sensitive to it. Classification accuracy is not sensitive to the shift and actually can benefit from it, but genes selected for the classification can be greatly affected.

  10. Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds

    PubMed Central

    Yung, Pui Yi; Grasso, Letizia Lo; Mohidin, Abeed Fatima; Acerbi, Enzo; Hinks, Jamie; Seviour, Thomas; Marsili, Enrico; Lauro, Federico M.

    2016-01-01

    Volatile organic compounds (VOCs) are commonly used as solvents in various industrial settings. Many of them present a challenge to receiving environments, due to their toxicity and low bioavailability for degradation. Microorganisms are capable of sensing and responding to their surroundings and this makes them ideal detectors for toxic compounds. This study investigates the global transcriptomic responses of Escherichia coli K-12 to selected VOCs at sub-toxic levels. Cells grown in the presence of VOCs were harvested during exponential growth, followed by whole transcriptome shotgun sequencing (RNAseq). The analysis of the data revealed both shared and unique genetic responses compared to cells without exposure to VOCs. Results suggest that various functional gene categories, for example, those relating to Fe/S cluster biogenesis, oxidative stress responses and transport proteins, are responsive to selected VOCs in E. coli. The differential expression (DE) of genes was validated using GFP-promoter fusion assays. A variety of genes were differentially expressed even at non-inhibitory concentrations and when the cells are at their balanced-growth. Some of these genes belong to generic stress response and others could be specific to VOCs. Such candidate genes and their regulatory elements could be used as the basis for designing biosensors for selected VOCs. PMID:26818886

  11. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.

    PubMed

    He, Zhili; Zhou, Aifen; Baidoo, Edward; He, Qiang; Joachimiak, Marcin P; Benke, Peter; Phan, Richard; Mukhopadhyay, Aindrila; Hemme, Christopher L; Huang, Katherine; Alm, Eric J; Fields, Matthew W; Wall, Judy; Stahl, David; Hazen, Terry C; Keasling, Jay D; Arkin, Adam P; Zhou, Jizhong

    2010-03-01

    The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels.

  12. Heme Signaling Impacts Global Gene Expression, Immunity and Dengue Virus Infectivity in Aedes aegypti

    PubMed Central

    Bottino-Rojas, Vanessa; Talyuli, Octávio A. C.; Jupatanakul, Natapong; Sim, Shuzhen; Dimopoulos, George; Venancio, Thiago M.; Bahia, Ana C.; Sorgine, Marcos H.; Oliveira, Pedro L.; Paiva-Silva, Gabriela O.

    2015-01-01

    Blood-feeding mosquitoes are exposed to high levels of heme, the product of hemoglobin degradation. Heme is a pro-oxidant that influences a variety of cellular processes. We performed a global analysis of heme-regulated Aedes aegypti (yellow fever mosquito) transcriptional changes to better understand influence on mosquito physiology at the molecular level. We observed an iron- and reactive oxygen species (ROS)-independent signaling induced by heme that comprised genes related to redox metabolism. By modulating the abundance of these transcripts, heme possibly acts as a danger signaling molecule. Furthermore, heme triggered critical changes in the expression of energy metabolism and immune response genes, altering the susceptibility towards bacteria and dengue virus. These findings seem to have implications on the adaptation of mosquitoes to hematophagy and consequently on their ability to transmit diseases. Altogether, these results may also contribute to the understanding of heme cell biology in eukaryotic cells. PMID:26275150

  13. Global relationships in fluctuation and response in adaptive evolution

    PubMed Central

    Furusawa, Chikara; Kaneko, Kunihiko

    2015-01-01

    Cells change their internal state to adapt to environmental changes, and evolve in response to the new conditions. The phenotype changes first via adaptation in response to environmental changes, and then through mutational changes in the genomic sequence, followed by selection in evolution. Here, we analysed simulated adaptive evolution using a simple cell model consisting of thousands of intracellular components, and found that the changes in their concentrations by adaptation are proportional to those by evolution across all the components, where the proportion coefficient between the two agreed well with the change in the growth rate of a cell. Furthermore, we demonstrate that the phenotypic variance in concentrations of cellular components due to (non-genetic) noise and to genomic alternations is proportional across all components. This implies that the specific phenotypes that are highly evolvable were already given by non-genetic fluctuations. These global relationships in cellular states were also supported by phenomenological theory based on steady reproduction and transcriptome analysis of laboratory evolution in Escherichia coli. These findings demonstrate that a possible evolutionary change in phenotypic state is highly restricted. Our results provide a basis for the development of a quantitative theory of plasticity and robustness in phenotypic evolution. PMID:26202686

  14. Improving models to predict phenological responses to global change

    SciTech Connect

    Richardson, Andrew D.

    2015-11-25

    The term phenology describes both the seasonal rhythms of plants and animals, and the study of these rhythms. Plant phenological processes, including, for example, when leaves emerge in the spring and change color in the autumn, are highly responsive to variation in weather (e.g. a warm vs. cold spring) as well as longer-term changes in climate (e.g. warming trends and changes in the timing and amount of rainfall). We conducted a study to investigate the phenological response of northern peatland communities to global change. Field work was conducted at the SPRUCE experiment in northern Minnesota, where we installed 10 digital cameras. Imagery from the cameras is being used to track shifts in plant phenology driven by elevated carbon dioxide and elevated temperature in the different SPRUCE experimental treatments. Camera imagery and derived products (“greenness”) is being posted in near-real time on a publicly available web page (http://phenocam.sr.unh.edu/webcam/gallery/). The images will provide a permanent visual record of the progression of the experiment over the next 10 years. Integrated with other measurements collected as part of the SPRUCE program, this study is providing insight into the degree to which phenology may mediate future shifts in carbon uptake and storage by peatland ecosystems. In the future, these data will be used to develop improved models of vegetation phenology, which will be tested against ground observations collected by a local collaborator.

  15. The Role of Civil Society Organizations in Monitoring the Global AIDS Response.

    PubMed

    Smith, Julia; Mallouris, Christoforos; Lee, Kelley; Alfvén, Tobias

    2016-10-12

    Civil society organizations (CSOs) are recognized as playing an exceptional role in the global AIDS response. However, there is little detailed research to date on how they contribute to specific governance functions. This article uses Haas' framework on global governance functions to map CSO's participation in the monitoring of global commitments to the AIDS response by institutions and states. Drawing on key informant interviews and primary documents, it focuses specifically on CSO participation in Global AIDS Response Progress Reporting and in Global Fund to Fight AIDS, Tuberculosis and Malaria processes. It argues that the AIDS response is unique within global health governance, in that CSOs fulfill both formal and informal monitoring functions, and considers the strengths and weaknesses of these contributions. It concludes that future global health governance arrangements should include provisions and resources for monitoring by CSOs because their participation creates more inclusive global health governance and contributes to strengthening commitments to human rights.

  16. Global and App Express Updates, 2002-2003. EDExpress Training. Participant Guide.

    ERIC Educational Resources Information Center

    Office of Student Financial Assistance (ED), Washington, DC.

    This manual identifies the major changes for 2002-2003 in EDExpress, the electronic data exchange aspect of the Title IV student financial aid application process. It describes the major changes in the global EDExpress module and the App Express module and discusses locations for other resources describing changes in EDExpress. The Global Module…

  17. Promoting health in response to global tourism expansion in Cuba.

    PubMed

    Spiegel, J M; Gonzalez, M; Cabrera, G J; Catasus, S; Vidal, C; Yassi, A

    2008-03-01

    The ability of communities to respond to the pressures of globalization is an important determinant of community health. Tourism is a rapidly growing industry and there is an increasing concern about its health impact on local communities. Nonetheless, little research has been conducted to identify potential mitigating measures. We therefore took advantage of the 'natural experiment' provided by the expansion of tourism in Cuba, and conducted four focus groups and key informants interviews in each of two coastal communities. Participants expressed concerns about psycho-social impacts as well as occupational and environmental concerns, and both infectious and chronic diseases. A wide array of programs that had been developed to mitigate potential negative were described. Some of the programs were national in scope and others were locally developed. The programs particularly targeted youth as the most vulnerable population at risk of addictions and sexually transmitted infections. Occupational health concerns for workers in the tourism sector were also addressed, with many of the measures implemented protecting tourists as well. The health promotion and various other participatory action initiatives implemented showed a strong commitment to address the impacts of tourism and also contributed to building capacity in the two communities. Although longitudinal studies are needed to assess the sustainability of these programs and to evaluate their long-term impact in protecting health, other communities can learn from the initiatives taken.

  18. Global Proteomics Analysis of the Response to Starvation in C. elegans.

    PubMed

    Larance, Mark; Pourkarimi, Ehsan; Wang, Bin; Brenes Murillo, Alejandro; Kent, Robert; Lamond, Angus I; Gartner, Anton

    2015-07-01

    Periodic starvation of animals induces large shifts in metabolism but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass-spectrometry-based quantitative proteomics to identify global changes in the Caenorhabditis elegans proteome due to acute starvation of young adult animals. Measuring changes in the abundance of over 5,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin-associated proteins, including specific linker histones, histone variants, and histone posttranslational modifications associated with the epigenetic control of gene expression. To maximize community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).

  19. Global Proteomics Analysis of the Response to Starvation in C. elegans*

    PubMed Central

    Larance, Mark; Pourkarimi, Ehsan; Wang, Bin; Brenes Murillo, Alejandro; Kent, Robert; Lamond, Angus I.; Gartner, Anton

    2015-01-01

    Periodic starvation of animals induces large shifts in metabolism but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass-spectrometry-based quantitative proteomics to identify global changes in the Caenorhabditis elegans proteome due to acute starvation of young adult animals. Measuring changes in the abundance of over 5,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin-associated proteins, including specific linker histones, histone variants, and histone posttranslational modifications associated with the epigenetic control of gene expression. To maximize community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/). PMID:25963834

  20. Global proteomic analysis of the chromate response in Arthrobacter sp strain FB24.

    SciTech Connect

    Henne, K. L.; Turse, J. E.; Nicora, C. D.; Lipton, M. S.; Tollaksen, S. L.; Lindberg, C.; Babnigg, G.; Giometti, C. S.; Nakatsu, C. H.; Thompson, D. K.; Konopka, A. E.; Biosciences Division; Purdue Univ.; PNNL

    2009-04-01

    A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO{sub 4}{sup 2-}) transporter by the chromate (CrO{sub 4}{sup 2-}) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceeded 5 mM.

  1. Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24

    SciTech Connect

    Henne, Kristene L.; Turse, Joshua E.; Nicora, Carrie D.; Lipton, Mary S.; Tollaksen, Sandra L.; Lindberg, Carl; Babbnig, Gyorgy; Giometti, Carol S.; Nakatsu, Cindy N.; Thompson, Dorothea K.; Konopka, Allan

    2009-04-01

    A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 mM and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled to tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO42-) transporter by the chromate (CrO42-) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceed 5 mM.

  2. Global transcriptome and physiological responses of Acinetobacter oleivorans DR1 exposed to distinct classes of antibiotics.

    PubMed

    Heo, Aram; Jang, Hyun-Jin; Sung, Jung-Suk; Park, Woojun

    2014-01-01

    The effects of antibiotics on environment-originated nonpathogenic Acinetobacter species have been poorly explored. To understand the antibiotic-resistance mechanisms that function in nonpathogenic Acinetobacter species, we used an RNA-sequencing (RNA-seq) technique to perform global gene-expression profiling of soil-borne Acinetobacter oleivorans DR1 after exposing the bacteria to 4 classes of antibiotics (ampicillin, Amp; kanamycin, Km; tetracycline, Tc; norfloxacin, Nor). Interestingly, the well-known two global regulators, the soxR and the rpoE genes are present among 41 commonly upregulated genes under all 4 antibiotic-treatment conditions. We speculate that these common genes are essential for antibiotic resistance in DR1. Treatment with the 4 antibiotics produced diverse physiological and phenotypic changes. Km treatment induced the most dramatic phenotypic changes. Examination of mutation frequency and DNA-repair capability demonstrated the induction of the SOS response in Acinetobacter especially under Nor treatment. Based on the RNA-seq analysis, the glyoxylate-bypass genes of the citrate cycle were specifically upregulated under Amp treatment. We also identified newly recognized non-coding small RNAs of the DR1 strain, which were also confirmed by Northern blot analysis. These results reveal that treatment with antibiotics of distinct classes differentially affected the gene expression and physiology of DR1 cells. This study expands our understanding of the molecular mechanisms of antibiotic-stress response of environment-originated bacteria and provides a basis for future investigations.

  3. Global gene expression analysis of Saccharomyces cerevisiae grown under redox potential-controlled very-high-gravity conditions.

    PubMed

    Liu, Chen-Guang; Lin, Yen-Han; Bai, Feng-Wu

    2013-11-01

    Redox potential (ORP) plays a pivotal role in yeast viability and ethanol production during very-high-gravity (VHG) ethanol fermentation. In order to identify the correlation between redox potential profiles and gene expression patterns, global gene expression of Saccharomyces cerevisiae was investigated. Results indicated that significant changes in gene expression occurred at the periods of 0 - 6 h and 30 - 36 h, respectively. Changes noted in the period of 0 - 6 h were mainly related to carbohydrate metabolism. In contrast, gene expression variation at 30 - 36 h could be attributed primarily to stress response. Although CDC19 was down-regulated, expression of PYK2, PDC6 and ADH2 correlated inversely with ORP. Meanwhile, expression of GPD1 decreased due to the depletion of dissolved oxygen in the fermentation broth, but expression of GPD2 correlated with ORP. Transcription of genes encoding heat shock proteins was characterized by uphill, downhill, valley and plateau expression profiles, accordingly to specific function in stress response. These results highlight the role of ORP in modulating yeast physiology and metabolism under VHG conditions.

  4. Global Expression for Representing Diatomic Potential-Energy Curves

    NASA Technical Reports Server (NTRS)

    Ferrante, John; Schlosser, Herbert; Smith, John R.

    1991-01-01

    A three-parameter expression that gives an accurate fit to diatomic potential curves over the entire range of separation for charge transfers between 0 and 1. It is based on a generalization of the universal binding-energy relation of Smith et al. (1989) with a modification that describes the crossover from a partially ionic state to the neutral state at large separations. The expression is tested by comparison with first-principles calculations of the potential curves ranging from covalently bonded to ionically bonded. The expression is also used to calculate spectroscopic constants form a curve fit to the first-principles curves. A comparison is made with experimental values of the spectroscopic constants.

  5. DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks

    PubMed Central

    Gan, Rui; Wu, Xiaolin; He, Wei; Liu, Zhenhua; Wu, Shuangju; Chen, Chao; Chen, Si; Xiang, Qianrong; Deng, Zixin; Liang, Dequan; Chen, Shi; Wang, Lianrong

    2014-01-01

    The modification of DNA by phosphorothioate (PT) occurs when the non-bridging oxygen in the sugar-phosphate backbone of DNA is replaced with sulfur. This DNA backbone modification was recently discovered and is governed by the dndABCDE genes in a diverse group of bacteria and archaea. However, the biological function of DNA PT modifications is poorly understood. In this study, we employed the RNA-seq analysis to characterize the global transcriptional changes in response to PT modifications. Our results show that DNA without PT protection is susceptible to DNA damage caused by the dndFGHI gene products. The DNA double-stranded breaks then trigger the SOS response, cell filamentation and prophage induction. Heterologous expression of dndBCDE conferring DNA PT modifications at GPSA and GPST prevented the damage in Salmonella enterica. Our data provide insights into the physiological role of the DNA PT system. PMID:25319634

  6. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough.

    SciTech Connect

    Chhabra, S.R.; He, Q.; Huang, K.H.; Gaucher, S.P.; Alm, E.J.; He,Z.; Hadi, M.Z.; Hazen, T.C.; Wall, J.D.; Zhou, J.; Arkin, A.P.; Singh, A.K.

    2005-09-16

    Desulfovibrio vulgaris Hildenborough belongs to a class ofsulfate-reducing bacteria (SRB) and is found ubiquitously in nature.Given the importance of SRB-mediated reduction for bioremediation ofmetal ion contaminants, ongoing research on D. vulgaris has been in thedirection of elucidating regulatory mechanisms for this organism under avariety of stress conditions. This work presents a global view of thisorganism's response to elevated growth temperature using whole-celltranscriptomics and proteomics tools. Transcriptional response (1.7-foldchange or greater; Z>1.5) ranged from 1,135 genes at 15 min to 1,463genes at 120 min for a temperature up-shift of 13oC from a growthtemperature of 37oC for this organism and suggested both direct andindirect modes of heat sensing. Clusters of orthologous group categoriesthat were significantly affected included posttranslationalmodifications; protein turnover and chaperones (up-regulated); energyproduction and conversion (down-regulated), nucleotide transport,metabolism (down-regulated), and translation; ribosomal structure; andbiogenesis (down-regulated). Analysis of the genome sequence revealed thepresence of features of both negative and positive regulation whichincluded the CIRCE element and promoter sequences corresponding to thealternate sigma factors ?32 and ?54. While mechanisms of heat shockcontrol for some genes appeared to coincide with those established forEscherichia coli and Bacillus subtilis, the presence of unique controlschemes for several other genes was also evident. Analysis of proteinexpression levels using differential in-gel electrophoresis suggestedgood agreement with transcriptional profiles of several heat shockproteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), andAhpC (DVU2247). The proteomics study also suggested the possibility ofposttranslational modifications in the chaperones DnaK, AhpC, GroES(DVU1977), and GroEL (DVU1976) and also several periplasmic ABCtransporters.

  7. Seasonal Climate Extremes : Mechanism, Predictability and Responses to Global Warming

    NASA Astrophysics Data System (ADS)

    Shongwe, M. E.

    2010-01-01

    Climate extremes are rarely occurring natural phenomena in the climate system. They often pose one of the greatest environmental threats to human and natural systems. Statistical methods are commonly used to investigate characteristics of climate extremes. The fitted statistical properties are often interpolated or extrapolated to give an indication of the likelihood of a certain event within a given period or interval. Under changing climatic conditions, the statistical properties of climate extremes are also changing. It is an important scientific goal to predict how the properties of extreme events change. To achieve this goal, observational and model studies aimed at revealing important features are a necessary prerequisite. Notable progress has been made in understanding mechanisms that influence climate variability and extremes in many parts of the globe including Europe. However, some of the recently observed unprecedented extremes cannot be fully explained from the already identified forcing factors. A better understanding of why these extreme events occur and their sensitivity to certain reinforcing and/or competing factors is useful. Understanding their basic form as well as their temporal variability is also vital and can contribute to global scientific efforts directed at advancing climate prediction capabilities, particularly making skilful forecasts and realistic projections of extremes. In this thesis temperature and precipitation extremes in Europe and Africa, respectively, are investigated. Emphasis is placed on the mechanisms underlying the occurrence of the extremes, their predictability and their likely response to global warming. The focus is on some selected seasons when extremes typically occur. An atmospheric energy budget analysis for the record-breaking European Autumn 2006 event has been carried out with the goal to identify the sources of energy for the extreme event. Net radiational heating is compared to surface turbulent fluxes of

  8. Global cellular response to chemotherapy-induced apoptosis

    PubMed Central

    Wiita, Arun P; Ziv, Etay; Wiita, Paul J; Urisman, Anatoly; Julien, Olivier; Burlingame, Alma L; Weissman, Jonathan S; Wells, James A

    2013-01-01

    How cancer cells globally struggle with a chemotherapeutic insult before succumbing to apoptosis is largely unknown. Here we use an integrated systems-level examination of transcription, translation, and proteolysis to understand these events central to cancer treatment. As a model we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line therapy. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. Simultaneous ribosome profiling further reveals potential translational regulation of stress response genes. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of upstream bortezomib effects. Moreover, previously uncharacterized non-caspase proteolytic events also participate in cellular deconstruction. Our systems-level data also support co-targeting the anti-apoptotic regulator HSF1 to promote cell death by bortezomib. This integrated approach offers unique, in-depth insight into apoptotic dynamics that may prove important to preclinical evaluation of any anti-cancer compound. DOI: http://dx.doi.org/10.7554/eLife.01236.001 PMID:24171104

  9. Response of a temperate demersal fish community to global warming

    NASA Astrophysics Data System (ADS)

    Punzón, A.; Serrano, A.; Sánchez, F.; Velasco, F.; Preciado, I.; González-Irusta, J. M.; López-López, L.

    2016-09-01

    Changes in the distribution of the demersal fish species have been identified in north-European Atlantic waters. The consequence of these changes has been a northward shift of the distribution limits and changes in richness. In this study a notable increase in demersal fish species richness per sampling station was detected in the southern Bay of Biscay. This rise was due to an increase in frequency of occurrence and abundance of the majority of fish species in the area (53% from the total species). A fisheries relate explanation was discarded because the mismatch between the changes in the fishing effort and the augment in frequency of occurrence and abundance. On the contrary, these changes are in agreement with expected response under the increasing temperature of the sea observed over the last three decades, associated to global warming. These changes were positively correlated with an increase in temperature of intermediate waters in the study area. In addition, some of these species showed a notable western displacements of the Centre of Gravity in the study area, which would be expected if temperate water species would be favoured by an increase in water temperature. Our results are consistent with studies in the North Sea, where many of these species showing widened distribution limits towards north. The analysis of the results shows that the studied ecosystem, the Bay of Biscay is under a meridionalization process. On the other hand, only one tropicalization event (Lepidotrigla dieuzeidei), was recorded, maybe due to the conservative restrictions applied in species selection.

  10. Global frequency response analysis of gravitationally stretched liquid jets

    NASA Astrophysics Data System (ADS)

    Consoli-Lizzi, Paula; Coenen, Wilfried; Sevilla, Alejandro

    2013-11-01

    The convective capillary break-up of freely falling axisymmetric jets of Newtonian liquid is theoretically studied with a one-dimensional description of the mass and momentum conservation equations. Instead of using the classical quasi-parallel assumption in the stability analysis, here we compute the global linear response of the flow to harmonic inputs at the exit of the jet, allowing us to predict its break-up length in cases where the base flow is not slender. Our theory compares favourably with recent experiments by Javadi et al. (PRL 110, 144501, 2013), who measured the break-up length of unforced liquid jets of several viscosities. From the physical point of view, our main finding is that the meniscus region near the injector outlet, where the jet experiences the strongest axial stretching, delays the growth of capillary disturbances due to a spatial counterpart of the kinematic stabilizing mechanism firstly described by Tomotika (Proc. Roy. Soc. 153, 1936) in a temporal setting. Supported by Spanish MINECO under project DPI 2011-28356-C03-02.

  11. Global transcriptome analysis of Bacillus cereus ATCC 14579 in response to silver nitrate stress.

    PubMed

    Babu, Malli Mohan Ganesh; Sridhar, Jayavel; Gunasekaran, Paramasamy

    2011-11-10

    Silver nanoparticles (AgNPs) were synthesized using Bacillus cereus strains. Earlier, we had synthesized monodispersive crystalline silver nanoparticles using B. cereus PGN1 and ATCC14579 strains. These strains have showed high level of resistance to silver nitrate (1 mM) but their global transcriptomic response has not been studied earlier. In this study, we investigated the cellular and metabolic response of B. cereus ATCC14579 treated with 1 mM silver nitrate for 30 & 60 min. Global expression profiling using genomic DNA microarray indicated that 10% (n = 524) of the total genes (n = 5234) represented on the microarray were up-regulated in the cells treated with silver nitrate. The majority of genes encoding for chaperones (GroEL), nutrient transporters, DNA replication, membrane proteins, etc. were up-regulated. A substantial number of the genes encoding chemotaxis and flagellar proteins were observed to be down-regulated. Motility assay of the silver nitrate treated cells revealed reduction in their chemotactic activity compared to the control cells. In addition, 14 distinct transcripts overexpressed from the 'empty' intergenic regions were also identified and proposed as stress-responsive non-coding small RNAs.

  12. Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation

    SciTech Connect

    Lee, Patrick K. H.; Dill, Brian; Louie, Tiffany S.; Shah, Manesh B; Verberkmoes, Nathan C; Andersen, Gary L.; Zinder, Stephen H.; Alvarez-Cohen, Lisa

    2012-01-01

    Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL) as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly up-regulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally down regulated in response to FNL and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and post-translational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.

  13. Global expression profiling in leaves of free-growing aspen

    PubMed Central

    Sjödin, Andreas; Wissel, Kirsten; Bylesjö, Max; Trygg, Johan; Jansson, Stefan

    2008-01-01

    Background Genomic studies are routinely performed on young plants in controlled environments which is very different from natural conditions. In reality plants in temperate countries are exposed to large fluctuations in environmental conditions, in the case of perennials over several years. We have studied gene expression in leaves of a free-growing aspen (Populus tremula) throughout multiple growing seasons Results We show that gene expression during the first month of leaf development was largely determined by a developmental program although leaf expansion, chlorophyll accumulation and the speed of progression through this program was regulated by the temperature. We were also able to define "transcriptional signatures" for four different substages of leaf development. In mature leaves, weather factors were important for gene regulation. Conclusion This study shows that multivariate methods together with high throughput transcriptional methods in the field can provide additional, novel information as to plant status under changing environmental conditions that is impossible to mimic in laboratory conditions. We have generated a dataset that could be used to e.g. identify marker genes for certain developmental stages or treatments, as well as to assess natural variation in gene expression. PMID:18500984

  14. Mineral supply constraints necessitate a global policy response

    NASA Astrophysics Data System (ADS)

    Nickless, Edmund

    2016-04-01

    Adoption on 12 December 2015 of The Paris Agreement, the first universal climate agreement, suggests that nations will invest in infrastructures for renewable energy sources paving the way to a global low-carbon society. These large-scale changes will require vast amounts of metals and minerals. Regardless of whether known supplies are enough to meet demand in the near future, efforts must be made now to forestall unpredictable yet inevitable supply shortages in the decades to come, shortages that would dramatically impact the building of additional generation and distribution capacity, and deployment of low-carbon technology. But in response to the current downturn in commodity prices, the global mining industry is downsizing and reducing investment in the new exploration, putting at risk future security of supply. Mining and climate change are inextricably linked; the new adaptive technologies needed to tackle climate change depend on extraction of minerals and metals. An interdisciplinary group supported by the International Union of Geological Sciences, the International Council for Science Unions and UNESCO proposes measures to avert the looming minerals crisis that is developing in the context of current recycling capacity and exploration trends. Our immediate goal is to stimulate discussion of supply constraints using available data on mineral reserves. We build on recent discussions of supply risk and criticality with a focus on the source of primary resources over the next two to three decades when the availability of metals for recycling will remain low. Current massive production of iron ore and other such commodities despite record low prices indicates a failure of the traditional supply and demand constraints. Broader discussions of metal and mineral supply beyond current criticality are needed given the pace of technological and demographic change as well as rapid development spurts. Furthermore, accessible mineral deposits are irregularly distributed

  15. Global Regulation of Gene Expression by the MafR Protein of Enterococcus faecalis

    PubMed Central

    Ruiz-Cruz, Sofía; Espinosa, Manuel; Goldmann, Oliver; Bravo, Alicia

    2016-01-01

    Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. However, as an opportunistic pathogen, it is able to colonize other host niches and cause life-threatening infections. Its adaptation to new environments involves global changes in gene expression. The EF3013 gene (here named mafR) of E. faecalis strain V583 encodes a protein (MafR, 482 residues) that has sequence similarity to global response regulators of the Mga/AtxA family. The enterococcal OG1RF genome also encodes the MafR protein (gene OG1RF_12293). In this work, we have identified the promoter of the mafR gene using several in vivo approaches. Moreover, we show that MafR influences positively the transcription of many genes on a genome-wide scale. The most significant target genes encode components of PTS-type membrane transporters, components of ABC-type membrane transporters, and proteins involved in the metabolism of carbon sources. Some of these genes were previously reported to be up-regulated during the growth of E. faecalis in blood and/or in human urine. Furthermore, we show that a mafR deletion mutant strain induces a significant lower degree of inflammation in the peritoneal cavity of mice, suggesting that enterococcal cells deficient in MafR are less virulent. Our work indicates that MafR is a global transcriptional regulator. It might facilitate the adaptation of E. faecalis to particular host niches and, therefore, contribute to its potential virulence. PMID:26793169

  16. Terrestrial Ecosystem Responses to Global Change: A Research Strategy

    SciTech Connect

    Ecosystems Working Group,

    1998-09-23

    Uncertainty about the magnitude of global change effects on terrestrial ecosystems and consequent feedbacks to the atmosphere impedes sound policy planning at regional, national, and global scales. A strategy to reduce these uncertainties must include a substantial increase in funding for large-scale ecosystem experiments and a careful prioritization of research efforts. Prioritization criteria should be based on the magnitude of potential changes in environmental properties of concern to society, including productivity; biodiversity; the storage and cycling of carbon, water, and nutrients; and sensitivity of specific ecosystems to environmental change. A research strategy is proposed that builds on existing knowledge of ecosystem responses to global change by (1) expanding the spatial and temporal scale of experimental ecosystem manipulations to include processes known to occur at large scales and over long time periods; (2) quantifying poorly understood linkages among processes through the use of experiments that manipulate multiple interacting environmental factors over a broader range of relevant conditions than did past experiments; and (3) prioritizing ecosystems for major experimental manipulations on the basis of potential positive and negative impacts on ecosystem properties and processes of intrinsic and/or utilitarian value to humans and on feedbacks of terrestrial ecosystems to the atmosphere. Models and experiments are equally important for developing process-level understanding into a predictive capability. To support both the development and testing of mechanistic ecosystem models, a two-tiered design of ecosystem experiments should be used. This design should include both (1) large-scale manipulative experiments for comprehensive testing of integrated ecosystem models and (2) multifactor, multilevel experiments for parameterization of process models across the critical range of interacting environmental factors (CO{sub 2}, temperature, water

  17. Global gene expression profiles induced by phytoestrogens in human breast cancer cells.

    PubMed

    Dip, Ramiro; Lenz, Sarah; Antignac, Jean-Philippe; Le Bizec, Bruno; Gmuender, Hans; Naegeli, Hanspeter

    2008-03-01

    The nutritional intake of phytoestrogens seems to reduce the risk of breast cancer or other neoplastic diseases. However, these epidemiological findings remain controversial because low doses of phytoestrogens, achievable through soy-rich diets, stimulate the proliferation of estrogen-sensitive tumor cells. The question of whether such phytochemicals prevent cancer or rather pose additional health hazards prompted us to examine global gene expression programs induced by a typical soy product. After extraction from soymilk, phytoestrogens were deconjugated and processed through reverse- and normal-phase cartridges. The resulting mixture was used to treat human target cells that represent a common model system for mammary tumorigenesis. Analysis of mRNA on high-density microarrays revealed that soy phytoestrogens induce a genomic fingerprint that is indistinguishable from the transcriptional effects of the endogenous hormone 17beta-estradiol. Highly congruent responses were also observed by comparing the physiologic estradiol with daidzein, coumestrol, enterolactone, or resveratrol, each representing distinct phytoestrogen structures. More diverging transcriptional profiles were generated when an inducible promoter was used to reconstitute the expression of estrogen receptor beta (ERbeta). Therefore, phytoestrogens appear to mitigate estrogenic signaling in the presence of both ER subtypes but, in late-stage cancer cells lacking ERbeta, these phytochemicals contribute to a tumor-promoting transcriptional signature.

  18. Global Responses to Potential Climate Change: A Simulation.

    ERIC Educational Resources Information Center

    Williams, Mary Louise; Mowry, George

    This interdisciplinary five-day unit provides students with an understanding of the issues in the debate on global climate change. Introductory lessons enhance understanding of the "greenhouse gases" and their sources with possible global effects of climate change. Students then roleplay negotiators from 10 nations in a simulation of the…

  19. A Critique and Response to Multicultural Visions of Globalization

    ERIC Educational Resources Information Center

    Sriraman, Bharath; Adrian, Harry

    2008-01-01

    The paper by White in this issue of Interchange contains an interesting model for a global educational perspective based on the writings of Aurobindo and Pierre Teilhard de Chardin. White proposes a foundation for this new perspective based on the synthesis of Aurobindo's and de Chardin's theories of global, social, and conscious evolution. In our…

  20. Global responses of Escherichia coli to adverse conditions determined by microarrays and FT-IR spectroscopy.

    PubMed

    Moen, Birgitte; Janbu, Astrid Oust; Langsrud, Solveig; Langsrud, Oyvind; Hobman, Jon L; Constantinidou, Chrystala; Kohler, Achim; Rudi, Knut

    2009-06-01

    The global gene expression and biomolecular composition in an Escherichia coli model strain exposed to 10 adverse conditions (sodium chloride, ethanol, glycerol, hydrochloric and acetic acid, sodium hydroxide, heat (46 degrees C), and cold (15 degrees C), as well as ethidium bromide and the disinfectant benzalkonium chloride) were determined using DNA microarrays and Fourier transform infrared (FT-IR) spectroscopy. In total, approximately 40% of all investigated genes (1682/4279 genes) significantly changed expression, compared with a nonstressed control. There were, however, only 3 genes (ygaW (unknown function), rmf (encoding a ribosomal modification factor), and ghrA (encoding a glyoxylate/hydroxypyruvate reductase)) that significantly changed expression under all conditions (not including benzalkonium chloride). The FT-IR analysis showed an increase in unsaturated fatty acids during ethanol and cold exposure, and a decrease during acid and heat exposure. Cold conditions induced changes in the carbohydrate composition of the cell, possibly related to the upregulation of outer membrane genes (glgAP and rcsA). Although some covariance was observed between the 2 data sets, principle component analysis and regression analyses revealed that the gene expression and the biomolecular responses are not well correlated in stressed populations of E. coli, underlining the importance of multiple strategies to begin to understand the effect on the whole cell.

  1. Global Transcriptional Profiles of the Copper Responses in the Cyanobacterium Synechocystis sp. PCC 6803

    PubMed Central

    Giner-Lamia, Joaquin; López-Maury, Luis; Florencio, Francisco J.

    2014-01-01

    Copper is an essential element involved in fundamental processes like respiration and photosynthesis. However, it becomes toxic at high concentration, which has forced organisms to control its cellular concentration. We have recently described a copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803, which is mediated by the two-component system, CopRS, a RND metal transport system, CopBAC and a protein of unknown function, CopM. Here, we report the transcriptional responses to copper additions at non-toxic (0.3 µM) and toxic concentrations (3 µM) in the wild type and in the copper sensitive copR mutant strain. While 0.3 µM copper slightly stimulated metabolism and promoted the exchange between cytochrome c6 and plastocyanin as soluble electron carriers, the addition of 3 µM copper catalyzed the formation of ROS, led to a general stress response and induced expression of Fe-S cluster biogenesis genes. According to this, a double mutant strain copRsufR, which expresses constitutively the sufBCDS operon, tolerated higher copper concentration than the copR mutant strain, suggesting that Fe-S clusters are direct targets of copper toxicity in Synechocystis. In addition we have also demonstrated that InrS, a nickel binding transcriptional repressor that belong to the CsoR family of transcriptional factor, was involved in heavy metal homeostasis, including copper, in Synechocystis. Finally, global gene expression analysis of the copR mutant strain suggested that CopRS only controls the expression of copMRS and copBAC operons in response to copper. PMID:25268225

  2. Global transcriptional profiles of the copper responses in the cyanobacterium Synechocystis sp. PCC 6803.

    PubMed

    Giner-Lamia, Joaquin; López-Maury, Luis; Florencio, Francisco J

    2014-01-01

    Copper is an essential element involved in fundamental processes like respiration and photosynthesis. However, it becomes toxic at high concentration, which has forced organisms to control its cellular concentration. We have recently described a copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803, which is mediated by the two-component system, CopRS, a RND metal transport system, CopBAC and a protein of unknown function, CopM. Here, we report the transcriptional responses to copper additions at non-toxic (0.3 µM) and toxic concentrations (3 µM) in the wild type and in the copper sensitive copR mutant strain. While 0.3 µM copper slightly stimulated metabolism and promoted the exchange between cytochrome c6 and plastocyanin as soluble electron carriers, the addition of 3 µM copper catalyzed the formation of ROS, led to a general stress response and induced expression of Fe-S cluster biogenesis genes. According to this, a double mutant strain copRsufR, which expresses constitutively the sufBCDS operon, tolerated higher copper concentration than the copR mutant strain, suggesting that Fe-S clusters are direct targets of copper toxicity in Synechocystis. In addition we have also demonstrated that InrS, a nickel binding transcriptional repressor that belong to the CsoR family of transcriptional factor, was involved in heavy metal homeostasis, including copper, in Synechocystis. Finally, global gene expression analysis of the copR mutant strain suggested that CopRS only controls the expression of copMRS and copBAC operons in response to copper.

  3. The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes.

    PubMed

    Reddy, Timothy E; Gertz, Jason; Crawford, Gregory E; Garabedian, Michael J; Myers, Richard M

    2012-09-01

    Glucocorticoids regulate gene expression by binding and activating the glucocorticoid receptor (GR). While ligand affinity determines the global sensitivity of the response, additional proteins act on the genome to tune sensitivity of some genes. However, the genomic extent and specificity of dose-specific glucocorticoid responses are unknown. We show that dose-specific glucocorticoid responses are extraordinarily specific at the genomic scale, able to distinctly express a single gene, the circadian rhythm gene for Period 1 (PER1), at concentrations consistent with the nighttime nadir of human cortisol. We mapped the PER1 response to a single GR binding site. The specific GR binding sequence did not impact sensitivity, and we instead attributed the response to a combination of additional transcription factors and chromatin accessibility acting in the same locus. The PER1 hypersensitive response element is conserved in the mouse, where we found similar upregulation of Per1 in pituitary cells. Targeted and transient overexpression of PER1 led to regulation of additional circadian rhythm genes hours later, suggesting that hypersensitive expression of PER1 impacts circadian gene expression. These findings show that hypersensitive GR binding occurs throughout the genome, drives targeted gene expression, and may be important to endocrine mediation of peripheral circadian rhythms.

  4. Spontaneous Facial Mimicry in Response to Dynamic Facial Expressions

    ERIC Educational Resources Information Center

    Sato, Wataru; Yoshikawa, Sakiko

    2007-01-01

    Based on previous neuroscientific evidence indicating activation of the mirror neuron system in response to dynamic facial actions, we hypothesized that facial mimicry would occur while subjects viewed dynamic facial expressions. To test this hypothesis, dynamic/static facial expressions of anger/happiness were presented using computer-morphing…

  5. Cell types differ in global coordination of splicing and proportion of highly expressed genes

    PubMed Central

    Trakhtenberg, Ephraim F.; Pho, Nam; Holton, Kristina M.; Chittenden, Thomas W.; Goldberg, Jeffrey L.; Dong, Lingsheng

    2016-01-01

    Balance in the transcriptome is regulated by coordinated synthesis and degradation of RNA molecules. Here we investigated whether mammalian cell types intrinsically differ in global coordination of gene splicing and expression levels. We analyzed RNA-seq transcriptome profiles of 8 different purified mouse cell types. We found that different cell types vary in proportion of highly expressed genes and the number of alternatively spliced transcripts expressed per gene, and that the cell types that express more variants of alternatively spliced transcripts per gene are those that have higher proportion of highly expressed genes. Cell types segregated into two clusters based on high or low proportion of highly expressed genes. Biological functions involved in negative regulation of gene expression were enriched in the group of cell types with low proportion of highly expressed genes, and biological functions involved in regulation of transcription and RNA splicing were enriched in the group of cell types with high proportion of highly expressed genes. Our findings show that cell types differ in proportion of highly expressed genes and the number of alternatively spliced transcripts expressed per gene, which represent distinct properties of the transcriptome and may reflect intrinsic differences in global coordination of synthesis, splicing, and degradation of RNA molecules. PMID:27577089

  6. The Global Economic Crisis: Impact on Sub-Saharan Africa and Global Policy Responses

    DTIC Science & Technology

    2009-08-25

    The State of Food Insecurity in the World, 2008. 20 CRS Report R40127, The Impact of Food Insecurity and Hunger on Global Health: Issues for Congress...Report R40127, The Impact of Food Insecurity and Hunger on Global Health: Issues for Congress, by Tiaji Salaam-Blyther and Charles E. Hanrahan

  7. Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics.

    PubMed

    Urano, Kaoru; Maruyama, Kyonoshin; Ogata, Yoshiyuki; Morishita, Yoshihiko; Takeda, Migiwa; Sakurai, Nozomu; Suzuki, Hideyuki; Saito, Kazuki; Shibata, Daisuke; Kobayashi, Masatomo; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

    2009-03-01

    Drought is the major environmental threat to agricultural production and distribution worldwide. Adaptation by plants to dehydration stress is a complex biological process that involves global changes in gene expression and metabolite composition. Here, using one type of functional genomics analysis, metabolomics, we characterized the metabolic phenotypes of Arabidopsis wild-type and a knockout mutant of the NCED3 gene (nc3-2) under dehydration stress. NCED3 plays a role in the dehydration-inducible biosynthesis of abscisic acid (ABA), a phytohormone that is important in the dehydration-stress response in higher plants. Metabolite profiling performed using two types of mass spectrometry (MS) systems, gas chromatography/time-of-flight MS (GC/TOF-MS) and capillary electrophoresis MS (CE-MS), revealed that accumulation of amino acids depended on ABA production, but the level of the oligosaccharide raffinose was regulated by ABA independently under dehydration stress. Metabolic network analysis showed that global metabolite-metabolite correlations occurred in dehydration-increased amino acids in wild-type, and strong correlations with raffinose were reconstructed in nc3-2. An integrated metabolome and transcriptome analysis revealed ABA-dependent transcriptional regulation of the biosynthesis of the branched-chain amino acids, saccharopine, proline and polyamine. This metabolomics analysis revealed new molecular mechanisms of dynamic metabolic networks in response to dehydration stress.

  8. Global Gene Expression Profiling of a Population Exposed to a Range of Benzene Levels

    PubMed Central

    McHale, Cliona M.; Zhang, Luoping; Lan, Qing; Vermeulen, Roel; Li, Guilan; Hubbard, Alan E.; Porter, Kristin E.; Thomas, Reuben; Portier, Christopher J.; Shen, Min; Rappaport, Stephen M.; Yin, Songnian; Smith, Martyn T.; Rothman, Nathaniel

    2011-01-01

    Background Benzene, an established cause of acute myeloid leukemia (AML), may also cause one or more lymphoid malignancies in humans. Previously, we identified genes and pathways associated with exposure to high (> 10 ppm) levels of benzene through transcriptomic analyses of blood cells from a small number of occupationally exposed workers. Objectives The goals of this study were to identify potential biomarkers of benzene exposure and/or early effects and to elucidate mechanisms relevant to risk of hematotoxicity, leukemia, and lymphoid malignancy in occupationally exposed individuals, many of whom were exposed to benzene levels < 1 ppm, the current U.S. occupational standard. Methods We analyzed global gene expression in the peripheral blood mononuclear cells of 125 workers exposed to benzene levels ranging from < 1 ppm to > 10 ppm. Study design and analysis with a mixed-effects model minimized potential confounding and experimental variability. Results We observed highly significant widespread perturbation of gene expression at all exposure levels. The AML pathway was among the pathways most significantly associated with benzene exposure. Immune response pathways were associated with most exposure levels, potentially providing biological plausibility for an association between lymphoma and benzene exposure. We identified a 16-gene expression signature associated with all levels of benzene exposure. Conclusions Our findings suggest that chronic benzene exposure, even at levels below the current U.S. occupational standard, perturbs many genes, biological processes, and pathways. These findings expand our understanding of the mechanisms by which benzene may induce hematotoxicity, leukemia, and lymphoma and reveal relevant potential biomarkers associated with a range of exposures. PMID:21147609

  9. Global expression for representing cohesive-energy curves. II

    NASA Technical Reports Server (NTRS)

    Schlosser, Herbert; Ferrante, John

    1993-01-01

    Schlosser et al. (1991) showed that the R dependence of the cohesive energy of partially ionic solids may be characterized by a two-term energy relationship consisting of a Coulomb term arising from the charge transfer, delta-Z, and a scaled universal energy function, E*(a *), which accounts for the partially covalent character of the bond and for repulsion between the atomic cores for small R; a* is a scaled length. In the paper by Schlosser et al., the normalized cohesive-energy curves of NaCl-structure alkali-halide crystals were generated with this expression. In this paper we generate the cohesive-energy curves of several families of partially ionic solids with different crystal structures and differing degrees of ionicity. These include the CsCl-structure Cs halides, and the Tl and Ag halides, which have weaker ionic bonding than the alkali halides, and which have the CsCl and NaCl structures, respectively. The cohesive-energy-curve parameters are then used to generate theoretical isothermal compression curves for the Li, Na, K, Cs, and Ag halides. We find good agreement with the available experimental compression data.

  10. Response styles in the assessment of anger expression.

    PubMed

    Gollwitzer, Mario; Eid, Michael; Jürgensen, Ralph

    2005-03-01

    This study demonstrates how mixture distribution item response models can be used to detect different response styles in the clinical assessment of anger expression. Analyses of 3 subscales of the State-Trait Anger Expression Inventory in a clinical sample of 4,497 patients revealed that there are different response styles that manifest themselves in 2- and 3-class solutions. These solutions are robust across subsamples. Response styles reflect both psychologically meaningful biases (i.e., social desirability) and nonmeaningful response category preferences. Person parameters that correct for class membership (and thus, for response styles) are computed and compared with raw scores. The implications of these results for research on clinical assessment are discussed.

  11. Integrated Transcriptomic and Proteomic Analysis of the Global Response of Synechococcus to High Light Stress*

    PubMed Central

    Xiong, Qian; Feng, Jie; Li, Si-ting; Zhang, Gui-ying; Qiao, Zhi-xian; Chen, Zhuo; Wu, Ying; Lin, Yan; Li, Tao; Ge, Feng; Zhao, Jin-dong

    2015-01-01

    Sufficient light is essential for the growth and physiological functions of photosynthetic organisms, but prolonged exposure to high light (HL) stress can cause cellular damage and ultimately result in the death of these organisms. Synechococcus sp. PCC 7002 (hereafter Synechococcus 7002) is a unicellular cyanobacterium with exceptional tolerance to HL intensities. However, the molecular mechanisms involved in HL response by Synechococcus 7002 are not well understood. Here, an integrated RNA sequencing transcriptomic and quantitative proteomic analysis was performed to investigate the cellular response to HL in Synechococcus 7002. A total of 526 transcripts and 233 proteins were identified to be differentially regulated under HL stress. Data analysis revealed major changes in mRNAs and proteins involved in the photosynthesis pathways, resistance to light-induced damage, DNA replication and repair, and energy metabolism. A set of differentially expressed mRNAs and proteins were validated by quantitative RT-PCR and Western blot, respectively. Twelve genes differentially regulated under HL stress were selected for knockout generation and growth analysis of these mutants led to the identification of key genes involved in the response of HL in Synechococcus 7002. Taken altogether, this study established a model for global response mechanisms to HL in Synechococcus 7002 and may be valuable for further studies addressing HL resistance in photosynthetic organisms. PMID:25681118

  12. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation

    SciTech Connect

    He, Z.; Zhou, A.; Baidoo, E.; He, Q.; Joachimiak, M. P.; Benke, P.; Phan, R.; Mukhopadhyay, A.; Hemme, C.L.; Huang, K.; Alm, E.J.; Fields, M.W.; Wall, J.; Stahl, D.; Hazen, T.C.; Keasling, J.D.; Arkin, A.P.; Zhou, J.

    2009-12-01

    The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by physiological, global transcriptional, and metabolite analyses. The growth of D. vulgaris was inhibited by high levels of NaCl, and the growth inhibition could be relieved by the addition of exogenous amino acids (e.g., glutamate, alanine, tryptophan) or yeast extract. Salt adaptation induced the expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). Genes involved in carbon metabolism, cell motility, and phage structures were repressed. Comparison of transcriptomic profiles of D. vulgaris responses to salt adaptation with those of salt shock (short-term NaCl exposure) showed some similarity as well as a significant difference. Metabolite assays showed that glutamate and alanine were accumulated under salt adaptation, suggesting that they may be used as osmoprotectants in D. vulgaris. A conceptual model is proposed to link the observed results to currently available knowledge for further understanding the mechanisms of D. vulgaris adaptation to elevated NaCl.

  13. Differentially Expressed Genes in Bordetella pertussis Strains Belonging to a Lineage Which Recently Spread Globally

    PubMed Central

    de Gouw, Daan; Hermans, Peter W. M.; Bootsma, Hester J.; Zomer, Aldert; Heuvelman, Kees; Diavatopoulos, Dimitri A.; Mooi, Frits R.

    2014-01-01

    Pertussis is a highly contagious, acute respiratory disease in humans caused by the Gram-negative pathogen Bordetella pertussis. Pertussis has resurged in the face of intensive vaccination and this has coincided with the emergence of strains carrying a particular allele for the pertussis toxin promoter, ptxP3, which is associated with higher levels of pertussis toxin (Ptx) production. Within 10 to 20 years, ptxP3 strains have nearly completely replaced the previously dominant ptxP1 strains resulting in a worldwide selective sweep. In order to identify B. pertussis genes associated with the selective sweep, we compared the expression of genes in ptxP1 and ptxP3 strains that are under control of the Bordetella master virulence regulatory locus (bvgASR). The BvgAS proteins comprise a two component sensory transduction system which is regulated by temperature, nicotinic acid and sulfate. By increasing the sulfate concentration, it is possible to change the phase of B. pertussis from virulent to avirulent. Until recently, the only distinctive phenotype of ptxP3 strains was a higher Ptx production. Here we identify additional phenotypic differences between ptxP1 and ptxP3 strains which may have contributed to its global spread by comparing global transcriptional responses under sulfate-modulating conditions. We show that ptxP3 strains are less sensitive to sulfate-mediated gene suppression, resulting in an increased production of the vaccine antigens pertactin (Prn) and Ptx and a number of other virulence genes, including a type III secretion toxin, Vag8, a protein involved in complement resistance, and lpxE involved in lipid A modification. Furthermore, enhanced expression of the vaccine antigens Ptx and Prn by ptxP3 strains was confirmed at the protein level. Identification of genes differentially expressed between ptxP1 and ptxP3 strains may elucidate how B. pertussis has adapted to vaccination and allow the improvement of pertussis vaccines by identifying novel

  14. The Global Economic Crisis: Impact on Sub-Saharan Africa and Global Policy Responses

    DTIC Science & Technology

    2009-10-19

    Insecurity in the World, 2008. 21 CRS Report R40127, The Impact of Food Insecurity and Hunger on Global Health: Issues for Congress, by Tiaji Salaam...Poverty,” July 10, 2009. 106 See CRS Report R40127, The Impact of Food Insecurity and Hunger on Global Health: Issues for Congress, by Tiaji Salaam...Strengthening Regional Economic Integration for Africa’s Development, June 25, 2009. 20 See e.g. Food and Agriculture Organization (FAO), The State of Food

  15. The Global Economic Crisis: Impact on Sub-Saharan Africa and Global Policy Responses

    DTIC Science & Technology

    2010-04-06

    Insecurity in the World, 2008. 29 CRS Report R40127, The Impact of Food Insecurity and Hunger on Global Health: Issues for Congress, by Tiaji Salaam-Blyther...Development to Reduce Hunger and Poverty,” July 10, 2009. 114 See CRS Report R40127, The Impact of Food Insecurity and Hunger on Global Health: Issues for...Regional Economic Integration for Africa’s Development, June 25, 2009. 28 See e.g. Food and Agriculture Organization (FAO), The State of Food

  16. GLUT-1 expression and response to chemoradiotherapy in rectal cancer.

    PubMed

    Brophy, Sarah; Sheehan, Katherine M; McNamara, Deborah A; Deasy, Joseph; Bouchier-Hayes, David J; Kay, Elaine W

    2009-12-15

    Preoperative chemoradiotherapy is used in locally advanced rectal cancer to reduce local recurrence and improve operability, however a proportion of tumors do not undergo significant regression. Identification of predictive markers of response to chemoradiotherapy would improve patient selection and may allow response modification by targeting of specific pathways. The aim of this study was to determine whether expression of glucose transporter-1 (GLUT-1) and p53 in pretreatment rectal cancer biopsies was predictive of tumor response to chemoradiotherapy. Immunohistochemical staining for GLUT-1 and p53 was performed on 69 pretreatment biopsies and compared to tumor response in the resected specimen as determined by the tumor regression grade (TRG) scoring system. GLUT-1 expression was significantly associated with reduced response to chemoradiotherapy and increasing GLUT expression correlated with poorer response (p=0.02). GLUT-1 negative tumors had a 70% probability of good response (TRG3/4) compared to a 31% probability of good response in GLUT-1 positive tumors. GLUT-1 may be a useful predictive marker of response to chemoradiotherapy in rectal cancer.

  17. Understanding gene expression in coronary artery disease through global profiling, network analysis and independent validation of key candidate genes.

    PubMed

    Arvind, Prathima; Jayashree, Shanker; Jambunathan, Srikarthika; Nair, Jiny; Kakkar, Vijay V

    2015-12-01

    Molecular mechanism underlying the patho-physiology of coronary artery disease (CAD) is complex. We used global expression profiling combined with analysis of biological network to dissect out potential genes and pathways associated with CAD in a representative case-control Asian Indian cohort. We initially performed blood transcriptomics profiling in 20 subjects, including 10 CAD patients and 10 healthy controls on the Agilent microarray platform. Data was analysed with Gene Spring Gx12.5, followed by network analysis using David v 6.7 and Reactome databases. The most significant differentially expressed genes from microarray were independently validated by real time PCR in 97 cases and 97 controls. A total of 190 gene transcripts showed significant differential expression (fold change>2,P<0.05) between the cases and the controls of which 142 genes were upregulated and 48 genes were downregulated. Genes associated with inflammation, immune response, cell regulation, proliferation and apoptotic pathways were enriched, while inflammatory and immune response genes were displayed as hubs in the network, having greater number of interactions with the neighbouring genes. Expression of EGR1/2/3, IL8, CXCL1, PTGS2, CD69, IFNG, FASLG, CCL4, CDC42, DDX58, NFKBID and NR4A2 genes were independently validated; EGR1/2/3 and IL8 showed >8-fold higher expression in cases relative to the controls implying their important role in CAD. In conclusion, global gene expression profiling combined with network analysis can help in identifying key genes and pathways for CAD.

  18. Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature

    PubMed Central

    Aguado-Urda, Mónica; Gibello, Alicia; Blanco, M. del Mar; Fernández-Garayzábal, José F.; López-Alonso, Victoria; López-Campos, Guillermo H.

    2013-01-01

    Lactococcus garvieae is an important fish and an opportunistic human pathogen. The genomic sequences of several L. garvieae strains have been recently published, opening the possibility of global studies on the biology of this pathogen. In this study, a whole genome DNA microarray of two strains of L. garvieae was designed and validated. This DNA microarray was used to investigate the effects of growth temperature (18°C and 37°C) on the transcriptome of two clinical strains of L. garvieae that were isolated from fish (Lg8831) and from a human case of septicemia (Lg21881). The transcriptome profiles evidenced a strain-specific response to temperature, which was more evident at 18°C. Among the most significant findings, Lg8831 was found to up-regulate at 18°C several genes encoding different cold-shock and cold-induced proteins involved in an efficient adaptive response of this strain to low-temperature conditions. Another relevant result was the description, for the first time, of respiratory metabolism in L. garvieae, whose gene expression regulation was temperature-dependent in Lg21881. This study provides new insights about how environmental factors such as temperature can affect L. garvieae gene expression. These data could improve our understanding of the regulatory networks and adaptive biology of this important pathogen. PMID:24223997

  19. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure.

    PubMed

    Lim, Jia Chun; Thevarajoo, Suganthi; Selvaratnam, Chitra; Goh, Kian Mau; Shamsir, Mohd Shahir; Ibrahim, Zaharah; Chong, Chun Shiong

    2017-02-01

    Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L(-1) of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.

  20. Carbon Monoxide Gas Is Not Inert, but Global, in Its Consequences for Bacterial Gene Expression, Iron Acquisition, and Antibiotic Resistance

    PubMed Central

    Wareham, Lauren K.; Begg, Ronald; Jesse, Helen E.; van Beilen, Johan W.A.; Ali, Salar; Svistunenko, Dimitri; McLean, Samantha; Hellingwerf, Klaas J.; Sanguinetti, Guido

    2016-01-01

    Abstract Aims: Carbon monoxide is a respiratory poison and gaseous signaling molecule. Although CO-releasing molecules (CORMs) deliver CO with temporal and spatial specificity in mammals, and are proven antimicrobial agents, we do not understand the modes of CO toxicity. Our aim was to explore the impact of CO gas per se, without intervention of CORMs, on bacterial physiology and gene expression. Results: We used tightly controlled chemostat conditions and integrated transcriptomic datasets with statistical modeling to reveal the global effects of CO. CO is known to inhibit bacterial respiration, and we found expression of genes encoding energy-transducing pathways to be significantly affected via the global regulators, Fnr, Arc, and PdhR. Aerobically, ArcA—the response regulator—is transiently phosphorylated and pyruvate accumulates, mimicking anaerobiosis. Genes implicated in iron acquisition, and the metabolism of sulfur amino acids and arginine, are all perturbed. The global iron-related changes, confirmed by modulation of activity of the transcription factor Fur, may underlie enhanced siderophore excretion, diminished intracellular iron pools, and the sensitivity of CO-challenged bacteria to metal chelators. Although CO gas (unlike H2S and NO) offers little protection from antibiotics, a ruthenium CORM is a potent adjuvant of antibiotic activity. Innovation: This is the first detailed exploration of global bacterial responses to CO, revealing unexpected targets with implications for employing CORMs therapeutically. Conclusion: This work reveals the complexity of bacterial responses to CO and provides a basis for understanding the impacts of CO from CORMs, heme oxygenase activity, or environmental sources. Antioxid. Redox Signal. 24, 1013–1028. PMID:26907100

  1. Global and regional air quality responses to regional CO reductions

    NASA Astrophysics Data System (ADS)

    Fry, M. M.; Adelman, Z.; Dolwick, P.; Jang, C.; West, J. J.

    2011-12-01

    Ozone (O3) precursor emissions influence global and regional air quality and climate through changes in the tropospheric concentrations of O3, methane (CH4), and aerosols. Here we examine the influence of regional carbon monoxide (CO) emissions on air quality by simulating 50% reductions in anthropogenic CO emissions from 10 world regions (Australia/New Zealand, Southeast Asia, East Asia, India, Southern Africa, Northern Africa/Middle East, Former Soviet Union, Europe, South America, and North America), using the global chemical transport model MOZART-4. The IPCC AR5 Representative Concentration Pathway 8.5 (RCP 8.5) emissions inventory for 2005 and global meteorology from the Goddard Earth Observing System Model, version 5 (GEOS-5) for 2004-2005 are used as inputs to MOZART-4, run at 1.9 x 2.5 degree horizontal resolution. Base case global air quality is first simulated for the year 2005, and the resulting distributions of tropospheric O3 and related species are compared with observations. Then CO emission reductions from each of the 10 regions are simulated individually. We quantify global and regional changes in O3 and PM2.5 at the surface and within the troposphere, including the influence of each regional reduction on long-term O3 concentrations via CH4 and the long-range transport of O3 and CO. This analysis shows the sensitivity of global and regional air quality to anthropogenic CO emissions from many world regions, in contrast to previous studies of only a few regions. Beyond this study, these simulations will be used to estimate the net radiative forcing due to CO emission reductions from these world regions.

  2. Global transcriptome analysis of the heat shock response of the deep-sea bacterium Shewanella piezotolerans WP3.

    PubMed

    Jian, Huahua; Li, Shengkang; Feng, Xiaoyuan; Xiao, Xiang

    2016-12-01

    For microorganisms, heat shock is a major stressful condition. Heat shock is characterized by sudden temperature increases that damage important protein structures and interfere with essential cellular functions. In this study, global gene expression patterns of the deep-sea bacterium Shewanella piezotolerans WP3 in response to heat shock were studied by DNA microarray analysis. Overall, 438, 573, and 627 genes were found to be differentially expressed after heat shock for 30, 60, and 90min, respectively. Functional classification of differentially transcribed genes was performed using the Clusters of Orthologous Groups of Proteins database. Additionally, 361 genes were identified as common differentially expressed genes. These genes may comprise the core genes responsible for coping with heat shock stress of WP3. Moreover, comparative analysis of gene expression pattern in WP3 and other bacteria indicated the presence of different adaptive strategies. These data represent the first transcriptome resource for the response of this deep-sea bacterium to high-temperature stress. This study contributes to the understanding of the global adaptation mechanisms of benthic bacteria toward environmental stresses.

  3. Gene Expression Response of Mice after a Single Dose of 137Cs as an Internal Emitter

    PubMed Central

    Paul, Sunirmal; Ghandhi, Shanaz A.; Weber, Waylon; Doyle-Eisele, Melanie; Melo, Dunstana; Guilmette, Raymond; Amundson, Sally A.

    2014-01-01

    Cesium-137 is a radionuclide of concern in fallout from reactor accidents or nuclear detonations. When ingested or inhaled, it can expose the entire body for an extended period of time, potentially contributing to serious health consequences ranging from acute radiation syndrome to increased cancer risks. To identify changes in gene expression that may be informative for detecting such exposure, and to begin examining the molecular responses involved, we have profiled global gene expression in blood of male C57BL/6 mice injected with 137CsCl. We extracted RNA from the blood of control or 137CsCl-injected mice at 2, 3, 5, 20 or 30 days after exposure. Gene expression was measured using Agilent Whole Mouse Genome Microarrays, and the data was analyzed using BRB-ArrayTools. Between 466–6,213 genes were differentially expressed, depending on the time after 137Cs administration. At early times (2–3 days), the majority of responsive genes were expressed above control levels, while at later times (20–30 days) most responding genes were expressed below control levels. Numerous genes were overexpressed by day 2 or 3, and then underexpressed by day 20 or 30, including many Tp53-regulated genes. The same pattern was seen among significantly enriched gene ontology categories, including those related to nucleotide binding, protein localization and modification, actin and the cytoskeleton, and in the integrin signaling canonical pathway. We compared the expression of several genes three days after 137CsCl injection and three days after an acute external gamma-ray exposure, and found that the internal exposure appeared to produce a more sustained response. Many common radiation-responsive genes are altered by internally administered 137Cs, but the gene expression pattern resulting from continued irradiation at a decreasing dose rate is extremely complex, and appears to involve a late reversal of much of the initial response. PMID:25162453

  4. Global gene expression analysis of peripheral blood mononuclear cells in rhesus monkey infants with CA16 infection-induced HFMD.

    PubMed

    Song, Jie; Hu, Yajie; Hu, Yunguang; Wang, Jingjing; Zhang, Xiaolong; Wang, Lichun; Guo, Lei; Wang, Yancui; Ning, Ruotong; Liao, Yun; Zhang, Ying; Zheng, Huiwen; Shi, Haijing; He, Zhanlong; Li, Qihan; Liu, Longding

    2016-03-02

    Coxsackievirus A16 (CA16) is a dominant pathogen that results in hand, foot, and mouth disease and causes outbreaks worldwide, particularly in the Asia-Pacific region. However, the underlying molecular mechanisms remain unclear. Our previous study has demonstrated that the basic CA16 pathogenic process was successfully mimicked in rhesus monkey infant. The present study focused on the global gene expression changes in peripheral blood mononuclear cells of rhesus monkey infants with hand, foot, and mouth disease induced by CA16 infection at different time points. Genome-wide expression analysis was performed with Agilent whole-genome microarrays and established bioinformatics tools. Nine hundred and forty-eight significant differentially expressed genes that were associated with 5 gene ontology categories, including cell communication, cell cycle, immune system process, regulation of transcription and metabolic process were identified. Subsequently, the mapping of genes related to the immune system process by PANTHER pathway analysis revealed the predominance of inflammation mediated by chemokine and cytokine signaling pathways and the interleukin signaling pathway. Ultimately, co-expressed genes and their networks were analyzed. The results revealed the gene expression profile of the immune system in response to CA16 in rhesus monkey infants and suggested that such an immune response was generated as a result of the positive mobilization of the immune system. This initial microarray study will provide insights into the molecular mechanism of CA16 infection and will facilitate the identification of biomarkers for the evaluation of vaccines against this virus.

  5. Marek's disease virus-induced immunosuppression: array analysis of chicken immune response gene expression profiling.

    PubMed

    Heidari, Mohammad; Sarson, Aimie J; Huebner, Marianne; Sharif, Shayan; Kireev, Dmitry; Zhou, Huaijun

    2010-06-01

    Marek's disease (MD) is a lymphoproliferative disease of chickens induced by a highly cell-associated oncogenic alpha-herpesvirus, Marek's disease virus (MDV). MDV replicates in chicken lymphocytes and establishes a latency infection within CD4(+) T cells. Host-virus interaction, immune responses to infection, and transcriptional profiling of chicken gene expression in MD are poorly understood. In this study we conducted a global host gene expression analysis in the splenocytes of MDV-infected chickens using oligonucleotide-based Affymetrix GeneChip Chicken Genome Arrays. These arrays contain probes for more than 32,000 chicken transcripts and most of the known MDV genes and open reading frames. Two-week-old MD-susceptible chickens were inoculated with an oncogenic strain of MDV, and spleen samples were collected 5 and 15 days post-infection (dpi) for RNA isolation and microarray analysis. Array results displayed a significant differential pattern of immune response transcriptome between the two phases of MDV infection. The expression levels of more than 22 immune-response and related genes were downregulated, while the expression levels of at least 58 genes were increased at 5 dpi (cytolytic infection), compared to age-matched control birds. In comparison, out of 73 immune-response and related genes, 67 genes were downregulated, with only 6 genes having higher expression levels at 15 dpi (latency infection). Cytokines, chemokines, MHC molecules and related receptors, and adhesion molecules were among the many MDV-induced downregulated genes that are critical for an effective antiviral immune response. In addition, several apoptosis-associated genes were decreased in expression during latent infection, suggesting an MDV-induced blocking of initiation or progression of programmed cell death processes. These chicken arrays are valuable tools in understanding the molecular mechanisms behind viral pathogenesis and chicken gene expression patterns, and associated

  6. National Collections, Global Collecting: The Responsibilities of Librarians as Collectors.

    ERIC Educational Resources Information Center

    Prochaska, Alice

    2002-01-01

    Shared knowledge, while not a new concept, is receiving new emphasis in a global society. National and other research libraries can fruitfully collaborate to maximize the public value of their materials. The partnership of the British Library with the Harry Ransom Center (University of Texas at Austin) is one example of this. (Author)

  7. Global Information Justice: Rights, Responsibilities, and Caring Connections.

    ERIC Educational Resources Information Center

    Smith, Martha

    2001-01-01

    Explains the concept of global information justice and describes it as an ethical ideal, as an organizing principle for a model for analysis, and as a direction for policy making. Discusses the use of new technologies; access to technology; ownership; privacy; security; community; and the Universal Declaration of Human Rights. (Author/LRW)

  8. Interleukin-6 receptor expression and localization after transient global ischemia in gerbil hippocampus.

    PubMed

    Vollenweider, Florence; Herrmann, Martina; Otten, Uwe; Nitsch, Cordula

    2003-04-24

    Ischemia results in increased interleukin-6 (IL-6) expression in the brain. To prove a connection between IL-6 upregulation and IL-6 receptor (IL-6R) expression following ischemia, we analyzed cell-type specific expression changes of IL-6R using transient global ischemia in the gerbil as a model. In sham operated animals, IL-6R mRNA and protein were mainly detected in hippocampal pyramidal cells and interneurons. After ischemia, IL-6R was expressed in neurons but there was no increase during the peak IL-6 expression. Neuronal IL-6R mRNA and protein decreased in parallel with pyramidal cell death, starting 2 days after ischemia. Double-labeling experiments revealed that in postischemic hippocampus IL-6R was not present in GFAP-reactive astrocytes but that the surviving parvalbumin containing interneurons expressed IL-6R mRNA.

  9. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato

    PubMed Central

    Wang, Guixiang; Weng, Lin; Li, Meng; Xiao, Han

    2017-01-01

    Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops. PMID:28257093

  10. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato.

    PubMed

    Wang, Guixiang; Weng, Lin; Li, Meng; Xiao, Han

    2017-03-02

    Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.

  11. Global gene expression in channel catfish after vaccination with an attenuated Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To understand the global gene expression in channel catfish after immersion vaccination with an attenuated Edwardsiella ictaluri (AquaVac ESCTM), microarray analysis of 65,182 UniGene transcripts were performed. With a filter of false-discovery rate less than 0.05 and fold change greater than 2, a t...

  12. Edwardsiella tarda Hfq: impact on host infection and global protein expression

    PubMed Central

    2014-01-01

    Hfq is an RNA-binding protein that plays an important role in many cellular processes. In this study, we examined the biological effect of the Hfq of Edwardsiella tarda, a severe fish pathogen with a broad host range that includes humans. To facilitate the study, a markerless hfq in-frame deletion wild type, TXhfq, was constructed. Compared to the wild type TX01, TXhfq exhibited (i) retarded planktonic and biofilm growth, (ii) decreased resistance against oxidative stress, (iii) attenuated overall virulence and tissue dissemination and colonization capacity, (iv) impaired ability to replicate in host macrophages and to block host immune response. Introduction of a trans-expressed hfq gene into TXhfq restored the lost virulence of TXhfq. To identify potential Hfq targets, comparative global proteomic analysis was conducted, which revealed that 20 proteins belonging to different functional categories were differentially expressed in TXhfq and TX01. Quantitative real time RT-PCR analysis showed that the mRNA levels of two thirds of the genes of the identified proteins were consistent with the proteomic results. Since TXhfq is dramatically attenuated in virulence, we further examined its potential as a naturally delivered vaccine administered via the immersion route in a flounder model. The results showed that TXhfq induced effective protection against lethal E. tarda challenge. Taken together, our study indicated that Hfq is required for the normal operation of E. tarda in multiple aspects, and that Hfq probably exerts a regulatory effect on a wide range of target genes at both transcription and post-transcription levels. PMID:24568370

  13. A global response to a global problem: the epidemic of overnutrition.

    PubMed Central

    Chopra, Mickey; Galbraith, Sarah; Darnton-Hill, Ian

    2002-01-01

    It is estimated that by 2020 two-thirds of the global burden of disease will be attributable to chronic noncommunicable diseases, most of them strongly associated with diet. The nutrition transition towards refined foods, foods of animal origin, and increased fats plays a major role in the current global epidemics of obesity, diabetes and cardiovascular diseases, among other noncommunicable conditions. Sedentary lifestyles and the use of tobacco are also significant risk factors. The epidemics cannot be ended simply by encouraging people to reduce their risk factors and adopt healthier lifestyles, although such encouragement is undoubtedly beneficial if the targeted people can respond. Unfortunately, increasingly obesogenic environments, reinforced by many of the cultural changes associated with globalization, make even the adoption of healthy lifestyles, especially by children and adolescents, more and more difficult. The present paper examines some possible mechanisms for, and WHO's role in, the development of a coordinated global strategy on diet, physical activity and health. The situation presents many countries with unmanageable costs. At the same time there are often continuing problems of undernutrition. A concerted multisectoral approach, involving the use of policy, education and trade mechanisms, is necessary to address these matters. PMID:12571723

  14. Global Gene Expression Profiling in PAI-1 Knockout Murine Heart and Kidney: Molecular Basis of Cardiac-Selective Fibrosis

    PubMed Central

    Ghosh, Asish K.; Murphy, Sheila B.; Kishore, Raj; Vaughan, Douglas E.

    2013-01-01

    Fibrosis is defined as an abnormal matrix remodeling due to excessive synthesis and accumulation of extracellular matrix proteins in tissues during wound healing or in response to chemical, mechanical and immunological stresses. At present, there is no effective therapy for organ fibrosis. Previous studies demonstrated that aged plasminogen activator inhibitor-1(PAI-1) knockout mice develop spontaneously cardiac-selective fibrosis without affecting any other organs. We hypothesized that differential expressions of profibrotic and antifibrotic genes in PAI-1 knockout hearts and unaffected organs lead to cardiac selective fibrosis. In order to address this prediction, we have used a genome-wide gene expression profiling of transcripts derived from aged PAI-1 knockout hearts and kidneys. The variations of global gene expression profiling were compared within four groups: wildtype heart vs. knockout heart; wildtype kidney vs. knockout kidney; knockout heart vs. knockout kidney and wildtype heart vs. wildtype kidney. Analysis of illumina-based microarray data revealed that several genes involved in different biological processes such as immune system processing, response to stress, cytokine signaling, cell proliferation, adhesion, migration, matrix organization and transcriptional regulation were affected in hearts and kidneys by the absence of PAI-1, a potent inhibitor of urokinase and tissue-type plasminogen activator. Importantly, the expressions of a number of genes, involved in profibrotic pathways including Ankrd1, Pi16, Egr1, Scx, Timp1, Timp2, Klf6, Loxl1 and Klotho, were deregulated in PAI-1 knockout hearts compared to wildtype hearts and PAI-1 knockout kidneys. While the levels of Ankrd1, Pi16 and Timp1 proteins were elevated during EndMT, the level of Timp4 protein was decreased. To our knowledge, this is the first comprehensive report on the influence of PAI-1 on global gene expression profiling in the heart and kidney and its implication in fibrogenesis and

  15. Sustainable water future with global implications: everyone's responsibility.

    PubMed

    Kuylenstierna, J L; Bjorklund, G; Najlis, P

    1997-01-01

    The current use and management of freshwater is not sustainable in many countries and regions of the world. If current trends are maintained, about two-thirds of the world's population will face moderate to severe water stress by 2025 compared to one-third at present. This water stress will hamper economic and social development unless action is taken to deal with the emerging problems. The Comprehensive Assessment of the Freshwater Resources of the World, prepared by the UN and the Stockholm Environment Institute, calls for immediate action to prevent further deterioration of freshwater resources. Although most problems related to water quantity and quality require national and regional solutions, only a global commitment can achieve the necessary agreement on principles, as well as financial means to attain sustainability. Due to the central and integrated role played by water in human activities, any measures taken need to incorporate a wide range of social, ecological and economic factors and needs. The Assessment thus addresses the many issues related to freshwater use, such as integrated land and water management at the watershed level, global food security, water supply and sanitation, ecosystem requirements, pollution, strengthening of major groups, and national water resource assessment capabilities and monitoring networks. Governments are urged to work towards a consensus regarding global principles and guidelines for integrated water management, and towards their implementation in local and regional water management situations. The alternative development options available to countries facing water stress, or the risk thereof, needs to be considered in all aspects of development planning.

  16. Global changes in biogeochemical cycles in response to human activities

    NASA Technical Reports Server (NTRS)

    Moore, Berrien, III; Melillo, Jerry

    1994-01-01

    The main objective of our research was to characterize biogeochemical cycles at continental and global scales in both terrestrial and aquatic ecosystems. This characterization applied to both natural ecosystems and those disturbed by human activity. The primary elements of interest were carbon and nitrogen and the analysis sought to quantify standing stocks and dynamic cycling processes. The translocation of major nutrients from the terrestrial landscape to the atmosphere (via trace gases) and to fluvial systems (via leaching, erosional losses, and point source pollution) were of particular importance to this study. Our aim was to develop the first generation of Earth System Models. Our research was organized around the construction and testing of component biogeochemical models which treated terrestrial ecosystem processes, aquatic nutrient transport through drainage basins, and trace gas exchanges at the continental and global scale. A suite of three complementary models were defined within this construct. The models were organized to operate at a 1/2 degree latitude by longitude level of spatial resolution and to execute at a monthly time step. This discretization afforded us the opportunity to understand the dynamics of the biosphere down to subregional scales, while simultaneously placing these dynamics into a global context.

  17. Expression of human hyaluronan synthases in response to external stimuli.

    PubMed Central

    Jacobson, A; Brinck, J; Briskin, M J; Spicer, A P; Heldin, P

    2000-01-01

    In the present study we have investigated the expression of mRNAs for hyaluronan synthase isoforms (HAS1, HAS2 and HAS3) in different cells in response to various stimuli. Human mesothelial cells, which synthesize large amounts of hyaluronan, express mRNAs encoding all three HAS isoforms, whereas their transformed counterparts, mesothelioma cells, which produce only minute amounts of hyaluronan, express only HAS3 mRNA. Human lung fibroblasts and the glioma cell line U-118 MG express only the HAS2 and HAS3 genes. The expression of the transcripts was higher in subconfluent than in confluent cultures and was well correlated with the production of hyaluronan by the cells. Stimulation of mesothelial cells with platelet-derived growth factor-BB induced an up-regulation of mRNA for HAS2 to a maximum after 6 h of stimulation; HAS1 and HAS3 genes were only induced slightly. Transforming growth factor-beta1 reduced HAS2 mRNA slightly, and hydrocortisone reduced it strongly, within 6 h of stimulation in mesothelial cell cultures but did not significantly affect the expression of mRNAs for HAS1 and HAS3. Induction of HAS1 and HAS2 protein levels in response to the stimuli above correlated with HAS transcript levels. Thus the expression of the three HAS isoforms is more prominent in growing cells than in resting cells and is differentially regulated by various stimuli suggesting distinct functional roles of the three proteins. PMID:10794710

  18. Progress in Global Surveillance and Response Capacity 10 Years after Severe Acute Respiratory Syndrome

    PubMed Central

    Braden, Christopher R.; Dowell, Scott F.; Jernigan, Daniel B.

    2013-01-01

    Ten years have elapsed since the World Health Organization issued its first global alert for an unexplained illness named severe acute respiratory syndrome (SARS). The anniversary provides an opportunity to reflect on the international response to this new global microbial threat. While global surveillance and response capacity for public health threats have been strengthened, critical gaps remain. Of 194 World Health Organization member states that signed on to the International Health Regulations (2005), <20% had achieved compliance with the core capacities required by the deadline in June 2012. Lessons learned from the global SARS outbreak highlight the need to avoid complacency, strengthen efforts to improve global capacity to address the next pandemic using all available 21st century tools, and support research to develop new treatment options, countermeasures, and insights while striving to address the global inequities that are the root cause of many of these challenges. PMID:23731871

  19. Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning.

    PubMed

    Smith, Sadie L; Everts, Robin E; Tian, X Cindy; Du, Fuliang; Sung, Li-Ying; Rodriguez-Zas, Sandra L; Jeong, Byeong-Seon; Renard, Jean-Paul; Lewin, Harris A; Yang, Xiangzhong

    2005-12-06

    Nuclear transfer (NT) has potential applications in agriculture and biomedicine, but the technology is hindered by low efficiency. Global gene expression analysis of clones is important for the comprehensive study of nuclear reprogramming. Here, we compared global gene expression profiles of individual bovine NT blastocysts with their somatic donor cells and fertilized control embryos using cDNA microarray technology. The NT embryos' gene expression profiles were drastically different from those of their donor cells and closely resembled those of the naturally fertilized embryos. Our findings demonstrate that the NT embryos have undergone significant nuclear reprogramming by the blastocyst stage; however, problems may occur during redifferentiation for tissue genesis and organogenesis, and small reprogramming errors may be magnified downstream in development.

  20. Microtubule-Associated Protein Expression and Predicting Taxane Response

    DTIC Science & Technology

    2009-10-01

    taxanes. Our results indicate that MAP- tau functions as a prognostic factor in both the Yale cohort and the TAX 307 cohort with high MAP- tau ...expression associated with longer overall survival and TTP. Tau does NOT behave as a predictor of response to taxane-based chemotherapy since differences...between low and high MAP- tau groups by treatment arm and response rate were not observed in the TAX 307 clinical trial cohort. Our data supports the

  1. Protein-energy malnutrition alters hippocampal plasticity-associated protein expression following global ischemia in the gerbil.

    PubMed

    Prosser-Loose, Erin J; Verge, Valerie M K; Cayabyab, Francisco S; Paterson, Phyllis G

    2010-11-01

    Previously it has been demonstrated that protein-energy malnutrition (PEM) impairs habituation in the open field test following global ischemia. The present study examined the hypothesis that PEM exerts some of its deleterious effects on functional outcome by altering the post-ischemic expression of the plasticity-associated genes brain-derived neurotrophic factor (BDNF), its receptor tropomyosin-related kinase B (trkB), and growth-associated protein-43 (GAP-43). Male, Mongolian gerbils (11-12 wk) were randomized to either control diet (12.5% protein) or PEM (2% protein) for 4 wk, and then underwent 5 min bilateral common carotid artery occlusion or sham surgery. Tympanic temperature was maintained at 36.5 ± 0.5°C during surgery. Brains collected at 1, 3 and 7 d post-surgery were processed by in-situ hybridization or immunofluorescence. BDNF and trkB mRNA expression was increased in hippocampal CA1 neurons after ischemia at all time points and was not significantly influenced by diet. However, increased trkB protein expression after ischemia was exacerbated by PEM at 7 d in the CA1 region. Post-ischemic GAP-43 protein increased at 3 and 7 d in the CA1 region, and PEM intensified this response and extended it to the CA3 and hilar regions. PEM exerted these effects without exacerbating CA1 neuron loss caused by global ischemia. The findings suggest that PEM increases the stress response and/or hyper-excitability in the hippocampus after global ischemia. Nutritional care appears to have robust effects on plasticity mechanisms important to recovery after brain ischemia.

  2. MGMT expression predicts response to temozolomide in pancreatic neuroendocrine tumors.

    PubMed

    Cros, J; Hentic, O; Rebours, V; Zappa, M; Gille, N; Theou-Anton, N; Vernerey, D; Maire, F; Lévy, P; Bedossa, P; Paradis, V; Hammel, P; Ruszniewski, P; Couvelard, A

    2016-08-01

    Temozolomide (TEM) showed encouraging results in well-differentiated pancreatic neuroendocrine tumors (WDPNETs). Low O(6)-methylguanine-DNA methyltransferase (MGMT) expression and MGMT promoter methylation within tumors correlate with a better outcome under TEM-based chemotherapy in glioblastoma. We aimed to assess whether MGMT expression and MGMT promoter methylation could help predict the efficacy of TEM-based chemotherapy in patients with WDPNET. Consecutive patients with progressive WDPNET and/or liver involvement over 50% who received TEM between 2006 and 2012 were retrospectively studied. Tumor response was assessed according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 guidelines. Nuclear expression of MGMT was assessed by immunochemistry (H-score, 0-300) and MGMT promoter methylation by pyrosequencing. Forty-three patients (21 men, 58years (27-84)) with grade 1 WDPNET (n=6) or 2 (n=36) were analyzed. Objective response, stable disease, and progression rates were seen in 17 patients (39.5%), 18 patients (41.9%), and 8 patients (18.6%), respectively. Low MGMT expression (≤50) was associated with radiological objective response (P=0.04) and better progression-free survival (PFS) (HR=0.35 (0.15-0.81), P=0.01). Disease control rate at 18months of treatment remained satisfying with an MGMT score up to 100 (74%) but dropped with a higher expression. High MGMT promoter methylation was associated with a low MGMT expression and longer PFS (HR=0.37 (0.29-1.08), P=0.05). Low MGMT score (≤50) appears to predict an objective tumor response, whereas an intermediate MGMT score (50-100) seems to be associated with prolonged stable disease.

  3. Chemopreventive agents alters global gene expression pattern: predicting their mode of action and targets.

    PubMed

    Narayanan, Bhagavathi A

    2006-12-01

    Chemoprevention has the potential to be a major component of colon, breast, prostate and lung cancer control. Epidemiological, experimental, and clinical studies provide evidence that antioxidants, anti-inflammatory agents, n-3 polyunsaturated fatty acids and several other phytochemicals possess unique modes of action against cancer growth. However, the mode of action of several of these agents at the gene transcription level is not completely understood. Completion of the human genome sequence and the advent of DNA microarrays using cDNAs enhanced the detection and identification of hundreds of differentially expressed genes in response to anticancer drugs or chemopreventive agents. In this review, we are presenting an extensive analysis of the key findings from studies using potential chemopreventive agents on global gene expression patterns, which lead to the identification of cancer drug targets. The summary of the study reports discussed in this review explains the extent of gene alterations mediated by more than 20 compounds including antioxidants, fatty acids, NSAIDs, phytochemicals, retinoids, selenium, vitamins, aromatase inhibitor, lovastatin, oltipraz, salvicine, and zinc. The findings from these studies further reveal the utility of DNA microarray in characterizing and quantifying the differentially expressed genes that are possibly reprogrammed by the above agents against colon, breast, prostate, lung, liver, pancreatic and other cancer types. Phenolic antioxidant resveratrol found in berries and grapes inhibits the formation of prostate tumors by acting on the regulatory genes such as p53 while activating a cascade of genes involved in cell cycle and apoptosis including p300, Apaf-1, cdk inhibitor p21, p57 (KIP2), p53 induced Pig 7, Pig 8, Pig 10, cyclin D, DNA fragmentation factor 45. The group of genes significantly altered by selenium includes cyclin D1, cdk5, cdk4, cdk2, cdc25A and GADD 153. Vitamine D shows impact on p21(Waf1/Cip1) p27 cyclin B

  4. A Conceptual Framework for Responsive Global Engagement in Communication Sciences and Disorders

    ERIC Educational Resources Information Center

    Hyter, Yvette D.

    2014-01-01

    The field of speech-language pathology needs a conceptual framework to guide the provision of services in a globalized world. Proposed in this article is a conceptual framework designed to facilitate responsive global engagement for professionals such as speech-language pathologists, who are increasingly serving diverse populations around the…

  5. Trends in TIMSS Responses over Time: Evidence of Global Forces in Education?

    ERIC Educational Resources Information Center

    Rutkowski, Leslie; Rutkowski, David

    2009-01-01

    In this article, the influence of global processes on international mathematics curricula as evidenced by item responses to 3 Trends in International Mathematics and Science Study (TIMSS) administrations (1995, 1999, and 2003) is considered. Based on Dale's (2000) argument, we set out to test 2 plausible impacts of global processes on education.…

  6. Globalism and Tribalism and the State of the Discipline: A Response to Mary Snell-Hornby.

    ERIC Educational Resources Information Center

    Salama-Carr, Myriam

    1999-01-01

    This response to an article on the effect of recent developments (particularly globalization and advances in technology) on the production and perception of language argues that the two opposing directions of globalization and tribalism can be equally related to what is going on within the discipline of translation studies. (Author/VWL)

  7. Global SUMO Proteome Responses Guide Gene Regulation, mRNA Biogenesis, and Plant Stress Responses.

    PubMed

    Mazur, Magdalena J; van den Burg, Harrold A

    2012-01-01

    Small Ubiquitin-like MOdifier (SUMO) is a key regulator of abiotic stress, disease resistance, and development in plants. The identification of >350 plant SUMO targets has revealed many processes modulated by SUMO and potential consequences of SUMO on its targets. Importantly, highly related proteins are SUMO-modified in plants, yeast, and metazoans. Overlapping SUMO targets include heat-shock proteins (HSPs), transcription regulators, histones, histone-modifying enzymes, proteins involved in DNA damage repair, but also proteins involved in mRNA biogenesis and nucleo-cytoplasmic transport. Proteomics studies indicate key roles for SUMO in gene repression by controlling histone (de)acetylation activity at genomic loci. The responsible heavily sumoylated transcriptional repressor complexes are recruited by plant transcription factors (TFs) containing an (ERF)-associated Amphiphilic Repression (EAR) motif. These TFs are not necessarily themselves a SUMO target. Conversely, SUMO acetylation (Ac) prevents binding of downstream partners by blocking binding of their SUMO-interaction peptide motifs to Ac-SUMO. In addition, SUMO acetylation has emerged as a mechanism to recruit specifically bromodomains. Bromodomains are generally linked with gene activation. These findings strengthen the idea of a bi-directional sumo-acetylation switch in gene regulation. Quantitative proteomics has highlighted that global sumoylation provides a dynamic response to protein damage involving SUMO chain-mediated protein degradation, but also SUMO E3 ligase-dependent transcription of HSP genes. With these insights in SUMO function and novel technical advancements, we can now study SUMO dynamics in responses to (a)biotic stress in plants.

  8. Emotional Responses to Music: Experience, Expression, and Physiology

    ERIC Educational Resources Information Center

    Lundqvist, Lars-Olov; Carlsson, Fredrik; Hilmersson, Per; Juslin, Patrik N.

    2009-01-01

    A crucial issue in research on music and emotion is whether music evokes genuine emotional responses in listeners (the emotivist position) or whether listeners merely perceive emotions expressed by the music (the cognitivist position). To investigate this issue, we measured self-reported emotion, facial muscle activity, and autonomic activity in…

  9. First cellular approach of the effects of global warming on groundwater organisms: a study of the HSP70 gene expression.

    PubMed

    Colson-Proch, Céline; Morales, Anne; Hervant, Frédéric; Konecny, Lara; Moulin, Colette; Douady, Christophe J

    2010-05-01

    Whereas the consequences of global warming at population or community levels are well documented, studies at the cellular level are still scarce. The study of the physiological or metabolic effects of such small increases in temperature (between +2 degrees C and +6 degrees C) is difficult because they are below the amplitude of the daily or seasonal thermal variations occurring in most environments. In contrast, subterranean biotopes are highly thermally buffered (+/-1 degrees C within a year), and underground water organisms could thus be particularly well suited to characterise cellular responses of global warming. To this purpose, we studied genes encoding chaperone proteins of the HSP70 family in amphipod crustaceans belonging to the ubiquitous subterranean genus Niphargus. An HSP70 sequence was identified in eight populations of two complexes of species of the Niphargus genus (Niphargus rhenorhodanensis and Niphargus virei complexes). Expression profiles were determined for one of these by reverse transcription and quantitative polymerase chain reaction, confirming the inducible nature of this gene. An increase in temperature of 2 degrees C seemed to be without effect on N. rhenorhodanensis physiology, whereas a heat shock of +6 degrees C represented an important thermal stress for these individuals. Thus, this study shows that although Niphargus individuals do not undergo any daily or seasonal thermal variations in underground water, they display an inducible HSP70 heat shock response. This controlled laboratory-based physiological experiment constitutes a first step towards field investigations of the cellular consequences of global warming on subterranean organisms.

  10. The Induced Affect Response: 10-Week-Old Infants' Responses to Three Emotion Expressions.

    ERIC Educational Resources Information Center

    Haviland, Jeannette M.; Lelwica, Mary

    1987-01-01

    When mothers of 12 infants 10 weeks of age displayed noncontingent, practiced facial and vocal expressions of joy, anger, and sadness, infants responded differently to each expression. Infants' matching responses to maternal affects were only part of complex but predictable behavioral patterns that indicate meaningful affect states and possibly…

  11. Microbial legacies alter decomposition in response to simulated global change

    PubMed Central

    Martiny, Jennifer BH; Martiny, Adam C; Weihe, Claudia; Lu, Ying; Berlemont, Renaud; Brodie, Eoin L; Goulden, Michael L; Treseder, Kathleen K; Allison, Steven D

    2017-01-01

    Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities. PMID:27740610

  12. Global analysis of the regulatory network structure of gene expression in Saccharomyces cerevisiae.

    PubMed

    Gunji, Wataru; Kai, Takahito; Takahashi, Yoriko; Maki, Yukihiro; Kurihara, Wataru; Utsugi, Takahiko; Fujimori, Fumihiro; Murakami, Yasufumi

    2004-06-30

    Gene expression in eukaryotic cells is controlled by the concerted action of various transcription factors. To help clarify these complex mechanisms, we attempted to develop a method for extracting maximal information regarding the transcriptional control pathways. To this end, we first analyzed the expression profiles of numerous transcription factors in yeast cells, under the assumption that the expression levels of these factors would be elevated under conditions in which the factors were active in the cells. Based on the results, we successfully categorized about 400 transcription factors into three groups based on their expression profiles. We then analyzed the effect of the loss of function of various induced transcription factors on the global expression profile to investigate the above-mentioned assumption of a correlation between transcription elevation and functional activity. By comparing the expression profiles of wild-type with those of disruption mutants using microarrays, we were able to detect a substantial number of relations between transcription factors and the genes they regulate. The results of these experiments suggested that our approach is useful for understanding the global transcriptional networks of eukaryotic cells, in which most genes are regulated in a temporal and conditional manner.

  13. Drug effects on responses to emotional facial expressions: recent findings

    PubMed Central

    Miller, Melissa A.; Bershad, Anya K.; de Wit, Harriet

    2016-01-01

    Many psychoactive drugs increase social behavior and enhance social interactions, which may, in turn, increase their attractiveness to users. Although the psychological mechanisms by which drugs affect social behavior are not fully understood, there is some evidence that drugs alter the perception of emotions in others. Drugs can affect the ability to detect, attend to, and respond to emotional facial expressions, which in turn may influence their use in social settings. Either increased reactivity to positive expressions or decreased response to negative expressions may facilitate social interaction. This article reviews evidence that psychoactive drugs alter the processing of emotional facial expressions using subjective, behavioral, and physiological measures. The findings lay the groundwork for better understanding how drugs alter social processing and social behavior more generally. PMID:26226144

  14. Drug effects on responses to emotional facial expressions: recent findings.

    PubMed

    Miller, Melissa A; Bershad, Anya K; de Wit, Harriet

    2015-09-01

    Many psychoactive drugs increase social behavior and enhance social interactions, which may, in turn, increase their attractiveness to users. Although the psychological mechanisms by which drugs affect social behavior are not fully understood, there is some evidence that drugs alter the perception of emotions in others. Drugs can affect the ability to detect, attend to, and respond to emotional facial expressions, which in turn may influence their use in social settings. Either increased reactivity to positive expressions or decreased response to negative expressions may facilitate social interaction. This article reviews evidence that psychoactive drugs alter the processing of emotional facial expressions using subjective, behavioral, and physiological measures. The findings lay the groundwork for better understanding how drugs alter social processing and social behavior more generally.

  15. Family health nursing: a response to the global health challenges.

    PubMed

    Martin, Paul; Duffy, Tim; Johnston, Brian; Banks, Pauline; Harkess-Murphy, Eileen; Martin, Colin R

    2013-02-01

    The European Family Health Nursing Project is a revitalized World Health Organization initiative led by the University of the West of Scotland. Partner countries include Armenia, Austria, Germany, Italy, Poland, Portugal, Romania, Slovenia, and Spain. European Union Lifelong Learning funding was received in 2011 to facilitate a consistency of approach in the development of a definition of family health nursing, required core competencies and capabilities, and consequent education and training requirements. Global health challenges have informed the development of the project: increasingly aging populations, the increasing incidence in noncommunicable diseases that are currently the main cause of death, and the significant progress made in the way health systems have developed to meet the demands in relation to access and equality of health services. Governments and policy makers should develop a health workforce based on the principles of teamwork and interdisciplinarity while recognizing the core contribution of the "specialist generalist" role in the primary care setting.

  16. A Robust Response of the Hadley Circulation to Global Warming

    NASA Technical Reports Server (NTRS)

    Lau, William K M.; Kim, Kyu-Myong

    2014-01-01

    Tropical rainfall is expected to increase in a warmer climate. Yet, recent studies have inferred that the Hadley Circulation (HC), which is primarily driven by latent heating from tropical rainfall, is weakened under global warming. Here, we show evidence of a robust intensification of the HC from analyses of 33 CMIP5 model projections under a scenario of 1 per year CO2 emission increase. The intensification is manifested in a deep-tropics squeeze, characterized by a pronounced increase in the zonal mean ascending motion in the mid and upper troposphere, a deepening and narrowing of the convective zone and enhanced rainfall in the deep tropics. These changes occur in conjunction with a rise in the region of maximum outflow of the HC, with accelerated meridional mass outflow in the uppermost branch of the HC away from the equator, coupled to a weakened inflow in the return branches of the HC in the lower troposphere.

  17. Global reductions in seafloor biomass in response to climate change.

    PubMed

    Jones, Daniel O B; Yool, Andrew; Wei, Chih-Lin; Henson, Stephanie A; Ruhl, Henry A; Watson, Reg A; Gehlen, Marion

    2014-06-01

    Seafloor organisms are vital for healthy marine ecosystems, contributing to elemental cycling, benthic remineralization, and ultimately sequestration of carbon. Deep-sea life is primarily reliant on the export flux of particulate organic carbon from the surface ocean for food, but most ocean biogeochemistry models predict global decreases in export flux resulting from 21st century anthropogenically induced warming. Here we show that decadal-to-century scale changes in carbon export associated with climate change lead to an estimated 5.2% decrease in future (2091-2100) global open ocean benthic biomass under RCP8.5 (reduction of 5.2 Mt C) compared with contemporary conditions (2006-2015). Our projections use multi-model mean export flux estimates from eight fully coupled earth system models, which contributed to the Coupled Model Intercomparison Project Phase 5, that have been forced by high and low representative concentration pathways (RCP8.5 and 4.5, respectively). These export flux estimates are used in conjunction with published empirical relationships to predict changes in benthic biomass. The polar oceans and some upwelling areas may experience increases in benthic biomass, but most other regions show decreases, with up to 38% reductions in parts of the northeast Atlantic. Our analysis projects a future ocean with smaller sized infaunal benthos, potentially reducing energy transfer rates though benthic multicellular food webs. More than 80% of potential deep-water biodiversity hotspots known around the world, including canyons, seamounts, and cold-water coral reefs, are projected to experience negative changes in biomass. These major reductions in biomass may lead to widespread change in benthic ecosystems and the functions and services they provide.

  18. Global reductions in seafloor biomass in response to climate change

    PubMed Central

    Jones, Daniel O B; Yool, Andrew; Wei, Chih-Lin; Henson, Stephanie A; Ruhl, Henry A; Watson, Reg A; Gehlen, Marion

    2014-01-01

    Seafloor organisms are vital for healthy marine ecosystems, contributing to elemental cycling, benthic remineralization, and ultimately sequestration of carbon. Deep-sea life is primarily reliant on the export flux of particulate organic carbon from the surface ocean for food, but most ocean biogeochemistry models predict global decreases in export flux resulting from 21st century anthropogenically induced warming. Here we show that decadal-to-century scale changes in carbon export associated with climate change lead to an estimated 5.2% decrease in future (2091–2100) global open ocean benthic biomass under RCP8.5 (reduction of 5.2 Mt C) compared with contemporary conditions (2006–2015). Our projections use multi-model mean export flux estimates from eight fully coupled earth system models, which contributed to the Coupled Model Intercomparison Project Phase 5, that have been forced by high and low representative concentration pathways (RCP8.5 and 4.5, respectively). These export flux estimates are used in conjunction with published empirical relationships to predict changes in benthic biomass. The polar oceans and some upwelling areas may experience increases in benthic biomass, but most other regions show decreases, with up to 38% reductions in parts of the northeast Atlantic. Our analysis projects a future ocean with smaller sized infaunal benthos, potentially reducing energy transfer rates though benthic multicellular food webs. More than 80% of potential deep-water biodiversity hotspots known around the world, including canyons, seamounts, and cold-water coral reefs, are projected to experience negative changes in biomass. These major reductions in biomass may lead to widespread change in benthic ecosystems and the functions and services they provide. PMID:24382828

  19. The acute phase response of cod (Gadus morhua L.): expression of immune response genes.

    PubMed

    Audunsdottir, Sigridur S; Magnadottir, Bergljot; Gisladottir, Berglind; Jonsson, Zophonias O; Bragason, Birkir Th

    2012-02-01

    An acute phase response (APR) was experimentally induced in Atlantic cod (Gadus morhua L.) by intramuscular injection of turpentine oil. The change in the expression of immune related genes was monitored in the anterior kidney and the spleen over a period of 7 days. The genes examined were two types of pentraxins, apolipoprotein A1 (ApoA-I), the complement component C3, interleukin-1β (IL-1β), transferrin, cathelicidin, and hepcidin. All genes were constitutively expressed in both organs and their expression amplified by the turpentine injection. A pattern of response was observed both with respect to the organ preference and to the timing of a maximum response. The increased gene expression of the pentraxins, ApoA-I and C3 was restricted to the anterior kidney, the gene expression of IL-1β, cathelicidin, and transferrin increased in both organs, while hepcidin gene expression was only significantly increased in the spleen. The pentraxins and ApoA-I appear to be early mediators of APR in cod, possibly stimulating C3 and IL-1β response, while the antimicrobial peptides may play a minor role. The increase in transferrin gene expression in both organs, and apparent indifference to cortisol release associated with the turpentine injection, suggests that this could be a typical acute phase protein in cod.

  20. Global variability in gene expression and alternative splicing is modulated by mitochondrial content.

    PubMed

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J

    2015-05-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype.

  1. Global variability in gene expression and alternative splicing is modulated by mitochondrial content

    PubMed Central

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J.

    2015-01-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype. PMID:25800673

  2. Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens

    PubMed Central

    Hao, Hai-Ting; Zhao, Xia; Shang, Qian-Han; Wang, Yun; Guo, Zhi-Hong; Zhang, Yu-Bao; Xie, Zhong-Kui; Wang, Ruo-Yu

    2016-01-01

    Some plant growth-promoting rhizobacteria (PGPR) regulated plant growth and elicited plant basal immunity by volatiles. The response mechanism to the Bacillus amyloliquefaciens volatiles in plant has not been well studied. We conducted global gene expression profiling in Arabidopsis after treatment with Bacillus amyloliquefaciens FZB42 volatiles by Illumina Digital Gene Expression (DGE) profiling of different growth stages (seedling and mature) and tissues (leaves and roots). Compared with the control, 1,507 and 820 differentially expressed genes (DEGs) were identified in leaves and roots at the seedling stage, respectively, while 1,512 and 367 DEGs were identified in leaves and roots at the mature stage. Seventeen genes with different regulatory patterns were validated using quantitative RT-PCR. Numerous DEGs were enriched for plant hormones, cell wall modifications, and protection against stress situations, which suggests that volatiles have effects on plant growth and immunity. Moreover, analyzes of transcriptome difference in tissues and growth stage using DGE profiling showed that the plant response might be tissue-specific and/or growth stage-specific. Thus, genes encoding flavonoid biosynthesis were downregulated in leaves and upregulated in roots, thereby indicating tissue-specific responses to volatiles. Genes related to photosynthesis were downregulated at the seedling stage and upregulated at the mature stage, respectively, thereby suggesting growth period-specific responses. In addition, the emission of bacterial volatiles significantly induced killing of cells of other organism pathway with up-regulated genes in leaves and the other three pathways (defense response to nematode, cell morphogenesis involved in differentiation and trichoblast differentiation) with up-regulated genes were significantly enriched in roots. Interestingly, some important alterations in the expression of growth-related genes, metabolic pathways, defense response to biotic

  3. Global antibody response to Staphylococcus aureus live-cell vaccination.

    PubMed

    Selle, Martina; Hertlein, Tobias; Oesterreich, Babett; Klemm, Theresa; Kloppot, Peggy; Müller, Elke; Ehricht, Ralf; Stentzel, Sebastian; Bröker, Barbara M; Engelmann, Susanne; Ohlsen, Knut

    2016-04-22

    The pathogen Staphylococcus aureus causes a broad range of severe diseases and is feared for its ability to rapidly develop resistance to antibiotic substances. The increasing number of highly resistant S. aureus infections has accelerated the search for alternative treatment options to close the widening gap in anti-S. aureus therapy. This study analyses the humoral immune response to vaccination of Balb/c mice with sublethal doses of live S. aureus. The elicited antibody pattern in the sera of intravenously and intramuscularly vaccinated mice was determined using of a recently developed protein array. We observed a specific antibody response against a broad set of S. aureus antigens which was stronger following i.v. than i.m. vaccination. Intravenous but not intramuscular vaccination protected mice against an intramuscular challenge infection with a high bacterial dose. Vaccine protection was correlated with the strength of the anti-S. aureus antibody response. This study identified novel vaccine candidates by using protein microarrays as an effective tool and showed that successful vaccination against S. aureus relies on the optimal route of administration.

  4. Global antibody response to Staphylococcus aureus live-cell vaccination

    PubMed Central

    Selle, Martina; Hertlein, Tobias; Oesterreich, Babett; Klemm, Theresa; Kloppot, Peggy; Müller, Elke; Ehricht, Ralf; Stentzel, Sebastian; Bröker, Barbara M.; Engelmann, Susanne; Ohlsen, Knut

    2016-01-01

    The pathogen Staphylococcus aureus causes a broad range of severe diseases and is feared for its ability to rapidly develop resistance to antibiotic substances. The increasing number of highly resistant S. aureus infections has accelerated the search for alternative treatment options to close the widening gap in anti-S. aureus therapy. This study analyses the humoral immune response to vaccination of Balb/c mice with sublethal doses of live S. aureus. The elicited antibody pattern in the sera of intravenously and intramuscularly vaccinated mice was determined using of a recently developed protein array. We observed a specific antibody response against a broad set of S. aureus antigens which was stronger following i.v. than i.m. vaccination. Intravenous but not intramuscular vaccination protected mice against an intramuscular challenge infection with a high bacterial dose. Vaccine protection was correlated with the strength of the anti-S. aureus antibody response. This study identified novel vaccine candidates by using protein microarrays as an effective tool and showed that successful vaccination against S. aureus relies on the optimal route of administration. PMID:27103319

  5. Child organ trafficking: global reality and inadequate international response.

    PubMed

    Bagheri, Alireza

    2016-06-01

    In organ transplantation, the demand for human organs has grown far faster than the supply of organs. This has opened the door for illegal organ trade and trafficking including from children. Organized crime groups and individual organ brokers exploit the situation and, as a result, black markets are becoming more numerous and organized organ trafficking is expanding worldwide. While underprivileged and vulnerable men and women in developing countries are a major source of trafficked organs, and may themselves be trafficked for the purpose of illegal organ removal and trade, children are at especial risk of exploitation. With the confirmed cases of children being trafficked for their organs, child organ trafficking, which once called a "modern urban legend", is a sad reality in today's world. By presenting a global picture of child organ trafficking, this paper emphasizes that child organ trafficking is no longer a myth but a reality which has to be addressed. It argues that the international efforts against organ trafficking and trafficking in human beings for organ removal have failed to address child organ trafficking adequately. This chapter suggests that more orchestrated international collaboration as well as development of preventive measure and legally binding documents are needed to fight child organ trafficking and to support its victims.

  6. Global monsoon precipitation responses to large volcanic eruptions

    PubMed Central

    Liu, Fei; Chai, Jing; Wang, Bin; Liu, Jian; Zhang, Xiao; Wang, Zhiyuan

    2016-01-01

    Climate variation of global monsoon (GM) precipitation involves both internal feedback and external forcing. Here, we focus on strong volcanic forcing since large eruptions are known to be a dominant mechanism in natural climate change. It is not known whether large volcanoes erupted at different latitudes have distinctive effects on the monsoon in the Northern Hemisphere (NH) and the Southern Hemisphere (SH). We address this issue using a 1500-year volcanic sensitivity simulation by the Community Earth System Model version 1.0 (CESM1). Volcanoes are classified into three types based on their meridional aerosol distributions: NH volcanoes, SH volcanoes and equatorial volcanoes. Using the model simulation, we discover that the GM precipitation in one hemisphere is enhanced significantly by the remote volcanic forcing occurring in the other hemisphere. This remote volcanic forcing-induced intensification is mainly through circulation change rather than moisture content change. In addition, the NH volcanic eruptions are more efficient in reducing the NH monsoon precipitation than the equatorial ones, and so do the SH eruptions in weakening the SH monsoon, because the equatorial eruptions, despite reducing moisture content, have weaker effects in weakening the off-equatorial monsoon circulation than the subtropical-extratropical volcanoes do. PMID:27063141

  7. Global monsoon precipitation responses to large volcanic eruptions.

    PubMed

    Liu, Fei; Chai, Jing; Wang, Bin; Liu, Jian; Zhang, Xiao; Wang, Zhiyuan

    2016-04-11

    Climate variation of global monsoon (GM) precipitation involves both internal feedback and external forcing. Here, we focus on strong volcanic forcing since large eruptions are known to be a dominant mechanism in natural climate change. It is not known whether large volcanoes erupted at different latitudes have distinctive effects on the monsoon in the Northern Hemisphere (NH) and the Southern Hemisphere (SH). We address this issue using a 1500-year volcanic sensitivity simulation by the Community Earth System Model version 1.0 (CESM1). Volcanoes are classified into three types based on their meridional aerosol distributions: NH volcanoes, SH volcanoes and equatorial volcanoes. Using the model simulation, we discover that the GM precipitation in one hemisphere is enhanced significantly by the remote volcanic forcing occurring in the other hemisphere. This remote volcanic forcing-induced intensification is mainly through circulation change rather than moisture content change. In addition, the NH volcanic eruptions are more efficient in reducing the NH monsoon precipitation than the equatorial ones, and so do the SH eruptions in weakening the SH monsoon, because the equatorial eruptions, despite reducing moisture content, have weaker effects in weakening the off-equatorial monsoon circulation than the subtropical-extratropical volcanoes do.

  8. Global responses for recycling waste CRTs in e-waste.

    PubMed

    Singh, Narendra; Li, Jinhui; Zeng, Xianlai

    2016-11-01

    The management of used cathode ray tube (CRT) devices is a major problem worldwide due to rapid uptake of the technology and early obsolescence of CRT devices, which is considered an environment hazard if disposed improperly. Previously, their production has grown in step with computer and television demand but later on with rapid technological innovation; TVs and computer screens has been replaced by new products such as Liquid Crystal Displays (LCDs) and Plasma Display Panel (PDPs). This change creates a large volume of waste stream of obsolete CRTs waste in developed countries and developing countries will be becoming major CRTs waste producers in the upcoming years. We studied that there is also high level of trans-boundary movement of these devices as second-hand electronic equipment into developing countries in an attempt to bridge the 'digital divide'. Moreover, the current global production of e-waste is estimated to be '41million tonnes per year' where a major part of the e-waste stream consists of CRT devices. This review article provides a concise overview of world's current CRTs waste scenario, namely magnitude of the demand and processing, current disposal and recycling operations.

  9. A review of progress towards understanding the transient global mean surface temperature response to radiative perturbation

    NASA Astrophysics Data System (ADS)

    Yoshimori, Masakazu; Watanabe, Masahiro; Shiogama, Hideo; Oka, Akira; Abe-Ouchi, Ayako; Ohgaito, Rumi; Kamae, Youichi

    2016-12-01

    The correct understanding of the transient response to external radiative perturbation is important for the interpretation of observed climate change, the prediction of near-future climate change, and committed warming under climate stabilization scenarios, as well as the estimation of equilibrium climate sensitivity based on observation data. It has been known for some time that the radiative damping rate per unit of global mean surface temperature increase varies with time, and this inconstancy affects the transient response. Knowledge of the equilibrium response alone is insufficient, but understanding the transient response of the global mean surface temperature has made rapid progress. The recent progress accompanies the relatively new concept of the efficacies of ocean heat uptake and forcing. The ocean heat uptake efficacy associates the temperature response induced by ocean heat uptake with equilibrium temperature response, and the efficacy of forcing compares the temperature response caused by non-CO2 forcing with that by CO2 forcing.

  10. Assessing Global Transcriptome Changes in Response to South African Cassava Mosaic Virus [ZA-99] Infection in Susceptible Arabidopsis thaliana

    PubMed Central

    Pierce, Erica J.; Rey, M. E. Chrissie

    2013-01-01

    In susceptible plant hosts, co-evolution has favoured viral strategies to evade host defenses and utilize resources to their own benefit. The degree of manipulation of host gene expression is dependent on host-virus specificity and certain abiotic factors. In order to gain insight into global transcriptome changes for a geminivirus pathosystem, South African cassava mosaic virus [ZA:99] and Arabidopsis thaliana, 4×44K Agilent microarrays were adopted. After normalization, a log2 fold change filtering of data (p<0.05) identified 1,743 differentially expressed genes in apical leaf tissue. A significant increase in differential gene expression over time correlated with an increase in SACMV accumulation, as virus copies were 5-fold higher at 24 dpi and 6-fold higher at 36 dpi than at 14 dpi. Many altered transcripts were primarily involved in stress and defense responses, phytohormone signalling pathways, cellular transport, cell-cycle regulation, transcription, oxidation-reduction, and other metabolic processes. Only forty-one genes (2.3%) were shown to be continuously expressed across the infection period, indicating that the majority of genes were transient and unique to a particular time point during infection. A significant number of pathogen-responsive genes were suppressed during the late stages of pathogenesis, while during active systemic infection (14 to 24 dpi), there was an increase in up-regulated genes in several GO functional categories. An adaptive response was initiated to divert energy from growth-related processes to defense, leading to disruption of normal biological host processes. Similarities in cell-cycle regulation correlated between SACMV and Cabbage leaf curl virus (CaLCuV), but differences were also evident. Differences in gene expression between the two geminiviruses clearly demonstrated that, while some global transcriptome responses are generally common in plant virus infections, temporal host-specific interactions are required for

  11. Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response

    PubMed Central

    Bendjilali, Nasrine; MacLeon, Samuel; Kalra, Gurmannat; Willis, Stephen D.; Hossian, A. K. M. Nawshad; Avery, Erica; Wojtowicz, Olivia; Hickman, Mark J.

    2016-01-01

    Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen. PMID:27883312

  12. Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response.

    PubMed

    Bendjilali, Nasrine; MacLeon, Samuel; Kalra, Gurmannat; Willis, Stephen D; Hossian, A K M Nawshad; Avery, Erica; Wojtowicz, Olivia; Hickman, Mark J

    2017-01-05

    Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.

  13. Evolutionary History of Lagomorphs in Response to Global Environmental Change

    PubMed Central

    Ge, Deyan; Wen, Zhixin; Xia, Lin; Zhang, Zhaoqun; Erbajeva, Margarita; Huang, Chengming; Yang, Qisen

    2013-01-01

    Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C3 plants, while for the diet of leporids, more than 16% of plant species are identified as C4 (31% species are from Poaceae). The ability of several leporid species to consume C4 plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C4 plants in the late Miocene, the so-called ‘nature’s green revolution’, induced by global environmental change, is suggested to be one of the major ‘ecological opportunities’, which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of leporids

  14. Contrasting responses of Central Asian rock glaciers to global warming.

    PubMed

    Sorg, Annina; Kääb, Andreas; Roesch, Andrea; Bigler, Christof; Stoffel, Markus

    2015-02-06

    While the responses of Tien Shan glaciers--and glaciers elsewhere--to climatic changes are becoming increasingly well understood, this is less the case for permafrost in general and for rock glaciers in particular. We use a novel approach to describe the climate sensitivity of rock glaciers and to reconstruct periods of high and low rock glacier activity in the Tien Shan since 1895. Using more than 1500 growth anomalies from 280 trees growing on rock glacier bodies, repeat aerial photography from Soviet archives and high-resolution satellite imagery, we present here the world's longest record of rock glacier movements. We also demonstrate that the rock glaciers exhibit synchronous periods of activity at decadal timescales. Despite the complex energy-balance processes on rock glaciers, periods of enhanced activity coincide with warm summers, and the annual mass balance of Tuyuksu glacier fluctuates asynchronously with rock glacier activity. At multi-decadal timescales, however, the investigated rock glaciers exhibit site-specific trends reflecting different stages of inactivation, seemingly in response to the strong increase in air temperature since the 1970s.

  15. Expressive suppression and neural responsiveness to nonverbal affective cues

    PubMed Central

    Petrican, Raluca; Rosenbaum, R. Shayna; Grady, Cheryl

    2016-01-01

    responsiveness to nonverbal affective cues, while also suggesting one explanation for the suppressors’ poorer cognitive performance in social situations. Moreover, our results point to a potential neural mechanism supporting the development and perpetuation of expressive suppression as an emotion regulation strategy. PMID:26365712

  16. Strategies for rapid global earthquake impact estimation: the Prompt Assessment of Global Earthquakes for Response (PAGER) system

    USGS Publications Warehouse

    Jaiswal, Kishor; Wald, D.J.

    2013-01-01

    This chapter summarizes the state-of-the-art for rapid earthquake impact estimation. It details the needs and challenges associated with quick estimation of earthquake losses following global earthquakes, and provides a brief literature review of various approaches that have been used in the past. With this background, the chapter introduces the operational earthquake loss estimation system developed by the U.S. Geological Survey (USGS) known as PAGER (for Prompt Assessment of Global Earthquakes for Response). It also details some of the ongoing developments of PAGER’s loss estimation models to better supplement the operational empirical models, and to produce value-added web content for a variety of PAGER users.

  17. Developmental-stage-dependent transcriptional response to leukaemic oncogene expression

    PubMed Central

    Regha, Kakkad; Assi, Salam A.; Tsoulaki, Olga; Gilmour, Jane; Lacaud, Georges; Bonifer, Constanze

    2015-01-01

    Acute myeloid leukaemia (AML) is characterized by a block in myeloid differentiation the stage of which is dependent on the nature of the transforming oncogene and the developmental stage of the oncogenic hit. This is also true for the t(8;21) translocation that gives rise to the RUNX1-ETO fusion protein and initiates the most common form of human AML. Here we study the differentiation of mouse embryonic stem cells expressing an inducible RUNX1-ETO gene into blood cells as a model, combined with genome-wide analyses of transcription factor binding and gene expression. RUNX1-ETO interferes with both the activating and repressive function of its normal counterpart, RUNX1, at early and late stages of blood cell development. However, the response of the transcriptional network to RUNX1-ETO expression is developmental stage specific, highlighting the molecular mechanisms determining specific target cell expansion after an oncogenic hit. PMID:26018585

  18. Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax.

    PubMed

    Jackson, Andrew P; Goyard, Sophie; Xia, Dong; Foth, Bernardo J; Sanders, Mandy; Wastling, Jonathan M; Minoprio, Paola; Berriman, Matthew

    2015-01-01

    The parasitic flagellate Trypanosoma vivax is a cause of animal trypanosomiasis across Africa and South America. The parasite has a digenetic life cycle, passing between mammalian hosts and insect vectors, and a series of developmental forms adapted to each life cycle stage. Each point in the life cycle presents radically different challenges to parasite metabolism and physiology and distinct host interactions requiring remodeling of the parasite cell surface. Transcriptomic and proteomic studies of the related parasites T. brucei and T. congolense have shown how gene expression is regulated during their development. New methods for in vitro culture of the T. vivax insect stages have allowed us to describe global gene expression throughout the complete T. vivax life cycle for the first time. We combined transcriptomic and proteomic analysis of each life stage using RNA-seq and mass spectrometry respectively, to identify genes with patterns of preferential transcription or expression. While T. vivax conforms to a pattern of highly conserved gene expression found in other African trypanosomes, (e.g. developmental regulation of energy metabolism, restricted expression of a dominant variant antigen, and expression of 'Fam50' proteins in the insect mouthparts), we identified significant differences in gene expression affecting metabolism in the fly and a suite of T. vivax-specific genes with predicted cell-surface expression that are preferentially expressed in the mammal ('Fam29, 30, 42') or the vector ('Fam34, 35, 43'). T. vivax differs significantly from other African trypanosomes in the developmentally-regulated proteins likely to be expressed on its cell surface and thus, in the structure of the host-parasite interface. These unique features may yet explain the species differences in life cycle and could, in the form of bloodstream-stage proteins that do not undergo antigenic variation, provide targets for therapy.

  19. Escherichia coli Global Gene Expression in Urine from Women with Urinary Tract Infection

    PubMed Central

    Rasko, David A.; Faerber, Gary J.; Mobley, Harry L. T.

    2010-01-01

    Murine models of urinary tract infection (UTI) have provided substantial data identifying uropathogenic E. coli (UPEC) virulence factors and assessing their expression in vivo. However, it is unclear how gene expression in these animal models compares to UPEC gene expression during UTI in humans. To address this, we used a UPEC strain CFT073-specific microarray to measure global gene expression in eight E. coli isolates monitored directly from the urine of eight women presenting at a clinic with bacteriuria. The resulting gene expression profiles were compared to those of the same E. coli isolates cultured statically to exponential phase in pooled, sterilized human urine ex vivo. Known fitness factors, including iron acquisition and peptide transport systems, were highly expressed during human UTI and support a model in which UPEC replicates rapidly in vivo. While these findings were often consistent with previous data obtained from the murine UTI model, host-specific differences were observed. Most strikingly, expression of type 1 fimbrial genes, which are among the most highly expressed genes during murine experimental UTI and encode an essential virulence factor for this experimental model, was undetectable in six of the eight E. coli strains from women with UTI. Despite the lack of type 1 fimbrial expression in the urine samples, these E. coli isolates were generally capable of expressing type 1 fimbriae in vitro and highly upregulated fimA upon experimental murine infection. The findings presented here provide insight into the metabolic and pathogenic profile of UPEC in urine from women with UTI and represent the first transcriptome analysis for any pathogenic E. coli during a naturally occurring infection in humans. PMID:21085611

  20. Phenological Responses to ENSO in the Global Oceans

    NASA Astrophysics Data System (ADS)

    Racault, M.-F.; Sathyendranath, S.; Menon, N.; Platt, T.

    2017-01-01

    Phenology relates to the study of timing of periodic events in the life cycle of plants or animals as influenced by environmental conditions and climatic forcing. Phenological metrics provide information essential to quantify variations in the life cycle of these organisms. The metrics also allow us to estimate the speed at which living organisms respond to environmental changes. At the surface of the oceans, microscopic plant cells, so-called phytoplankton, grow and sometimes form blooms, with concentrations reaching up to 100 million cells per litre and extending over many square kilometres. These blooms can have a huge collective impact on ocean colour, because they contain chlorophyll and other auxiliary pigments, making them visible from space. Phytoplankton populations have a high turnover rate and can respond within hours to days to environmental perturbations. This makes them ideal indicators to study the first-level biological response to environmental changes. In the Earth's climate system, the El Niño-Southern Oscillation (ENSO) dominates large-scale inter-annual variations in environmental conditions. It serves as a natural experiment to study and understand how phytoplankton in the ocean (and hence the organisms at higher trophic levels) respond to climate variability. Here, the ENSO influence on phytoplankton is estimated through variations in chlorophyll concentration, primary production and timings of initiation, peak, termination and duration of the growing period. The phenological variabilities are used to characterise phytoplankton responses to changes in some physical variables: sea surface temperature, sea surface height and wind. It is reported that in oceanic regions experiencing high annual variations in the solar cycle, such as in high latitudes, the influence of ENSO may be readily measured using annual mean anomalies of physical variables. In contrast, in oceanic regions where ENSO modulates a climate system characterised by a seasonal

  1. The global workforce shortages and the migration of medical professions: the Australian policy response

    PubMed Central

    Smith, Saxon D

    2008-01-01

    Medical migration sees the providers of medical services (in particular medical practitioners) moving from one region or country to another. This creates problems for the provision of public health and medical services and poses challenges for laws in the nation state and for laws in the global community. There exists a global shortage of healthcare professionals. Nation states and health rights movements have been both responsible for, and responsive to, this global community shortage through a variety of health policy, regulation and legislation which directly affects the migration of medical providers. The microcosm responses adopted by individual nation states, such as Australia, to this workforce shortage further impact on the global workforce shortage through active recruitment of overseas-trained healthcare professionals. "Push" and "pull" factors exist which encourage medical migration of healthcare professionals. A nation state's approach to health policy, regulation and legislation dramatically helps to create these "push factors" and "pull factors". A co-ordinated global response is required with individual nation states being cognisant of the impact of their health policy, regulations and legislation on the global community through the medical migration of healthcare professionals. PMID:18507867

  2. Studying Biological Responses to Global Change in Atmospheric Oxygen

    PubMed Central

    Powell, Frank L.

    2010-01-01

    A popular book recently hypothesized that change in atmospheric oxygen over geological time is the most important physical factor in the evolution of many fundamental characteristics of modern terrestrial animals. This hypothesis is generated primarily using fossil data but the present paper considers how modern experimental biology can be used to test it. Comparative physiology and experimental evolution clearly show that changes in atmospheric O2 over the ages had the potential to drive evolution, assuming the physiological O2-sensitivity of animals today is similar to the past. Established methods, such as phylogenetically independent contrasts, as well new approaches, such as adding environmental history to phylogenetic analyses or modeling interactions between environmental stresses and biological responses with different rate constants, may be useful for testing (disproving) hypotheses about biological adaptations to changes in atmospheric O2. PMID:20385257

  3. Response of Vegetation in Northern China to Global Warming

    NASA Astrophysics Data System (ADS)

    Cui, H.; Huang, R.

    2009-05-01

    (Sophora japonica), tree of heaven (Ailanthus altissima), yellow locust (Robinia pseudoacacia), staghorn sumac (Rhus typhina), and gingko (Ginkgo biloba) have also been pushing northward to Huhhot, (41 degree N)Chifeng (42 degree N) and Tongliao (43 degree N), Inner Mongolia Autonomous Region. Alpine timberline has also been moved to higher altitude in Wutai Mt., Shanxi Province and Changbaishan Mt., Jilin Province. Although global warming seems to benefit agriculture in some cases, considering the decrease of wetness, the perspective is still uncertain. Drought and frost hazard are stress factors for the vegetation introduced to the northern areas. Chinese scholars are carefully watching the trend.

  4. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

    NASA Astrophysics Data System (ADS)

    Kaminski, Naftali; Allard, John D.; Pittet, Jean F.; Zuo, Fengrong; Griffiths, Mark J. D.; Morris, David; Huang, Xiaozhu; Sheppard, Dean; Heller, Renu A.

    2000-02-01

    The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin 6 subunit (6/-), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

  5. Personality traits modulate neural responses to emotions expressed in music.

    PubMed

    Park, Mona; Hennig-Fast, Kristina; Bao, Yan; Carl, Petra; Pöppel, Ernst; Welker, Lorenz; Reiser, Maximilian; Meindl, Thomas; Gutyrchik, Evgeny

    2013-07-26

    Music communicates and evokes emotions. The number of studies on the neural correlates of musical emotion processing is increasing but few have investigated the factors that modulate these neural activations. Previous research has shown that personality traits account for individual variability of neural responses. In this study, we used functional magnetic resonance imaging (fMRI) to investigate how the dimensions Extraversion and Neuroticism are related to differences in brain reactivity to musical stimuli expressing the emotions happiness, sadness and fear. 12 participants (7 female, M=20.33 years) completed the NEO-Five Factor Inventory (NEO-FFI) and were scanned while performing a passive listening task. Neurofunctional analyses revealed significant positive correlations between Neuroticism scores and activations in bilateral basal ganglia, insula and orbitofrontal cortex in response to music expressing happiness. Extraversion scores were marginally negatively correlated with activations in the right amygdala in response to music expressing fear. Our findings show that subjects' personality may have a predictive power in the neural correlates of musical emotion processing and should be considered in the context of experimental group homogeneity.

  6. Gene Expression of Corals in Response to Macroalgal Competitors

    PubMed Central

    Shearer, Tonya L.; Snell, Terry W.; Hay, Mark E.

    2014-01-01

    As corals decline and macroalgae proliferate on coral reefs, coral-macroalgal competition becomes more frequent and ecologically important. Whether corals are damaged by these interactions depends on susceptibility of the coral and traits of macroalgal competitors. Investigating changes in gene expression of corals and their intracellular symbiotic algae, Symbiodinium, in response to contact with different macroalgae provides insight into the biological processes and cellular pathways affected by competition with macroalgae. We evaluated the gene expression profiles of coral and Symbiodinium genes from two confamilial corals, Acropora millepora and Montipora digitata, after 6 h and 48 h of contact with four common macroalgae that differ in their allelopathic potency to corals. Contacts with macroalgae affected different biological pathways in the more susceptible (A. millepora) versus the more resistant (M. digitata) coral. Genes of coral hosts and of their associated Symbiodinium also responded in species-specific and time-specific ways to each macroalga. Changes in number and expression intensity of affected genes were greater after 6 h compared to 48 h of contact and were greater following contact with Chlorodesmis fastigiata and Amphiroa crassa than following contact with Galaxaura filamentosa or Turbinaria conoides. We documented a divergence in transcriptional responses between two confamilial corals and their associated Symbiodinium, as well as a diversity of dynamic responses within each coral species with respect to the species of macroalgal competitor and the duration of exposure to that competitor. These responses included early initiation of immune processes by Montipora, which is more resistant to damage after long-term macroalgal contact. Activation of the immune response by corals that better resist algal competition is consistent with the hypothesis that some macroalgal effects on corals may be mediated by microbial pathogens. PMID:25500576

  7. Global microRNA expression profiles in insulin target tissues in a spontaneous rat model of type 2 diabetes

    PubMed Central

    Herrera, B. M.; Lockstone, H. E.; Taylor, J. M.; Ria, M.; Barrett, A.; Collins, S.; Kaisaki, P.; Argoud, K.; Fernandez, C.; Travers, M. E.; Grew, J. P.; Randall, J. C.; Gloyn, A. L.; Gauguier, D.; McCarthy, M. I.

    2010-01-01

    Aims/hypothesis MicroRNAs regulate a broad range of biological mechanisms. To investigate the relationship between microRNA expression and type 2 diabetes, we compared global microRNA expression in insulin target tissues from three inbred rat strains that differ in diabetes susceptibility. Methods Using microarrays, we measured the expression of 283 microRNAs in adipose, liver and muscle tissue from hyperglycaemic (Goto–Kakizaki), intermediate glycaemic (Wistar Kyoto) and normoglycaemic (Brown Norway) rats (n = 5 for each strain). Expression was compared across strains and validated using quantitative RT-PCR. Furthermore, microRNA expression variation in adipose tissue was investigated in 3T3-L1 adipocytes exposed to hyperglycaemic conditions. Results We found 29 significantly differentiated microRNAs (padjusted < 0.05): nine in adipose tissue, 18 in liver and two in muscle. Of these, five microRNAs had expression patterns that correlated with the strain-specific glycaemic phenotype. MiR-222 (padjusted = 0.0005) and miR-27a (padjusted = 0.006) were upregulated in adipose tissue; miR-195 (padjusted = 0.006) and miR-103 (padjusted = 0.04) were upregulated in liver; and miR-10b (padjusted = 0.004) was downregulated in muscle. Exposure of 3T3-L1 adipocytes to increased glucose concentration upregulated the expression of miR-222 (p = 0.008), miR-27a (p = 0.02) and the previously reported miR-29a (p = 0.02). Predicted target genes of these differentially expressed microRNAs are involved in pathways relevant to type 2 diabetes. Conclusion The expression patterns of miR-222, miR-27a, miR-195, miR-103 and miR-10b varied with hyperglycaemia, suggesting a role for these microRNAs in the pathophysiology of type 2 diabetes, as modelled by the Gyoto–Kakizaki rat. We observed similar patterns of expression of miR-222, miR-27a and miR-29a in adipocytes as a response to increased glucose levels, which supports our hypothesis that altered

  8. Hemin and Magnesium-Protoporphyrin IX Induce Global Changes in Gene Expression in Chlamydomonas reinhardtii[C][W

    PubMed Central

    Voß, Björn; Meinecke, Linda; Kurz, Thorsten; Al-Babili, Salim; Beck, Christoph F.; Hess, Wolfgang R.

    2011-01-01

    Retrograde signaling is a pathway of communication from mitochondria and plastids to the nucleus in the context of cell differentiation, development, and stress response. In Chlamydomonas reinhardtii, the tetrapyrroles magnesium-protoporphyrin IX and heme are only synthesized within the chloroplast, and they have been implicated in the retrograde control of nuclear gene expression in this unicellular green alga. Feeding the two tetrapyrroles to Chlamydomonas cultures was previously shown to transiently induce five nuclear genes, three of which encode the heat shock proteins HSP70A, HSP70B, and HSP70E. In contrast, controversial results exist on the possible role of magnesium-protoporphyrin IX in the repression of genes for light-harvesting proteins in higher plants, raising the question of how important this mode of regulation is. Here, we used genome-wide transcriptional profiling to measure the global impact of these tetrapyrroles on gene regulation and the scope of the response. We identified almost 1,000 genes whose expression level changed transiently but significantly. Among them were only a few genes for photosynthetic proteins but several encoding enzymes of the tricarboxylic acid cycle, heme-binding proteins, stress-response proteins, as well as proteins involved in protein folding and degradation. More than 50% of the latter class of genes was also regulated by heat shock. The observed drastic fold changes at the RNA level did not correlate with similar changes in protein concentrations under the tested experimental conditions. Phylogenetic profiling revealed that genes of putative endosymbiontic origin are not overrepresented among the responding genes. This and the transient nature of changes in gene expression suggest a signaling role of both tetrapyrroles as secondary messengers for adaptive responses affecting the entire cell and not only organellar proteins. PMID:21148414

  9. Adaptation responses to climate change differ between global megacities

    NASA Astrophysics Data System (ADS)

    Georgeson, Lucien; Maslin, Mark; Poessinouw, Martyn; Howard, Steve

    2016-06-01

    Urban areas are increasingly at risk from climate change, with negative impacts predicted for human health, the economy and ecosystems. These risks require responses from cities to improve their resilience. Policymakers need to understand current adaptation spend to plan comprehensively and effectively. Through the measurement of spend in the newly defined `adaptation economy', we analyse current climate change adaptation efforts in ten megacities. In all cases, the adaptation economy remains a small part of the overall economy, representing a maximum of 0.33% of a city's gross domestic product (here referred to as GDPc). Differences in total spend are significant between cities in developed, emerging and developing countries, ranging from #15 million to #1,600 million. Comparing key subsectors, we demonstrate the differences in adaptation profiles. Developing cities have higher proportional spend on health and agriculture, whereas developed cities have higher spend on energy and water. Spend per capita and percentage of GDPc comparisons more clearly show disparities between cities. Developing country cities spend half the proportion of GDPc and significantly less per capita, suggesting that adaptation spend is driven by wealth rather than the number of vulnerable people. This indicates that current adaptation activities are insufficient in major population centres in developing and emerging economies.

  10. Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis.

    PubMed

    Marth, Christina D; Young, Neil D; Glenton, Lisa Y; Noden, Drew M; Browning, Glenn F; Krekeler, Natali

    2015-05-20

    The physiological changes associated with the varying hormonal environment throughout the oestrous cycle are linked to the different functions the uterus needs to fulfil. The aim of the present study was to generate global gene expression profiles for the equine uterus during oestrus and Day 5 of dioestrus. To achieve this, samples were collected from five horses during oestrus (follicle >35 mm in diameter) and dioestrus (5 days after ovulation) and analysed using high-throughput RNA sequencing techniques (RNA-Seq). Differentially expressed genes between the two cycle stages were further investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The expression of 1577 genes was found to be significantly upregulated during oestrus, whereas 1864 genes were expressed at significantly higher levels in dioestrus. Most genes upregulated during oestrus were associated with the extracellular matrix, signal interaction and transduction, cell communication or immune function, whereas genes expressed at higher levels in early dioestrus were most commonly associated with metabolic or transport functions, correlating well with the physiological functions of the uterus. These results allow for a more complete understanding of the hormonal influence on gene expression in the equine uterus by functional analysis of up- and downregulated genes in oestrus and dioestrus, respectively. In addition, a valuable baseline is provided for further research, including analyses of changes associated with uterine inflammation.

  11. Global stability for delay-dependent HTLV-I model with CTL immune response

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Liu, Jun

    2016-06-01

    We present a delay-dependent HTLV-I model with CTL immune response. The basic reproduction number is obtained for the existence of positive steady state. By constructing suitable Lyapunov functions, when the basic reproduction number is less than one, the infection-free steady state is globally asymptotically stable; when the basic reproduction number is greater than one, the infected steady state is globally asymptotically stable.

  12. The effect of blur on cortical responses to global form and motion

    PubMed Central

    Burton, Eliza A.; Wattam-Bell, John; Rubin, Gary S.; Atkinson, Janette; Braddick, Oliver; Nardini, Marko

    2015-01-01

    Global form and motion sensitivity undergo long development in childhood with motion sensitivity rather than form being impaired in a number of childhood disorders and both impaired in adult clinical populations. This suggests extended development and vulnerability of extrastriate cortical areas associated with global processing. However, in some developmental and clinical populations, it remains unclear to what extent impairments might reflect deficits at earlier stages of visual processing, such as reduced visual acuity and contrast sensitivity. To address this, we investigated the impact of degraded spatial vision on cortical global form and motion processing in healthy adults. Loss of high spatial frequencies was simulated using a diffuser to blur the stimuli. Participants completed behavioral and EEG tests of global form and motion perception under three levels of blur. For the behavioral tests, participants' form and motion coherence thresholds were measured using a two-alternative, forced-choice procedure. Steady-state visual evoked potentials were used to measure cortical responses to changes in the coherence of global form and motion stimuli. Both global form and global motion perception were impaired with increasing blur as measured by elevated behavioral thresholds and reduced cortical responses. However, form thresholds showed greater impairment in both behavioral and EEG measures than motion thresholds at the highest levels of blur. The results suggest that high spatial frequencies play an important role in the perception of both global form and motion but are especially significant for global form. Overall, the results reveal complex interactions between low-level factors and global visual processing, highlighting the importance of taking these factors into account when investigating extrastriate function in low vision populations. PMID:26605841

  13. Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation ▿ †

    PubMed Central

    He, Zhili; Zhou, Aifen; Baidoo, Edward; He, Qiang; Joachimiak, Marcin P.; Benke, Peter; Phan, Richard; Mukhopadhyay, Aindrila; Hemme, Christopher L.; Huang, Katherine; Alm, Eric J.; Fields, Matthew W.; Wall, Judy; Stahl, David; Hazen, Terry C.; Keasling, Jay D.; Arkin, Adam P.; Zhou, Jizhong

    2010-01-01

    The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels. PMID:20038696

  14. Atomic oxygen distributions in the Venus thermosphere: Comparisons between Venus Express observations and global model simulations

    NASA Astrophysics Data System (ADS)

    Brecht, A. S.; Bougher, S. W.; Gérard, J.-C.; Soret, L.

    2012-02-01

    Nightglow emissions provide insight into the global thermospheric circulation, specifically in the transition region (˜70-120 km). The O 2 IR nightglow statistical map created from Venus Express (VEx) Visible and InfraRed Thermal Imaging Spectrometer (VIRTIS) observations has been used to deduce a three-dimensional atomic oxygen density map. In this study, the National Center of Atmospheric Research (NCAR) Venus Thermospheric General Circulation Model (VTGCM) is utilized to provide a self-consistent global view of the atomic oxygen density distribution. More specifically, the VTGCM reproduces a 2D nightside atomic oxygen density map and vertical profiles across the nightside, which are compared to the VEx atomic oxygen density map. Both the simulated map and vertical profiles are in close agreement with VEx observations within a ˜30° contour of the anti-solar point. The quality of agreement decreases past ˜30°. This discrepancy implies the employment of Rayleigh friction within the VTGCM may be an over-simplification for representing wave drag effects on the local time variation of global winds. Nevertheless, the simulated atomic oxygen vertical profiles are comparable with the VEx profiles above 90 km, which is consistent with similar O 2 ( 1Δ) IR nightglow intensities. The VTGCM simulations demonstrate the importance of low altitude trace species as a loss for atomic oxygen below 95 km. The agreement between simulations and observations provides confidence in the validity of the simulated mean global thermospheric circulation pattern in the lower thermosphere.

  15. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)

    PubMed Central

    Ohtsu, Kazuhiro; Smith, Marianne B; Emrich, Scott J; Borsuk, Lisa A; Zhou, Ruilian; Chen, Tianle; Zhang, Xiaolan; Timmermans, Marja C P; Beck, Jon; Buckner, Brent; Janick-Buckner, Diane; Nettleton, Dan; Scanlon, Michael J; Schnable, Patrick S

    2007-01-01

    All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P<0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed. PMID:17764504

  16. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

    PubMed

    Ohtsu, Kazuhiro; Smith, Marianne B; Emrich, Scott J; Borsuk, Lisa A; Zhou, Ruilian; Chen, Tianle; Zhang, Xiaolan; Timmermans, Marja C P; Beck, Jon; Buckner, Brent; Janick-Buckner, Diane; Nettleton, Dan; Scanlon, Michael J; Schnable, Patrick S

    2007-11-01

    All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.

  17. Microbial response to simulated global change is phylogenetically conserved and linked with functional potential.

    PubMed

    Amend, Anthony S; Martiny, Adam C; Allison, Steven D; Berlemont, Renaud; Goulden, Michael L; Lu, Ying; Treseder, Kathleen K; Weihe, Claudia; Martiny, Jennifer B H

    2016-01-01

    The high diversity of microbial communities hampers predictions about their responses to global change. Here we investigate the potential for using a phylogenetic, trait-based framework to capture the response of bacteria and fungi to global change manipulations. Replicated grassland plots were subjected to 3+ years of drought and nitrogen fertilization. The responses of leaf litter bacteria and fungi to these simulated changes were significantly phylogenetically conserved. Proportional changes in abundance were highly correlated among related organisms, such that relatives with approximately 5% ribosomal DNA genetic distance showed similar responses to the treatments. A microbe's change in relative abundance was significantly correlated between the treatments, suggesting a compromise between numerical abundance in undisturbed environments and resistance to change in general, independent of disturbance type. Lineages in which at least 90% of the microbes shared the same response were circumscribed at a modest phylogenetic depth (τD 0.014-0.021), but significantly larger than randomized simulations predict. In several clades, phylogenetic depth of trait consensus was higher. Fungal response to drought was more conserved than was response to nitrogen fertilization, whereas bacteria responded equally to both treatments. Finally, we show that a bacterium's response to the manipulations is correlated with its potential functional traits (measured here as the number of glycoside hydrolase genes encoding the capacity to degrade different types of carbohydrates). Together, these results suggest that a phylogenetic, trait-based framework may be useful for predicting shifts in microbial composition and functioning in the face of global change.

  18. Social responses to expressive suppression: The role of personality judgments.

    PubMed

    Tackman, Allison M; Srivastava, Sanjay

    2016-04-01

    Why do people who suppress their emotion-expressive behavior have difficulty forming close, supportive relationships? Previous studies have found that suppression disrupts the dynamics of social interactions and existing relationships. We evaluated a complementary hypothesis: that suppression functions as a behavioral cue leading others to form negative personality impressions of suppressors, even at zero-acquaintance. In 2 studies, participants reported personality judgments and other impressions of targets who either suppressed or expressed their emotion-expressive behavior in response to amusing or sad film clips. In findings replicated across studies, targets who suppressed either amusement or sadness were judged as less extraverted, less agreeable, and more interpersonally avoidant and anxious than targets who expressed emotions, and participants were less interested in affiliating with suppressors compared with expressers. Effects were amplified when targets suppressed amusement (compared with sadness) and when participants knew the emotional context (compared with when they did not) and, thus, could form expectations about what emotions targets should be showing. Extraversion and agreeableness judgments mediated the effect of suppression on participants' disinterest in affiliating. In Study 2, which extended Study 1 in several ways, effects were pronounced for the enthusiasm aspect of extraversion and the compassion aspect of agreeableness. We also found evidence that judgments of suppressors do not simply fall between neutral and fully expressing targets; rather, judgments of suppressors are qualitatively different. We discuss implications for understanding the social consequences of emotion regulation-in particular, how beyond disrupting relationships, suppression may prevent some relationships from even forming in the first place.

  19. Gene Expression Analysis of Alfalfa Seedlings Response to Acid-Aluminum

    PubMed Central

    Lv, Aimin; Wang, Shengyin; Huang, Bingru

    2016-01-01

    Acid-Aluminum (Al) is toxic to plants and greatly affects crop production worldwide. To understand the responses of plants to acid soils and Aluminum toxicity, we examined global gene expression using microarray data in alfalfa seedlings with the treatment of acid-Aluminum. 3,926 genes that were identified significantly up- or downregulated in response to Al3+ ions with pH 4.5 treatment, 66.33% of which were found in roots. Their functional categories were mainly involved with phytohormone regulation, reactive oxygen species, and transporters. Both gene ontology (GO) enrichment and KEGG analysis indicated that phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis played a critical role on defense to Aluminum stress in alfalfa. In addition, we found that transcription factors such as the MYB and WRKY family proteins may be also involved in the regulation of reactive oxygen species reactions and flavonoid biosynthesis. Thus, the finding of global gene expression profile provided insights into the mechanisms of plant defense to acid-Al stress in alfalfa. Understanding the key regulatory genes and pathways would be advantageous for improving crop production not only in alfalfa but also in other crops under acid-Aluminum stress. PMID:28074175

  20. Effect of light on global gene expression in the neuroglobin-deficient mouse retina

    PubMed Central

    ILMJÄRV, STEN; REIMETS, RIIN; HUNDAHL, CHRISTIAN ANSGAR; LUUK, HENDRIK

    2014-01-01

    Several previous studies have raised controversy over the functional role of neuroglobin (Ngb) in the retina. Certain studies indicate a significant impact of Ngb on retinal physiology, whereas others are conflicting. The present is an observational study that tested the effect of Ngb deficiency on gene expression in dark- and light-adapted mouse retinas. Large-scale gene expression profiling was performed using GeneChip® Mouse Exon 1.0 ST arrays and the results were compared to publicly available data sets. The lack of Ngb was found to have a minor effect on the light-induced retinal gene expression response. In addition, there was no increase in the expression of marker genes associated with hypoxia, endoplasmic reticulum-stress and oxidative stress in the Ngb-deficient retina. By contrast, several genes were identified that appeared to be differentially expressed between the genotypes when the effect of light was ignored. The present study indicates that Ngb deficiency does not lead to major alternations in light-dependent gene expression response, but leads to subtle systemic differences of a currently unknown functional significance. PMID:25279145

  1. Gender Differences in Emotional Response: Inconsistency between Experience and Expressivity

    PubMed Central

    Deng, Yaling; Chang, Lei; Yang, Meng; Huo, Meng

    2016-01-01

    The present study investigated gender differences in both emotional experience and expressivity. Heart rate (HR) was recorded as an indicator of emotional experience while the participants watched 16 video clips that induced eight types of emotion (sadness, anger, horror, disgust, neutrality, amusement, surprise, and pleasure). We also asked the participants to report valence, arousal, and motivation as indicators of emotional expressivity. Overall, the results revealed gender differences in emotional experience and emotional expressivity. When watching videos that induced anger, amusement, and pleasure, men showed larger decreases in HR, whereas women reported higher levels of arousal. There was no gender difference in HR when the participants watched videos that induced horror and disgust, but women reported lower valence, higher arousal, and stronger avoidance motivation than did men. Finally, no gender difference was observed in sadness or surprise, although there was one exception—women reported higher arousal when watching videos that induced sadness. The findings suggest that, when watching videos that induce an emotional response, men often have more intense emotional experiences, whereas women have higher emotional expressivity, particularly for negative emotions. In addition, gender differences depend on the specific emotion type but not the valence. PMID:27362361

  2. Mitochondrial gene expression, antioxidant responses, and histopathology after cadmium exposure.

    PubMed

    Al Kaddissi, Simone; Legeay, Alexia; Elia, Antonia Concetta; Gonzalez, Patrice; Floriani, Magali; Cavalie, Isabelle; Massabuau, Jean-Charles; Gilbin, Rodolphe; Simon, Olivier

    2014-08-01

    The present study investigates cadmium effects on the transcription of mitochondrial genes of Procambarus clarkii after acute (0.05, 0.5, and 5 mg Cd/L; 4-10 days) and chronic exposures (10 μg Cd/L; 30-60 days). Transcriptional responses of cox1, atp6, and 12S using quantitative real-time RT-PCR were assessed in gills and hepatopancreas. Additionally, the expression levels of genes involved in detoxification and/or oxidative stress responses [mt, sod(Mn)] and enzymatic activities of antioxidants (SOD, CAT, GPX, and GST) were analyzed. The histopathological effects in hepatopancreas of crayfish were evaluated by light microscopy. Relationships between endpoints at different levels of biological organization and Cd bioaccumulation were also examined. Cd induced high levels of bioaccumulation, which was followed by mitochondrial dysfunction and histological alterations in both experiments. Moreover, perturbations in the defence mechanisms against oxidative stress tended to increase with time. Results also showed that molecular responses can vary depending on the intensity and duration of the chemical stress applied to the organisms and that the study of mt gene expression levels seemed to be the best tool to assess Cd intoxication.

  3. Global Transcriptome Analysis and Identification of Differentially Expressed Genes in Strawberry after Preharvest Application of Benzothiadiazole and Chitosan

    PubMed Central

    Landi, Lucia; De Miccolis Angelini, Rita M.; Pollastro, Stefania; Feliziani, Erica; Faretra, Franco; Romanazzi, Gianfranco

    2017-01-01

    The use of resistance inducers is a novel strategy to elicit defense responses in strawberry fruit to protect against preharvest and postharvest decay. However, the mechanisms behind the specific resistance inducers are not completely understood. Here, global transcriptional changes in strawberry fruit were investigated using RNA-Seq technology. Preharvest, benzothiadiazole (BTH) and chitosan were applied to the plant canopy, and the fruit were harvested at 6, 12, and 24 h post-treatment. Overall, 5,062 and 5,210 differentially expressed genes (fold change ≥ 2) were identified in these fruits under the BTH and chitosan treatments, respectively, as compared to the control expression. About 80% of these genes were differentially expressed by both elicitors. Comprehensive functional enrichment analysis highlighted different gene modulation over time for transcripts associated with photosynthesis and heat-shock proteins, according to elicitor. Up-regulation of genes associated with reprogramming of protein metabolism was observed in fruit treated with both elicitors, which led to increased storage proteins. Several genes associated with the plant immune system, hormone metabolism, systemic acquired resistance, and biotic and abiotic stresses were differentially expressed in treated versus untreated plants. The RNA-Seq output was confirmed using RT-qPCR for 12 selected genes. This study demonstrates that these two elicitors affect cell networks associated with plant defenses in different ways, and suggests a role for chloroplasts as the primary target in this modulation of the plant defense responses, which actively communicate these signals through changes in redox status. The genes identified in this study represent markers to better elucidate plant/pathogen/resistance-inducer interactions, and to plan novel sustainable disease management strategies. PMID:28286508

  4. Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination.

    PubMed

    Strakova, Eva; Bobek, Jan; Zikova, Alice; Vohradsky, Jiri

    2013-01-01

    Streptomycetes have been studied mostly as producers of secondary metabolites, while the transition from dormant spores to an exponentially growing culture has largely been ignored. Here, we focus on a comparative analysis of fluorescently and radioactively labeled proteome and microarray acquired transcriptome expressed during the germination of Streptomyces coelicolor. The time-dynamics is considered, starting from dormant spores through 5.5 hours of growth with 13 time points. Time series of the gene expressions were analyzed using correlation, principal components analysis and an analysis of coding genes utilization. Principal component analysis was used to identify principal kinetic trends in gene expression and the corresponding genes driving S. coelicolor germination. In contrast with the correlation analysis, global trends in the gene/protein expression reflected by the first principal components showed that the prominent patterns in both the protein and the mRNA domains are surprisingly well correlated. Analysis of the number of expressed genes identified functional groups activated during different time intervals of the germination.

  5. Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses

    PubMed Central

    2013-01-01

    Background In the intracellular pathogen Brucella spp., the activation of the stringent response, a global regulatory network providing rapid adaptation to growth-affecting stress conditions such as nutrient deficiency, is essential for replication in the host. A single, bi-functional enzyme Rsh catalyzes synthesis and hydrolysis of the alarmone (p)ppGpp, responsible for differential gene expression under stringent conditions. Results cDNA microarray analysis allowed characterization of the transcriptional profiles of the B. suis 1330 wild-type and Δrsh mutant in a minimal medium, partially mimicking the nutrient-poor intramacrophagic environment. A total of 379 genes (11.6% of the genome) were differentially expressed in a rsh-dependent manner, of which 198 were up-, and 181 were down-regulated. The pleiotropic character of the response was confirmed, as the genes encoded an important number of transcriptional regulators, cell envelope proteins, stress factors, transport systems, and energy metabolism proteins. Virulence genes such as narG and sodC, respectively encoding respiratory nitrate reductase and superoxide dismutase, were under the positive control of (p)ppGpp, as well as expression of the cbb3-type cytochrome c oxidase, essential for chronic murine infection. Methionine was the only amino acid whose biosynthesis was absolutely dependent on stringent response in B. suis. Conclusions The study illustrated the complexity of the processes involved in adaptation to nutrient starvation, and contributed to a better understanding of the correlation between stringent response and Brucella virulence. Most interestingly, it clearly indicated (p)ppGpp-dependent cross-talk between at least three stress responses playing a central role in Brucella adaptation to the host: nutrient, oxidative, and low-oxygen stress. PMID:23834488

  6. Gene expression in the placenta: maternal stress and epigenetic responses.

    PubMed

    Gheorghe, Ciprian P; Goyal, Ravi; Mittal, Ashwani; Longo, Lawrence D

    2010-01-01

    Successful placental development is crucial for optimal growth, development, maturation and survival of the embryo/fetus into adulthood. Numerous epidemiologic and experimental studies have demonstrated the profound influence of intrauterine environment on life, and the diseases to which one is subject as an adult. For the most part, these invidious influences, whether maternal hypoxia, protein or caloric deficiency or excess, and others, represent types of maternal stress. In the present review, we examine certain aspects of gene expression in the placenta as a consequence of maternal stressors. To examine these issues in a controlled manner, and in a species in which the genome has been sequenced, most of these reported studies have been performed in the mouse. Although each individual maternal stress is characterized by up- or down-regulation of specific genes in the placenta, functional analysis reveals some patterns of gene expression common to the several forms of stress. Of critical importance, these genes include those involved in DNA methylation and histone modification, cell cycle regulation, and related global pathways of great relevance to epigenesis and the developmental origins of adult health and disease.

  7. Histone H1 and heterochromatin protein 1 (HP1) regulate specific gene expression and not global transcription

    PubMed Central

    Jedrusik-Bode, Monika

    2013-01-01

    The highly conserved Hox transcription factors define positional identity along the anterior-posterior body axis during development. Inappropriate expression of Hox genes causes homeotic transformation, which leads to abnormal development of a specific region or segment. C. elegans offers an excellent model for studying factors required for the establishment of the spatially-restricted expression of Hox genes. We have recently identified chromatin factors, including a linker histone (H1) variant, HIS-24 and heterochromatin protein 1 (HP1) homolog, HPL-2, which contribute to the regulation of specific Hox gene expression through their binding to the repressive mark, H3K27me3. Furthermore, HIS-24 and HPL-2 act in a parallel pathway as members of the evolutionally conserved Polycomb group (PcG) silencing complex, MES-2/3/6. By microarray analysis, we found that HIS-24 and HPL-2 are not global transcriptional repressors as suggested by early studies, but rather are fine tuners of selected genes. Here, we discuss how HIS-24 and HPL-2 are responsible for the repression of specific genes in C. elegans. We suggest possible mechanisms for such an unanticipated function of an individual H1 variant and HP1 in the transcriptional repression of Hox genes. PMID:24058872

  8. Potential applications of global protein expression analysis (proteomics) in morbid obesity and bariatric surgery.

    PubMed

    Brandacher, Gerald; Golderer, Georg; Kienzl, Katrin; Werner, Ernst R; Margreiter, Raimund; Weiss, Helmut G

    2008-07-01

    Global protein expression analysis, known as proteomics, has emerged as a novel scientific technology currently successfully applied to several fields of medicine including cancer and transplantation. Thereby, a thorough exploration of the pathogenic mechanisms and a better understanding of the pathophysiology of diseases as well as identification of diagnostic biomarkers have been achieved. In this paper, we outline the basic principles and potential applications of this promising tool in bariatric surgery where proteomics might hold great potential for new insights into diagnostic and therapeutic decision making based on improved knowledge of metabolic regulations pre- and postsurgical interventions in morbidly obese patients.

  9. Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa.

    PubMed

    Zhang, Yu; Peng, Lifang; Wu, Ya; Shen, Yanyue; Wu, Xiaoming; Wang, Jianbo

    2014-11-01

    Embryo development represents a crucial developmental period in the life cycle of flowering plants. To gain insights into the genetic programs that control embryo development in Brassica rapa L., RNA sequencing technology was used to perform transcriptome profiling analysis of B. rapa developing embryos. The results generated 42,906,229 sequence reads aligned with 32,941 genes. In total, 27,760, 28,871, 28,384, and 25,653 genes were identified from embryos at globular, heart, early cotyledon, and mature developmental stages, respectively, and analysis between stages revealed a subset of stage-specific genes. We next investigated 9,884 differentially expressed genes with more than fivefold changes in expression and false discovery rate ≤ 0.001 from three adjacent-stage comparisons; 1,514, 3,831, and 6,633 genes were detected between globular and heart stage embryo libraries, heart stage and early cotyledon stage, and early cotyledon and mature stage, respectively. Large numbers of genes related to cellular process, metabolism process, response to stimulus, and biological process were expressed during the early and middle stages of embryo development. Fatty acid biosynthesis, biosynthesis of secondary metabolites, and photosynthesis-related genes were expressed predominantly in embryos at the middle stage. Genes for lipid metabolism and storage proteins were highly expressed in the middle and late stages of embryo development. We also identified 911 transcription factor genes that show differential expression across embryo developmental stages. These results increase our understanding of the complex molecular and cellular events during embryo development in B. rapa and provide a foundation for future studies on other oilseed crops.

  10. Time-lag effects of global vegetation responses to climate change.

    PubMed

    Wu, Donghai; Zhao, Xiang; Liang, Shunlin; Zhou, Tao; Huang, Kaicheng; Tang, Bijian; Zhao, Wenqian

    2015-09-01

    Climate conditions significantly affect vegetation growth in terrestrial ecosystems. Due to the spatial heterogeneity of ecosystems, the vegetation responses to climate vary considerably with the diverse spatial patterns and the time-lag effects, which are the most important mechanism of climate-vegetation interactive effects. Extensive studies focused on large-scale vegetation-climate interactions use the simultaneous meteorological and vegetation indicators to develop models; however, the time-lag effects are less considered, which tends to increase uncertainty. In this study, we aim to quantitatively determine the time-lag effects of global vegetation responses to different climatic factors using the GIMMS3g NDVI time series and the CRU temperature, precipitation, and solar radiation datasets. First, this study analyzed the time-lag effects of global vegetation responses to different climatic factors. Then, a multiple linear regression model and partial correlation model were established to statistically analyze the roles of different climatic factors on vegetation responses, from which the primary climate-driving factors for different vegetation types were determined. The results showed that (i) both the time-lag effects of the vegetation responses and the major climate-driving factors that significantly affect vegetation growth varied significantly at the global scale, which was related to the diverse vegetation and climate characteristics; (ii) regarding the time-lag effects, the climatic factors explained 64% variation of the global vegetation growth, which was 11% relatively higher than the model ignoring the time-lag effects; (iii) for the area with a significant change trend (for the period 1982-2008) in the global GIMMS3g NDVI (P < 0.05), the primary driving factor was temperature; and (iv) at the regional scale, the variation in vegetation growth was also related to human activities and natural disturbances. Considering the time-lag effects is quite

  11. Model-based synthesis of locally contingent responses to global market signals

    NASA Astrophysics Data System (ADS)

    Magliocca, N. R.

    2015-12-01

    Rural livelihoods and the land systems on which they depend are increasingly influenced by distant markets through economic globalization. Place-based analyses of land and livelihood system sustainability must then consider both proximate and distant influences on local decision-making. Thus, advancing land change theory in the context of economic globalization calls for a systematic understanding of the general processes as well as local contingencies shaping local responses to global signals. Synthesis of insights from place-based case studies of land and livelihood change is a path forward for developing such systematic knowledge. This paper introduces a model-based synthesis approach to investigating the influence of local socio-environmental and agent-level factors in mediating land-use and livelihood responses to changing global market signals. A generalized agent-based modeling framework is applied to six case-study sites that differ in environmental conditions, market access and influence, and livelihood settings. The largest modeled land conversions and livelihood transitions to market-oriented production occurred in sties with relatively productive agricultural land and/or with limited livelihood options. Experimental shifts in the distributions of agents' risk tolerances generally acted to attenuate or amplify responses to changes in global market signals. Importantly, however, responses of agents at different points in the risk tolerance distribution varied widely, with the wealth gap growing wider between agents with higher or lower risk tolerance. These results demonstrate model-based synthesis is a promising approach to overcome many of the challenges of current synthesis methods in land change science, and to identify generalized as well as locally contingent responses to global market signals.

  12. Global Cross-Talk of Genes of the Mosquito Aedes aegypti in Response to Dengue Virus Infection

    PubMed Central

    Behura, Susanta K.; Gomez-Machorro, Consuelo; Harker, Brent W.; deBruyn, Becky; Lovin, Diane D.; Hemme, Ryan R.; Mori, Akio; Romero-Severson, Jeanne; Severson, David W.

    2011-01-01

    Background The mosquito Aedes aegypti is the primary vector of dengue virus (DENV) infection in humans, and DENV is the most important arbovirus across most of the subtropics and tropics worldwide. The early time periods after infection with DENV define critical cellular processes that determine ultimate success or failure of the virus to establish infection in the mosquito. Methods and Results To identify genes involved in these processes, we performed genome-wide transcriptome profiling between susceptible and refractory A. aegypti strains at two critical early periods after challenging them with DENV. Genes that responded coordinately to DENV infection in the susceptible strain were largely clustered in one specific expression module, whereas in the refractory strain they were distributed in four distinct modules. The susceptible response module in the global transcriptional network showed significant biased representation with genes related to energy metabolism and DNA replication, whereas the refractory response modules showed biased representation across different metabolism pathway genes including cytochrome P450 and DDT [1,1,1-Trichloro-2,2-bis(4-chlorophenyl) ethane] degradation genes, and genes associated with cell growth and death. A common core set of coordinately expressed genes was observed in both the susceptible and refractory mosquitoes and included genes related to the Wnt (Wnt: wingless [wg] and integration 1 [int1] pathway), MAPK (Mitogen-activated protein kinase), mTOR (mammalian target of rapamycin) and JAK-STAT (Janus Kinase - Signal Transducer and Activator of Transcription) pathways. Conclusions Our data revealed extensive transcriptional networks of mosquito genes that are expressed in modular manners in response to DENV infection, and indicated that successfully defending against viral infection requires more elaborate gene networks than hosting the virus. These likely play important roles in the global-cross talk among the mosquito host

  13. Proteome investigation of the global regulatory role of sigma 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867.

    PubMed

    Zhao, Bing; Yeo, Chew Chieng; Poh, Chit Laa

    2005-05-01

    Pseudomonas alcaligenes NCIMB 9867 (strain P25X) utilizes the gentisate pathway for the degradation of aromatic hydrocarbons. The gene encoding the alternative sigma (sigma) factor sigma(54), rpoN, was cloned from strain P25X and a rpoN knock-out strain, designated G54, was constructed by insertional inactivation with a kanamycin resistance gene cassette. The role of sigma(54) in the physiological response of P. alcaligenes P25X to gentisate induction was assessed by comparing the global protein expression profiles of the wild-type P25X with the rpoN mutant strain G54. Analysis of two-dimensional polyacrylamide gel electrophoresis gels showed that 39 out of 355 prominent protein spots exhibited differential expression as a result of the insertional inactivation of rpoN. Identification of the protein spots by matrix-assisted laser desorption/ionization-time of flight/time of flight revealed a wide diversity of proteins that are affected by the sigma(54) mutation, the largest group being proteins that are involved in carbon metabolism. The strictly inducible gentisate 1,2-dioxygenase, one of two isofunctional copies of the key enzyme in the gentisate pathway, and enzymes of the TCA cycle, pyruvate metabolism and gluconeogenesis were part of this group. Other proteins that are part of the sigma(54) regulon include enzymes implicated in nitrogen metabolism, transport proteins, stress-response proteins and proteins involved in cell motility. The results of this study showed that sigma(54) plays a global regulatory role in the expression of a wide variety of genes in P. alcaligenes, including the wild-type response to the presence of the aromatic inducer, gentisate.

  14. Global measures: utility in defining and measuring treatment response in dementia.

    PubMed

    Reisberg, Barry

    2007-06-01

    Global measures used in treatment trials in dementia encompass two distinct categories: (1) clinician's interview-based global severity scales, and (2) clinician's interview-based global change scales. The global severity scales that have been used include: the Clinical Dementia Rating (CDR) and the related CDR-sum of boxes (CDR-SB), the Global Deterioration Scale (GDS), and the Functional Assessment Staging (FAST) procedure. The global severity scales are clearly useful in subject categorization in treatment trials, in part because they are relatively free of many of the sociocultural biases inherent in mental status and psychometric descriptors. Global severity scales can also be used to demonstrate therapeutic efficacy in terms of the general progression of the dementia process. These measures have also proven to be useful in sensitively assessing pharmacotherapeutic effects in Alzheimer's disease (AD) treatment trials. For example, in pivotal trials: (1) in Mild to Moderate AD, the GDS has shown significant change in response to medication, whereas the results on the Mini-mental State Examination (MMSE) were not significant, and (2) in Moderate to Severe AD, the FAST has shown significant pharmacotherapeutic efficacy, whereas the results using the MMSE were not significant. The global change scales employed in dementia trials differ widely in assessment methodology. Clinical Global Impressions of Change (CGIC) scales do not have defined methodologies, whereas Clinician's Interview-Based Impression of Change Plus Caregiver Input (CIBIC-Plus) scales are much more elaborate. The CIBIC-Plus procedures require an independent clinician assessment and can provide independent, comprehensive evidence of therapeutic efficacy. The CIBIC-Plus procedure may also be useful in sensitively assessing efficacy in future prevention trials, for example in subjects with Subjective Cognitive Impairment. For Mild Cognitive Impairment (MCI), global severity scales already appear to be

  15. Challenges to global surveillance and response to infectious disease outbreaks of international importance.

    PubMed

    Hitchcock, Penny; Chamberlain, Allison; Van Wagoner, Megan; Inglesby, Thomas V; O'Toole, Tara

    2007-09-01

    This article presents a notional scheme of global surveillance and response to infectious disease outbreaks and reviews 14 international surveillance and response programs. In combination, the scheme and the programs illustrate how, in an ideal world and in the real world, infectious disease outbreaks of public health significance could be detected and contained. Notable practices and achievements of the programs are cited; these may be useful when instituting new programs or redesigning existing ones. Insufficiencies are identified in four critical areas: health infrastructure; scientific methods and concepts of operation; essential human, technical, and financial resources; and international policies. These insufficiencies challenge global surveillance of and response to infectious disease outbreaks of international importance. This article is intended to help policymakers appreciate the complexity of the problem and assess the impact and cost-effectiveness of proposed solutions. An assessment of the potential contribution of appropriate diagnostic tests to surveillance and response is included.

  16. Evolutionary history underlies plant physiological responses to global change since the last glacial maximum.

    PubMed

    Becklin, Katie M; Medeiros, Juliana S; Sale, Kayla R; Ward, Joy K

    2014-06-01

    Assessing family- and species-level variation in physiological responses to global change across geologic time is critical for understanding factors that underlie changes in species distributions and community composition. Here, we used stable carbon isotopes, leaf nitrogen content and stomatal measurements to assess changes in leaf-level physiology in a mixed conifer community that underwent significant changes in composition since the last glacial maximum (LGM) (21 kyr BP). Our results indicate that most plant taxa decreased stomatal conductance and/or maximum photosynthetic capacity in response to changing conditions since the LGM. However, plant families and species differed in the timing and magnitude of these physiological responses, and responses were more similar within families than within co-occurring species assemblages. This suggests that adaptation at the level of leaf physiology may not be the main determinant of shifts in community composition, and that plant evolutionary history may drive physiological adaptation to global change over recent geologic time.

  17. Stress, and pathogen response gene expression in modeled microgravity

    NASA Technical Reports Server (NTRS)

    Sundaresan, Alamelu; Pellis, Neal R.

    2006-01-01

    Purpose: Immune suppression in microgravity has been well documented. With the advent of human exploration and long-term space travel, the immune system of the astronaut must be optimally maintained. It is important to investigate the expression patterns of cytokine genes, because they are directly related to immune response. Heat shock proteins (HSPs), also called stress proteins, are a group of proteins that are present in the cells of every life form. These proteins are induced when a cell responds to stressors such as heat, cold and oxygen deprivation. Microgravity is another stressor that may regulate HSPs. Heat shock proteins trigger immune response through activities that occur both inside the cell (intracellular) and outside the cell (extracellular). Knowledge about these two gene groups could lead to establishment of a blueprint of the immune response and adaptation-related genes in the microgravity environment. Methods: Human peripheral blood cells were cultured in 1g (T flask) and modeled microgravity (MMG, rotating-wall vessel) for 24 and 72 hours. Cell samples were collected and subjected to gene array analysis using the Affymetrix HG_U95 array. Data was collected and subjected to a two-way analysis of variance. The genes related to immune and stress responses were analyzed. Results and Conclusions: HSP70 was up-regulated by more than two fold in microgravity culture, while HSP90 was significantly down-regulated. HSP70 is not typically expressed in all kinds of cells, but it is expressed at high levels in stress conditions. HSP70 participates in translation, protein translocation, proteolysis and protein folding, suppressing aggregation and reactivating denatured proteins. Increased serum HSP70 levels correlate with a better outcome for heat-stroke or severe trauma patients. At the same time, elevated serum levels of HSP70 have been detected in patients with peripheral or renal vascular disease. HSP90 has been identified in the cytosol, nucleus and

  18. Impact of smoking cessation on global gene expression in the bronchial epithelium of chronic smokers

    PubMed Central

    Zhang, Li; Lee, Jack; Tang, Hongli; Fan, You-Hong; Xiao, Lianchun; Ren, Hening; Kurie, Jonathan; Morice, Rodolfo C; Hong, Waun Ki; Mao, Li

    2014-01-01

    Cigarette smoke is the major cause of lung cancer and can interact in complex ways with drugs for lung cancer prevention or therapy. Molecular genetic research promises to elucidate the biologic mechanisms underlying divergent drug effects in smokers versus non-smokers and to help in developing new approaches for controlling lung cancer. The present study compared global gene expression profiles (determined via Affymetrix microarray measurements in bronchial epithelial cells) between chronic smokers, former smokers, and never smokers. Smoking effects on global gene expression were determined from a combined analysis of three independent datasets. Differential expression between current and never smokers occurred in 591 of the 13,902 genes measured on the microarrays (P < 0.01 and >2 fold change; pooled data)—a profound effect. In contrast, differential expression between current and former smokers occurred in only 145 of the measured genes (P < 0.01 and >2 fold change; pooled data). Nine of these 145 genes showed consistent and significant changes in each of the three datasets (P < 0.01 and >2 fold change), with 8 being down-regulated in former smokers. Seven of the 8 down-regulated genes, including CYP1B1 and 3 AKR genes, influence the metabolism of carcinogens and/or therapeutic/chemopreventive agents. Our data comparing former and current smokers allowed us to pinpoint the genes involved in smoking–drug interactions in lung cancer prevention and therapy. These findings have important implications for developing new targeted and dosing approaches for prevention and therapy in the lung and other sites, highlighting the importance of monitoring smoking status in patients receiving oncologic drug interventions. PMID:19138944

  19. Earth's changing global atmospheric energy cycle in response to climate change

    NASA Astrophysics Data System (ADS)

    Pan, Yefeng; Li, Liming; Jiang, Xun; Li, Gan; Zhang, Wentao; Wang, Xinyue; Ingersoll, Andrew P.

    2017-01-01

    The Lorenz energy cycle is widely used to investigate atmospheres and climates on planets. However, the long-term temporal variations of such an energy cycle have not yet been explored. Here we use three independent meteorological data sets from the modern satellite era, to examine the temporal characteristics of the Lorenz energy cycle of Earth's global atmosphere in response to climate change. The total mechanical energy of the global atmosphere basically remains constant with time, but the global-average eddy energies show significant positive trends. The spatial investigations suggest that these positive trends are concentrated in the Southern Hemisphere. Significant positive trends are also found in the conversion, generation and dissipation rates of energies. The positive trends in the dissipation rates of kinetic energies suggest that the efficiency of the global atmosphere as a heat engine increased during the modern satellite era.

  20. Earth's changing global atmospheric energy cycle in response to climate change

    PubMed Central

    Pan, Yefeng; Li, Liming; Jiang, Xun; Li, Gan; Zhang, Wentao; Wang, Xinyue; Ingersoll, Andrew P.

    2017-01-01

    The Lorenz energy cycle is widely used to investigate atmospheres and climates on planets. However, the long-term temporal variations of such an energy cycle have not yet been explored. Here we use three independent meteorological data sets from the modern satellite era, to examine the temporal characteristics of the Lorenz energy cycle of Earth's global atmosphere in response to climate change. The total mechanical energy of the global atmosphere basically remains constant with time, but the global-average eddy energies show significant positive trends. The spatial investigations suggest that these positive trends are concentrated in the Southern Hemisphere. Significant positive trends are also found in the conversion, generation and dissipation rates of energies. The positive trends in the dissipation rates of kinetic energies suggest that the efficiency of the global atmosphere as a heat engine increased during the modern satellite era. PMID:28117324

  1. Earth's changing global atmospheric energy cycle in response to climate change.

    PubMed

    Pan, Yefeng; Li, Liming; Jiang, Xun; Li, Gan; Zhang, Wentao; Wang, Xinyue; Ingersoll, Andrew P

    2017-01-24

    The Lorenz energy cycle is widely used to investigate atmospheres and climates on planets. However, the long-term temporal variations of such an energy cycle have not yet been explored. Here we use three independent meteorological data sets from the modern satellite era, to examine the temporal characteristics of the Lorenz energy cycle of Earth's global atmosphere in response to climate change. The total mechanical energy of the global atmosphere basically remains constant with time, but the global-average eddy energies show significant positive trends. The spatial investigations suggest that these positive trends are concentrated in the Southern Hemisphere. Significant positive trends are also found in the conversion, generation and dissipation rates of energies. The positive trends in the dissipation rates of kinetic energies suggest that the efficiency of the global atmosphere as a heat engine increased during the modern satellite era.

  2. On the response of the global subduction rate to globalwarming in coupled climate models

    NASA Astrophysics Data System (ADS)

    Liu, Chengyan; Wang, Zhaomin

    2014-01-01

    The response of the global subduction rate to global warming was assessed based on a set of Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) models. It was found that the subduction rate of the global ocean could be significantly reduced under a warming climate, as compared to a simulation of the present-day climate. The reduction in the subduction volume was quantitatively estimated at about 40 Sv and was found to be primarily induced by the decreasing of the lateral induction term due to a shallower winter mixed layer depth. The shrinking of the winter mixed layer would result from intensified stratification caused by increased heat input into the ocean under a warming climate. A reduction in subduction associated with the vertical pumping term was estimated at about 5 Sv. Further, in the Southern Ocean, a significant reduction in subduction was estimated at around 24 Sv, indicating a substantial contribution to the weakening of global subduction.

  3. Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression

    PubMed Central

    Palumbo, Alex; Nagarajan, Radha; Gardiner, David M.; Muneoka, Ken; Stromberg, Arnold J.; Athippozhy, Antony T.

    2015-01-01

    Abstract While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post‐amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non‐injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well‐described stages of limb regeneration—amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set. PMID:27168937

  4. Global gene expression analysis using RNA-seq uncovered a new role for SR1/CAMTA3 transcription factor in salt stress

    PubMed Central

    Prasad, Kasavajhala V. S. K.; Abdel-Hameed, Amira A. E.; Xing, Denghui; Reddy, Anireddy S. N.

    2016-01-01

    Abiotic and biotic stresses cause significant yield losses in all crops. Acquisition of stress tolerance in plants requires rapid reprogramming of gene expression. SR1/CAMTA3, a member of signal responsive transcription factors (TFs), functions both as a positive and a negative regulator of biotic stress responses and as a positive regulator of cold stress-induced gene expression. Using high throughput RNA-seq, we identified ~3000 SR1-regulated genes. Promoters of about 60% of the differentially expressed genes have a known DNA binding site for SR1, suggesting that they are likely direct targets. Gene ontology analysis of SR1-regulated genes confirmed previously known functions of SR1 and uncovered a potential role for this TF in salt stress. Our results showed that SR1 mutant is more tolerant to salt stress than the wild type and complemented line. Improved tolerance of sr1 seedlings to salt is accompanied with the induction of salt-responsive genes. Furthermore, ChIP-PCR results showed that SR1 binds to promoters of several salt-responsive genes. These results suggest that SR1 acts as a negative regulator of salt tolerance by directly repressing the expression of salt-responsive genes. Overall, this study identified SR1-regulated genes globally and uncovered a previously uncharacterized role for SR1 in salt stress response. PMID:27251464

  5. A Robust Response of Precipitation to Global Warming from CMIP5 Models

    NASA Technical Reports Server (NTRS)

    Lau, K. -M.; Wu, H. -T.; Kim, K. -M.

    2012-01-01

    How precipitation responds to global warming is a major concern to society and a challenge to climate change research. Based on analyses of rainfall probability distribution functions of 14 state-of-the-art climate models, we find a robust, canonical global rainfall response to a triple CO2 warming scenario, featuring 100 250% more heavy rain, 5-10% less moderate rain, and 10-15% more very light or no-rain events. Regionally, a majority of the models project a consistent response with more heavy rain events over climatologically wet regions of the deep tropics, and more dry events over subtropical and tropical land areas. Results suggest that increased CO2 emissions induce basic structural changes in global rain systems, increasing risks of severe floods and droughts in preferred geographic locations worldwide.

  6. Global Agenda, Local Responses: Changing Education Governance in Hong Kong's Higher Education

    ERIC Educational Resources Information Center

    Chan, David K. K.

    2007-01-01

    Hong Kong has undergone a series of educational reforms since the mid 1990s in response to the tidal wave of globalisation. This article tries to examine the recent education reforms in Hong Kong's higher education within the global context, by putting into perspective a discussion of its policy implications of marketisation, privatisation and…

  7. Nonlinear, interacting responses to climate limit grassland production under global change.

    PubMed

    Zhu, Kai; Chiariello, Nona R; Tobeck, Todd; Fukami, Tadashi; Field, Christopher B

    2016-09-20

    Global changes in climate, atmospheric composition, and pollutants are altering ecosystems and the goods and services they provide. Among approaches for predicting ecosystem responses, long-term observations and manipulative experiments can be powerful approaches for resolving single-factor and interactive effects of global changes on key metrics such as net primary production (NPP). Here we combine both approaches, developing multidimensional response surfaces for NPP based on the longest-running, best-replicated, most-multifactor global-change experiment at the ecosystem scale-a 17-y study of California grassland exposed to full-factorial warming, added precipitation, elevated CO2, and nitrogen deposition. Single-factor and interactive effects were not time-dependent, enabling us to analyze each year as a separate realization of the experiment and extract NPP as a continuous function of global-change factors. We found a ridge-shaped response surface in which NPP is humped (unimodal) in response to temperature and precipitation when CO2 and nitrogen are ambient, with peak NPP rising under elevated CO2 or nitrogen but also shifting to lower temperatures. Our results suggest that future climate change will push this ecosystem away from conditions that maximize NPP, but with large year-to-year variability.

  8. Global Influences and Local Responses: The Restructuring of the University of Botswana, 1990-2000

    ERIC Educational Resources Information Center

    Tabulawa, Richard

    2007-01-01

    The University of Botswana has not escaped the reform fever currently gripping higher education institutions the world-over. In the late 1980s the University initiated an administrative/management restructuring exercise whose resultant structure was implemented between 1998 and 2000. The exercise, in many respects, was a response to globalization.…

  9. Nonlinear, interacting responses to climate limit grassland production under global change

    PubMed Central

    Zhu, Kai; Chiariello, Nona R.; Tobeck, Todd; Fukami, Tadashi; Field, Christopher B.

    2016-01-01

    Global changes in climate, atmospheric composition, and pollutants are altering ecosystems and the goods and services they provide. Among approaches for predicting ecosystem responses, long-term observations and manipulative experiments can be powerful approaches for resolving single-factor and interactive effects of global changes on key metrics such as net primary production (NPP). Here we combine both approaches, developing multidimensional response surfaces for NPP based on the longest-running, best-replicated, most-multifactor global-change experiment at the ecosystem scale—a 17-y study of California grassland exposed to full-factorial warming, added precipitation, elevated CO2, and nitrogen deposition. Single-factor and interactive effects were not time-dependent, enabling us to analyze each year as a separate realization of the experiment and extract NPP as a continuous function of global-change factors. We found a ridge-shaped response surface in which NPP is humped (unimodal) in response to temperature and precipitation when CO2 and nitrogen are ambient, with peak NPP rising under elevated CO2 or nitrogen but also shifting to lower temperatures. Our results suggest that future climate change will push this ecosystem away from conditions that maximize NPP, but with large year-to-year variability. PMID:27601643

  10. Internationalization as a Response to Globalization: Radical Shifts in University Environments

    ERIC Educational Resources Information Center

    Stromquist, Nelly P.

    2007-01-01

    This case study probes recent developments in a number of academic and non-academic aspects of a private research university in response to current globalization trends. Under the name of internationalization, university administrators and external firms are emerging as powerful decision-makers shaping academic content and even academic…

  11. Gene Expression Dynamics Accompanying the Sponge Thermal Stress Response

    PubMed Central

    Guzman, Christine; Conaco, Cecilia

    2016-01-01

    Marine sponges are important members of coral reef ecosystems. Thus, their responses to changes in ocean chemistry and environmental conditions, particularly to higher seawater temperatures, will have potential impacts on the future of these reefs. To better understand the sponge thermal stress response, we investigated gene expression dynamics in the shallow water sponge, Haliclona tubifera (order Haplosclerida, class Demospongiae), subjected to elevated temperature. Using high-throughput transcriptome sequencing, we show that these conditions result in the activation of various processes that interact to maintain cellular homeostasis. Short-term thermal stress resulted in the induction of heat shock proteins, antioxidants, and genes involved in signal transduction and innate immunity pathways. Prolonged exposure to thermal stress affected the expression of genes involved in cellular damage repair, apoptosis, signaling and transcription. Interestingly, exposure to sublethal temperatures may improve the ability of the sponge to mitigate cellular damage under more extreme stress conditions. These insights into the potential mechanisms of adaptation and resilience of sponges contribute to a better understanding of sponge conservation status and the prediction of ecosystem trajectories under future climate conditions. PMID:27788197

  12. Global vegetation productivity response to climatic oscillations during the satellite era.

    PubMed

    Gonsamo, Alemu; Chen, Jing M; Lombardozzi, Danica

    2016-10-01

    Climate control on global vegetation productivity patterns has intensified in response to recent global warming. Yet, the contributions of the leading internal climatic variations to global vegetation productivity are poorly understood. Here, we use 30 years of global satellite observations to study climatic variations controls on continental and global vegetation productivity patterns. El Niño-Southern Oscillation (ENSO) phases (La Niña, neutral, and El Niño years) appear to be a weaker control on global-scale vegetation productivity than previously thought, although continental-scale responses are substantial. There is also clear evidence that other non-ENSO climatic variations have a strong control on spatial patterns of vegetation productivity mainly through their influence on temperature. Among the eight leading internal climatic variations, the East Atlantic/West Russia Pattern extensively controls the ensuing year vegetation productivity of the most productive tropical and temperate forest ecosystems of the Earth's vegetated surface through directionally consistent influence on vegetation greenness. The Community Climate System Model (CCSM4) simulations do not capture the observed patterns of vegetation productivity responses to internal climatic variations. Our analyses show the ubiquitous control of climatic variations on vegetation productivity and can further guide CCSM and other Earth system models developments to represent vegetation response patterns to unforced variability. Several winter time internal climatic variation indices show strong potentials on predicting growing season vegetation productivity two to six seasons ahead which enables national governments and farmers forecast crop yield to ensure supplies of affordable food, famine early warning, and plan management options to minimize yield losses ahead of time.

  13. Mitochondrial and Nuclear Genomic Responses to Loss of LRPPRC Expression*

    PubMed Central

    Gohil, Vishal M.; Nilsson, Roland; Belcher-Timme, Casey A.; Luo, Biao; Root, David E.; Mootha, Vamsi K.

    2010-01-01

    Rapid advances in genotyping and sequencing technology have dramatically accelerated the discovery of genes underlying human disease. Elucidating the function of such genes and understanding their role in pathogenesis, however, remain challenging. Here, we introduce a genomic strategy to characterize such genes functionally, and we apply it to LRPPRC, a poorly studied gene that is mutated in Leigh syndrome, French-Canadian type (LSFC). We utilize RNA interference to engineer an allelic series of cellular models in which LRPPRC has been stably silenced to different levels of knockdown efficiency. We then combine genome-wide expression profiling with gene set enrichment analysis to identify cellular responses that correlate with the loss of LRPPRC. Using this strategy, we discovered a specific role for LRPPRC in the expression of all mitochondrial DNA-encoded mRNAs, but not the rRNAs, providing mechanistic insights into the enzymatic defects observed in the disease. Our analysis shows that nuclear genes encoding mitochondrial proteins are not collectively affected by the loss of LRPPRC. We do observe altered expression of genes related to hexose metabolism, prostaglandin synthesis, and glycosphingolipid biology that may either play an adaptive role in cell survival or contribute to pathogenesis. The combination of genetic perturbation, genomic profiling, and pathway analysis represents a generic strategy for understanding disease pathogenesis. PMID:20220140

  14. Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing.

    PubMed

    Chen, Zhiyuan; Hagen, Darren E; Wang, Juanbin; Elsik, Christine G; Ji, Tieming; Siqueira, Luiz G; Hansen, Peter J; Rivera, Rocío M

    2016-07-02

    Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ∼105 Bos taurus indicus × Bos taurus taurus F1 conceptuses using RNA sequencing. To accomplish this, we developed a bioinformatics pipeline to identify parent-specific single nucleotide polymorphism alleles after filtering adenosine to inosine (A-to-I) RNA editing sites. We identified 53 genes subject to monoallelic expression. Twenty three are genes known to be imprinted in the cow and an additional 7 have previously been characterized as imprinted in human and/or mouse that have not been reported as imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinted clusters, whereas the other 13 genes are distributed throughout the bovine genome and are not close to any known imprinted clusters. To exclude potential cis-eQTL effects on allele expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus × Bos taurus taurus conceptuses and identified 8 novel bovine imprinted genes. Further, we identified 671 candidate A-to-I RNA editing sites and describe random X-inactivation in day 15 bovine extraembryonic membranes. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effects.

  15. DCX-expressing neurons decrease in the retrosplenial cortex after global brain ischemia.

    PubMed

    Kutsuna, Nobuo; Murata, Yoshihiro; Eriguchi, Takashi; Takada, Yoshiyuki; Oshima, Hideki; Sakatani, Kaoru; Katayama, Yoichi

    2013-01-01

    Many studies have demonstrated cognitive function disorders including space learning disorders after global brain ischemia (GBI). Previous research on space perception and learning has indicated that the retrosplenial cortex (RS) is strongly involved. We performed immunostaining with doublecortin (DCX) for neurons with plasticity potential in the RS and investigated the neuronal numbers to assess the changes of plasticity in the RS following GBI. We employed male Sprague-Dawley rats and carried out bilateral carotid arterial occlusion for 10 min as a GBI model (control, n = 5; GBI model, n = 5). We counted the right and left hemispheres separately on two serial sections, for a total of four regions per animal to examine the differences in expression related to GBI. Additionally, we performed Fluoro-Jade B (FJB) staining to investigate the cause of any DCX-expressing neuron decrease. The total number of DCX-expressing neurons was 1,652 and 912 in the controls and GBI model, respectively. The mean number of DCX-expressing neurons per unit area was significantly lower in the GBI model than in the controls. FJB positive neurons were not found in the RS, while many were present in the -hippocampus CA1 after GBI. The decrease of DCX-expressing neurons in the RS indicated a plasticity decrease following GBI. The lack of FJB positive neurons in the RS after GBI suggested that the decrease of DCX-expressing neurons in the RS was not due to neuronal cell death in contrast to the hippocampus CA1, while the FJB positive neurons in the hippocampus indicated a delayed neuronal cell death as observed in many previous studies.

  16. Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing

    PubMed Central

    Chen, Zhiyuan; Hagen, Darren E.; Wang, Juanbin; Elsik, Christine G.; Ji, Tieming; Siqueira, Luiz G.; Hansen, Peter J.; Rivera, Rocío M.

    2016-01-01

    ABSTRACT Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ∼105 Bos taurus indicus × Bos taurus taurus F1 conceptuses using RNA sequencing. To accomplish this, we developed a bioinformatics pipeline to identify parent-specific single nucleotide polymorphism alleles after filtering adenosine to inosine (A-to-I) RNA editing sites. We identified 53 genes subject to monoallelic expression. Twenty three are genes known to be imprinted in the cow and an additional 7 have previously been characterized as imprinted in human and/or mouse that have not been reported as imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinted clusters, whereas the other 13 genes are distributed throughout the bovine genome and are not close to any known imprinted clusters. To exclude potential cis-eQTL effects on allele expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus × Bos taurus taurus conceptuses and identified 8 novel bovine imprinted genes. Further, we identified 671 candidate A-to-I RNA editing sites and describe random X-inactivation in day 15 bovine extraembryonic membranes. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effects. PMID:27245094

  17. [Global expression profiling of Saccharomyces cerevisiae: metabolic remodeling in post-log phase].

    PubMed

    Ye, Yanrui; Tang, Yuqian; Chen, Hongyun; Zheng, Suiping; Pan, Li; Lin, Ying

    2008-06-01

    For the purpose of revealing the mechanism of the reduction of yeasts ethanol production rate after entrance of post-log phase, we used microarray to study expression profiles of the yeast Saccharomyces cerevisiae during the transition from mid-log growth phase to post-log growth. The results demonstrate that the global pattern of gene expression is very stable during the mid-log phase. However, a dramatic metabolic remodeling was found when the yeast entries post-log phase, during which many of amino acid synthesis and metabolism related genes are up-regulated, moreover, ion transport, energy generation and storage related genes are also up regulated during this phase, while a large number of genes involved in transposition and DNA recombination are repressed. Central metabolic pathways also engage in metabolic remodeling, within which the genes involved in succinate and a-ketoglutarate synthesis pathways are up regulated, accordance with those of amino acid synthesis and metabolism. These results demonstrate that the increasing demand for amino acids in post-log phase lead to a metabolic transition into TCA cycle and glyoxylate cycle, which subsequently reduce the ethanol production rate. This suggests a global insight into the process of yeast ethanol fermentation.

  18. Effects of the cryptochrome CryB from Rhodobacter sphaeroides on global gene expression in the dark or blue light or in the presence of singlet oxygen.

    PubMed

    Frühwirth, Sebastian; Teich, Kristin; Klug, Gabriele

    2012-01-01

    Several regulators are controlling the formation of the photosynthetic apparatus in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. Among the proteins affecting photosynthesis gene expression is the blue light photoreceptor cryptochrome CryB. This study addresses the effect of CryB on global gene expression. The data reveal that CryB does not only influence photosynthesis gene expression but also genes for the non-photosynthetic energy metabolism like citric acid cycle and oxidative phosphorylation. In addition several genes involved in RNA processing and in transcriptional regulation are affected by a cryB deletion. Although CryB was shown to undergo a photocycle it does not only affect gene expression in response to blue light illumination but also in response to singlet oxygen stress conditions. While there is a large overlap in these responses, some CryB-dependent effects are specific for blue-light or photooxidative stress. In addition to protein-coding genes some genes for sRNAs show CryB-dependent expression. These findings give new insight into the function of bacterial cryptochromes and demonstrate for the first time a function in the oxidative stress response.

  19. Global microRNA expression is essential for murine mast cell development in vivo.

    PubMed

    Oh, Sun Young; Brandal, Stephanie; Kapur, Reuben; Zhu, Zhou; Takemoto, Clifford M

    2014-10-01

    MicroRNAs (miRNAs) are small, noncoding RNAs that have been shown to play a critical role in normal physiology and disease, such as hematopoietic development and cancer. However, their role in mast-cell function and development is poorly understood. The major objective of this study was to determine how global miRNA expression affects mast-cell physiology. The RNase III endonuclease, Dicer, is required for the processing of pre-miRNAs into mature miRNAs. To investigate the effect of global miRNA depletion on mast cells in vivo, we generated a mast-cell-specific knock out of Dicer in mice. Transgenic mice (Mcpt5-Cre) that express Cre selectively in connective tissue mast cells were crossed with mice carrying the floxed conditional Dicer allele (Dicer fl/fl). Mcpt5-Cre × Dicer fl/fl mice with homozygous Dicer gene deletion in mast cells were found to have a profound mast-cell deficiency with near complete loss of peritoneal, gastrointestinal, and skin mast cells. We examined the in vivo functional consequence of mast-cell-specific Dicer deletion using an immunoglobulin-E-dependent passive systemic anaphylaxis murine model. Immunoglobulin-E-sensitized wild type Mcpt5-Cre × Dicer +/+ and heterozygous Mcpt5-Cre × Dicer fl/+ mice show marked hypothermia with antigen; however, homozygous Mcpt5-Cre × Dicer fl/fl mice were completely unresponsive to antigen challenge. These studies suggest a critical role for Dicer and miRNA expression for establishment of tissue compartments of functional mast cells in vivo.

  20. Testing the relationship between local cue-response patterns and the global structure of communication behaviour.

    PubMed

    Taylor, Paul J; Donald, Ian

    2007-06-01

    A central assumption of negotiation research is that organized sequences of cues and responses underlie the dimensions and constructs found to structure interaction. We empirically tested this assumption using a new 'proximity' coefficient, which measures the global interrelationships among behaviours based on their intrinsic local organization within an interaction sequence. An analysis of sequences from 21 hostage negotiations showed that local cue-response dependencies are organized in a way that corresponds with an established structural model of communication. Further analysis of case-specific coefficients showed that criminal, political and domestic incidents involve very different cue-response dynamics, with criminal incidents dividing into two distinct types of interaction. The importance of the proximity concept for unifying local and global accounts of negotiation behaviour, and the avenues of research made possible by the proximity coefficient, are discussed.

  1. The metabolic background is a global player in Saccharomyces gene expression epistasis

    PubMed Central

    Shliaha, Pavel; Schwarz, Roland; Capuano, Floriana; Vowinckel, Jakob; Radmanesfahar, Elahe; Krüger, Antje; Calvani, Enrica; Michel, Steve; Börno, Stefan; Christen, Stefan; Patil, Kiran Raosaheb; Timmermann, Bernd; Lilley, Kathryn S; Ralser, Markus

    2016-01-01

    Regulation of gene expression in response to nutrient availability is fundamental to the genotype-phenotype relationship. The metabolic-genetic make-up of the cell, as reflected in auxotrophy, is hence a likely determinant of gene expression. Here, we addressed the importance of the metabolic-genetic background by monitoring transcriptome, proteome, and metabolome in a repertoire of sixteen Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes showed, on average, 83% overlap between unrelated auxotrophs, and 35% with previously published transcriptomes generated for non-metabolic gene knock-outs. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging for a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale. PMID:27572163

  2. The global gene expression profile of the secondary transition during pancreatic development.

    PubMed

    Willmann, Stefanie J; Mueller, Nikola S; Engert, Silvia; Sterr, Michael; Burtscher, Ingo; Raducanu, Aurelia; Irmler, Martin; Beckers, Johannes; Sass, Steffen; Theis, Fabian J; Lickert, Heiko

    2016-02-01

    Pancreas organogenesis is a highly dynamic process where neighboring tissue interactions lead to dynamic changes in gene regulatory networks that orchestrate endocrine, exocrine, and ductal lineage formation. To understand the spatio-temporal regulatory logic we have used the Forkhead transcription factor Foxa2-Venus fusion (FVF) knock-in reporter mouse to separate the FVF(+) pancreatic epithelium from the FVF(−) surrounding tissue (mesenchyme, neurons, blood, and blood vessels) to perform a genome-wide mRNA expression profiling at embryonic days (E) 12.5-15.5. Annotating genes and molecular processes suggest that FVF marks endoderm-derived multipotent epithelial progenitors at several lineage restriction steps, when the bulk of endocrine, exocrine and ductal cells are formed during the secondary transition. In the pancreatic epithelial compartment, we identified most known endocrine and exocrine lineage determining factors and diabetes-associated genes, but also unknown genes with spatio-temporal regulated pancreatic expression. In the non-endoderm-derived compartment, we identified many well-described regulatory genes that are not yet functionally annotated in pancreas development, emphasizing that neighboring tissue interactions are still ill defined. Pancreatic expression of over 635 genes was analyzed with them RNA in situ hybridization Genepaint public database. This validated the quality of the profiling data set and identified hundreds of genes with spatially restricted expression patterns in the pancreas. Some of these genes are also targeted by pancreatic transcription factors and show active chromatin marks in human islets of Langerhans. Thus, with the highest spatio-temporal resolution of a global gene expression profile during the secondary transition, our study enables to shed light on neighboring tissue interactions, developmental timing and diabetes gene regulation.

  3. Effects of hypergravity stimulus on global gene expression during reproductive growth in Arabidopsis.

    PubMed

    Tamaoki, D; Karahara, I; Nishiuchi, T; Wakasugi, T; Yamada, K; Kamisaka, S

    2014-01-01

    The life cycle of higher plants consists of successive vegetative and reproductive growth phases. Understanding effects of altered gravity conditions on the reproductive growth is essential, not only to elucidate how higher plants evolved under gravitational condition on Earth but also to approach toward realization of agriculture in space. In the present study, a comprehensive analysis of global gene expression of floral buds under hypergravity was carried out to understand effects of altered gravity on reproductive growth at molecular level. Arabidopsis plants grown for 20-26 days were exposed to hypergravity of 300 g for 24 h. Total RNA was extracted from flower buds and microarray (44 K) analysis performed. As a result, hypergravity up-regulated expression of a gene related to β-1,3-glucanase involved in pectin modification, and down-regulated β-galactosidase and amino acid transport, which supports a previous study reporting inhibition of pollen development and germination under hypergravity. With regard to genes related to seed storage accumulation, hypergravity up-regulated expression of genes of aspartate aminotransferase, and down-regulated those related to cell wall invertase and sugar transporter, supporting a previous study reporting promotion of protein body development and inhibition of starch accumulation under hypergravity, respectively. In addition, hypergravity up-regulated expression of G6PDH and GPGDH, which supports a previous study reporting promotion of lipid deposition under hypergravity. In addition, analysis of the metabolic pathway revealed that hypergravity substantially changed expression of genes involved in the biosynthesis of phytohormones such as abscisic acid and auxin.

  4. PSR1 Is a Global Transcriptional Regulator of Phosphorus Deficiency Responses and Carbon Storage Metabolism in Chlamydomonas reinhardtii1[OPEN

    PubMed Central

    Bajhaiya, Amit K.; Dean, Andrew P.; Zeef, Leo A.H.; Webster, Rachel E.; Pittman, Jon K.

    2016-01-01

    Many eukaryotic microalgae modify their metabolism in response to nutrient stresses such as phosphorus (P) starvation, which substantially induces storage metabolite biosynthesis, but the genetic mechanisms regulating this response are poorly understood. Here, we show that P starvation-induced lipid and starch accumulation is inhibited in a Chlamydomonas reinhardtii mutant lacking the transcription factor Pi Starvation Response1 (PSR1). Transcriptomic analysis identified specific metabolism transcripts that are induced by P starvation but misregulated in the psr1 mutant. These include transcripts for starch and triacylglycerol synthesis but also transcripts for photosynthesis-, redox-, and stress signaling-related proteins. To further examine the role of PSR1 in regulating lipid and starch metabolism, PSR1 complementation lines in the psr1 strain and PSR1 overexpression lines in a cell wall-deficient strain were generated. PSR1 expression in the psr1 lines was shown to be functional due to rescue of the psr1 phenotype. PSR1 overexpression lines exhibited increased starch content and number of starch granules per cell, which correlated with a higher expression of specific starch metabolism genes but reduced neutral lipid content. Furthermore, this phenotype was consistent in the presence and absence of acetate. Together, these results identify a key transcriptional regulator in global metabolism and demonstrate transcriptional engineering in microalgae to modulate starch biosynthesis. PMID:26704642

  5. PSR1 Is a Global Transcriptional Regulator of Phosphorus Deficiency Responses and Carbon Storage Metabolism in Chlamydomonas reinhardtii.

    PubMed

    Bajhaiya, Amit K; Dean, Andrew P; Zeef, Leo A H; Webster, Rachel E; Pittman, Jon K

    2016-03-01

    Many eukaryotic microalgae modify their metabolism in response to nutrient stresses such as phosphorus (P) starvation, which substantially induces storage metabolite biosynthesis, but the genetic mechanisms regulating this response are poorly understood. Here, we show that P starvation-induced lipid and starch accumulation is inhibited in a Chlamydomonas reinhardtii mutant lacking the transcription factor Pi Starvation Response1 (PSR1). Transcriptomic analysis identified specific metabolism transcripts that are induced by P starvation but misregulated in the psr1 mutant. These include transcripts for starch and triacylglycerol synthesis but also transcripts for photosynthesis-, redox-, and stress signaling-related proteins. To further examine the role of PSR1 in regulating lipid and starch metabolism, PSR1 complementation lines in the psr1 strain and PSR1 overexpression lines in a cell wall-deficient strain were generated. PSR1 expression in the psr1 lines was shown to be functional due to rescue of the psr1 phenotype. PSR1 overexpression lines exhibited increased starch content and number of starch granules per cell, which correlated with a higher expression of specific starch metabolism genes but reduced neutral lipid content. Furthermore, this phenotype was consistent in the presence and absence of acetate. Together, these results identify a key transcriptional regulator in global metabolism and demonstrate transcriptional engineering in microalgae to modulate starch biosynthesis.

  6. Global gene expression in neuroendocrine tumors from patients with the MEN1 syndrome

    PubMed Central

    Dilley, William G; Kalyanaraman, Somasundaram; Verma, Sulekha; Cobb, J Perren; Laramie, Jason M; Lairmore, Terry C

    2005-01-01

    Background Multiple Endocrine Neoplasia type 1 (MEN1, OMIM 131100) is an autosomal dominant disorder characterized by endocrine tumors of the parathyroids, pancreatic islets and pituitary. The disease is caused by the functional loss of the tumor suppressor protein menin, coded by the MEN1 gene. The protein sequence has no significant homology to known consensus motifs. In vitro studies have shown menin binding to JunD, Pem, Smad3, NF-kappaB, nm23H1, and RPA2 proteins. However, none of these binding studies have led to a convincing theory of how loss-of-menin leads to neoplasia. Results Global gene expression studies on eight neuroendocrine tumors from MEN1 patients and 4 normal islet controls was performed utilizing Affymetrix U95Av2 chips. Overall hierarchical clustering placed all tumors in one group separate from the group of normal islets. Within the group of tumors, those of the same type were mostly clustered together. The clustering analysis also revealed 19 apoptosis-related genes that were under-expressed in the group of tumors. There were 193 genes that were increased/decreased by at least 2-fold in the tumors relative to the normal islets and that had a t-test significance value of p < = 0.005. Forty-five of these genes were increased and 148 were decreased in the tumors relative to the controls. One hundred and four of the genes could be classified as being involved in cell growth, cell death, or signal transduction. The results from 11 genes were selected for validation by quantitative RT-PCR. The average correlation coefficient was 0.655 (range 0.235–0.964). Conclusion This is the first analysis of global gene expression in MEN1-associated neuroendocrine tumors. Many genes were identified which were differentially expressed in neuroendocrine tumors arising in patients with the MEN1 syndrome, as compared with normal human islet cells. The expression of a group of apoptosis-related genes was significantly suppressed, suggesting that these genes may

  7. Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays.

    PubMed

    Badri, Hanène; Monsieurs, Pieter; Coninx, Ilse; Nauts, Robin; Wattiez, Ruddy; Leys, Natalie

    2015-01-01

    The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response was investigated by monitoring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed during early response, suggested a reduction of photosystem II and I activity and reduced tricarboxylic acid (TCA) and Calvin-Benson-Bassham (CBB) cycles, combined with an activation of the pentose phosphate pathway (PPP). For reactive oxygen species detoxification and restoration of the redox balance in Arthrospira cells, the results suggested a powerful contribution of the antioxidant molecule glutathione. The repair mechanisms of Arthrospira cells that were immediately switched on, involve mainly proteases for damaged protein removal, single strand DNA repair and restriction modification systems, while recA was not induced. Additionally, the exposed cells showed significant increased expression of arh genes, coding for a novel group of protein of unknown function, also seen in our previous irradiation studies. This observation confirms our hypothesis that arh genes are key elements in radiation resistance of Arthrospira, requiring further investigation. This study provides new insights into phasic response and the cellular pathways involved in the radiation resistance of

  8. Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays

    PubMed Central

    Badri, Hanène; Monsieurs, Pieter; Coninx, Ilse; Nauts, Robin; Wattiez, Ruddy; Leys, Natalie

    2015-01-01

    The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response was investigated by monitoring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed during early response, suggested a reduction of photosystem II and I activity and reduced tricarboxylic acid (TCA) and Calvin-Benson-Bassham (CBB) cycles, combined with an activation of the pentose phosphate pathway (PPP). For reactive oxygen species detoxification and restoration of the redox balance in Arthrospira cells, the results suggested a powerful contribution of the antioxidant molecule glutathione. The repair mechanisms of Arthrospira cells that were immediately switched on, involve mainly proteases for damaged protein removal, single strand DNA repair and restriction modification systems, while recA was not induced. Additionally, the exposed cells showed significant increased expression of arh genes, coding for a novel group of protein of unknown function, also seen in our previous irradiation studies. This observation confirms our hypothesis that arh genes are key elements in radiation resistance of Arthrospira, requiring further investigation. This study provides new insights into phasic response and the cellular pathways involved in the radiation resistance of

  9. Global transcriptomic profiling of bovine endometrial immune response in vitro. I. Effect of lipopolysaccharide on innate immunity.

    PubMed

    Oguejiofor, Chike F; Cheng, Zhangrui; Abudureyimu, Ayimuguli; Fouladi-Nashta, Ali A; Wathes, D Claire

    2015-10-01

    The dysregulation of endometrial immune response to bacterial lipopolysaccharide (LPS) has been implicated in uterine disease and infertility in the postpartum dairy cow, although the mechanisms are not clear. Here, we investigated whole-transcriptomic gene expression in primary cultures of mixed bovine epithelial and stromal endometrial cells. Cultures were exposed to LPS for 6 h, and cellular response was measured by bovine microarray. Approximately 30% of the 1006 genes altered by LPS were classified as being involved in immune response. Cytokines and chemokines (IL1A, CX3CL1, CXCL2, and CCL5), interferon (IFN)-stimulated genes (RSAD2, MX2, OAS1, ISG15, and BST2), and the acute phase molecule SAA3 were the most up-regulated genes. Ingenuity Pathway Analysis identified up-regulation of many inflammatory cytokines and chemokines, which function to attract immune cells to the endometrium, together with vascular adhesion molecules and matrix metalloproteinases, which can facilitate immune cell migration from the tissue toward the uterine lumen. Increased expression of many IFN-signaling genes, immunoproteasomes, guanylate-binding proteins, and genes involved in the intracellular recognition of pathogens suggests important roles for these molecules in the innate defense against bacterial infections. Our findings confirmed the important role of endometrial cells in uterine innate immunity, whereas the global approach used identified several novel immune response pathways triggered by LPS in the endometrium. Additionally, many genes involved in endometrial response to the conceptus in early pregnancy were also altered by LPS, suggesting one mechanism whereby an ongoing response to infection may interfere with the establishment of pregnancy.

  10. Microbial response to simulated global change is phylogenetically conserved and linked with functional potential

    PubMed Central

    Amend, Anthony S; Martiny, Adam C; Allison, Steven D; Berlemont, Renaud; Goulden, Michael L; Lu, Ying; Treseder, Kathleen K; Weihe, Claudia; Martiny, Jennifer B H

    2016-01-01

    The high diversity of microbial communities hampers predictions about their responses to global change. Here we investigate the potential for using a phylogenetic, trait-based framework to capture the response of bacteria and fungi to global change manipulations. Replicated grassland plots were subjected to 3+ years of drought and nitrogen fertilization. The responses of leaf litter bacteria and fungi to these simulated changes were significantly phylogenetically conserved. Proportional changes in abundance were highly correlated among related organisms, such that relatives with approximately 5% ribosomal DNA genetic distance showed similar responses to the treatments. A microbe's change in relative abundance was significantly correlated between the treatments, suggesting a compromise between numerical abundance in undisturbed environments and resistance to change in general, independent of disturbance type. Lineages in which at least 90% of the microbes shared the same response were circumscribed at a modest phylogenetic depth (τD 0.014–0.021), but significantly larger than randomized simulations predict. In several clades, phylogenetic depth of trait consensus was higher. Fungal response to drought was more conserved than was response to nitrogen fertilization, whereas bacteria responded equally to both treatments. Finally, we show that a bacterium's response to the manipulations is correlated with its potential functional traits (measured here as the number of glycoside hydrolase genes encoding the capacity to degrade different types of carbohydrates). Together, these results suggest that a phylogenetic, trait-based framework may be useful for predicting shifts in microbial composition and functioning in the face of global change. PMID:26046258

  11. Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature

    PubMed Central

    Schneider, Igor; Aneas, Ivy; Gehrke, Andrew R.; Dahn, Randall D.; Nobrega, Marcelo A.; Shubin, Neil H.

    2011-01-01

    The evolutionary transition of the fins of fish into tetrapod limbs involved genetic changes to developmental systems that resulted in novel skeletal patterns and functions. Approaches to understanding this issue have entailed the search for antecedents of limb structure in fossils, genes, and embryos. Comparative genetic analyses have produced ambiguous results: although studies of posterior Hox genes from homology group 13 (Hoxa-13 and Hoxd-13) reveal similarities in gene expression between the distal segments of fins and limbs, this functional homology has not been supported by genomic comparisons of the activity of their cis-regulatory elements, namely the Hoxd Global Control Region. Here, we show that cis-regulatory elements driving Hoxd gene expression in distal limbs are present in fish. Using an interspecies transgenesis approach, we find functional conservation between gnathostome Hoxd enhancers, demonstrating that orthologous sequences from tetrapods, zebrafish and skate can drive reporter gene expression in mouse limbs and zebrafish fins. Our results support the notion that some of the novelties associated with tetrapod limbs arose by modification of deeply conserved cis- and trans-acting mechanisms of Hox regulation in gnathostomes. PMID:21765002

  12. Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile

    PubMed Central

    Wang, Huaishan; Yang, Jia; Yang, Qi; Fu, Yi; Hu, Yu; Liu, Fang; Wang, Weiqing; Cui, Lianxian; Chen, Hui; Zhang, Jianmin; He, Wei

    2016-01-01

    Translocator Protein (18kDa, TSPO) is a mitochondrial outer membrane transmembrane protein. Its expression is elevated during inflammation and injury. However, the function of TSPO in vivo is still controversial. Here, we constructed a TSPO global knockout (KO) mouse with a Cre-LoxP system that abolished TSPO protein expression in all tissues and showed normal phenotypes in the physiological condition. The birth rates of TSPO heterozygote (Het) x Het or KO x KO breeding were consistent with Mendel’s Law, suggesting a normal viability of TSPO KO mice at birth. RNA-seq analysis showed no significant difference in the gene expression profile of lung tissues from TSPO KO mice compared with wild type mice, including the genes associated with bronchial alveoli immune homeostasis. The alveolar macrophage population was not affected by TSPO deletion in the physiological condition. Our findings contradict the results of Papadopoulos, but confirmed Selvaraj’s findings. This study confirms TSPO deficiency does not affect viability and bronchial alveolar immune homeostasis. PMID:27907096

  13. Developmental Control of Stress Stimulons in Streptomyces coelicolor Revealed by Statistical Analyses of Global Gene Expression Patterns

    PubMed Central

    Vohradsky, J.; Li, X.-M.; Dale, G.; Folcher, M.; Nguyen, L.; Viollier, P. H.; Thompson, C. J.

    2000-01-01

    Stress-induced regulatory networks coordinated with a procaryotic developmental program were revealed by two-dimensional gel analyses of global gene expression. Four developmental stages were identified by their distinctive protein synthesis patterns using principal component analysis. Statistical analyses focused on five stress stimulons (induced by heat, cold, salt, ethanol, or antibiotic shock) and their synthesis during development. Unlike other bacteria, for which various stresses induce expression of similar sets of protein spots, in Streptomyces coelicolor heat, salt, and ethanol stimulons were composed of independent sets of proteins. This suggested independent control by different physiological stress signals and their corresponding regulatory systems. These stress proteins were also under developmental control. Cluster analysis of stress protein synthesis profiles identified 10 different developmental patterns or “synexpression groups.” Proteins induced by cold, heat, or salt shock were enriched in three developmental synexpression groups. In addition, certain proteins belonging to the heat and salt shock stimulons were coregulated during development. Thus, stress regulatory systems controlling these stimulons were implicated as integral parts of the developmental program. This correlation suggested that thermal shock and salt shock stress response regulatory systems either allow the cell to adapt to stresses associated with development or directly control the developmental program. PMID:10940043

  14. Avermectin induced global DNA hypomethylation and over-expression of heat shock proteins in cardiac tissues of pigeon.

    PubMed

    Liu, Ci; Cao, Ye; Zhou, Shuo; Khoso, Pervez Ahmed; Li, Shu

    2017-01-01

    Despite increasing evidences pointing to residues of avermectin (AVM) pose toxic effects on non-target organisms in environment, but the data in pigeon is insufficient. The alteration of global DNA methylation and response of heat shock proteins (Hsps) are important for assessing the AVM toxicity in cardiac tissues of pigeon (Columba livia). To investigate the effects of AVM exposure in cardiac tissues of pigeon, we detected the expression levels of DNA methyltransferases (Dnmts), methylated DNA-binding domain protein 2 (MBD2), and Hsp 60, 70 and 90. Pigeons were exposed to feed containing AVM (0, 20, 40 and 60mg/kg diet) for 30, 60, 90days respectively, and cardiac tissues were collected and analyzed. We found the transcriptional levels of Dnmt1, Dnmt3a and Dnmt3b mRNA were down-regulated, but the transcriptional levels of MBD2 mRNA were up-regulated by AVM exposure in cardiac tissues of pigeon. Necrocytosis, hemorrhage, infiltration of inflammatory cells and abundant vacuoles appeared in cardiac tissues after AVM exposure. Accompanying this phenotype, the mRNA transcriptional and/or protein levels of Hsp30, Hsp60, Hsp70 and Hsp90 increased. In conclusion, these results underscored AVM exposure caused DNA methylation machinery malfunctions, and induced over-expression of Hsps to improve the protective function against cardiac injury.

  15. Expression of ethylene response genes during persimmon fruit astringency removal.

    PubMed

    Yin, Xue-ren; Shi, Yan-na; Min, Ting; Luo, Zheng-rong; Yao, Yun-Cong; Xu, Qian; Ferguson, Ian; Chen, Kun-song

    2012-05-01

    Thirteen ethylene signaling related genes were isolated and studied during ripening of non-astringent 'Yangfeng' and astringent 'Mopan' persimmon fruit. Some of these genes were characterized as ethylene responsive. Treatments, including ethylene and CO(2), had different effects on persimmon ripening, but overlapping roles in astringency removal, such as increasing the reduction in levels of soluble tannins. DkERS1, DkETR2, and DkERF8, may participate in persimmon fruit ripening and softening. The expression patterns of DkETR2, DkERF4, and DkERF5 had significant correlations with decreases in soluble tannins in 'Mopan' persimmon fruit, suggesting that these genes might be key components in persimmon fruit astringency removal and be the linkage between different treatments, while DkERF1 and DkERF6 may be specifically involved in CO(2) induced astringency removal. The possible roles of ethylene signaling genes in persimmon fruit astringency removal are discussed.

  16. Gene expression responses in Suaeda salsa after cadmium exposure.

    PubMed

    Cong, Ming; Lv, Jiasen; Liu, Xiaoli; Zhao, Jianmin; Wu, Huifeng

    2013-12-01

    Coastal line is now polluted by many kinds of sewage including heavy metals discharged by intensive human activities. Cadmium is a nonessential heavy metal for organisms and can cause many kinds of adverse effect on the organisms. Suaeda salsa, a pioneer halophyte in intertidal zone of the Bohai coast, was proved to have cadmium-tolerant capacity. Given that, S. salsa was suggested as a potential coastal bio-indicator plant for cadmium contamination in the intertidal zone. Therefore, it is essential to investigate the responsive mechanism of S. salsa to cadmium since few studies focus on this subject till now. In the present study, six genes were selected to investigate the variation profiles of mRNA expression by fluorescent real-time quantitative PCR, including those involved in myo-inositol synthesis, redox reaction, salt-tolerant reaction. Results showed that cadmium exposure significantly modulate the mRNA expressions of MIPS, Nhx1, CAT2, GST, Prx Q genes. It suggested that cadmium exposure exerted an oxidative stress on S. salsa, disturbed Na(+) homeostasis across membranes and interfered with the metabolism of inositol. In addition, CAT2 gene could be used as a gene marker in S. salsa to indicate cadmium pollution.

  17. [Emotional intelligence and oscillatory responses on the emotional facial expressions].

    PubMed

    Kniazev, G G; Mitrofanova, L G; Bocharov, A V

    2013-01-01

    Emotional intelligence-related differences in oscillatory responses to emotional facial expressions were investigated in 48 subjects (26 men and 22 women) in age 18-30 years. Participants were instructed to evaluate emotional expression (angry, happy and neutral) of each presented face on an analog scale ranging from -100 (very hostile) to + 100 (very friendly). High emotional intelligence (EI) participants were found to be more sensitive to the emotional content of the stimuli. It showed up both in their subjective evaluation of the stimuli and in a stronger EEG theta synchronization at an earlier (between 100 and 500 ms after face presentation) processing stage. Source localization using sLORETA showed that this effect was localized in the fusiform gyrus upon the presentation of angry faces and in the posterior cingulate gyrus upon the presentation of happy faces. At a later processing stage (500-870 ms) event-related theta synchronization in high emotional intelligence subject was higher in the left prefrontal cortex upon the presentation of happy faces, but it was lower in the anterior cingulate cortex upon presentation of angry faces. This suggests the existence of a mechanism that can be selectively increase the positive emotions and reduce negative emotions.

  18. Trypanosoma cruzi Gene Expression in Response to Gamma Radiation

    PubMed Central

    Grynberg, Priscila; Passos-Silva, Danielle Gomes; Mourão, Marina de Moraes; Hirata Jr, Roberto; Macedo, Andrea Mara; Machado, Carlos Renato; Bartholomeu, Daniella Castanheira; Franco, Glória Regina

    2012-01-01

    Trypanosoma cruzi is an organism highly resistant to ionizing radiation. Following a dose of 500 Gy of gamma radiation, the fragmented genomic DNA is gradually reconstructed and the pattern of chromosomal bands is restored in less than 48 hours. Cell growth arrests after irradiation but, while DNA is completely fragmented, RNA maintains its integrity. In this work we compared the transcriptional profiles of irradiated and non-irradiated epimastigotes at different time points after irradiation using microarray. In total, 273 genes were differentially expressed; from these, 160 were up-regulated and 113 down-regulated. We found that genes with predicted functions are the most prevalent in the down-regulated gene category. Translation and protein metabolic processes, as well as generation of precursor of metabolites and energy pathways were affected. In contrast, the up-regulated category was mainly composed of obsolete sequences (which included some genes of the kinetoplast DNA), genes coding for hypothetical proteins, and Retrotransposon Hot Spot genes. Finally, the tyrosyl-DNA phosphodiesterase 1, a gene involved in double-strand DNA break repair process, was up-regulated. Our study demonstrated the peculiar response to ionizing radiation, raising questions about how this organism changes its gene expression to manage such a harmful stress. PMID:22247781

  19. Global gene expression changes in human embryonic lung fibroblasts induced by organic extracts from respirable air particles

    PubMed Central

    2012-01-01

    Background Recently, we used cell-free assays to demonstrate the toxic effects of complex mixtures of organic extracts from urban air particles (PM2.5) collected in four localities of the Czech Republic (Ostrava-Bartovice, Ostrava-Poruba, Karvina and Trebon) which differed in the extent and sources of air pollution. To obtain further insight into the biological mechanisms of action of the extractable organic matter (EOM) from ambient air particles, human embryonic lung fibroblasts (HEL12469) were treated with the same four EOMs to assess changes in the genome-wide expression profiles compared to DMSO treated controls. Method For this purpose, HEL cells were incubated with subtoxic EOM concentrations of 10, 30, and 60 μg EOM/ml for 24 hours and global gene expression changes were analyzed using human whole genome microarrays (Illumina). The expression of selected genes was verified by quantitative real-time PCR. Results Dose-dependent increases in the number of significantly deregulated transcripts as well as dose-response relationships in the levels of individual transcripts were observed. The transcriptomic data did not differ substantially between the localities, suggesting that the air pollution originating mainly from various sources may have similar biological effects. This was further confirmed by the analysis of deregulated pathways and by identification of the most contributing gene modulations. The number of significantly deregulated KEGG pathways, as identified by Goeman's global test, varied, depending on the locality, between 12 to 29. The Metabolism of xenobiotics by cytochrome P450 exhibited the strongest upregulation in all 4 localities and CYP1B1 had a major contribution to the upregulation of this pathway. Other important deregulated pathways in all 4 localities were ABC transporters (involved in the translocation of exogenous and endogenous metabolites across membranes and DNA repair), the Wnt and TGF-β signaling pathways (associated

  20. A meta-analysis of responses of soil biota to global change.

    PubMed

    Blankinship, Joseph C; Niklaus, Pascal A; Hungate, Bruce A

    2011-03-01

    Global environmental changes are expected to impact the abundance of plants and animals aboveground, but comparably little is known about the responses of belowground organisms. Using meta-analysis, we synthesized results from over 75 manipulative experiments in order to test for patterns in the effects of elevated CO(2), warming, and altered precipitation on the abundance of soil biota related to taxonomy, body size, feeding habits, ecosystem type, local climate, treatment magnitude and duration, and greenhouse CO(2) enrichment. We found that the positive effect size of elevated CO(2) on the abundance of soil biota diminished with time, whereas the negative effect size of warming and positive effect size of precipitation intensified with time. Trophic group, body size, and experimental approaches best explained the responses of soil biota to elevated CO(2), whereas local climate and ecosystem type best explained responses to warming and altered precipitation. The abundance of microflora and microfauna, and particularly detritivores, increased with elevated CO(2), indicative of microbial C limitation under ambient CO(2). However, the effects of CO(2) were smaller in field studies than in greenhouse studies and were not significant for higher trophic levels. Effects of warming did not depend on taxon or body size, but reduced abundances were more likely to occur at the colder and drier sites. Precipitation limited all taxa and trophic groups, particularly in forest ecosystems. Our meta-analysis suggests that the responses of soil biota to global change are predictable and unique for each global change factor.

  1. Global Regulation of the Response to Sulfur Availability in the Cheese-Related Bacterium Brevibacterium aurantiacum▿ †

    PubMed Central

    Forquin, Marie-Pierre; Hébert, Agnès; Roux, Aurélie; Aubert, Julie; Proux, Caroline; Heilier, Jean-François; Landaud, Sophie; Junot, Christophe; Bonnarme, Pascal; Martin-Verstraete, Isabelle

    2011-01-01

    In this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, at least one gene of the transsulfuration pathway (aecD), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression of metX, metY, metE1, metE2, and BL613, encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase (BL929) and a methionine transporter (metPS) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production. PMID:21169450

  2. Global Expression Profiling of Globose Basal Cells and Neurogenic Progression Within the Olfactory Epithelium

    PubMed Central

    Krolewski, Richard C.; Packard, Adam; Schwob, James E.

    2013-01-01

    Ongoing, lifelong neurogenesis maintains the neuronal population of the olfactory epithelium in the face of piecemeal neuronal turnover and restores it following wholesale loss. The molecular phenotypes corresponding to different stages along the progression from multipotent globose basal cell (GBC) progenitor to differentiated olfactory sensory neuron are poorly characterized. We used the transgenic expression of enhanced green fluorescent protein (eGFP) and cell surface markers to FACS-isolate ΔSox2-eGFP(+) GBCs, Neurog1-eGFP(+) GBCs and immature neurons, and ΔOMP-eGFP(+) mature neurons from normal adult mice. In addition, the latter two populations were also collected 3 weeks after olfactory bulb ablation, a lesion that results in persistently elevated neurogenesis. Global profiling of mRNA from the populations indicates that all stages of neurogenesis share a cohort of >2,100 genes that are upregulated compared to sustentacular cells. A further cohort of >1,200 genes are specifically upregulated in GBCs as compared to sustentacular cells and differentiated neurons. The increased rate of neurogenesis caused by olfactory bulbectomy had little effect on the transcriptional profile of the Neurog1-eGFP(+) population. In contrast, the abbreviated lifespan of ΔOMP-eGFP(+) neurons born in the absence of the bulb correlated with substantial differences in gene expression as compared to the mature neurons of the normal epithelium. Detailed examination of the specific genes upregulated in the different progenitor populations revealed that the chromatin modifying complex proteins LSD1 and coREST were expressed sequentially in upstream ΔSox2-eGFP(+) GBCs and Neurog1-eGFP(+) GBCs/immature neurons. The expression patterns of these proteins are dynamically regulated after activation of the epithelium by methyl bromide lesion. PMID:22847514

  3. A Canonical Response in Rainfall Characteristics to Global Warming: Projections by IPCC CMIP5 Models

    NASA Technical Reports Server (NTRS)

    Lau, William K. M.; Wu, H. T.; Kim, K. M.

    2012-01-01

    Changes in rainfall characteristics induced by global warming are examined based on probability distribution function (PDF) analysis, from outputs of 14 IPCC (Intergovernmental Panel on Climate Change), CMIP (5th Coupled Model Intercomparison Project) models under various scenarios of increased CO2 emissions. Results show that collectively CMIP5 models project a robust and consistent global and regional rainfall response to CO2 warming. Globally, the models show a 1-3% increase in rainfall per degree rise in temperature, with a canonical response featuring large increase (100-250 %) in frequency of occurrence of very heavy rain, a reduction (5-10%) of moderate rain, and an increase (10-15%) of light rain events. Regionally, even though details vary among models, a majority of the models (>10 out of 14) project a consistent large scale response with more heavy rain events in climatologically wet regions, most pronounced in the Pacific ITCZ and the Asian monsoon. Moderate rain events are found to decrease over extensive regions of the subtropical and extratropical oceans, but increases over the extratropical land regions, and the Southern Oceans. The spatial distribution of light rain resembles that of moderate rain, but mostly with opposite polarity. The majority of the models also show increase in the number of dry events (absence or only trace amount of rain) over subtropical and tropical land regions in both hemispheres. These results suggest that rainfall characteristics are changing and that increased extreme rainfall events and droughts occurrences are connected, as a consequent of a global adjustment of the large scale circulation to global warming.

  4. NusA-dependent transcription termination prevents misregulation of global gene expression

    PubMed Central

    Mondal, Smarajit; Yakhnin, Alexander V.; Sebastian, Aswathy; Albert, Istvan; Babitzke, Paul

    2017-01-01

    Intrinsic transcription terminators consist of an RNA hairpin followed by a U-rich tract, and these signals can trigger termination without the involvement of additional factors. Although NusA is known to stimulate intrinsic termination in vitro, the in vivo targets and global impact of NusA are not known because it is essential for viability. Using genome-wide 3′ end-mapping on an engineered Bacillus subtilis NusA depletion strain, we show that weak suboptimal terminators are the principle NusA substrates. Moreover, a subclass of weak non-canonical terminators was identified that completely depend on NusA for effective termination. NusA-dependent terminators tend to have weak hairpins and/or distal U-tract interruptions, supporting a model in which NusA is directly involved in the termination mechanism. Depletion of NusA altered global gene expression directly and indirectly via readthrough of suboptimal terminators. Readthrough of NusA-dependent terminators caused misregulation of genes involved in essential cellular functions, especially DNA replication and metabolism. We further show that nusA is autoregulated by a transcription attenuation mechanism that does not rely on antiterminator structures. Instead, NusA-stimulated termination in its 5′ UTR dictates the extent of transcription into the operon, thereby ensuring tight control of cellular NusA levels. PMID:27571753

  5. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

    PubMed Central

    Smits, Arne H.; Lindeboom, Rik G.H.; Perino, Matteo; van Heeringen, Simon J.; Veenstra, Gert Jan C.; Vermeulen, Michiel

    2014-01-01

    While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs. PMID:25056316

  6. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

    PubMed

    Smits, Arne H; Lindeboom, Rik G H; Perino, Matteo; van Heeringen, Simon J; Veenstra, Gert Jan C; Vermeulen, Michiel

    2014-09-01

    While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs.

  7. Weak response of oceanic dimethylsulfide to upper mixing shoaling induced by global warming.

    PubMed

    Vallina, S M; Simó, R; Manizza, M

    2007-10-09

    The solar radiation dose in the oceanic upper mixed layer (SRD) has recently been identified as the main climatic force driving global dimethylsulfide (DMS) dynamics and seasonality. Because DMS is suggested to exert a cooling effect on the earth radiative budget through its involvement in the formation and optical properties of tropospheric clouds over the ocean, a positive relationship between DMS and the SRD supports the occurrence of a negative feedback between the oceanic biosphere and climate, as postulated 20 years ago. Such a natural feedback might partly counteract anthropogenic global warming through a shoaling of the mixed layer depth (MLD) and a consequent increase of the SRD and DMS concentrations and emission. By applying two globally derived DMS diagnostic models to global fields of MLD and chlorophyll simulated with an Ocean General Circulation Model coupled to a biogeochemistry model for a 50% increase of atmospheric CO(2) and an unperturbed control run, we have estimated the response of the DMS-producing pelagic ocean to global warming. Our results show a net global increase in surface DMS concentrations, especially in summer. This increase, however, is so weak (globally 1.2%) that it can hardly be relevant as compared with the radiative forcing of the increase of greenhouse gases. This contrasts with the seasonal variability of DMS (1000-2000% summer-to-winter ratio). We suggest that the "plankton-DMS-clouds-earth albedo feedback" hypothesis is less strong a long-term thermostatic system than a seasonal mechanism that contributes to regulate the solar radiation doses reaching the earth's biosphere.

  8. Regulation of microcin C51 operon expression: the role of global regulators of transcription.

    PubMed

    Fomenko, D; Veselovskii, A; Khmel, I

    2001-06-01

    Expression of the microcin C51 operon in Escherichia coli cells is regulated as a function of the phase of growth; it is stimulated during the decelerating phase of growth. Using single-copy P(mcc)-lac transcriptional fusion (the promoter region of the microcin C51 operon fused to a promoterless lac operon in lambda phage), we showed that transcription from the microcin operon promoter is dependent on sigma(s) (RpoS) factor. However, some level of P(mcc)-lac expression is possible in rpoS null mutants, indicating that another sigma factor might be involved in transcription of the microcin C51 operon. Overproduction of sigma70 decreased Pmcc-directed transcription, presumably as a result of competition of sigma factors for the limited amount of core RNA polymerase. The cyclic AMP-CRP complex was shown to stimulate transcription from Pmcc: the absence of CRP or cAMP in crp or cya mutant cells strongly decreased the level of P(mcc)-lac expression. The production of C51 microcin decreased or was absent in rpoS, crp and cya mutant cells. Leucine-responsive protein Lrp and histone-like protein H-NS repressed P(mcc)-lac expression in the exponential and decelerating phases of growth. In studies of P(mcc)-lac expression in double mutant cells, we showed that proteins CRP, Lrp and H-NS acted in rpoS-dependent and rpoS-independent ways in transcription of the microcin C51 operon. Mutation hns(-) resulted in an increase in P(mcc)-lac expression in crp, rpoS and lrp mutant cells, as in wild-type cells.

  9. Soil Microbial Community Responses to Long-Term Global Change Factors in a California Grassland

    NASA Astrophysics Data System (ADS)

    Qin, K.; Peay, K.

    2015-12-01

    Soil fungal and bacterial communities act as mediators of terrestrial carbon and nutrient cycling, and interact with the aboveground plant community as both pathogens and mutualists. However, these soil microbial communities are sensitive to changes in their environment. A better understanding of the response of soil microbial communities to global change may help to predict future soil microbial diversity, and assist in creating more comprehensive models of terrestrial carbon and nutrient cycles. This study examines the effects of four global change factors (increased temperature, increased variability in precipitation, nitrogen deposition, and CO2 enrichment) on soil microbial communities at the Jasper Ridge Global Change Experiment (JRGCE), a full-factorial global change manipulative experiment on three hectares of California grassland. While similar studies have examined the effects of global change on soil microbial communities, few have manipulated more factors or been longer in duration than the JRGCE, which began field treatments in 1998. We find that nitrogen deposition, CO2 enrichment, and increased variability in precipitation significantly affect the structure of both fungal and bacterial communities, and explain more of the variation in the community structures than do local soil chemistry or aboveground plant community. Fungal richness is correlated positively with soil nitrogen content and negatively with soil water content. Arbuscular mycorrhizal fungi (AMF), which associate closely with herbaceous plants' roots and assist in nutrient uptake, decrease in both richness and relative abundance in elevated CO2 treatments.

  10. The TRY Plant Trait Database - a Tool to Characterize Plant Responses to Global Changes

    NASA Astrophysics Data System (ADS)

    Kattge, J.

    2015-12-01

    Plant traits are fundamental for understanding and predicting vegetation responses to global changes, and they provide a promising basis towards a more quantitative and predictive approach to ecology. Plant traits have therefore been collected for a long time, but mostly been stored in small, separated and private databases, not accessible to the research community. The TRY initiative, a network of vegetation scientists (https://www.try-db.org), provides a global archive of plant traits, curated to be applicable for the characterization of species-specific responses in the context of terrestrial biosphere models. This contribution will (1) introduce the TRY initiative and the current state of the plant trait database, (2) provide examples of trait-based approaches to improve terrestrial biosphere models, (3) highlight future perspectives and challenges for trait based approaches in ecology and vegetation modeling.

  11. Regional and Global Climate Response to Anthropogenic SO2 Emissions from China in Three Climate Models

    NASA Technical Reports Server (NTRS)

    Kasoar, M.; Voulgarakis, Apostolos; Lamarque, Jean-Francois; Shindell, Drew T.; Bellouin, Nicholas; Collins, William J.; Faluvegi, Greg; Tsigaridis, Kostas

    2016-01-01

    We use the HadGEM3-GA4, CESM1, and GISS ModelE2 climate models to investigate the global and regional aerosol burden, radiative flux, and surface temperature responses to removing anthropogenic sulfur dioxide (SO2) emissions from China. We find that the models differ by up to a factor of 6 in the simulated change in aerosol optical depth (AOD) and shortwave radiative flux over China that results from reduced sulfate aerosol, leading to a large range of magnitudes in the regional and global temperature responses. Two of the three models simulate a near-ubiquitous hemispheric warming due to the regional SO2 removal, with similarities in the local and remote pattern of response, but overall with a substantially different magnitude. The third model simulates almost no significant temperature response. We attribute the discrepancies in the response to a combination of substantial differences in the chemical conversion of SO2 to sulfate, translation of sulfate mass into AOD, cloud radiative interactions, and differences in the radiative forcing efficiency of sulfate aerosol in the models. The model with the strongest response (HadGEM3-GA4) compares best with observations of AOD regionally, however the other two models compare similarly (albeit poorly) and still disagree substantially in their simulated climate response, indicating that total AOD observations are far from sufficient to determine which model response is more plausible. Our results highlight that there remains a large uncertainty in the representation of both aerosol chemistry as well as direct and indirect aerosol radiative effects in current climate models, and reinforces that caution must be applied when interpreting the results of modelling studies of aerosol influences on climate. Model studies that implicate aerosols in climate responses should ideally explore a range of radiative forcing strengths representative of this uncertainty, in addition to thoroughly evaluating the models used against

  12. Regional and global temperature response to anthropogenic SO2 emissions from China in three climate models

    NASA Astrophysics Data System (ADS)

    Kasoar, Matthew; Voulgarakis, Apostolos; Lamarque, Jean-François; Shindell, Drew T.; Bellouin, Nicolas; Collins, William J.; Faluvegi, Greg; Tsigaridis, Kostas

    2016-08-01

    We use the HadGEM3-GA4, CESM1, and GISS ModelE2 climate models to investigate the global and regional aerosol burden, radiative flux, and surface temperature responses to removing anthropogenic sulfur dioxide (SO2) emissions from China. We find that the models differ by up to a factor of 6 in the simulated change in aerosol optical depth (AOD) and shortwave radiative flux over China that results from reduced sulfate aerosol, leading to a large range of magnitudes in the regional and global temperature responses. Two of the three models simulate a near-ubiquitous hemispheric warming due to the regional SO2 removal, with similarities in the local and remote pattern of response, but overall with a substantially different magnitude. The third model simulates almost no significant temperature response. We attribute the discrepancies in the response to a combination of substantial differences in the chemical conversion of SO2 to sulfate, translation of sulfate mass into AOD, cloud radiative interactions, and differences in the radiative forcing efficiency of sulfate aerosol in the models. The model with the strongest response (HadGEM3-GA4) compares best with observations of AOD regionally, however the other two models compare similarly (albeit poorly) and still disagree substantially in their simulated climate response, indicating that total AOD observations are far from sufficient to determine which model response is more plausible. Our results highlight that there remains a large uncertainty in the representation of both aerosol chemistry as well as direct and indirect aerosol radiative effects in current climate models, and reinforces that caution must be applied when interpreting the results of modelling studies of aerosol influences on climate. Model studies that implicate aerosols in climate responses should ideally explore a range of radiative forcing strengths representative of this uncertainty, in addition to thoroughly evaluating the models used against

  13. Testicular Dnmt3 expression and global DNA methylation are down-regulated by gonadotropin releasing hormones in the ricefield eel Monopterus albus

    PubMed Central

    Zhang, Yize; Sun, Xin; Zhang, Lihong; Zhang, Weimin

    2017-01-01

    In vertebrates, DNA methyltransferase 3 (Dnmt3) homologues are responsible for de novo DNA methylation and play important roles in germ cell development. In the present study, four dnmt3 genes, dnmt3aa, dnmt3ab, dnmt3ba and dnmt3bb.1, were identified in ricefield eels. Real-time quantitative PCR analysis showed that all four dnmt3 mRNAs were detected broadly in tissues examined, with testicular expression at relatively high levels. In the testis, immunostaining for all four Dnmt3 forms was mainly localized to spermatocytes, which also contained highly methylated DNA. All three forms of Gonadotropin-releasing hormone (Gnrh) in the ricefield eel were shown to decrease the expression of dnmt3 genes in the in vitro incubated testicular fragments through cAMP and IP3/Ca2+ pathways. Moreover, in vivo treatment of male fish with three forms of Gnrh decreased significantly the testicular Dnmt3 expression at both mRNA and protein levels, and the global DNA methylation levels. These results suggest that the expression of Dnmt3 and global DNA methylation in the testis of ricefield eels are potentially down-regulated by Gnrh, and reveal a novel regulatory mechanism of testicular Dnmt3 expression in vertebrates. PMID:28225069

  14. Effects of chronic cortisol administration on global expression of GR and the liver transcriptome in Sparus aurata.

    PubMed

    Teles, Mariana; Boltaña, Sebastian; Reyes-López, Felipe; Santos, Maria Ana; Mackenzie, Simon; Tort, Lluis

    2013-02-01

    The present work was designed to assess the effects of artificially increased high plasma cortisol levels induced by slow-release cortisol implants on the mRNA abundance of the glucocorticoid receptor (GR) in different organs of Sparus aurata (Gilthead sea bream), as well as to evaluate global transcriptional changes in the liver, using the Aquagenomics S. aurata oligo-nucleotide microarray technology. For that purpose, groups of fish were intraperitoneally injected with implants containing two different concentrations of cortisol (50 or 200 μg/g body weight). Blood and organs were sampled after 7 and 14 days of cortisol implantation. Only fish with 200 μg/g implants exhibited a significant rise in plasma cortisol. Thus, we evaluated the expression of the GR in different organs in these fish 7 and 14 days post-implantation. GR mRNA abundance was upregulated in head kidney and heart of fish at both sampling times. In liver and muscle, GR mRNA abundance was upregulated after 14 days, whereas in gills, the GR mRNA transcript was upregulated earlier, at day 7. These results suggest that increased plasma cortisol induced by a slow-release implant of cortisol mimics the overall effects of stress and affects the expression of GR mRNA in a time- and organ-specific manner. Data obtained with the Aquagenomics S. aurata oligo-nucleotide microarray allowed the identification of a total of 491 cortisol-responsive transcripts and highlight the strong intensity of transcriptional modulation in liver of fish implanted with cortisol after 7 days, in contrast to that observed at day 14. Transcriptional remodeling highlighted a significant activity in carbohydrate metabolism mainly in the gluconeogenic pathway linked to downregulation of inflammatory and immune response processes in implanted fish.

  15. Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus.

    PubMed

    Park, Dan M; Overton, K Wesley; Liou, Megan J; Jiao, Yongqin

    2016-12-30

    Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA ) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, named UzcRS, which is responsible for U-dependent activation of PurcA . UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a noncanonical DNA-binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug-resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples the perception of U, Zn and Cu with a novel extracytoplasmic stress response.

  16. Multiple determinants, common vulnerabilities, and creative responses: addressing the AIDS pandemic in diverse populations globally.

    PubMed

    Mayer, Kenneth H; Pape, Jean W; Wilson, Phill; Diallo, Dazon D; Saavedra, Jorge; Mimiaga, Matthew J; Koenig, Serena; Farmer, Paul

    2012-08-01

    The AIDS epidemic has been fueled by global inequities. Ranging from sexual inequality and underdevelopment to homophobia impeding health care access for men who have sex with men, imbalanced resource allocations, and social biases have potentiated the spread of the epidemic. However, recognition of culturally specific aspects of each microepidemic has yielded development of community-based organizations, which have resulted in locally effective responses to AIDS. This effective approach to HIV prevention, care, and treatment is illustrated through examples of community-based responses in Haiti, the United States, Africa, and other impoverished settings.

  17. Multiple Determinants, Common Vulnerabilities, and Creative Responses: Addressing the AIDS Pandemic in Diverse Populations Globally

    PubMed Central

    Mayer, Kenneth H.; Pape, Jean William; Wilson, Phill; Diallo, Dazon Dixon; Saavedra, Jorge; Mimiaga, Matthew J.; Koenig, Serena; Farmer, Paul

    2012-01-01

    The AIDS epidemic has been fueled by global inequities. Ranging from gender inequality and underdevelopment to homophobia impeding health care access for men who have sex with men (MSM), imbalanced resource allocations and social biases have potentiated the epidemic’s spread. However, recognition of culturally specific aspects of each microepidemic has yielded development of community-based organizations, which have resulted in locally effective responses to AIDS. This effective approach to HIV prevention, care and treatment is illustrated through examples of community-based responses in Haiti, the United States, Africa, and other impoverished settings. PMID:22772387

  18. The financial crisis and global health: the International Monetary Fund's (IMF) policy response.

    PubMed

    Ruckert, Arne; Labonté, Ronald

    2013-09-01

    In this article, we interrogate the policy response of the International Monetary Fund (IMF) to the global financial crisis, and discuss the likely global health implications, especially in low-income countries. In doing so, we ask if the IMF has meaningfully loosened its fiscal deficit targets in light of the economic challenges posed by the financial crisis and adjusted its macro-economic policy advice to this new reality; or has the rhetoric of counter-cyclical spending failed to translate into additional fiscal space for IMF loan-recipient countries, with negative health consequences? To answer these questions, we assess several post-crisis IMF lending agreements with countries requiring financial assistance, and draw upon recent academic studies and civil society reports examining policy conditionalities still being prescribed by the IMF. We also reference recent studies examining the health impacts of these conditionalities. We demonstrate that while the IMF has been somewhat more flexible in its crisis response than in previous episodes of financial upheaval, there has been no meaningful rethinking in the application of dominant neoliberal macro-economic policies. After showing some flexibility in the initial crisis response, the IMF is pushing for excessive contraction in most low and middle-income countries. We conclude that there remains a wide gap between the rhetoric and the reality of the IMF's policy and programming advice, with negative implications for global health.

  19. Temporal variation overshadows the response of leaf litter microbial communities to simulated global change.

    PubMed

    Matulich, Kristin L; Weihe, Claudia; Allison, Steven D; Amend, Anthony S; Berlemont, Renaud; Goulden, Michael L; Kimball, Sarah; Martiny, Adam C; Martiny, Jennifer B H

    2015-11-01

    Bacteria and fungi drive the decomposition of dead plant biomass (litter), an important step in the terrestrial carbon cycle. Here we investigate the sensitivity of litter microbial communities to simulated global change (drought and nitrogen addition) in a California annual grassland. Using 16S and 28S rDNA amplicon pyrosequencing, we quantify the response of the bacterial and fungal communities to the treatments and compare these results to background, temporal (seasonal and interannual) variability of the communities. We found that the drought and nitrogen treatments both had significant effects on microbial community composition, explaining 2-6% of total compositional variation. However, microbial composition was even more strongly influenced by seasonal and annual variation (explaining 14-39%). The response of microbial composition to drought varied by season, while the effect of the nitrogen addition treatment was constant through time. These compositional responses were similar in magnitude to those seen in microbial enzyme activities and the surrounding plant community, but did not correspond to a consistent effect on leaf litter decomposition rate. Overall, these patterns indicate that, in this ecosystem, temporal variability in the composition of leaf litter microorganisms largely surpasses that expected in a short-term global change experiment. Thus, as for plant communities, future microbial communities will likely be determined by the interplay between rapid, local background variability and slower, global changes.

  20. Histopathologic Alterations Associated with Global Gene Expression Due to Chronic Dietary TCDD Exposure in Juvenile Zebrafish

    PubMed Central

    Liu, Qing; Spitsbergen, Jan M.; Cariou, Ronan; Huang, Chun-Yuan; Jiang, Nan; Goetz, Giles; Hutz, Reinhold J.; Tonellato, Peter J.; Carvan, Michael J.

    2014-01-01

    The goal of this project was to investigate the effects and possible developmental disease implication of chronic dietary TCDD exposure on global gene expression anchored to histopathologic analysis in juvenile zebrafish by functional genomic, histopathologic and analytic chemistry methods. Specifically, juvenile zebrafish were fed Biodiet starter with TCDD added at 0, 0.1, 1, 10 and 100 ppb, and fish were sampled following 0, 7, 14, 28 and 42 d after initiation of the exposure. TCDD accumulated in a dose- and time-dependent manner and 100 ppb TCDD caused TCDD accumulation in female (15.49 ppb) and male (18.04 ppb) fish at 28 d post exposure. Dietary TCDD caused multiple lesions in liver, kidney, intestine and ovary of zebrafish and functional dysregulation such as depletion of glycogen in liver, retrobulbar edema, degeneration of nasal neurosensory epithelium, underdevelopment of intestine, and diminution in the fraction of ovarian follicles containing vitellogenic oocytes. Importantly, lesions in nasal epithelium and evidence of endocrine disruption based on alternatively spliced vasa transcripts are two novel and significant results of this study. Microarray gene expression analysis comparing vehicle control to dietary TCDD revealed dysregulated genes involved in pathways associated with cardiac necrosis/cell death, cardiac fibrosis, renal necrosis/cell death and liver necrosis/cell death. These baseline toxicological effects provide evidence for the potential mechanisms of developmental dysfunctions induced by TCDD and vasa as a biomarker for ovarian developmental disruption. PMID:24988445

  1. Using global gene expression to discriminate thin melanomas with poor outcomes.

    PubMed

    Hothem, Zachary; Bayci, Andrew; Thibodeau, Bryan J; Ketelsen, Billie E; Fortier, Laura E; Uzieblo, Alison F; Cosner, Diane; Totoraitis, Kristin; Keidan, Richard D; Wilson, George D

    2017-01-01

    Most melanomas present as thin lesions (≤1.0 mm) with a good prognosis; however, a small percentage of patients with thin lesions experience recurrence or metastasis. The aim of our study was to identify a distinct pattern of gene expression within thin melanomas known to have eventually metastasized to regional lymph nodes or distant sites compared with those that followed the typical course with good response to wide local excision alone. Patients who were disease-free for a minimum of 10 y served as controls (n = 10) to the experimental group who developed metastasis (n = 9). Laser capture microdissection was used to specifically isolate cancer cells from formalin-fixed paraffin-embedded tissue with subsequent gene expression analysis on Affymetrix Human Transcriptome Array 2.0 Arrays. Although gene expression differences were observed between the patients with thin melanoma with poor clinical outcome and those with good clinical outcome, neither the number of genes nor the magnitude of the fold difference was very substantial or significant. Cluster analysis with this subset of genes could definitively separate a subset of the poor responders from the good responders, but there remained a mixed group of tumors that could not be predicted from gene expression alone. Pathway analysis identified cellular processes that were regulated based on the response, including categories commonly associated with melanoma progression. Ultimately, we concluded that there were very few differences between these groups. Future research will be required and investigation of the mutational landscape may be another strategy to uncover genomic changes that drive recurrence and metastasis in thin melanoma.

  2. A statistical study of the observed and modeled global thermosphere response to magnetic activity

    NASA Astrophysics Data System (ADS)

    Lathuillère, Chantal; Menvielle, Michel; Marchaudon, Aurelie

    Total density retrieved from CHAMP/STAR accelerometer measurements from years 2002 to 2005 is compared to the NRLMSISE00 and JB2006 model predictions. Special emphasis is put on the low and mid latitude global response of the thermosphere to the varying geomagnetic forcing. CHAMP densities are used to define a disturbance coefficient that characterizes this response. We show that this disturbance coefficient is better correlated with the magnetic am indices than with the magnetic ap indices used in the models for quantifying the geomagnetic forcing. It is found that the NRLMISISE-00 model correctly estimates the main features of the thermosphere density response to geomagnetic activity, i.e. the morphology of UT variations and the larger increases during night than during day-time. However it statistically underestimates the amplitude of the density response by about 45 %. Similar comparison with JB2006 will also be shown.

  3. Global Average Upper Ocean Temperature Response To Changing Solar Irradiance: Exciting The Internal Decadal Mode

    NASA Astrophysics Data System (ADS)

    White, W. B.; Dettinger, M. D.; Cayan, D. R.; White, Warren B.; Dettinger, Michael D.; Cayan, Daniel R.

    Global average upper ocean temperatures anomalies of +/-0.05°K fluctuate in fixed phase with decadal signals in the Sun's irradiance of +/-0.5 Watts m-2 over the past 100 years (White et al., 1997), but its amplitude is 2 to 3 times that expected from the transient Stefan-Boltzmann radiation balance (White et al., 1988). Examining global patterns of upper ocean temperature and lower troposphere winds, we find the internal interannual mode of variability in Earth's ocean-atmosphere-terrestrial system with global-average upper ocean temperature anomalies of +/-0.05°K occurring naturally, independent of changing solar irradiance (White et al., 2000). Yet coherence and phase statistics indicate that the observed internal decadal mode in Earth's ocean -atmosphere terrestrial system is excited by the decadal signal in the Sun's irradiance. To understand the thermodynamics of this association we conduct a global-average upper ocean heat budget utilizing upper ocean temperatures from the SIO reanalysis and air-sea heat and momentum fluxes from the COADS reanalysis, finding the source of decadal global warming to be the reduction in trade wind intensity across the tropics, decreasing global average latent heat flux out of the ocean. We demonstrate that this reduction in trade wind intensity in the Pacific Ocean is governed by a delayed action oscillator mechanism in the ocean-atmosphere system differing little from that used to explain the El Niño-Southern Oscillation (Graham and White, 1988). We operate an intermediate coupled model of this delayed action oscillator, normally driven by white noise, by superimposing the Stefan-Boltzmann upper ocean temperature response to decadal changes in the Sun's irradiance. We find the latter, with weak amplitude of +/-0.02°K and non-random phase, is able to excite a decadal signal in this delayed action oscillator, yielding a damped resonance response of +/-0.1°K in the equatorial Pacific Ocean, with dissipation provided by

  4. The Northern Hemisphere winter stationary wave response to global warming in CMIP5

    NASA Astrophysics Data System (ADS)

    Simpson, Isla; Seager, Richard; Ting, Mingfang; Shaw, Tiffany

    2015-04-01

    During the Northern Hemisphere winter, models tend to predict a poleward shifting of the zonal mean mid-latitude westerlies under anthropogenic greenhouse gas emissions. Locally, however, changes in the stationary waves tend to dominate, resulting in considerable deviation from this around the longitude circle, with important implications for regional climate change. Past studies have demonstrated diversity in the stationary wave response to global warming and differ in their views of the mechanisms involved in producing it. Here we will explore the stationary wave response to global warming in the CMIP5 dataset and demonstrate a strong consensus on a wavenumber 5 stationary wave response with a particular phasing that contributes to hydroclimate change across North America and Europe, such as wetting on the west coast of the USA, drying in the south west USA and drying in the eastern Mediterranean. The mechanisms responsible for producing this multi-model mean response are explored using a stationary wave model. It is demonstrated that, to first order, it is produced by changes in the zonal mean basic state, in agreement with the majority of previous stationary wave modelling studies. The relative importance of different features of this basic state change such as Arctic amplification, enhanced tropical upper tropospheric warming, stratospheric cooling and their associated zonal mean zonal wind responses will be explored. Through an understanding of the mechanisms involved in this stationary wave response we can begin to assess our confidence in whether the real world will behave as the models do and understand any diversity among the modelled responses.

  5. Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium

    PubMed Central

    Bergholz, Teresa M; Wick, Lukas M; Qi, Weihong; Riordan, James T; Ouellette, Lindsey M; Whittam, Thomas S

    2007-01-01

    Background: Global patterns of gene expression of Escherichia coli K-12 during growth transitions have been deeply investigated, however, comparable studies of E. coli O157:H7 have not been explored, particularly with respect to factors regulating virulence genes and genomic islands specific to this pathogen. To examine the impact of growth phase on the dynamics of the transcriptome, O157:H7 Sakai strain was cultured in MOPS minimal media (0.1% glucose), RNA harvested at 10 time points from early exponential to full stationary phase, and relative gene expression was measured by co-hybridization on high-density DNA microarrays. Expression levels of 14 genes, including those encoding Shiga toxins and other virulence factors associated with the locus of enterocyte effacement (LEE), were confirmed by Q-PCR. Results: Analysis of variance (R/MAANOVA, Fs test) identified 442 (36%) of 1239 O157-specific ORFs and 2110 (59%) of 3647 backbone ORFs that changed in expression significantly over time. QT cluster analysis placed 2468 of the 2552 significant ORFs into 12 groups; each group representing a distinct expression pattern. ORFs from the largest cluster (n = 1078) decreased in expression from late exponential to early stationary phase: most of these ORFs are involved in functions associated with steady state growth. Also represented in this cluster are ORFs of the TAI island, encoding tellurite resistance and urease activity, which decreased ~4-fold. Most ORFs of the LEE pathogenicity island also decreased ~2-fold by early stationary phase. The ORFs encoding proteins secreted via the LEE encoded type III secretion system, such as tccP and espJ, also decreased in expression from exponential to stationary phase. Three of the clusters (n = 154) comprised genes that are transiently upregulated at the transition into stationary phase and included genes involved in nutrient scavenging. Upregulated genes with an increase in mRNA levels from late exponential to early stationary

  6. Identification of Listeria monocytogenes Genes Expressed in Response to Growth at Low Temperature

    PubMed Central

    Liu, Siqing; Graham, James E.; Bigelow, Lance; Morse, Philip D.; Wilkinson, Brian J.

    2002-01-01

    Listeria monocytogenes is a food-borne bacterial pathogen that is able to grow at refrigeration temperatures. To investigate microbial gene expression associated with cold acclimation, we used a differential cDNA cloning procedure known as selective capture of transcribed sequences (SCOTS) to identify bacterial RNAs that were expressed at elevated levels in bacteria grown at 10°C compared to those grown at 37°C. A total of 24 different cDNA clones corresponding to open reading frames in the L. monocytogenes strain EGD-e genome were obtained by SCOTS. These included cDNAs for L. monocytogenes genes involved in previously described cold-adaptive responses (flaA and flp), regulatory adaptive responses (rpoN, lhkA, yycJ, bglG, adaB, and psr), general microbial stress responses (groEL, clpP, clpB, flp, and trxB), amino acid metabolism (hisJ, trpG, cysS, and aroA), cell surface alterations (fbp, psr, and flaA), and degradative metabolism (eutB, celD, and mleA). Four additional cDNAs were obtained corresponding to genes potentially unique to L. monocytogenes and showing no significant similarity to any other previously described genes. Northern blot analyses confirmed increased steady-state levels of RNA for all members of a subset of genes examined during growth at a low temperature. These results indicated that L. monocytogenes acclimation to growth at 10°C likely involves amino acid starvation, oxidative stress, aberrant protein synthesis, cell surface remodeling, alterations in degradative metabolism, and induction of global regulatory responses. PMID:11916687

  7. Changes of global gene expression and secondary metabolite accumulation during light-dependent Aspergillus nidulans development.

    PubMed

    Bayram, Özgür; Feussner, Kirstin; Dumkow, Marc; Herrfurth, Cornelia; Feussner, Ivo; Braus, Gerhard H

    2016-02-01

    Fungal development and secondary metabolite production are coordinated by regulatory complexes as the trimeric velvet complex. Light accelerates asexual but decreases sexual development of the filamentous fungus Aspergillus nidulans. Changes in gene expression and secondary metabolite accumulation in response to environmental stimuli have been the focus of many studies, but a comprehensive comparison during entire development is lacking. We compared snapshots of transcript and metabolite profiles during fungal development in dark or light. Overall 2.014 genes corresponding to 19% of the genome were differentially expressed when submerged vegetative hyphae were compared to surface development. Differentiation was preferentially asexual in light or preferentially sexual connected to delayed asexual development in dark. Light induces significantly gene expression within the first 24-48h after the transfer to surfaces. Many light induced genes are also expressed in dark after a delay of up to two days, which might be required for preparation of enhanced sexual development. Darkness results in a massive transcriptional reprogramming causing a peak of lipid-derived fungal pheromone synthesis (psi factors) during early sexual development and the expression of genes for cell-wall degradation presumably to mobilize the energy for sexual differentiation. Accumulation of secondary metabolites like antitumoral terrequinone A or like emericellamide start under light conditions, whereas the mycotoxin sterigmatocystin or asperthecin and emodin appear under dark conditions during sexual development. Amino acid synthesis and pool rapidly drop after 72-96h in dark. Subsequent initiation of apoptotic cell-death pathways in darkness happens significantly later than in light. This illustrates that fungal adaptation in differentiation and secondary metabolite production to light conditions requires the reprogramming of one fifth of the potential of its genome.

  8. Electromyographic response of global abdominal stabilisers in response to stable- and unstable-base isometric exercise.

    PubMed

    Atkins, Stephen

    2014-12-24

    Core stability training traditionally uses stable base techniques. Less is known as to the use of unstable base techniques, such as suspension training, to activate core musculature. This study sought to assess the neuromuscular activation of global core stabilisers when using suspension training techniques, compared to more traditional forms of isometric exercise. Eighteen elite level, male youth swimmers (Age 15.5yrs ± 2.3yrs; Stature - 163.3cm ± 12.7cm; Body Mass 62.2kg ± 11.9 kg) participated in the current study. Surface electromyography (sEMG) was used to determine the rate of muscle contraction in postural musculature, associated with core stability and torso bracing (rectus abdominus-RA, external oblique's-EO, erector spinae-ES). A maximal voluntary contraction (MVC) test was used to determine peak amplitude for all muscles. Static bracing of the core was achieved using a modified 'plank' position, with and without a Swiss ball, and held for 30 seconds. A mechanically similar 'plank' was then held using suspension straps. Analysis of sEMG revealed that suspension produced higher peak amplitude in the RA than using a prone or Swiss Ball 'plank' (p=0.04). This difference was not replicated in either the EO or ES musculature. We conclude that suspension training noticeably improves engagement of anterior core musculature when compared to both lateral and posterior muscles. Further research is required to determine how best to activate both posterior and lateral musculature when using all forms of core stability training.

  9. Quantitative Assessment of the Integrated Response in Global Heat and Moisture Budgets to Changing Solar Irradiance

    NASA Technical Reports Server (NTRS)

    White, Warren B.; Cayan, Daniel R.; Dettinger, Michael; Sharber, James (Technical Monitor)

    2001-01-01

    Earlier, we found time sequences of basin- and global-average upper ocean temperature (that is, diabatic heat storage above the main pycnocline) for 40 years from 1955-1994 and of sea surface temperature for 95 years from 1900-1994 associated with changes in the Sun's radiative forcing on decadal and interdecadal timescales, lagging by 10 deg.- 30 deg. of phase and confined to the upper 60-120 m. Yet, the observed changes in upper ocean temperature (approx. 0.1 K) were approximately twice those expected from the Stefan-Boltzmann black-body radiation law for the Earth's surface, with phase lags (0 deg. to 30 deg. of phase) much shorter than the 90 deg. phase shift expected as well. Moreover, White et al. (1997, 1998) found the Earth's global decadal mode in covarying SST and SLP anomalies phase locked to the decadal signal in the Sun's irradiance. Yet, Allan (2000) found this decadal signal also characterized by patterns similar to those observed on biennial and interannual time scales; that is, the Troposphere Biennial Oscillation (TBO) and the El Nino and the Southern Oscillation (ENSO). This suggested that small changes in the Sun's total irradiance could excite this global decadal mode in the Earth's ocean-atmosphere-terrestrial system similar to those excited internally on biennial and interannual period scales. This is a significant finding, proving that energy budget models (that is, models based on globally-averaged radiation balances) yield unrealistic responses. Thus, the true response must include positive and negative feedbacks in the Earth's ocean-atmosphere-terrestrial system as its internal mode (that is, the natural mode of the system) respond in damped resonance to quasi-periodic decadal changes in the Sun's irradiance. Moreover, these responses are not much different from those occurring internally on biennial and interannual period scales.

  10. Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

    PubMed Central

    McCrow, John P.; Badger, Jonathan H.; Zheng, Hong; New, Ashley M.; Dupont, Chris L.; Obata, Toshihiro; Fernie, Alisdair R.; Allen, Andrew E.

    2016-01-01

    Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic

  11. Global pressures, specific responses: effects of nutrient enrichment in streams from different biomes

    NASA Astrophysics Data System (ADS)

    Artigas, Joan; García-Berthou, Emili; Bauer, Delia E.; Castro, Maria I.; Cochero, Joaquín; Colautti, Darío C.; Cortelezzi, Agustina; Donato, John C.; Elosegi, Arturo; Feijoó, Claudia; Giorgi, Adonis; Gómez, Nora; Leggieri, Leonardo; Muñoz, Isabel; Rodrigues-Capítulo, Alberto; Romaní, Anna M.; Sabater, Sergi

    2013-03-01

    We assessed the effects of nutrient enrichment on three stream ecosystems running through distinct biomes (Mediterranean, Pampean and Andean). We increased the concentrations of N and P in the stream water 1.6-4-fold following a before-after control-impact paired series (BACIPS) design in each stream, and evaluated changes in the biomass of bacteria, primary producers, invertebrates and fish in the enriched (E) versus control (C) reaches after nutrient addition through a predictive-BACIPS approach. The treatment produced variable biomass responses (2-77% of explained variance) among biological communities and streams. The greatest biomass response was observed for algae in the Andean stream (77% of the variance), although fish also showed important biomass responses (about 9-48%). The strongest biomass response to enrichment (77% in all biological compartments) was found in the Andean stream. The magnitude and seasonality of biomass responses to enrichment were highly site specific, often depending on the basal nutrient concentration and on windows of ecological opportunity (periods when environmental constraints other than nutrients do not limit biomass growth). The Pampean stream, with high basal nutrient concentrations, showed a weak response to enrichment (except for invertebrates), whereas the greater responses of Andean stream communities were presumably favored by wider windows of ecological opportunity in comparison to those from the Mediterranean stream. Despite variation among sites, enrichment globally stimulated the algal-based food webs (algae and invertebrate grazers) but not the detritus-based food webs (bacteria and invertebrate shredders). This study shows that nutrient enrichment tends to globally enhance the biomass of stream biological assemblages, but that its magnitude and extent within the food web are complex and are strongly determined by environmental factors and ecosystem structure.

  12. Global patterns in lake ecosystem responses to warming based on the temperature dependence of metabolism.

    PubMed

    Kraemer, Benjamin M; Chandra, Sudeep; Dell, Anthony I; Dix, Margaret; Kuusisto, Esko; Livingstone, David M; Schladow, S Geoffrey; Silow, Eugene; Sitoki, Lewis M; Tamatamah, Rashid; McIntyre, Peter B

    2017-05-01

    Climate warming is expected to have large effects on ecosystems in part due to the temperature dependence of metabolism. The responses of metabolic rates to climate warming may be greatest in the tropics and at low elevations because mean temperatures are warmer there and metabolic rates respond exponentially to temperature (with exponents >1). However, if warming rates are sufficiently fast in higher latitude/elevation lakes, metabolic rate responses to warming may still be greater there even though metabolic rates respond exponentially to temperature. Thus, a wide range of global patterns in the magnitude of metabolic rate responses to warming could emerge depending on global patterns of temperature and warming rates. Here we use the Boltzmann-Arrhenius equation, published estimates of activation energy, and time series of temperature from 271 lakes to estimate long-term (1970-2010) changes in 64 metabolic processes in lakes. The estimated responses of metabolic processes to warming were usually greatest in tropical/low-elevation lakes even though surface temperatures in higher latitude/elevation lakes are warming faster. However, when the thermal sensitivity of a metabolic process is especially weak, higher latitude/elevation lakes had larger responses to warming in parallel with warming rates. Our results show that the sensitivity of a given response to temperature (as described by its activation energy) provides a simple heuristic for predicting whether tropical/low-elevation lakes will have larger or smaller metabolic responses to warming than higher latitude/elevation lakes. Overall, we conclude that the direct metabolic consequences of lake warming are likely to be felt most strongly at low latitudes and low elevations where metabolism-linked ecosystem services may be most affected.

  13. The Global Emerging Infection Surveillance and Response System (GEIS), a U.S. government tool for improved global biosurveillance: a review of 2009

    PubMed Central

    2011-01-01

    The Armed Forces Health Surveillance Center, Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) has the mission of performing surveillance for emerging infectious diseases that could affect the United States (U.S.) military. This mission is accomplished by orchestrating a global portfolio of surveillance projects, capacity-building efforts, outbreak investigations and training exercises. In 2009, this portfolio involved 39 funded partners, impacting 92 countries. This article discusses the current biosurveillance landscape, programmatic details of organization and implementation, and key contributions to force health protection and global public health in 2009. PMID:21388562

  14. The Global Emerging Infection Surveillance and Response System (GEIS), a U.S. government tool for improved global biosurveillance: a review of 2009.

    PubMed

    Russell, Kevin L; Rubenstein, Jennifer; Burke, Ronald L; Vest, Kelly G; Johns, Matthew C; Sanchez, Jose L; Meyer, William; Fukuda, Mark M; Blazes, David L

    2011-03-04

    The Armed Forces Health Surveillance Center, Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) has the mission of performing surveillance for emerging infectious diseases that could affect the United States (U.S.) military. This mission is accomplished by orchestrating a global portfolio of surveillance projects, capacity-building efforts, outbreak investigations and training exercises. In 2009, this portfolio involved 39 funded partners, impacting 92 countries. This article discusses the current biosurveillance landscape, programmatic details of organization and implementation, and key contributions to force health protection and global public health in 2009.

  15. Local and global responses of insect motion detectors to the spatial structure of natural scenes.

    PubMed

    O'Carroll, David C; Barnett, Paul D; Nordström, Karin

    2011-12-27

    As a consequence of the non-linear correlation mechanism underlying motion detection, the variability in local pattern structure and contrast inherent within natural scenes profoundly influences local motion responses. To accurately interpret optic flow induced by self-motion, neurons in many dipteran flies smooth this "pattern noise" by wide-field spatial integration. We investigated the role that size and shape of the receptive field plays in smoothing out pattern noise in two unusual hoverfly optic flow neurons: one (HSN) with an exceptionally small receptive field and one (HSNE) with a larger receptive field. We compared the local and global responses to a sequence of panoramic natural images in these two neurons with a parsimonious model for elementary motion detection weighted for their spatial receptive fields. Combined with manipulation of size and contrast of the stimulus images, this allowed us to separate spatial integration properties arising from the receptive field, from other local and global non-linearities, such as motion adaptation and dendritic gain control. We show that receptive field properties alone are poor predictors of the response to natural scenes. If anything, additional non-linearity enhances the pattern dependence of HSN's response, particularly to vertically elongated features, suggesting that it may serve a role in forward fixation during hovering.

  16. Laboratory test simulation for non-flat response calibration of global Earth albedo monitor

    NASA Astrophysics Data System (ADS)

    Seong, Sehyun; Kim, Sug-Whan; Ryu, Dongok; Hong, Jinsuk; Lockwood, Mike

    2012-09-01

    In this report, we present laboratory test simulation for directional responsivity of a global Earth albedo monitoring instrument. The sensor is to observe the Sun and the Earth, alternately, and measure their shortwave (<4μm) radiations around the L1 halo orbit to obtain global Earth albedo. The instrument consists of a broadband scanning radiometer (energy channel instrument) and an imager (visible channel instrument) with ±2° field-of-view. In the case of the energy channel instrument, radiations arriving at the viewing ports from the Sun and the Earth are directed toward the pyroelectric detector via two spherical folding mirrors and a 3D compound parabolic concentrator (CPC). The instrument responsivity is defined by the ratio of the incident radiation input to the instrument output signal. The radiometer's relative directional responsivity needs to be characterized across the field-of-view to assist output signal calibration. For the laboratory test, the distant small source configuration consists of an off-axis collimator and the instrument with adjustable mounts. Using reconstructed 3D CPC surface, the laboratory test simulation for predicting the instrument directional responsivity was conducted by a radiative transfer computation with ray tracing technique. The technical details of the laboratory test simulation are presented together with future plan.

  17. USE OF GENE EXPRESSION ANALYSIS INCORPORATING OPERON-TRANSCRIPTIONAL COUPLING AND TOXICANT DOSE RESPONSE TO DISTINGUISH AMONG STRUCTURAL HOMOLOGUES OF MX

    EPA Science Inventory

    We recently described a general method that can improve microarray analysis of toxicant-exposed cells that uses the intrinsic power of transcriptional coupling and toxicant concentration-expression response data. In this analysis, we characterized changes in global gene expressio...

  18. Prostaglandin F2a activates stress response signaling and induces expression of activating transcription factor 3 (ATF3) in bovine large luteal cells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The pulsatile uterine secretion of prostaglandin F2 alpha (PGF) triggers the regression of the corpus luteum (CL). Recent studies have explored global changes in gene expression in response to PGF that may contribute to structural and functional regression of the CL. Activating transcription facto...

  19. Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions.

    PubMed

    Becker, Anke; Bergès, Hélène; Krol, Elizaveta; Bruand, Claude; Rüberg, Silvia; Capela, Delphine; Lauber, Emmanuelle; Meilhoc, Eliane; Ampe, Frédéric; de Bruijn, Frans J; Fourment, Joëlle; Francez-Charlot, Anne; Kahn, Daniel; Küster, Helge; Liebe, Carine; Pühler, Alfred; Weidner, Stefan; Batut, Jacques

    2004-03-01

    Sinorhizobium meliloti is an alpha-proteobacterium that alternates between a free-living phase in bulk soil or in the rhizosphere of plants and a symbiotic phase within the host plant cells, where the bacteria ultimately differentiate into nitrogen-fixing organelle-like cells, called bacteroids. As a step toward understanding the physiology of S. meliloti in its free-living and symbiotic forms and the transition between the two, gene expression profiles were determined under two sets of biological conditions: growth under oxic versus microoxic conditions, and in free-living versus symbiotic state. Data acquisition was based on both macro- and microarrays. Transcriptome profiles highlighted a profound modification of gene expression during bacteroid differentiation, with 16% of genes being altered. The data are consistent with an overall slow down of bacteroid metabolism during adaptation to symbiotic life and acquisition of nitrogen fixation capability. A large number of genes of unknown function, including potential regulators, that may play a role in symbiosis were identified. Transcriptome profiling in response to oxygen limitation indicated that up to 5% of the genes were oxygen regulated. However, the microoxic and bacteroid transcriptomes only partially overlap, implying that oxygen contributes to a limited extent to the control of symbiotic gene expression.

  20. The Global and Local Climatic Response to the Collapse of the West Antarctic Ice Sheet

    NASA Astrophysics Data System (ADS)

    Huybers, K. M.; Singh, H.; Steiger, N. J.; Frierson, D. M.; Steig, E. J.; Bitz, C. M.

    2014-12-01

    Glaciologists have suggested that a relatively small external forcing may compromise the stability of the West Antarctic Ice Sheet (WAIS). Further, there is compelling physical evidence that the WAIS has collapsed in the past, at times when the mean global temperature was only a few degrees warmer than it is today. In addition to a rapid increase in global sea level, the collapse of the WAIS could also affect the global circulation of the atmosphere. Ice sheets are some of the largest topographic features on Earth, causing large regional anomalies in albedo and radiative balance. Our work uses idealized aquaplanet models in tandem with a fully coupled ocean/atmosphere/sea-ice model (CCSM4) to compare the atmospheric, radiative, and oceanic response to a complete loss of the WAIS. Initial findings indicate that the loss of the WAIS leads to a weakening and equator-ward shift of the zonal winds, a development of strong zonal asymmetries in the meridional wind, and a northward migration of the Intertropical Convergence Zone. We aim to characterize how the local and global climate is affected by the presence of the WAIS, and how changes in the distribution of Southern Hemisphere ice may be represented in the proxy record.

  1. Global biodiversity, stoichiometry and ecosystem function responses to human-induced C-N-P imbalances.

    PubMed

    Carnicer, Jofre; Sardans, Jordi; Stefanescu, Constantí; Ubach, Andreu; Bartrons, Mireia; Asensio, Dolores; Peñuelas, Josep

    2015-01-01

    Global change analyses usually consider biodiversity as a global asset that needs to be preserved. Biodiversity is frequently analysed mainly as a response variable affected by diverse environmental drivers. However, recent studies highlight that gradients of biodiversity are associated with gradual changes in the distribution of key dominant functional groups characterized by distinctive traits and stoichiometry, which in turn often define the rates of ecosystem processes and nutrient cycling. Moreover, pervasive links have been reported between biodiversity, food web structure, ecosystem function and species stoichiometry. Here we review current global stoichiometric gradients and how future distributional shifts in key functional groups may in turn influence basic ecosystem functions (production, nutrient cycling, decomposition) and therefore could exert a feedback effect on stoichiometric gradients. The C-N-P stoichiometry of most primary producers (phytoplankton, algae, plants) has been linked to functional trait continua (i.e. to major axes of phenotypic variation observed in inter-specific analyses of multiple traits). In contrast, the C-N-P stoichiometry of higher-level consumers remains less precisely quantified in many taxonomic groups. We show that significant links are observed between trait continua across trophic levels. In spite of recent advances, the future reciprocal feedbacks between key functional groups, biodiversity and ecosystem functions remain largely uncertain. The reported evidence, however, highlights the key role of stoichiometric traits and suggests the need of a progressive shift towards an ecosystemic and stoichiometric perspective in global biodiversity analyses.

  2. Multiplex immune-related genes expression analysis response to bacterial challenge in mud crab, Scylla paramamosain.

    PubMed

    Zhang, Fengying; Jiang, Keji; Sun, Manman; Zhang, Dan; Ma, Lingbo

    2013-02-01

    Crabs lack an acquired adaptive immune system and host defense is believed to depend entirely on innate, non-adaptive mechanisms to resist invasion by pathogens. Discovery of immune-related factors are helpful for understanding the molecular response of crabs to pathogens. The mud crab Scylla paramamosain is an important marine species for aquaculture in China because of its high nutritional value for humans. In recent years, the crab is prone to being infected by microbes with the enlargement of breeding scale. In this study, eight immune-related genes were analyzed by multiplex genes expression analysis using the GenomeLab GeXP analysis system (Beckman Coulter). The expression levels of all the detected genes rose after challenged by the live bacteria, but the levels of only four genes (C-type lectin, alpha 2-macroglobulin, HSP70 and thioredoxin 1) increased after challenge in heat-killed bacteria group. So the live bacteria were more effective in motivating expressions of immune factors than heat-killed bacteria. However, the transcript of C-type lectin firstly increased at 1 h after challenge in both heat-killed and live bacteria group. This indicated that C-type lectin was a quite susceptive immune factor responding to external pathogen. In group challenged by live bacteria, the genes of alpha 2-macroglobulin, HSP40, thioredoxin 1 and prophenoloxidase activating factor (PPAF) showed response earlier than the other genes. The rise of PPAF expression preceded prophenoloxidase (proPO), which suggested that PPAF might trigger production of proPO transcripts in the early stage of phenoloxidase reaction system. C-type lectin, proPO, thioredoxin 1, HSP40, and alpha 2-macroglobulin are very important immunity factors in response to bacterial infection. According to the result of heat-killed group, HSP70 is a sensitively inductive factor to foreign stimulus compared with the other genes. The multi-gene analysis presented an alternative approach for screening of immune

  3. Expression of heat shock protein genes in insect stress responses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The heat shock proteins (HSPs) that are abundantly expressed in insects are important modulators of insect survival. Expression of HSP genes in insects is not only developmentally regulated, but also induced by various stressors in order to confer protection against such stressors. The expression o...

  4. A growing global network's role in outbreak response: AFHSC-GEIS 2008-2009.

    PubMed

    Johns, Matthew C; Burke, Ronald L; Vest, Kelly G; Fukuda, Mark; Pavlin, Julie A; Shrestha, Sanjaya K; Schnabel, David C; Tobias, Steven; Tjaden, Jeffrey A; Montgomery, Joel M; Faix, Dennis J; Duffy, Mark R; Cooper, Michael J; Sanchez, Jose L; Blazes, David L; Wangchuk, Sonam; Dorji, Tandin; Gibbons, Robert; Iamsirithaworn, Sopon; Richardson, Jason; Buathong, Rome; Jarman, Richard; Yoon, In-Kyu; Shakya, Geeta; Ofula, Victor; Coldren, Rodney; Bulimo, Wallace; Sang, Rosemary; Omariba, Duke; Obura, Beryl; Mwala, Dennis; Kasper, Matthew; Brice, Gary; Williams, Maya; Yasuda, Chad; Barthel, Robert V; Pimentel, Guillermo; Meyers, Chris; Kammerer, Peter; Baynes, Darcie E; Metzgar, David; Hawksworth, Anthony; Blair, Patrick; Ellorin, Melody; Coon, Robert; Macintosh, Victor; Burwell, Kristen; Macias, Elizabeth; Palys, Thomas; Jerke, Kurt

    2011-03-04

    A cornerstone of effective disease surveillance programs comprises the early identification of infectious threats and the subsequent rapid response to prevent further spread. Effectively identifying, tracking and responding to these threats is often difficult and requires international cooperation due to the rapidity with which diseases cross national borders and spread throughout the global community as a result of travel and migration by humans and animals. From Oct.1, 2008 to Sept. 30, 2009, the United States Department of Defense's (DoD) Armed Forces Health Surveillance Center Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) identified 76 outbreaks in 53 countries. Emerging infectious disease outbreaks were identified by the global network and included a wide spectrum of support activities in collaboration with host country partners, several of which were in direct support of the World Health Organization's (WHO) International Health Regulations (IHR) (2005). The network also supported military forces around the world affected by the novel influenza A/H1N1 pandemic of 2009. With IHR (2005) as the guiding framework for action, the AFHSC-GEIS network of international partners and overseas research laboratories continues to develop into a far-reaching system for identifying, analyzing and responding to emerging disease threats.

  5. Comparison of a separated flow response to localized and global-type disturbances

    NASA Astrophysics Data System (ADS)

    Monnier, Bruno; Williams, David R.; Weier, Tom; Albrecht, Thomas

    2016-07-01

    The flow structure and lift response of a separated flow over an airfoil that is subjected to an impulsive type of pitching motion are compared to the response produced by a localized pulse disturbance at the leading edge of an airfoil. Time-resolved PIV data are used to obtain the velocity field on the suction side of the airfoil. POD analysis shows that the majority of energy is contained within the first four modes. Strong similarities in the shapes of the POD basis functions are found, especially for the second mode, irrespective of the type of actuation (global or local). The time-varying coefficient of this second POD mode tracks the negative of the lift coefficient or circulation in each case. Basis functions from the localized actuation data were projected on the velocity field of the globally actuated flow to obtain a hybrid set of coefficients. The hybrid coefficients matched reasonably well with the coefficients obtained from the original POD analysis for the globally excited flow. Both types of actuation were found to generate very similar Lagrangian flow structures. The results suggest a certain degree of universality in the POD modes/flow structures for the separated flow over an airfoil, irrespective of the type of excitation.

  6. Separating the nature and nurture of the allocation of energy in response to global change.

    PubMed

    Applebaum, Scott L; Pan, T-C Francis; Hedgecock, Dennis; Manahan, Donal T

    2014-07-01

    Understanding and predicting biological stability and change in the face of rapid anthropogenic modifications of ecosystems and geosystems are grand challenges facing environmental and life scientists. Physiologically, organisms withstand environmental stress through changes in biochemical regulation that maintain homeostasis, which necessarily demands tradeoffs in the use of metabolic energy. Evolutionarily, in response to environmentally forced energetic tradeoffs, populations adapt based on standing genetic variation in the ability of individual organisms to reallocate metabolic energy. Combined study of physiology and genetics, separating "Nature and Nurture," is, thus, the key to understanding the potential for evolutionary adaptation to future global change. To understand biological responses to global change, we need experimentally tractable model species that have the well-developed physiological, genetic, and genomic resources necessary for partitioning variance in the allocation of metabolic energy into its causal components. Model species allow for discovery and for experimental manipulation of relevant phenotypic contrasts and enable a systems-biology approach that integrates multiple levels of analyses to map genotypic-to-phenotypic variation. Here, we illustrate how combined physiological and genetic studies that focus on energy metabolism in developmental stages of a model marine organism contribute to an understanding of the potential to adapt to environmental change. This integrative research program provides insights that can be readily incorporated into individual-based ecological models of population persistence under global change.

  7. Coralline algae (Rhodophyta) in a changing world: integrating ecological, physiological, and geochemical responses to global change.

    PubMed

    McCoy, Sophie J; Kamenos, Nicholas A

    2015-02-01

    Coralline algae are globally distributed benthic primary producers that secrete calcium carbonate skeletons. In the context of ocean acidification, they have received much recent attention due to the potential vulnerability of their high-Mg calcite skeletons and their many important ecological roles. Herein, we summarize what is known about coralline algal ecology and physiology, providing context to understand their responses to global climate change. We review the impacts of these changes, including ocean acidification, rising temperatures, and pollution, on coralline algal growth and calcification. We also assess the ongoing use of coralline algae as marine climate proxies via calibration of skeletal morphology and geochemistry to environmental conditions. Finally, we indicate critical gaps in our understanding of coralline algal calcification and physiology and highlight key areas for future research. These include analytical areas that recently have become more accessible, such as resolving phylogenetic relationships at all taxonomic ranks, elucidating the genes regulating algal photosynthesis and calcification, and calibrating skeletal geochemical metrics, as well as research directions that are broadly applicable to global change ecology, such as the importance of community-scale and long-term experiments in stress response.

  8. The Response Regulator RcsB Activates Expression of Mat Fimbriae in Meningitic Escherichia coli

    PubMed Central

    Lehti, Timo A.; Heikkinen, Johanna; Korhonen, Timo K.

    2012-01-01

    The common colonization factor of Escherichia coli, the Mat (also termed ECP) fimbria, functions to advance biofilm formation on inert surfaces as well as bacterial adherence to epithelial cells and subsequent colonization. We used global mini-Tn5 transposon mutagenesis to identify novel regulators of biofilm formation by the meningitic E. coli isolate IHE 3034. Of the 4,418 transformants, we found 17 that were impaired in biofilm formation. Most of these mutants were affected in lipopolysaccharide synthesis and were reduced in growth but not in Mat fimbria expression. In contrast, two mutants grew well but did not express Mat fimbria. The insertions in these two mutants were located at different sites of the rcsB gene, which encodes a DNA-binding response regulator of the Rcs response regulon. The mutations abrogated temperature-dependent biofilm formation by IHE 3034, and the phenotype correlated with loss of mat expression. The defect in biofilm formation in the rcsB mutant was reversed upon complementation with rcsB as well as by overexpression of structural mat genes but not by overexpression of the fimbria-specific activator gene matA. Monitoring of the mat operon promoter activity with chromosomal reporter fusions showed that the RcsB protein and an RcsAB box in the mat regulatory region, but not RcsC, RcsD, AckA, and Pta, are essential for initiation of mat transcription. Gel retardation assays showed that RcsB specifically binds to the mat promoter DNA, which enables its function in promoting biofilm formation by E. coli. PMID:22522901

  9. Plant species' origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands.

    PubMed

    Seabloom, Eric W; Borer, Elizabeth T; Buckley, Yvonne M; Cleland, Elsa E; Davies, Kendi F; Firn, Jennifer; Harpole, W Stanley; Hautier, Yann; Lind, Eric M; MacDougall, Andrew S; Orrock, John L; Prober, Suzanne M; Adler, Peter B; Anderson, T Michael; Bakker, Jonathan D; Biederman, Lori A; Blumenthal, Dana M; Brown, Cynthia S; Brudvig, Lars A; Cadotte, Marc; Chu, Chengjin; Cottingham, Kathryn L; Crawley, Michael J; Damschen, Ellen I; Dantonio, Carla M; DeCrappeo, Nicole M; Du, Guozhen; Fay, Philip A; Frater, Paul; Gruner, Daniel S; Hagenah, Nicole; Hector, Andy; Hillebrand, Helmut; Hofmockel, Kirsten S; Humphries, Hope C; Jin, Virginia L; Kay, Adam; Kirkman, Kevin P; Klein, Julia A; Knops, Johannes M H; La Pierre, Kimberly J; Ladwig, Laura; Lambrinos, John G; Li, Qi; Li, Wei; Marushia, Robin; McCulley, Rebecca L; Melbourne, Brett A; Mitchell, Charles E; Moore, Joslin L; Morgan, John; Mortensen, Brent; O'Halloran, Lydia R; Pyke, David A; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Simonsen, Anna; Smith, Melinda D; Stevens, Carly J; Sullivan, Lauren; Wolkovich, Elizabeth; Wragg, Peter D; Wright, Justin; Yang, Louie

    2015-07-15

    Exotic species dominate many communities; however the functional significance of species' biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands.

  10. Global Transcriptomic Analysis of the Response of Corynebacterium glutamicum to Vanillin

    PubMed Central

    Chen, Can; Pan, Junfeng; Yang, Xiaobing; Guo, Chenghao; Ding, Wei; Si, Meiru; Zhang, Yi; Shen, Xihui; Wang, Yao

    2016-01-01

    Lignocellulosic biomass is an abundant and renewable resource for biofuels and bio-based chemicals. Vanillin is one of the major phenolic inhibitors in biomass production using lignocellulose. To assess the response of Corynebacterium glutamicum to vanillin stress, we performed a global transcriptional response analysis. The transcriptional data showed that the vanillin stress not only affected the genes involved in degradation of vanillin, but also differentially regulated several genes related to the stress response, ribosome/translation, protein secretion, and the cell envelope. Moreover, deletion of the sigH or msrA gene in C. glutamicum resulted in a decrease in cell viability under vanillin stress. These insights will promote further engineering of model industrial strains, with enhanced tolerance or degradation ability to vanillin to enable suitable production of biofuels and bio-based chemicals from lignocellulosic biomass. PMID:27760214

  11. Global Transcriptomic Analysis of the Response of Corynebacterium glutamicum to Vanillin.

    PubMed

    Chen, Can; Pan, Junfeng; Yang, Xiaobing; Guo, Chenghao; Ding, Wei; Si, Meiru; Zhang, Yi; Shen, Xihui; Wang, Yao

    2016-01-01

    Lignocellulosic biomass is an abundant and renewable resource for biofuels and bio-based chemicals. Vanillin is one of the major phenolic inhibitors in biomass production using lignocellulose. To assess the response of Corynebacterium glutamicum to vanillin stress, we performed a global transcriptional response analysis. The transcriptional data showed that the vanillin stress not only affected the genes involved in degradation of vanillin, but also differentially regulated several genes related to the stress response, ribosome/translation, protein secretion, and the cell envelope. Moreover, deletion of the sigH or msrA gene in C. glutamicum resulted in a decrease in cell viability under vanillin stress. These insights will promote further engineering of model industrial strains, with enhanced tolerance or degradation ability to vanillin to enable suitable production of biofuels and bio-based chemicals from lignocellulosic biomass.

  12. Engineers' Responsibilities for Global Electronic Waste: Exploring Engineering Student Writing Through a Care Ethics Lens.

    PubMed

    Campbell, Ryan C; Wilson, Denise

    2017-04-01

    This paper provides an empirically informed perspective on the notion of responsibility using an ethical framework that has received little attention in the engineering-related literature to date: ethics of care. In this work, we ground conceptual explorations of engineering responsibility in empirical findings from engineering student's writing on the human health and environmental impacts of "backyard" electronic waste recycling/disposal. Our findings, from a purposefully diverse sample of engineering students in an introductory electrical engineering course, indicate that most of these engineers of tomorrow associated engineers with responsibility for the electronic waste (e-waste) problem in some way. However, a number of responses suggested attempts to deflect responsibility away from engineers towards, for example, the government or the companies for whom engineers work. Still other students associated both engineers and non-engineers with responsibility, demonstrating the distributed/collective nature of responsibility that will be required to achieve a solution to the global problem of excessive e-waste. Building upon one element of a framework for care ethics adopted from the wider literature, these empirical findings are used to facilitate a preliminary, conceptual exploration of care-ethical responsibility within the context of engineering and e-waste recycling/disposal. The objective of this exploration is to provide a first step toward understanding how care-ethical responsibility applies to engineering. We also hope to seed dialogue within the engineering community about its ethical responsibilities on the issue. We conclude the paper with a discussion of its implications for engineering education and engineering ethics that suggests changes for educational policy and the practice of engineering.

  13. Face inversion decreased information about facial identity and expression in face-responsive neurons in macaque area TE.

    PubMed

    Sugase-Miyamoto, Yasuko; Matsumoto, Narihisa; Ohyama, Kaoru; Kawano, Kenji

    2014-09-10

    To investigate the effect of face inversion and thatcherization (eye inversion) on temporal processing stages of facial information, single neuron activities in the temporal cortex (area TE) of two rhesus monkeys were recorded. Test stimuli were colored pictures of monkey faces (four with four different expressions), human faces (three with four different expressions), and geometric shapes. Modifications were made in each face-picture, and its four variations were used as stimuli: upright original, inverted original, upright thatcherized, and inverted thatcherized faces. A total of 119 neurons responded to at least one of the upright original facial stimuli. A majority of the neurons (71%) showed activity modulations depending on upright and inverted presentations, and a lesser number of neurons (13%) showed activity modulations depending on original and thatcherized face conditions. In the case of face inversion, information about the fine category (facial identity and expression) decreased, whereas information about the global category (monkey vs human vs shape) was retained for both the original and thatcherized faces. Principal component analysis on the neuronal population responses revealed that the global categorization occurred regardless of the face inversion and that the inverted faces were represented near the upright faces in the principal component analysis space. By contrast, the face inversion decreased the ability to represent human facial identity and monkey facial expression. Thus, the neuronal population represented inverted faces as faces but failed to represent the identity and expression of the inverted faces, indicating that the neuronal representation in area TE cause the perceptual effect of face inversion.

  14. Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa.

    PubMed

    Li, Jimeng; Liu, Bo; Cheng, Feng; Wang, Xiaowu; Aarts, Mark G M; Wu, Jian

    2014-07-01

    Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana.

  15. Spacial and Temporal Patterns of Gene Expression After Cardiac MEK1 Gene Transfer Improve Post-Infarction Remodeling Without Inducing Global Hypertrophy.

    PubMed

    Fan, Yanying; Yang, Yi-Lin; Yeh, Che-Chung; Mann, Michael J

    2017-04-01

    Alteration of mitogen activated protein (MAP) kinase signaling in transgenic mice can ameliorate post-myocardial infarction (MI) remodeling. However, pre-existing changes in transgenic hearts and clinically unrealistic transgene expression likely affect the response to injury; it is unknown whether clinically relevant induction of transgene expression in an otherwise normal heart can yield similar benefits. Constitutively active MEK1 (aMEK1) or LacZ adeno-associated virus 9 (AAV9) vectors were injected into the left ventricular (LV) chambers of mice either just before or after coronary ligation. Hearts were evaluated via Western blot, quantitative polymerase chain reaction, histology, and echocardiography. AAV9-mediated aMEK1 delivery altered ERK1/2 expression/activation as in transgenic mice. Transgene expression was not immediately detectable but plateaued at 17 days, and therefore did not likely impact acute ischemia as it would in transgenics. With AAV9-aMEK1 injection just prior to MI, robust expression in the infarct border zone during post-MI remodeling increased border zone wall thickness and reduced infarct size versus controls at 4 weeks, but did not induce global hypertrophy. Significant improvements in local and global LV function were observed, as were trends toward a preservation of LV volume. Delivery after ligation significantly lowered transgene expression in the infarct border zone and did not yield structural or functional benefits. The primary benefits observed in transgenic mice, ameliorated remodeling, and reduced chronic infarct size, were achievable via clinically relevant gene transfer of aMEK1, supporting ongoing translational efforts. Important differences, however, were observed, and consideration must be given to the timing and distribution of transgene delivery and expression. J. Cell. Biochem. 118: 775-784, 2017. © 2016 Wiley Periodicals, Inc.

  16. The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally

    PubMed Central

    Park, Dan M.; Akhtar, Md. Sohail; Ansari, Aseem Z.; Landick, Robert; Kiley, Patricia J.

    2013-01-01

    Despite the importance of maintaining redox homeostasis for cellular viability, how cells control redox balance globally is poorly understood. Here we provide new mechanistic insight into how the balance between reduced and oxidized electron carriers is regulated at the level of gene expression by mapping the regulon of the response regulator ArcA from Escherichia coli, which responds to the quinone/quinol redox couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that ArcA reprograms metabolism under anaerobic conditions such that carbon oxidation pathways that recycle redox carriers via respiration are transcriptionally repressed by ArcA. We propose that this strategy favors use of catabolic pathways that recycle redox carriers via fermentation akin to lactate production in mammalian cells. Unexpectedly, bioinformatic analysis of the sequences bound by ArcA in ChIP-seq revealed that most ArcA binding sites contain additional direct repeat elements beyond the two required for binding an ArcA dimer. DNase I footprinting assays suggest that non-canonical arrangements of cis-regulatory modules dictate both the length and concentration-sensitive occupancy of DNA sites. We propose that this plasticity in ArcA binding site architecture provides both an efficient means of encoding binding sites for ArcA, σ70-RNAP and perhaps other transcription factors within the same narrow sequence space and an effective mechanism for global control of carbon metabolism to maintain redox homeostasis. PMID:24146625

  17. Global Transcriptome Analysis of Gracilaria changii (Rhodophyta) in Response to Agarolytic Enzyme and Bacterium.

    PubMed

    Lim, Ee-Leen; Siow, Rouh-San; Abdul Rahim, Raha; Ho, Chai-Ling

    2016-04-01

    Many bacterial epiphytes of agar-producing seaweeds secrete agarase that degrade algal cell wall matrix into oligoagars which elicit defense-related responses in the hosts. The molecular defense responses of red seaweeds are largely unknown. In this study, we surveyed the defense-related transcripts of an agarophyte, Gracilaria changii, treated with β-agarase through next generation sequencing (NGS). We also compared the defense responses of seaweed elicited by agarase with those elicited by an agarolytic bacterium isolated from seaweed, by profiling the expression of defense-related genes using quantitative reverse transcription real-time PCR (qRT-PCR). NGS detected a total of 391 differentially expressed genes (DEGs) with a higher abundance (>2-fold change with a p value <0.001) in the agarase-treated transcriptome compared to that of the non-treated G. changii. Among these DEGs were genes related to signaling, bromoperoxidation, heme peroxidation, production of aromatic amino acids, chorismate, and jasmonic acid. On the other hand, the genes encoding a superoxide-generating NADPH oxidase and related to photosynthesis were downregulated. The expression of these DEGs was further corroborated by qRT-PCR results which showed more than 90 % accuracy. A comprehensive analysis of their gene expression profiles between 1 and 24 h post treatments (hpt) revealed that most of the genes analyzed were consistently upregulated or downregulated by both agarase and agarolytic bacterial treatments, indicating that the defense responses induced by both treatments are highly similar except for genes encoding vanadium bromoperoxidase and animal heme peroxidase. Our study has provided the first glimpse of the molecular defense responses of G. changii to agarase and agarolytic bacterial treatments.

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

    PubMed

    Behringer, David; Zimmermann, Heike; Ziegenhagen, Birgit; Liepelt, Sascha

    2015-01-01

    Increasing drought periods as a result of global climate change pose a threat to many tree species by possibly outpacing their adaptive capabilities. Revealing the genetic basis of drought stress response is therefore implemental for future conservation strategies and risk assessment. Access to informative genomic regions is however challenging, especially for conifers, partially due to their large genomes, which puts constraints on the feasibility of whole genome scans. Candidate genes offer a valuable tool to reduce the complexity of the analysis and the amount of sequencing work and costs. For this study we combined an improved drought stress phenotyping of needles via a novel terahertz water monitoring technique with Massive Analysis of cDNA Ends to identify candidate genes for drought stress response in European silver fir (Abies alba Mill.). A pooled cDNA library was constructed from the cotyledons of six drought stressed and six well-watered silver fir seedlings, respectively. Differential expression analyses of these libraries revealed 296 candidate genes for drought stress response in silver fir (247 up- and 49 down-regulated) of which a subset was validated by RT-qPCR of the twelve individual cotyledons. A majority of these genes code for currently uncharacterized proteins and hint on new genomic resources to be explored in conifers. Furthermore, we could show that some traditional reference genes from model plant species (GAPDH and eIF4A2) are not suitable for differential analysis and we propose a new reference gene, TPC1, for drought stress expression profiling in needles of conifer seedlings.

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

    PubMed Central

    Ziegenhagen, Birgit; Liepelt, Sascha

    2015-01-01

    Increasing drought periods as a result of global climate change pose a threat to many tree species by possibly outpacing their adaptive capabilities. Revealing the genetic basis of drought stress response is therefore implemental for future conservation strategies and risk assessment. Access to informative genomic regions is however challenging, especially for conifers, partially due to their large genomes, which puts constraints on the feasibility of whole genome scans. Candidate genes offer a valuable tool to reduce the complexity of the analysis and the amount of sequencing work and costs. For this study we combined an improved drought stress phenotyping of needles via a novel terahertz water monitoring technique with Massive Analysis of cDNA Ends to identify candidate genes for drought stress response in European silver fir (Abies alba Mill.). A pooled cDNA library was constructed from the cotyledons of six drought stressed and six well-watered silver fir seedlings, respectively. Differential expression analyses of these libraries revealed 296 candidate genes for drought stress response in silver fir (247 up- and 49 down-regulated) of which a subset was validated by RT-qPCR of the twelve individual cotyledons. A majority of these genes code for currently uncharacterized proteins and hint on new genomic resources to be explored in conifers. Furthermore, we could show that some traditional reference genes from model plant species (GAPDH and eIF4A2) are not suitable for differential analysis and we propose a new reference gene, TPC1, for drought stress expression profiling in needles of conifer seedlings. PMID:25924061

  20. Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat.

    PubMed

    Mochida, Keiichi; Kawaura, Kanako; Shimosaka, Etsuo; Kawakami, Naoto; Shin-I, Tadasu; Kohara, Yuji; Yamazaki, Yukiko; Ogihara, Yasunari

    2006-09-01

    In order to assess global changes in gene expression patterns in stress-induced tissues, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Twenty-one cDNA libraries derived from stress-induced tissues, such as callus, as well as liquid cultures and abiotic stress conditions (temperature treatment, desiccation, photoperiod, moisture and ABA) were constructed. Several thousand colonies were randomly selected from each of these 21 cDNA libraries and sequenced from both the 5' and 3' ends. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were monitored. Furthermore, the relationships between gene expression profiles among the stress-induced tissues were inferred from the gene expression patterns. Multi-dimensional analysis of EST data is analogous to microarray experiments. As an example, genes specifically induced and/or suppressed by cold acclimation and heat-shock treatments were selected in silico. Four hundred and ninety genes showing fivefold induction or 218 genes for suppression in comparison to the control expression level were selected. These selected genes were annotated with the BLAST search. Furthermore, gene ontology was conducted for these genes with the InterPro search. Because genes regulated in response to temperature treatment were successfully selected, this method can be applied to other stress-treated tissues. Then, the method was applied to screen genes in response to abiotic stresses such as drought and ABA treatments. In silico selection of screened genes from virtual display should provide a powerful tool for functional plant genomics.

  1. Regulators of coastal wetland methane production and responses to simulated global change

    NASA Astrophysics Data System (ADS)

    Vizza, Carmella; West, William E.; Jones, Stuart E.; Hart, Julia A.; Lamberti, Gary A.

    2017-01-01

    Wetlands are the largest natural source of methane (CH4) emissions to the atmosphere, which vary along salinity and productivity gradients. Global change has the potential to reshape these gradients and therefore alter future contributions of wetlands to the global CH4 budget. Our study examined CH4 production along a natural salinity gradient in fully inundated coastal Alaska wetlands. In the laboratory, we incubated natural sediments to compare CH4 production rates between non-tidal freshwater and tidal brackish wetlands, and quantified the abundances of methanogens and sulfate-reducing bacteria in these ecosystems. We also simulated seawater intrusion and enhanced organic matter availability, which we predicted would have contrasting effects on coastal wetland CH4 production. Tidal brackish wetlands produced less CH4 than non-tidal freshwater wetlands probably due to high sulfate availability and generally higher abundances of sulfate-reducing bacteria, whereas non-tidal freshwater wetlands had significantly greater methanogen abundances. Seawater addition experiments with freshwater sediments, however, did not reduce CH4 production, perhaps because the 14-day incubation period was too short to elicit a shift in microbial communities. In contrast, increased organic matter enhanced CH4 production in 75 % of the incubations, but this response depended on the macrophyte species added, with half of the species treatments having no significant effect. Our study suggests that CH4 production in coastal wetlands, and therefore their overall contribution to the global CH4 cycle, will be sensitive to increased organic matter availability and potentially seawater intrusion. To better predict future wetland contributions to the global CH4 budget, future studies and modeling efforts should investigate how multiple global change mechanisms will interact to impact CH4 dynamics.

  2. Escherichia coli O157:H7 survives within human macrophages: global gene expression profile and involvement of the Shiga toxins.

    PubMed

    Poirier, Katherine; Faucher, Sébastien P; Béland, Maxime; Brousseau, Roland; Gannon, Victor; Martin, Christine; Harel, Josée; Daigle, France

    2008-11-01

    Escherichia coli O157:H7 is an important food-borne pathogen that specifically binds to the follicle-associated epithelium in the intestine, which rapidly brings this bacterial pathogen in contact with underlying human macrophages. Very little information is available about the interaction between E. coli O157:H7 and human macrophages. We evaluated the uptake and survival of strain EDL933 during infection of human macrophages. Surprisingly, EDL933 survived and multiplied in human macrophages at 24 h postinfection. The global gene expression profile of this pathogen during macrophage infection was determined. Inside human macrophages, upregulation of E. coli O157:H7 genes carried on O islands (such as pagC, the genes for both of the Shiga toxins, and the two iron transport system operons fit and chu) was observed. Genes involved in acid resistance and in the SOS response were upregulated. However, genes of the locus of enterocyte effacement or genes involved in peroxide resistance were not differentially expressed. Many genes with putative or unknown functions were upregulated inside human macrophages and may be newly discovered virulence factors. As the Shiga toxin genes were upregulated in macrophages, survival and cytotoxicity assays were performed with isogenic Shiga toxin mutants. The initial uptake of Shiga toxins mutants was higher than that of the wild type; however, the survival rates were significantly lower at 24 h postinfection. Thus, Shiga toxins are implicated in the interaction between E. coli O157:H7 and human macrophages. Understanding the molecular mechanisms used by E. coli to survive within macrophages may help in the identification of targets for new therapeutic agents.

  3. Specific regulatory motifs predict glucocorticoid responsiveness of hippocampal gene expression.

    PubMed

    Datson, N A; Polman, J A E; de Jonge, R T; van Boheemen, P T M; van Maanen, E M T; Welten, J; McEwen, B S; Meiland, H C; Meijer, O C

    2011-10-01

    The glucocorticoid receptor (GR) is an ubiquitously expressed ligand-activated transcription factor that mediates effects of cortisol in relation to adaptation to stress. In the brain, GR affects the hippocampus to modulate memory processes through direct binding to glucocorticoid response elements (GREs) in the DNA. However, its effects are to a high degree cell specific, and its target genes in different cell types as well as the mechanisms conferring this specificity are largely unknown. To gain insight in hippocampal GR signaling, we characterized to which GRE GR binds in the rat hippocampus. Using a position-specific scoring matrix, we identified evolutionary-conserved putative GREs from a microarray based set of hippocampal target genes. Using chromatin immunoprecipitation, we were able to confirm GR binding to 15 out of a selection of 32 predicted sites (47%). The majority of these 15 GREs are previously undescribed and thus represent novel GREs that bind GR and therefore may be functional in the rat hippocampus. GRE nucleotide composition was not predictive for binding of GR to a GRE. A search for conserved flanking sequences that may predict GR-GRE interaction resulted in the identification of GC-box associated motifs, such as Myc-associated zinc finger protein 1, within 2 kb of GREs with GR binding in the hippocampus. This enrichment was not present around nonbinding GRE sequences nor around proven GR-binding sites from a mesenchymal stem-like cell dataset that we analyzed. GC-binding transcription factors therefore may be unique partners for DNA-bound GR and may in part explain cell-specific transcriptional regulation by glucocorticoids in the context of the hippocampus.

  4. On Modeling the Upper Atmosphere and Ionosphere Response to Global Change

    NASA Astrophysics Data System (ADS)

    Roble, R. G.; Solomon, S. C.

    2005-05-01

    Ice core records indicate that the temperature and composition of the atmosphere can change significantly over geologic times. These changes occur naturally, however, recently the releases of trace gases from human activity have been recognized to have a potential for causing a significant change in the climate of the Earth. Most of the effort in investigating the global response to these trace gases has been directed toward the troposphere and stratosphere. Studies have shown that the troposphere will warm and the stratosphere will cool as trace gas concentrations increase in the 21st century. Studies have also been made that suggest that the mesosphere and thermosphere could also cool and affect the compositional structure of the upper atmosphere and ionosphere. We first review previous studies of the upper atmosphere and ionosphere response to trace gas increases. We then use both a global average model and the NCAR Thermosphere - Ionosphere - Mesosphere - Electrodynamics General Circulation Model (TIME-GCM) to investigate the atmospheric response to various scenarios of trace gas increases and compare the modeling results to the present day upper atmosphere and ionosphere structure. We will also discuss the key aeronomic processes that control the structure of the upper atmosphere as well as the extent to which these processes are known.

  5. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression.

    PubMed

    Almassalha, L M; Tiwari, A; Ruhoff, P T; Stypula-Cyrus, Y; Cherkezyan, L; Matsuda, H; Dela Cruz, M A; Chandler, J E; White, C; Maneval, C; Subramanian, H; Szleifer, I; Roy, H K; Backman, V

    2017-01-24

    Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis.

  6. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression

    PubMed Central

    Almassalha, L. M.; Tiwari, A.; Ruhoff, P. T.; Stypula-Cyrus, Y.; Cherkezyan, L.; Matsuda, H.; Dela Cruz, M. A.; Chandler, J. E.; White, C.; Maneval, C.; Subramanian, H.; Szleifer, I.; Roy, H. K.; Backman, V.

    2017-01-01

    Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis. PMID:28117353

  7. Ecohydrological responses to multifactor global change in a tallgrass prairie: A modeling analysis

    NASA Astrophysics Data System (ADS)

    Bell, Jesse Eugene; Weng, Ensheng; Luo, Yiqi

    2010-12-01

    Relative impacts of multiple global change factors on ecohydrological processes in terrestrial ecosystems have not been carefully studied. In this study, we used a terrestrial ecosystem (TECO) model to examine effects of three global change factors (i.e., climate warming, elevated CO2, and altered precipitation) individually and in combination on runoff, evaporation, transpiration, rooting zone soil moisture content, water use efficiency (WUE), and rain use efficiency (RUE) in a North American tallgrass prairie. We conducted a total of 200 different scenarios with gradual changes of the three factors for 100 years. Our modeling results show strong responses of runoff, evaporation, transpiration, and rooting zone soil moisture to changes in temperature and precipitation, while effects of CO2 changes were relatively minor. For example, runoff decreased by 50% with a 10°C increase in temperature and increased by 250% with doubled precipitation. Ecosystem-level RUE increased with CO2, decreased with precipitation, and optimized at 4-6°C of warming. In contrast, plant-level WUE was highest at doubled CO2, doubled precipitation, and ambient temperature. The different response patterns of RUE and WUE signify that processes at different scales responded uniquely to climate change. Combinations of temperature, CO2, and precipitation anomalies interactively affected response magnitude and/or patterns of ecohydrological processes. Our results suggest that ecohydrological processes were considerably affected by global change factors and then likely regulate other ecosystem processes, such as carbon and nitrogen cycling. In particular, substantial changes in runoff to different climate change scenarios could have policy implications because it is a major component to replenishing freshwater. These modeling results should be tested by and could influence design of field experiments on ecohydrological processes.

  8. Health workforce responses to global health initiatives funding: a comparison of Malawi and Zambia

    PubMed Central

    2010-01-01

    Background Shortages of health workers are obstacles to utilising global health initiative (GHI) funds effectively in Africa. This paper reports and analyses two countries' health workforce responses during a period of large increases in GHI funds. Methods Health facility record reviews were conducted in 52 facilities in Malawi and 39 facilities in Zambia in 2006/07 and 2008; quarterly totals from the last quarter of 2005 to the first quarter of 2008 inclusive in Malawi; and annual totals for 2004 to 2007 inclusive in Zambia. Topic-guided interviews were conducted with facility and district managers in both countries, and with health workers in Malawi. Results Facility data confirm significant scale-up in HIV/AIDS service delivery in both countries. In Malawi, this was supported by a large increase in lower trained cadres and only a modest increase in clinical staff numbers. Routine outpatient workload fell in urban facilities, in rural health centres and in facilities not providing antiretroviral treatment (ART), while it increased at district hospitals and in facilities providing ART. In Zambia, total staff and clinical staff numbers stagnated between 2004 and 2007. In rural areas, outpatient workload, which was higher than at urban facilities, increased further. Key informants described the effects of increased workloads in both countries and attributed staff migration from public health facilities to non-government facilities in Zambia to PEPFAR. Conclusions Malawi, which received large levels of GHI funding from only the Global Fund, managed to increase facility staff across all levels of the health system: urban, district and rural health facilities, supported by task-shifting to lower trained staff. The more complex GHI arena in Zambia, where both Global Fund and PEPFAR provided large levels of support, may have undermined a coordinated national workforce response to addressing health worker shortages, leading to a less effective response in rural areas

  9. Ecosystem Responses in the Jasper Ridge Global Change Experiment Over Seven Years

    NASA Astrophysics Data System (ADS)

    Gurwick, N. P.; Field, C. B.; Chiariello, N.; Vitousek, P. M.

    2007-12-01

    Field plots within a California grassland at Jasper Ridge, USA, have been exposed for 9 years to enhanced levels of CO2, nitrogen, heat, and precipitation, singly and in all possible combinations. We here report an updated analysis of major trends in NPP response, based on an analysis of data collected through 2006. First, as reported in earlier syntheses of NPP response at the JRGCE, NPP responded most strongly and consistently to enhanced N deposition. However, the magnitude of this response peaked in 2003 and had been markedly less pronounced since then. Second, all statistically significant effects emerged as interactions with year, highlighting the dependence of ecosystem responses to global change factors on temporal variation in uncontrolled drivers. Third, the influence of enhanced CO2 on NPP varied regularly across years, and correlated strongly with annual precipitation (R2=0.89, p<0.05). Contrary to expectations, enriched CO2 concentrations diminished NPP in dry years and enhanced NPP in wet years. Two observations point to the seasonal pattern of precipitation (vs. total amount) as mediating the ecosystem response to interactions among global change factors. First, although the effect of CO2 varied regularly with annual precipitation, the interaction of the CO2 and precipitation treatments did not produce a parallel result. The enhanced precipitation treatment in the JRGCE adds 50% to each rain event and adds two rain events to the end of the growing season but does not shift the pattern of rainfall during the growing season. Second, enhanced CO2 appears to diminish the positive effect of N deposition on NPP, contrary to a traditional model of co-limitation by C and N, but only in years with minimal precipitation during March.

  10. Global seabird responses to forage fish depletion: one-third for the birds

    USGS Publications Warehouse

    Cury, P.M.; Boyd, I.L.; Bonhommeau, S.; Anker-Nilssen, T.; Crawford, R.J.M.; Furness, R.W.; Mills, J.A.; Murphy, E.J.; Osterblom, H.; Paleczny, M.; Piatt, John F.; Roux, J.-P.; Shannon, L.; Sydeman, W.J.

    2011-01-01

    Determining the form of key predator-prey relationships is critical for understanding marine ecosystem dynamics. Using a comprehensive global database, we quantified the effect of fluctuations in food abundance on seabird breeding success. We identified a threshold in prey (fish and krill, termed "forage fish") abundance below which seabirds experience consistently reduced and more variable productivity. This response was common to all seven ecosystems and 14 bird species examined within the Atlantic, Pacific, and Southern Oceans. The threshold approximated one-third of the maximum prey biomass observed in long-term studies. This provides an indicator of the minimal forage fish biomass needed to sustain seabird productivity over the long term.

  11. Global seabird response to forage fish depletion - One-third for the birds

    USGS Publications Warehouse

    Cury, P.M.; Boyd, I.L.; Bonhommeau, S.; Anker-Nilssen, T.; Crawford, R.J.M.; Furness, R.W.; Mills, J.A.; Murphy, E.J.; Osterblom, H.; Paleczny, M.; Piatt, J.F.; Roux, J.-P.; Shannon, L.; Sydeman, W.J.

    2011-01-01

    Determining the form of key predator-prey relationships is critical for understanding marine ecosystem dynamics. Using a comprehensive global database, we quantified the effect of fluctuations in food abundance on seabird breeding success. We identified a threshold in prey (fish and krill, termed "forage fish") abundance below which seabirds experience consistently reduced and more variable productivity. This response was common to all seven ecosystems and 14 bird species examined within the Atlantic, Pacific, and Southern Oceans. The threshold approximated one-third of the maximum prey biomass observed in long-term studies. This provides an indicator of the minimal forage fish biomass needed to sustain seabird productivity over the long term.

  12. Managing the global commons decision making and conflict resolution in response to climate change

    SciTech Connect

    Rayner, S. ); Naegeli, W.; Lund, P. )

    1990-07-01

    A workshop was convened to develop a better understanding of decision-making matters concerning management of the global commons and to resolve conflicts in response to climate change. This workshop report does not provide a narrative of the proceedings. The workshop program is included, as are the abstracts of the papers that were presented. Only the introductory paper on social science research by William Riebsame and the closing summary by Richard Rockwell are reprinted here. This brief report focuses instead on the deliberations of the working groups that developed during the workshop. 4 figs., 1 tab.

  13. Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique

    SciTech Connect

    Smith, Daniel P.; Kitner, J. B.; Norbeck, Angela D.; Clauss, Therese RW; Lipton, Mary S.; Schwalbach, M. S.; Steindler, L.; Nicora, Carrie D.; Smith, Richard D.; Giovannoni, Stephen J.

    2010-05-05

    Abstract Background: Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Methodology/Principal Findings: Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. Conclusions/Significance: We propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. We propose a model in which the RNA-binding activity of cspE and cspL selectively enables protein synthesis of the iron acquisition protein sfuC during transient growth-limiting episodes of iron scarcity.

  14. Global alteration in gene expression profiles of deciduas from women with idiopathic recurrent pregnancy loss

    PubMed Central

    Krieg, S.A.; Fan, X.; Hong, Y.; Sang, Q.-X.; Giaccia, A.; Westphal, L.M.; Lathi, R.B.; Krieg, A.J.; Nayak, N.R.

    2012-01-01

    Recurrent pregnancy loss (RPL) occurs in ∼5% of women. However, the etiology is still poorly understood. Defects in decidualization of the endometrium during early pregnancy contribute to several pregnancy complications, such as pre-eclampsia and intrauterine growth restriction (IUGR), and are believed to be important in the pathogenesis of idiopathic RPL. We performed microarray analysis to identify gene expression alterations in the deciduas of idiopathic RPL patients. Control patients had one antecedent term delivery, but were undergoing dilation and curettage for current aneuploid miscarriage. Gene expression differences were evaluated using both pathway and gene ontology (GO) analysis. Selected genes were validated using quantitative reverse transcription–polymerase chain reaction (qRT–PCR). A total of 155 genes were found to be significantly dysregulated in the deciduas of RPL patients (>2-fold change, P < 0.05), with 22 genes up-regulated and 133 genes down-regulated. GO analysis linked a large percentage of genes to discrete biological functions, including immune response (23%), cell signaling (18%) and cell invasion (17.1%), and pathway analysis revealed consistent changes in both the interleukin 1 (IL-1) and IL-8 pathways. All genes in the IL-8 pathway were up-regulated while genes in the IL-1 pathway were down-regulated. Although both pathways can promote inflammation, IL-1 pathway activity is important for normal implantation. Additionally, genes known to be critical for degradation of the extracellular matrix, including matrix metalloproteinase 26 and serine peptidase inhibitor Kazal-type 1, were also highly up-regulated. In this first microarray approach to decidual gene expression in RPL patients, our data suggest that dysregulation of genes associated with cell invasion and immunity may contribute significantly to idiopathic recurrent miscarriage. PMID:22505054

  15. Changes in global gene expression in rat myometrium in transition from late pregnancy to parturition.

    PubMed

    Helguera, Gustavo; Eghbali, Mansoureh; Sforza, Daniel; Minosyan, Tamara Y; Toro, Ligia; Stefani, Enrico

    2009-01-08

    The process of parturition involves the complex interplay of factors that change the excitability and contractile activity of the uterus. We have compared the relative gene expression profile of myometrium from rats before parturition (21 days pregnant) and during delivery, using high-density DNA microarray. Of 8,740 sequences available in the array, a total of 3,782 were detected as present. From the sequences that were significantly altered, 59 genes were upregulated and 82 genes were downregulated. We were able to detect changes in genes described to have altered expression level at term, including connexin 43 and 26, cyclooxygenase 2, and oxytocin receptor, as well as novel genes that have been not previously associated with parturition. Quantitative real-time PCR on selected genes further confirmed the microarray data. Here we report for the first time that aquaporin5 (AQP5), a member of the aquaporin water channel family, was dramatically downregulated during parturition (approximately 100-fold by microarray and approximately 50-fold by real-time PCR). The emerging profile highlights biochemical cascades occurring in a period of approximately 36 h that trigger parturition and the initiation of myometrium reverse remodeling postpartum. The microarray analysis uncovered genes that were previously suspected to play a role in parturition. This regulation involves genes from immune/inflammatory response, steroid/lipid metabolism, calcium homeostasis, cell volume regulation, cell signaling, cell division, and tissue remodeling, suggesting the presence of multiple and redundant mechanisms altered in the process of birth.

  16. Analysis of grape ESTs: global gene expression patterns in leaf and berry.

    PubMed

    Ablett; Seaton; Scott; Shelton; Graham; Baverstock; Lee; Henry

    2000-10-16

    Analysis of 2479 ESTs from Vitis vinifera berry tissue and 2438 from leaf revealed that 1% of the ESTs match to known Vitis proteins, 72% to plant proteins, 11% to non-plant, and 16% had no match (P[N]>0.5). The levels of redundancy were similar in the leaf and berry libraries. Only 12% of the genes matched by the ESTs were common to both libraries indicating marked differences in the genes expressed in the two tissues. The abundance of transcripts with predicted cellular roles in leaf and berry were estimated by classifying the primary BLAST matches to known proteins (score >80) into functional categories. Thirty-six percent of the leaf transcripts were involved in photosynthesis, compared to 3% in the berry. This is a much higher proportion of transcripts involved with a function limited to specialized cells, than was found when transcripts of 33 human tissues were compared using a similar approach, suggesting plant cells may involve their cellular machinery to a greater extent in specialized activities than animal cells. Relatively enhanced expression of specific transcription factors, and genes involved in defense, detoxification, stress response, proteolysis, trafficing, and signal transduction, suggests berry tissue is actively engaged in responding to environmental stimuli.

  17. Global Gene Expression Differences in Joints of Mice with Divergent Post Traumatic Osteoarthritis Phenotypes

    SciTech Connect

    Kibui, J.

    2016-07-28

    Osteoarthritis (OA) is a debilitating joint disease characterized by cartilage degradation which prompts pain, stiffness and swelling. Contributing factors include age, genetics, obesity, injury and overuse of joints. OA is defined by an acute phase and a chronic phase whereby inflammation and degeneration of articular cartilage and other tissues is followed by joint pain and limited mobility. Patients remain asymptomatic until substantial joint damage has occurred and therefore rely on long term surgical joint replacement and pain management as their sole treatment options. For this reason, there is an increasing need to identify early stage osteoarthritis biomarkers. Our study aimed to identify and characterize gene expression variances in 3 different mouse strains (STR/ort, C57BL/6 and MRL/MpJ) with different susceptibility to post traumatic osteoarthritis (PTOA). Through RNA sequence analysis of whole knee joint RNA, we identified differentially expressed genes associated with the initial stages of PTOA in relation to mice with divergent phenotypes. These results will help elucidate potential mechanisms responsible for PTOA outcomes.

  18. Unpredictable, unpreventable and impersonal medicine: global disaster response in the 21st century.

    PubMed

    Andrews, Russell J; Quintana, Leonidas M

    2015-01-01

    The United Nations has recognized the devastating consequences of "unpredictable, unpreventable and impersonal" disasters-at least US $2 trillion in economic damage and more than 1.3 million lives lost from natural disasters in the last two decades alone. In many disasters (both natural and man-made) hundreds-and in major earthquakes, thousands-of lives are lost in the first days following the event because of the lack of medical/surgical facilities to treat those with potentially survivable injuries. Disasters disrupt and destroy not only medical facilities in the disaster zone but also infrastructure (roads, airports, electricity) and potentially local healthcare personnel as well. To minimize morbidity and mortality from disasters, medical treatment must begin immediately, within minutes ideally, but certainly within 24 h (not the days to weeks currently seen in medical response to disasters). This requires that all resources-medical equipment and support, and healthcare personnel-be portable and readily available; transport to the disaster site will usually require helicopters, as military medical response teams in developed countries have demonstrated. Some of the resources available and in development for immediate medical response for disasters-from portable CT scanners to telesurgical capabilities-are described. For immediate deployment, these resources-medical equipment and personnel-must be ready for deployment on a moment's notice and not require administrative approvals or bureaucratic authorizations from numerous national and international agencies, as is presently the case. Following the "trauma center/stroke center" model, disaster response incorporating "disaster response centers" would be seamlessly integrated into the ongoing daily healthcare delivery systems worldwide, from medical education and specialty training (resident/registrar) to acute and subacute intensive care to long-term rehabilitation. The benefits of such a global disaster

  19. The positive Indian Ocean Dipole-like response in the tropical Indian Ocean to global warming

    SciTech Connect

    Luo, Yiyong; Lu, Jian; Liu, Fukai; Wan, Xiuquan

    2016-02-04

    Climate models project a positive Indian Ocean Dipole (pIOD)-like SST response in the tropical Indian Ocean to global warming. By employing the Community Earth System Model (CESM) and applying an overriding technique to its ocean component Parallel Ocean Program version 2 (POP2), this study investigates the similarity and difference of the formation mechanisms for the changes in the tropical Indian Ocean during the pIOD versus global warming. Results show that their formation processes and related seasonality are quite similar; in particular, the Bjerknes feedback is the leading mechanism in producing the anomalous cooling over the eastern tropics in both cases. Some differences are also found, including that the cooling effect of the vertical advection over the eastern tropical Indian Ocean is dominated by the anomalous vertical velocity during the pIOD while it is dominated by the anomalous upper-ocean stratification under global warming. Lastly, these findings above are further examined with an analysis of the mixed layer heat budget.

  20. The positive Indian Ocean Dipole-like response in the tropical Indian Ocean to global warming

    DOE PAGES

    Luo, Yiyong; Lu, Jian; Liu, Fukai; ...

    2016-02-04

    Climate models project a positive Indian Ocean Dipole (pIOD)-like SST response in the tropical Indian Ocean to global warming. By employing the Community Earth System Model (CESM) and applying an overriding technique to its ocean component Parallel Ocean Program version 2 (POP2), this study investigates the similarity and difference of the formation mechanisms for the changes in the tropical Indian Ocean during the pIOD versus global warming. Results show that their formation processes and related seasonality are quite similar; in particular, the Bjerknes feedback is the leading mechanism in producing the anomalous cooling over the eastern tropics in both cases.more » Some differences are also found, including that the cooling effect of the vertical advection over the eastern tropical Indian Ocean is dominated by the anomalous vertical velocity during the pIOD while it is dominated by the anomalous upper-ocean stratification under global warming. Lastly, these findings above are further examined with an analysis of the mixed layer heat budget.« less

  1. Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes.

    PubMed

    Cornelissen, Johannes H C; van Bodegom, Peter M; Aerts, Rien; Callaghan, Terry V; van Logtestijn, Richard S P; Alatalo, Juha; Chapin, F Stuart; Gerdol, Renato; Gudmundsson, Jon; Gwynn-Jones, Dylan; Hartley, Anne E; Hik, David S; Hofgaard, Annika; Jónsdóttir, Ingibjörg S; Karlsson, Staffan; Klein, Julia A; Laundre, Jim; Magnusson, Borgthor; Michelsen, Anders; Molau, Ulf; Onipchenko, Vladimir G; Quested, Helen M; Sandvik, Sylvi M; Schmidt, Inger K; Shaver, Gus R; Solheim, Bjørn; Soudzilovskaia, Nadejda A; Stenström, Anna; Tolvanen, Anne; Totland, Ørjan; Wada, Naoya; Welker, Jeffrey M; Zhao, Xinquan

    2007-07-01

    Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide. Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition.

  2. A global analysis of ENSO synchrony: The oceans' biological response to physical forcing

    NASA Astrophysics Data System (ADS)

    Messié, Monique; Chavez, Francisco P.

    2012-09-01

    A global-scale Empirical Orthogonal Function (EOF) analysis of physical (sea surface temperatures, sea level height anomalies, atmospheric sea level pressure, photosynthetically active radiation, zonal surface currents and wind-driven upwelling velocities) and biological (surface chlorophyll concentrations and primary production) variables shows synchronous variations from 1993 to 2010 in the first mode of variability associated with El Niño Southern Oscillation (ENSO). The first EOF of vertical temperature structure along the equatorial Pacific shows identical temporal patterns. The ENSO-driven biological changes are explained both qualitatively and quantitatively from a subset of the physical variables. During the strong 1997-1998 El Niño a global new production decrease of ˜0.6-0.9 PgC yr-1 is estimated from changes in the depth of the nutricline and wind-driven upwelling. This is consistent with the 3.0 PgC yr-1 decrease in global primary production observed by satellite remote sensing. A simple two-layer model of chlorophyll and primary production driven by changes in nitrate and light reproduces the patterns and magnitude of changes observed by satellite. Changes in the depth of the nutricline are found to be the primary driver of the biological anomalies. The ENSO mode of zonal currents in the equatorial Pacific shows that horizontal advection is responsible for changes in chlorophyll in the central Pacific not explained by the two-layer model.

  3. Leveraging the laboratory response network model for the global health security agenda.

    PubMed

    Mangal, Chris N; Maryogo-Robinson, Lucy

    2014-01-01

    Promoting global health security as an international priority is a challenge; the US Centers for Disease Control and Prevention (CDC) in its Global Health Security Agenda has articulated the importance of accelerating progress toward a world safe and secure from infectious disease threats. The goals are to (1) prevent and reduce the likelihood of outbreaks-natural, accidental, or intentional; (2) detect threats early to save lives; and (3) respond rapidly and effectively using multisectoral, international coordination and communication. Foundational to this agenda is the World Health Organization (WHO) Revised International Health Regulations (IHR) of 2005, which provide the legal framework for countries to strengthen their health systems in order to be able to respond to any public health emergency of international concern. This article proposes leveraging the distributed structure of the US-managed Laboratory Response Network for Biological Threats Preparedness (LRN-B) to develop the core capacity of laboratory testing and to fulfill the laboratory-strengthening component of the Global Health Security Agenda. The LRN model offers an effective mechanism to detect and respond to public health emergencies of international concern.

  4. Leveraging the Laboratory Response Network Model for the Global Health Security Agenda

    PubMed Central

    Maryogo-Robinson, Lucy

    2014-01-01

    Promoting global health security as an international priority is a challenge; the US Centers for Disease Control and Prevention (CDC) in its Global Health Security Agenda has articulated the importance of accelerating progress toward a world safe and secure from infectious disease threats. The goals are to (1) prevent and reduce the likelihood of outbreaks—natural, accidental, or intentional; (2) detect threats early to save lives; and (3) respond rapidly and effectively using multisectoral, international coordination and communication. Foundational to this agenda is the World Health Organization (WHO) Revised International Health Regulations (IHR) of 2005, which provide the legal framework for countries to strengthen their health systems in order to be able to respond to any public health emergency of international concern. This article proposes leveraging the distributed structure of the US-managed Laboratory Response Network for Biological Threats Preparedness (LRN-B) to develop the core capacity of laboratory testing and to fulfill the laboratory-strengthening component of the Global Health Security Agenda. The LRN model offers an effective mechanism to detect and respond to public health emergencies of international concern. PMID:25254916

  5. Global mode and frequency response analysis of low-density jets

    NASA Astrophysics Data System (ADS)

    Coenen, W.; Lesshafft, L.; Garnaud, X.; Sevilla, A.

    2014-11-01

    We present a global stability analysis of a low-density jet, where the wavepacket structures are temporal eigenmodes of the linearized equations of motion in a 2D domain. As a base state we employ a numerical solution of the low-Mach number Navier-Stokes equations. The jet is characterized through the jet-to-ambient density ratio, the Reynolds number, and the momentum thickness of the velocity profile at the jet exit plane. The linear global mode analysis shows that for certain combinations of the control parameters, an isolated eigenmode dominates the eigenvalue spectrum. Its associated growth rate can be used to construct a neutral curve in the parameter space that agrees well with the experimentally observed onset of self-sustained oscillations (Hallberg & Strykowski, JFM, 2006). However, for high values of the Reynolds number, the construction of a neutral curve based on the spectrum loses validity, since for these cases the spectrum is dominated by a continuous branch of eigenvalues, sensitive to changes in domain length and grid refinement. Finally, the flow response to external forcing in a globally stable setting is investigated through the computation of the pseudospectrum, and is found to be dominated by a resonance of the stable eigenmode. Supported by Spanish MINECO under Project DPI 2011-28356-C03-02.

  6. Analysis of Global and Absorption, Distribution, Metabolism, and Elimination Gene Expression in the Progressive Stages of Human Nonalcoholic Fatty Liver DiseaseS⃞

    PubMed Central

    Lake, April D.; Novak, Petr; Fisher, Craig D.; Jackson, Jonathan P.; Hardwick, Rhiannon N.; Billheimer, D. Dean; Klimecki, Walter T.

    2011-01-01

    Nonalcoholic fatty liver disease (NAFLD) is characterized by a series of pathological changes that range from simple fatty liver to nonalcoholic steatohepatitis (NASH). The objective of this study is to describe changes in global gene expression associated with the progression of human NAFLD. This study is focused on the expression levels of genes responsible for the absorption, distribution, metabolism, and elimination (ADME) of drugs. Differential gene expression between three clinically defined pathological groups—normal, steatosis, and NASH—was analyzed. Genome-wide mRNA levels in samples of human liver tissue were assayed with Affymetrix GeneChip Human 1.0ST arrays. A total of 11,633 genes exhibited altered expression out of 33,252 genes at a 5% false discovery rate. Most gene expression changes occurred in the progression from steatosis to NASH. Principal component analysis revealed that hepatic disease status was the major determinant of differential ADME gene expression rather than age or sex of sample donors. Among the 515 drug transporters and 258 drug-metabolizing enzymes (DMEs) examined, uptake transporters but not efflux transporters or DMEs were significantly over-represented in the number of genes down-regulated. These results suggest that uptake transporter genes are coordinately targeted for down-regulation at the global level during the pathological development of NASH and that these patients may have decreased drug uptake capacity. This coordinated regulation of uptake transporter genes is indicative of a hepatoprotective mechanism acting to prevent accumulation of toxic intermediates in disease-compromised hepatocytes. PMID:21737566

  7. Are treelines advancing? A global meta-analysis of treeline response to climate warming.

    PubMed

    Harsch, Melanie A; Hulme, Philip E; McGlone, Matt S; Duncan, Richard P

    2009-10-01

    Treelines are temperature sensitive transition zones that are expected to respond to climate warming by advancing beyond their current position. Response to climate warming over the last century, however, has been mixed, with some treelines showing evidence of recruitment at higher altitudes and/or latitudes (advance) whereas others reveal no marked change in the upper limit of tree establishment. To explore this variation, we analysed a global dataset of 166 sites for which treeline dynamics had been recorded since 1900 AD. Advance was recorded at 52% of sites with only 1% reporting treeline recession. Treelines that experienced strong winter warming were more likely to have advanced, and treelines with a diffuse form were more likely to have advanced than those with an abrupt or krummholz form. Diffuse treelines may be more responsive to warming because they are more strongly growth limited, whereas other treeline forms may be subject to additional constraints.

  8. Orbit response matrix measurements for 10Hz global orbit feedback in RHIC

    SciTech Connect

    Liu, C.; Minty, M.

    2010-10-01

    The 10 Hz global orbit feedback system (gofb) was designed to correct the 10 Hz horizontal beam perturbations in both rings that are suspected to be caused by vibrations of the final focusing quadrupoles (triplets). The full system envisioned for Run-11 consists of 36 BPMs, corresponding to 2 per triplet in each of the 12 triplet locations and two in each of the 6 arcs, and 1 dipole corrector at each triplet location for a total of 12 correctors. Prototype testing was successfully carried out during RHIC Run-10 in store condition with 4 new dipole correctors (with independent power supplies) and 8 stripline beam position monitors (BPMs) per accelerator. An SVD-based algorithm was used to compute the applied corrections. For Run-10, the response matrix was provided by W. W. MacKay. The response matrix R relates corrector angles to beam displacements at BPMs.

  9. Plasticity in habitat use determines metabolic response of fish to global warming in stratified lakes.

    PubMed

    Busch, Susan; Kirillin, Georgiy; Mehner, Thomas

    2012-09-01

    We used a coupled lake physics and bioenergetics-based foraging model to evaluate how the plasticity in habitat use modifies the seasonal metabolic response of two sympatric cold-water fishes (vendace and Fontane cisco, Coregonus spp.) under a global warming scenario for the year 2100. In different simulations, the vertically migrating species performed either a plastic strategy (behavioral thermoregulation) by shifting their population depth at night to maintain the temperatures occupied at current in-situ observations, or a fixed strategy (no thermoregulation) by keeping their occupied depths at night but facing modified temperatures. The lake physics model predicted higher temperatures above 20 m and lower temperatures below 20 m in response to warming. Using temperature-zooplankton relationships, the density of zooplankton prey was predicted to increase at the surface, but to decrease in hypolimnetic waters. Simulating the fixed strategy, growth was enhanced only for the deeper-living cisco due to the shift in thermal regime at about 20 m. In contrast, simulating the plastic strategy, individual growth of cisco and young vendace was predicted to increase compared to growth currently observed in the lake. Only growth rates of older vendace are reduced under future global warming scenarios irrespective of the behavioral strategy. However, performing behavioral thermoregulation would drive both species into the same depth layers, and hence will erode vertical microhabitat segregation and intensify inter-specific competition between the coexisting coregonids.

  10. Contrasting responses of water use efficiency to drought across global terrestrial ecosystems

    NASA Astrophysics Data System (ADS)

    Yang, Yuting; Guan, Huade; Batelaan, Okke; McVicar, Tim R.; Long, Di; Piao, Shilong; Liang, Wei; Liu, Bing; Jin, Zhao; Simmons, Craig T.

    2016-03-01

    Drought is an intermittent disturbance of the water cycle that profoundly affects the terrestrial carbon cycle. However, the response of the coupled water and carbon cycles to drought and the underlying mechanisms remain unclear. Here we provide the first global synthesis of the drought effect on ecosystem water use efficiency (WUE = gross primary production (GPP)/evapotranspiration (ET)). Using two observational WUE datasets (i.e., eddy-covariance measurements at 95 sites (526 site-years) and global gridded diagnostic modelling based on existing observation and a data-adaptive machine learning approach), we find a contrasting response of WUE to drought between arid (WUE increases with drought) and semi-arid/sub-humid ecosystems (WUE decreases with drought), which is attributed to different sensitivities of ecosystem processes to changes in hydro-climatic conditions. WUE variability in arid ecosystems is primarily controlled by physical processes (i.e., evaporation), whereas WUE variability in semi-arid/sub-humid regions is mostly regulated by biological processes (i.e., assimilation). We also find that shifts in hydro-climatic conditions over years would intensify the drought effect on WUE. Our findings suggest that future drought events, when coupled with an increase in climate variability, will bring further threats to semi-arid/sub-humid ecosystems and potentially result in biome reorganization, starting with low-productivity and high water-sensitivity grassland.

  11. Terrestrial water flux responses to global warming in tropical rainforest areas

    NASA Astrophysics Data System (ADS)

    Lan, Chia-Wei; Lo, Min-Hui; Chou, Chia; Kumar, Sanjiv

    2016-05-01

    Precipitation extremes are expected to become more frequent in the changing global climate, which may considerably affect the terrestrial hydrological cycle. In this study, Coupled Model Intercomparison Project Phase 5 archives have been examined to explore the changes in normalized terrestrial water fluxes (precipitation minus evapotranspiration minus total runoff, divided by the precipitation climatology) in three tropical rainforest areas: Maritime Continent, Congo, and Amazon. Results show that a higher frequency of intense precipitation events is predicted for the Maritime Continent in the future climate than in the present climate, but not for the Amazon or Congo rainforests. Nonlinear responses to extreme precipitation lead to a reduced groundwater recharge and a proportionately greater amount of direct runoff, particularly for the Maritime Continent, where both the amount and intensity of precipitation increase under global warming. We suggest that the nonlinear response is related to the existence of a higher near-surface soil moisture over the Maritime Continent than that over the Amazon and Congo rainforests. The wetter soil over the Maritime Continent also leads to an increased subsurface runoff. Thus, increased precipitation extremes and concomitantly reduced terrestrial water fluxes lead to an intensified hydrological cycle for the Maritime Continent. This has the potential to result in a strong temporal heterogeneity in soil water distribution affecting the ecosystem of the rainforest region and increasing the risk of flooding and/or landslides.

  12. Earthquake casualty models within the USGS Prompt Assessment of Global Earthquakes for Response (PAGER) system

    USGS Publications Warehouse

    Jaiswal, Kishor; Wald, David J.; Earle, Paul S.; Porter, Keith A.; Hearne, Mike

    2011-01-01

    Since the launch of the USGS’s Prompt Assessment of Global Earthquakes for Response (PAGER) system in fall of 2007, the time needed for the U.S. Geological Survey (USGS) to determine and comprehend the scope of any major earthquake disaster anywhere in the world has been dramatically reduced to less than 30 min. PAGER alerts consist of estimated shaking hazard from the ShakeMap system, estimates of population exposure at various shaking intensities, and a list of the most severely shaken cities in the epicentral area. These estimates help government, scientific, and relief agencies to guide their responses in the immediate aftermath of a significant earthquake. To account for wide variability and uncertainty associated with inventory, structural vulnerability and casualty data, PAGER employs three different global earthquake fatality/loss computation models. This article describes the development of the models and demonstrates the loss estimation capability for earthquakes that have occurred since 2007. The empirical model relies on country-specific earthquake loss data from past earthquakes and makes use of calibrated casualty rates for future prediction. The semi-empirical and analytical models are engineering-based and rely on complex datasets including building inventories, time-dependent population distributions within different occupancies, the vulnerability of regional building stocks, and casualty rates given structural collapse.

  13. Human response to environmental change in the perspective of future, global climate

    NASA Astrophysics Data System (ADS)

    Butzer, Karl W.

    1983-05-01

    Human response to severe environmental stress is conceived and implemented by individuals, but must be approved by the group. These decisions are made with respect to perceived circumstances. Societies are enmeshed within adaptive systems that provide a matrix of opportunities and constraints for a wide range of potential behavioral variability. Such systems repeatedly readjust to short-term crises, e.g., droughts, but persistent and severe environmental stress may require substantial revision of adaptive strategies. The Sahel drought of 1968-1973 is an example of a brief but severe crisis, recurring along the Saharan margins perhaps once every 30 years. Closer inspection shows links between intensified intertribal warfare and ecological stress in the lower Omo Valley. The decline of the Egyptian New Kingdom during the 12th century B.C., in response to economic stagnation, sociopolitical instability, dynastic weakness, foreign pressures, and poor Nile floods over 50-70 years, represents a more complex and fundamental modification, with systemic simplification lasting 450 years. Such insights can be applied to future, global climatic change due to increasing atmospheric CO 2. Simulation and paleoclimatic experience suggest a drier climate for the North American and Soviet breadbaskets, to threaten world food supplies at a time of maximum demographic pressures and declining resources. Public perception and remedial planning should receive the attention of Quaternary scientists, in order to preempt an involuntary, global, systemic simplification.

  14. Contrasting responses of water use efficiency to drought across global terrestrial ecosystems

    PubMed Central

    Yang, Yuting; Guan, Huade; Batelaan, Okke; McVicar, Tim R.; Long, Di; Piao, Shilong; Liang, Wei; Liu, Bing; Jin, Zhao; Simmons, Craig T.

    2016-01-01

    Drought is an intermittent disturbance of the water cycle that profoundly affects the terrestrial carbon cycle. However, the response of the coupled water and carbon cycles to drought and the underlying mechanisms remain unclear. Here we provide the first global synthesis of the drought effect on ecosystem water use efficiency (WUE = gross primary production (GPP)/evapotranspiration (ET)). Using two observational WUE datasets (i.e., eddy-covariance measurements at 95 sites (526 site-years) and global gridded diagnostic modelling based on existing observation and a data-adaptive machine learning approach), we find a contrasting response of WUE to drought between arid (WUE increases with drought) and semi-arid/sub-humid ecosystems (WUE decreases with drought), which is attributed to different sensitivities of ecosystem processes to changes in hydro-climatic conditions. WUE variability in arid ecosystems is primarily controlled by physical processes (i.e., evaporation), whereas WUE variability in semi-arid/sub-humid regions is mostly regulated by biological processes (i.e., assimilation). We also find that shifts in hydro-climatic conditions over years would intensify the drought effect on WUE. Our findings suggest that future drought events, when coupled with an increase in climate variability, will bring further threats to semi-arid/sub-humid ecosystems and potentially result in biome reorganization, starting with low-productivity and high water-sensitivity grassland. PMID:26983909

  15. Case study on the utility of hepatic global gene expression profiling in the risk assessment of the carcinogen furan

    SciTech Connect

    Jackson, Anna Francina; Williams, Andrew; Recio, Leslie; Waters, Michael D.; Lambert, Iain B.; Yauk, Carole L.

    2014-01-01

    Furan is a chemical hepatocarcinogen in mice and rats. Its previously postulated cancer mode of action (MOA) is chronic cytotoxicity followed by sustained regenerative proliferation; however, its molecular basis is unknown. To this end, we conducted toxicogenomic analysis of B3C6F1 mouse livers following three week exposures to non-carcinogenic (0, 1, 2 mg/kg bw) or carcinogenic (4 and 8 mg/kg bw) doses of furan. We saw enrichment for pathways responsible for cytotoxicity: stress-activated protein kinase (SAPK) and death receptor (DR5 and TNF-alpha) signaling, and proliferation: extracellular signal-regulated kinases (ERKs) and TNF-alpha. We also noted the involvement of NF-kappaB and c-Jun in response to furan, which are genes that are known to be required for liver regeneration. Furan metabolism by CYP2E1 produces cis-2-butene-1,4-dial (BDA), which is required for ensuing cytotoxicity and oxidative stress. NRF2 is a master regulator of gene expression during oxidative stress and we suggest that chronic NFR2 activity and chronic inflammation may represent critical transition events between the adaptive (regeneration) and adverse (cancer) outcomes. Another objective of this study was to demonstrate the applicability of toxicogenomics data in quantitative risk assessment. We modeled benchmark doses for our transcriptional data and previously published cancer data, and observed consistency between the two. Margin of exposure values for both transcriptional and cancer endpoints were also similar. In conclusion, using furan as a case study we have demonstrated the value of toxicogenomics data in elucidating dose-dependent MOA transitions and in quantitative risk assessment. - Highlights: • Global gene expression changes in furan-exposed mouse livers were analyzed. • A molecular mode of action for furan-induced hepatocarcinogenesis is proposed. • Key pathways include NRF2, SAPK, ERK and death receptor signaling. • Important roles for TNF-alpha, c-Jun, and NF

  16. Comparative quantification of pharmacodynamic parameters of chiral compounds (RRR- vs. all-rac-alpha tocopherol) by global gene expression profiling.

    PubMed

    Muller, Patrick Y; Netscher, Thomas; Frank, Jan; Stoecklin, Elisabeth; Rimbach, Gerald; Barella, Luca

    2005-07-01

    Pharmacologically active compounds (e.g. from the groups of pharmaceutical drugs, cofactors or vitamins) often consist of two or more stereoisomers (enantiomers or diastereoisomers) which may differ in their pharmacodynamic/kinetic, toxicological and biological properties. A well-known example is vitamin E which is predominantly administered as two different forms, one derived from natural sources (mainly soybeans), and one from production by chemical total-synthesis. While vitamin E from natural sources occurs as a single stereoisomer (RRR-alpha-tocopherol), synthetic vitamin E (all-rac-alpha-tocopherol) is an equimolar mixture of eight stereoisomers. Based on a number of animal studies it has been suggested that the biological potency of natural-source vitamin E is 1.36 greater compared to its counterpart produced by chemical synthesis. In this study, we have used the Affymetrix GeneChip technology to evaluate the feasibility of a new bio-assay where the gene regulatory activities of RRR-alpha-tocopherol and all-rac-alpha-tocopherol were quantified and compared on the genome-wide level. For this purpose, HepG2 cells were supplemented with increasing amounts of RRR- or all-rac-alpha-tocopherol for 7 days. Genes showing a dose-related induction/repression were identified by global gene expression profiling. Our findings show that RRR- and all-rac-alpha-tocopherol share an identical transcriptional activity, i.e. induce/repress the expression of the same set of genes. Based on the transcriptional dose-response data, EC50 and IC50 values were determined for each of these genes. The feasibility of calculating a "transcriptional potency factor" of RRR- vs. all-rac-e-tocopherol was evaluated by dividing the EC50/IC50 of RRR-alpha-tocopherol by the corresponding EC50/IC50 of all-rac-alpha-tocopherol for every of the vitamin E responsive genes. Using this approach we have calculated 215 single biopotency ratios. Subsequently, the mean of all potency ratios was found to be

  17. Clouds, water vapor and the response of the extratropical jets to global warming

    NASA Astrophysics Data System (ADS)

    Voigt, A.; Shaw, T.

    2015-12-01

    Climate models suggest that global warming will cause substantial changes of the mid-latitude circulation, including meridional shifts of the extratropical jets and storm tracks. The magnitude, and in some circumstances even the sign, of these shifts remains subject to large model uncertainties, however. In this talk I will report on recent work that demonstrates the importance of longwave radiative effects of clouds and water vapor for the jet position and its response to warming. To this end, I will apply a hierarchy of climate models ranging from CMIP5 models in realisitic setups to dry idealized general circulation models. I will show that cloud changes, in particular those of the tropics and mid-latitudes, and high-latitude water vapor changes push the jet towards the pole under global warming, whereas equatorial water vapor changes pull the jet towards the equator. These radiative impacts of clouds and water vapor on the jet are found to be consistent with our understanding of the response of the dry circulation to diabatic heating. I will also discuss the extent to which mid-latitude clouds are controlled by the jet. Finally, I will show that CMIP5 model spread in warming-induced jet shifts is correlated with model spread in regional changes of clouds and water vapor. These results provide evidence that part of the climate model uncertainty in projections of future jet shifts might result from uncertainty in how clouds and water vapor respond to global warming, and how they modify the longwave radiation inside the atmosphere.

  18. Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response*

    PubMed Central

    Rose, Rebecca E.; Pazos, Manuel A.; Curcio, M. Joan; Fabris, Daniele

    2016-01-01

    The simultaneous detection of all the post-transcriptional modifications (PTMs) that decorate cellular RNA can provide comprehensive information on the effects of changing environmental conditions on the entire epitranscriptome. To capture this type of information, we performed the analysis of ribonucleotide mixtures produced by hydrolysis of total RNA extracts from S. cerevisiae that was grown under hyperosmotic and heat shock conditions. Their global PTM profiles clearly indicated that the cellular responses to these types of stresses involved profound changes in the production of specific PTMs. The observed changes involved not only up-/down-regulation of typical PTMs, but also the outright induction of new ones that were absent under normal conditions, or the elimination of others that were normally present. Pointing toward the broad involvement of different classes of RNAs, many of the newly observed PTMs differed from those engaged in the known tRNA-based mechanism of translational recoding, which is induced by oxidative stress. Some of the expression effects were stress-specific, whereas others were not, thus suggesting that RNA PTMs may perform multifaceted activities in stress response, which are subjected to distinctive regulatory pathways. To explore their signaling networks, we implemented a strategy based on the systematic deletion of genes that connect established response genes with PTM biogenetic enzymes in a putative interactomic map. The results clearly identified PTMs that were under direct HOG control, a well-known protein kinase pathway involved in stress response in eukaryotes. Activation of this signaling pathway has been shown to result in the stabilization of numerous mRNAs and the induction of selected lncRNAs involved in chromatin remodeling. The fact that PTMs are capable of altering the activity of the parent RNAs suggest their possible participation in feedback mechanisms aimed at modulating the regulatory functions of such RNAs. This

  19. Responsivity to Offspring's Expression of Emotion among Childhood-Onset Depressed Mothers

    ERIC Educational Resources Information Center

    Shaw, Daniel S.; Schonberg, Michael; Sherrill, Joel; Huffman, Drew; Lukon, Joella; Obrosky, David; Kovacs, Maria

    2006-01-01

    This study examined responsivity of mothers with childhood-onset depression (COD) in relation to children's overt expression of positive and negative emotion. It was hypothesized that COD and control mothers would differ in contingent responsivity to their children's expression of both positivity and different types of negative emotionality. Using…

  20. Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum.

    PubMed

    Gorshkov, Vladimir; Kwenda, Stanford; Petrova, Olga; Osipova, Elena; Gogolev, Yuri; Moleleki, Lucy N

    2017-01-01

    The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, Pectobacterium atrosepticum (Pba) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed Pba to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected Pba phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features

  1. Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum

    PubMed Central

    Gorshkov, Vladimir; Kwenda, Stanford; Petrova, Olga; Osipova, Elena; Gogolev, Yuri; Moleleki, Lucy N.

    2017-01-01

    The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, Pectobacterium atrosepticum (Pba) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed Pba to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected Pba phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features

  2. Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti.

    PubMed

    De Nisco, Nicole J; Abo, Ryan P; Wu, C Max; Penterman, Jon; Walker, Graham C

    2014-03-04

    In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. In the α-proteobacterium Caulobacter crescentus, cell cycle-regulated transcription plays an important role in the control of cell cycle progression but this has not been demonstrated in other α-proteobacteria. Here we describe a robust method for synchronizing cell growth that enabled global analysis of S. meliloti cell cycle-regulated gene expression. This analysis identified 462 genes with cell cycle-regulated transcripts, including several key cell cycle regulators, and genes involved in motility, attachment, and cell division. Only 28% of the 462 S. meliloti cell cycle-regulated genes were also transcriptionally cell cycle-regulated in C. crescentus. Furthermore, CtrA- and DnaA-binding motif analysis revealed little overlap between the cell cycle-dependent regulons of CtrA and DnaA in S. meliloti and C. crescentus. The predicted S. meliloti cell cycle regulon of CtrA, but not that of DnaA, was strongly conserved in more closely related α-proteobacteria with similar ecological niches as S. meliloti, suggesting that the CtrA cell cycle regulatory network may control functions of central importance to the specific lifestyles of α-proteobacteria.

  3. Regional Brain Responses Are Biased Toward Infant Facial Expressions Compared to Adult Facial Expressions in Nulliparous Women

    PubMed Central

    Zhang, Dajun; Wei, Dongtao; Qiao, Lei; Wang, Xiangpeng; Che, Xianwei

    2016-01-01

    Recent neuroimaging studies suggest that neutral infant faces compared to neutral adult faces elicit greater activity in brain areas associated with face processing, attention, empathic response, reward, and movement. However, whether infant facial expressions evoke larger brain responses than adult facial expressions remains unclear. Here, we performed event-related functional magnetic resonance imaging in nulliparous women while they were presented with images of matched unfamiliar infant and adult facial expressions (happy, neutral, and uncomfortable/sad) in a pseudo-randomized order. We found that the bilateral fusiform and right lingual gyrus were overall more activated during the presentation of infant facial expressions compared to adult facial expressions. Uncomfortable infant faces compared to sad adult faces evoked greater activation in the bilateral fusiform gyrus, precentral gyrus, postcentral gyrus, posterior cingulate cortex-thalamus, and precuneus. Neutral infant faces activated larger brain responses in the left fusiform gyrus compared to neutral adult faces. Happy infant faces compared to happy adult faces elicited larger responses in areas of the brain associated with emotion and reward processing using a more liberal threshold of p < 0.005 uncorrected. Furthermore, the level of the test subjects’ Interest-In-Infants was positively associated with the intensity of right fusiform gyrus response to infant faces and uncomfortable infant faces compared to sad adult faces. In addition, the Perspective Taking subscale score on the Interpersonal Reactivity Index-Chinese was significantly correlated with precuneus activity during uncomfortable infant faces compared to sad adult faces. Our findings suggest that regional brain areas may bias cognitive and emotional responses to infant facial expressions compared to adult facial expressions among nulliparous women, and this bias may be modulated by individual differences in Interest-In-Infants and

  4. Mitigation/adaptation and health: health policymaking in the global response to climate change and implications for other upstream determinants.

    PubMed

    Wiley, Lindsay F

    2010-01-01

    The time is ripe for innovation in global health governance if we are to achieve global health and development objectives in the face of formidable challenges. Integration of global health concerns into the law and governance of other, related disciplines should be given high priority. This article explores opportunities for health policymaking in the global response to climate change. Climate change and environmental degradation will affect weather disasters, food and water security, infectious disease patterns, and air pollution. Although scientific research has pointed to the interdependence of the global environment and human health, policymakers have been slow to integrate their approaches to environmental and health concerns. A robust response to climate change will require improved integration on two fronts: health concerns must be given higher priority in the response to climate change and threats associated with climate change and environmental degradation must be more adequately addressed by global health law and governance. The mitigation/adaptation response paradigm developing within and beyond the United Nations Framework Convention on Climate Change provides a useful framework for thinking about global health law and governance with respect to climate change, environmental degradation, and possibly other upstream determinants of health as well.

  5. MicroRNA-221 controls expression of intercellular adhesion molecule-1 in epithelial cells in response to Cryptosporidium parvum infection

    PubMed Central

    Gong, Ai-Yu; Hu, Guoku; Zhou, Rui; Liu, Jun; Feng, Yaoyu; Soukup, Garrett A.; Chen, Xian-Ming

    2011-01-01

    Cryptosporidium parvum is a protozoan parasite that infects gastrointestinal epithelial cells and causes diarrheal disease in humans and animals globally. Pathological changes following C. parvum infection include crypt hyperplasia, a modest inflammatory reaction with increased infiltration of lymphocytes into intestinal mucosa. Expression of adhesion molecules such as intercellular adhesion molecule-1 (ICAM-1), on infected epithelial cell surfaces may facilitate adhesion and recognition of lymphocytes at infection sites. MicroRNAs (miRNAs) are small RNA molecules of 23 nucleotides that negatively regulate protein-coding gene expression via translational suppression or mRNA degradation. We recently reported that microRNA-221 (miR-221) regulates ICAM-1 translation through targeting the ICAM-1 3′-untranslated region (UTR). In this study, we tested the role of miR-221 in regulating ICAM-1 expression in epithelial cells in response to C. parvum infection using an in vitro model of human biliary cryptosporidiosis. Up-regulation of ICAM-1 at both message and protein levels was detected in epithelial cells following C. parvum infection. Inhibition of ICAM-1 transcription with actinomycin D could only partially block C. parvum-induced ICAM-1 expression at the protein level. Cryptosporidium parvum infection decreased miR-221 expression in infected epithelial cells. When cells were transfected with a luciferase reporter construct covering the miR-221 binding site in the ICAM-1 3′-UTR and then exposed to C. parvum, an enhanced luciferase activity was detected. Transfection of miR-221 precursor abolished C. parvum-stimulated ICAM-1 protein expression. In addition, expression of ICAM-1 on infected epithelial cells facilitated epithelial adherence of co-cultured Jurkat cells. These results indicate that miR-221-mediated translational suppression controls ICAM-1 expression in epithelial cells in response to C. parvum infection. PMID:21236259

  6. Do cities simulate climate change? A comparison of herbivore response to urban and global warming

    USGS Publications Warehouse

    Youngsteadt, Elsa; Dale, Adam G.; Terando, Adam; Dunn, Robert R.; Frank, Steven D.

    2014-01-01

    Cities experience elevated temperature, CO2, and nitrogen deposition decades ahead of the global average, such that biological response to urbanization may predict response to future climate change. This hypothesis remains untested due to a lack of complementary urban and long-term observations. Here, we examine the response of an herbivore, the scale insect Melanaspis tenebricosa, to temperature in the context of an urban heat island, a series of historical temperature fluctuations, and recent climate warming. We survey M. tenebricosa on 55 urban street trees in Raleigh, NC, 342 herbarium specimens collected in the rural southeastern United States from 1895 to 2011, and at 20 rural forest sites represented by both modern (2013) and historical samples. We relate scale insect abundance to August temperatures and find that M. tenebricosa is most common in the hottest parts of the city, on historical specimens collected during warm time periods, and in present-day rural forests compared to the same sites when they were cooler. Scale insects reached their highest densities in the city, but abundance peaked at similar temperatures in urban and historical datasets and tracked temperature on a decadal scale. Although urban habitats are highly modified, species response to a key abiotic factor, temperature, was consistent across urban and rural-forest ecosystems. Cities may be an appropriate but underused system for developing and testing hypotheses about biological effects of climate change. Future work should test the applicability of this model to other groups of organisms.

  7. Do cities simulate climate change? A comparison of herbivore response to urban and global warming.

    PubMed

    Youngsteadt, Elsa; Dale, Adam G; Terando, Adam J; Dunn, Robert R; Frank, Steven D

    2015-01-01

    Cities experience elevated temperature, CO2 , and nitrogen deposition decades ahead of the global average, such that biological response to urbanization may predict response to future climate change. This hypothesis remains untested due to a lack of complementary urban and long-term observations. Here, we examine the response of an herbivore, the scale insect Melanaspis tenebricosa, to temperature in the context of an urban heat island, a series of historical temperature fluctuations, and recent climate warming. We survey M. tenebricosa on 55 urban street trees in Raleigh, NC, 342 herbarium specimens collected in the rural southeastern United States from 1895 to 2011, and at 20 rural forest sites represented by both modern (2013) and historical samples. We relate scale insect abundance to August temperatures and find that M. tenebricosa is most common in the hottest parts of the city, on historical specimens collected during warm time periods, and in present-day rural forests compared to the same sites when they were cooler. Scale insects reached their highest densities in the city, but abundance peaked at similar temperatures in urban and historical datasets and tracked temperature on a decadal scale. Although urban habitats are highly modified, species response to a key abiotic factor, temperature, was consistent across urban and rural-forest ecosystems. Cities may be an appropriate but underused system for developing and testing hypotheses about biological effects of climate change. Future work should test the applicability of this model to other groups of organisms.

  8. Quantifying Integrated Proteomic Responses to Iron Stress in the Globally Important Marine Diazotroph Trichodesmium

    PubMed Central

    Snow, Joseph T.; Polyviou, Despo; Skipp, Paul; Chrismas, Nathan A. M.; Hitchcock, Andrew; Geider, Richard; Moore, C. Mark; Bibby, Thomas S.

    2015-01-01

    Trichodesmium is a biogeochemically important marine cyanobacterium, responsible for a significant proportion of the annual ‘new’ nitrogen introduced into the global ocean. These non-heterocystous filamentous diazotrophs employ a potentially unique strategy of near-concurrent nitrogen fixation and oxygenic photosynthesis, potentially burdening Trichodesmium with a particularly high iron requirement due to the iron-binding proteins involved in these processes. Iron availability may therefore have a significant influence on the biogeography of Trichodesmium. Previous investigations of molecular responses to iron stress in this keystone marine microbe have largely been targeted. Here a holistic approach was taken using a label-free quantitative proteomics technique (MSE) to reveal a sophisticated multi-faceted proteomic response of Trichodesmium erythraeum IMS101 to iron stress. Increased abundances of proteins known to be involved in acclimation to iron stress and proteins known or predicted to be involved in iron uptake were observed, alongside decreases in the abundances of iron-binding proteins involved in photosynthesis and nitrogen fixation. Preferential loss of proteins with a high iron content contributed to overall reductions of 55–60% in estimated proteomic iron requirements. Changes in the abundances of iron-binding proteins also suggested the potential importance of alternate photosynthetic pathways as Trichodesmium reallocates the limiting resource under iron stress. Trichodesmium therefore displays a significant and integrated proteomic response to iron availability that likely contributes to the ecological success of this species in the ocean. PMID:26562022

  9. Global gene expression shift during the transition from early neural development to late neuronal differentiation in Drosophila melanogaster.

    PubMed

    Cantera, Rafael; Ferreiro, María José; Aransay, Ana María; Barrio, Rosa

    2014-01-01

    Regulation of transcription is one of the mechanisms involved in animal development, directing changes in patterning and cell fate specification. Large temporal data series, based on microarrays across the life cycle of the fly Drosophila melanogaster, revealed the existence of groups of genes which expression increases or decreases temporally correlated during the life cycle. These groups of genes are enriched in different biological functions. Here, instead of searching for temporal coincidence in gene expression using the entire genome expression data, we searched for temporal coincidence in gene expression only within predefined catalogues of functionally related genes and investigated whether a catalogue's expression profile can be used to generate larger catalogues, enriched in genes necessary for the same function. We analyzed the expression profiles from genes already associated with early neurodevelopment and late neurodifferentiation, at embryonic stages 16 and 17 of Drosophila life cycle. We hypothesized that during this interval we would find global downregulation of genes important for early neuronal development together with global upregulation of genes necessary for the final differentiation of neurons. Our results were consistent with this hypothesis. We then investigated if the expression profile of gene catalogues representing particular processes of neural development matched the temporal sequence along which these processes occur. The profiles of genes involved in patterning, neurogenesis, axogenesis or synaptic transmission matched the prediction, with largest transcript values at the time when the corresponding biological process takes place in the embryo. Furthermore, we obtained catalogues enriched in genes involved in temporally matching functions by performing a genome-wide systematic search for genes with their highest expression levels at the corresponding embryonic intervals. These findings imply the use of gene expression data in

  10. Constitutive versus responsive gene expression strategies for growth in changing environments.

    PubMed

    Geisel, Nico

    2011-01-01

    Microbes respond to changing environments by adjusting gene expression levels to the demand for the corresponding proteins. Adjusting protein levels is slow, consequently cells may reach the optimal protein level only by a time when the demand changed again. It is therefore not a priori clear whether expression "on demand" is always the optimal strategy. Indeed, many genes are constitutively expressed at intermediate levels, which represents a permanent cost but provides an immediate benefit when the protein is needed. Which are the conditions that select for a responsive or a constitutive expression strategy, what determines the optimal constitutive expression level in a changing environment, and how is the fitness of the two strategies affected by gene expression noise? Based on an established model of the lac- and gal-operon expression dynamics, we study the fitness of a constitutive and a responsive expression strategy in time-varying environments. We find that the optimal constitutive expression level differs from the average demand for the gene product and from the average optimal expression level; depending on the shape of the growth rate function, the optimal expression level either provides intermediate fitness in all environments, or maximizes fitness in only one of them. We find that constitutive expression can provide higher fitness than responsive expression even when regulatory machinery comes at no cost, and we determine the minimal response rate necessary for "expression on demand" to confer a benefit. Environmental and inter-cellular noise favor the responsive strategy while reducing fitness of the constitutive one. Our results show the interplay between the demand-frequency for a gene product, the genetic response rate, and the fitness, and address important questions on the evolution of gene regulation. Some of our predictions agree with recent yeast high throughput data, for others we propose the experiments that are needed to verify them.

  11. Host Gene Expression Responses to Biothreat and Infectious Agents: Implications for Mathematical Modeling of in vitro Responses

    DTIC Science & Technology

    2004-06-01

    genes of interest, complementary confirmatory techniques ( RT - PCR , real-time- PCR , etc) are used to verify the response profiles. All of these... RT - PCR . 2.4 Gene Profiles Showing Unique Patterns For Specific Biothreat Agents Figure 2 shows an example of a few selected genes that were...Figure 1. RT - PCR confirmation of selected gene responses initially identified from global gene analysis studies. In this graph, bright red

  12. A longitudinal analysis of the development of infant facial expressions in response to acute pain: immediate and regulatory expressions.

    PubMed

    Ahola Kohut, Sara; Pillai Riddell, Rebecca; Flora, David B; Oster, Harriet

    2012-12-01

    Facial expressions during infancy are important to examine, as infants do not have the language skills to describe their experiences. This is particularly vital in the context of pain, where infants depend solely on their caregivers for relief. The objective of the current study was to investigate the development of negative infant facial expressions in response to immunization pain over the first year of life. Infant facial expressions were examined longitudinally using a subsample of 100 infants that were each videotaped during their 2-, 4-, 6-, and 12-month routine immunization appointments. Infant facial expressions were coded using BabyFACS (facial action coding system) for the first minute after a painful needle prick. Facial expressions were examined with a catalogue of the most commonly occurring facial expressions. Results demonstrated that clear differences were seen over ages. Infants display a variety of facial expressions with some of the components of adult pain expressions immediately after the needle and they abate shortly after. However, infants did not display adult expressions of discrete negative emotions. Instead, infants displayed a variety of generalized pain and distress faces aimed at gaining caregiver aid. The development of nonverbal communication in infants, particularly facial expressions, remains an important area of inquiry. Further study into accurately measuring infant negative emotions, pain, and distress is warranted.

  13. Predicting Climate Change Using Response Theory: Global Averages and Spatial Patterns

    NASA Astrophysics Data System (ADS)

    Lucarini, Valerio; Ragone, Francesco; Lunkeit, Frank

    2016-04-01

    The provision of accurate methods for predicting the climate response to anthropogenic and natural forcings is a key contemporary scientific challenge. Using a simplified and efficient open-source general circulation model of the atmosphere featuring O(10^5 ) degrees of freedom, we show how it is possible to approach such a problem using nonequilibrium statistical mechanics. Response theory allows one to practically compute the time-dependent measure supported on the pullback attractor of the climate system, whose dynamics is non-autonomous as a result of time-dependent forcings. We propose a simple yet efficient method for predicting—at any lead time and in an ensemble sense—the change in climate properties resulting from increase in the concentration of CO_2 using test perturbation model runs. We assess strengths and limitations of the response theory in predicting the changes in the globally averaged values of surface temperature and of the yearly total precipitation, as well as in their spatial patterns. The quality of the predictions obtained for the surface temperature fields is rather good, while in the case of precipitation a good skill is observed only for the global average. We also show how it is possible to define accurately concepts like the inertia of the climate system or to predict when climate change is detectable given a scenario of forcing. Our analysis can be extended for dealing with more complex portfolios of forcings and can be adapted to treat, in principle, any climate observable. Our conclusion is that climate change is indeed a problem that can be effectively seen through a statistical mechanical lens, and that there is great potential for optimizing the current coordinated modelling exercises run for the preparation of the subsequent reports of the Intergovernmental Panel for Climate Change.

  14. Rights and Responsibilities of Tuberculosis Patients, and the Global Fund: A Qualitative Study

    PubMed Central

    Atif, Muhammad; Javaid, Sareema; Farooqui, Maryam; Sarwar, Muhammad Rehan

    2016-01-01

    Background Implementation of the Charter to protect patients’ rights is an important criterion to achieve patient-centered approach and receive financial support from the Global Fund. Our study aims to explore the knowledge of tuberculosis (TB) patients about their rights and responsibilities at the Chest Disease Unit of the Bahawal Victoria Hospital, Bahawalpur, Pakistan. Methods This was a qualitative study. The data from purposefully selected TB patients was collected by in-depth interviews. Eligibility criteria included confirmed diagnosis of TB and enrollment in the TB program. A pilot tested interview protocol was based upon the objectives of the study, and was used uniformly in each interview to maintain the consistency. The sample size was limited by applying the saturation criteria. All interviews were audiotaped and transcribed verbatim. Inductive thematic content analysis was applied to analyze the data and draw conclusions. Results Out of the total 16 patients, four were female, and seven were illiterate. Eight patients were known cases of multi-drug resistant TB. Analysis of the data yielded seven themes; tuberculosis care services, moral support and stigmatization, dignity and privacy, complaints, fear of losing job, information sharing and compliance to the treatment plan, and contribution to eradicate TB. First five represented the rights section while latter two were related to the responsibilities section of the Charter. Conclusion Discriminatory access to TB care services and the right to privacy were two major concerns identified in this study. However, the respondents recognized their responsibilities as a TB patient. To ensure uninterrupted investment from the Global Fund, there is a need to implement fair TB care policies which support human rights-based approach. PMID:26998830

  15. Predicting Climate Change Using Response Theory: Global Averages and Spatial Patterns

    NASA Astrophysics Data System (ADS)

    Lucarini, Valerio; Ragone, Francesco; Lunkeit, Frank

    2017-02-01

    The provision of accurate methods for predicting the climate response to anthropogenic and natural forcings is a key contemporary scientific challenge. Using a simplified and efficient open-source general circulation model of the atmosphere featuring O(10^5) degrees of freedom, we show how it is possible to approach such a problem using nonequilibrium statistical mechanics. Response theory allows one to practically compute the time-dependent measure supported on the pullback attractor of the climate system, whose dynamics is non-autonomous as a result of time-dependent forcings. We propose a simple yet efficient method for predicting—at any lead time and in an ensemble sense—the change in climate properties resulting from increase in the concentration of CO_2 using test perturbation model runs. We assess strengths and limitations of the response theory in predicting the changes in the globally averaged values of surface temperature and of the yearly total precipitation, as well as in their spatial patterns. The quality of the predictions obtained for the surface temperature fields is rather good, while in the case of precipitation a good skill is observed only for the global average. We also show how it is possible to define accurately concepts like the inertia of the climate system or to predict when climate change is detectable given a scenario of forcing. Our analysis can be extended for dealing with more complex portfolios of forcings and can be adapted to treat, in principle, any climate observable. Our conclusion is that climate change is indeed a problem that can be effectively seen through a statistical mechanical lens, and that there is great potential for optimizing the current coordinated modelling exercises run for the preparation of the subsequent reports of the Intergovernmental Panel for Climate Change.

  16. Global-change drivers of ecosystem functioning modulated by natural variability and saturating responses.

    PubMed

    Flombaum, Pedro; Yahdjian, Laura; Sala, Osvaldo E

    2017-02-01

    Humans are altering global environment at an unprecedented rate through changes in biodiversity, climate, nitrogen cycle, and land use. To address their effects on ecosystem functioning, experiments most frequently explore one driver at a