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  • expression
  • Termed 'functional genomics' or in some contexts 'systems biology' [ 1 ], a decade of work on the budding yeast Saccharomyces cerevisiae has resulted in a body of knowledge describing gene-expression patterns, gene-disruption phenotypes, and protein-protein and protein-DNA interactions. (biomedcentral.com)
  • Several groups have investigated gene expression in response to DNA damage in yeast. (biomedcentral.com)
  • Brown and co-workers [ 7 ] found a set of genes whose expression increased following methyl-methanesulfonate (MMS) and IR treatment: it included RAD51 , RAD54 , RNR2 and RNR4 . (biomedcentral.com)
  • Purpose: Our goal is to develop genomics-based tests of primary breast carcinoma for assessing risk of recurrence by comparing gene and tumor marker expression of primary lesions with those of lymph node and distant metastases. (aacrjournals.org)
  • Using microarray analyses from our studies and other reports, 32 candidate genes were selected from carcinoma and stromal cells, whose expression appears related to clinical outcome of breast cancer (Andres et al. (aacrjournals.org)
  • Expression of candidate genes was evaluated with estrogen (ER) and progestin receptor (PR) protein levels to ascertain their relationship during lymph node invasion. (aacrjournals.org)
  • Relative gene expression was calculated by the ddCt method, using β-actin as a reference and Universal Human Reference RNA (Stratagene) as a calibrator. (aacrjournals.org)
  • Conclusions: To ascertain genomic changes in primary breast carcinomas and lymph node metastases, we compared levels of 32 candidate genes whose expression appears related to clinical outcome of breast cancer. (aacrjournals.org)
  • Seldom was gene expression in the metastasis greater than that of the primary. (aacrjournals.org)
  • Gene expression and biological activities of their protein products are used to classify subsets of primary breast cancers according to metastatic spread. (aacrjournals.org)
  • Relative mRNA expression of TLR3/RIG-I signaling genes involved in IFN- β production was correlated with positive- and negative-strand HCV RNAs in pretreatment liver tissues responsive and nonresponsive to peginterferon and ribavirin for chronic hepatitis C genotype 1. (hindawi.com)
  • Thus mRNA expression of TLR3/RIG-I signaling genes was increased in relation to viral replication in nonresponders. (hindawi.com)
  • Under the circumstances, we hypothesized that HCV replication-associated interference with the host IFN system may cause changes in hepatic gene expression involved in IFN production at the mRNA levels and that, if so, this host feedback response may occur in different fashion according to responsiveness to IFN-based therapy as interference with the host IFN system is considered to be more severe in nonresponders. (hindawi.com)
  • The effect of changes in temperature/water activity ( a w ) on growth, deoxynivalenol (DON) production and trichothecene gene cluster expression (18 genes) for strains of Fusarium culmorum and Fusarium graminearum was studied. (royalsocietypublishing.org)
  • The expression data for six key transcription genes ( TRI4, TRI5 , TRI6, TRI10, TRI12 and TRI13 ) were analysed using multiple regression analyses to model the relationship between these various factors for the first time. (royalsocietypublishing.org)
  • Microarray data on expression of these genes were significantly related to DON production for both strains. (royalsocietypublishing.org)
  • Multi-regression analysis was done and polynomial models found to best fit the relationship between actual/predicted DON production relative to the expression of these TRI genes and environmental factors. (royalsocietypublishing.org)
  • This allowed prediction of the amounts of DON produced in two-dimensional contour maps to relate expression of these genes to either a w or temperature. (royalsocietypublishing.org)
  • These results suggest complex interactions between gene expression ( TRI genes), environmental factors and mycotoxin production. (royalsocietypublishing.org)
  • The recent development of a microarray that has subarrays for the gene clusters of key mycotoxigenic fungi has provided an excellent tool for examining in more detail the impact that changes in interacting environmental factors may have on the relative expression of these gene clusters and relating this to phenotypic mycotoxin production [ 14 , 15 ]. (royalsocietypublishing.org)
  • We found Osteocalcin gene expressed in brain in both genders, but Gprc6a expression is low in brain and BAT/WAT. (frontiersin.org)
  • A significant correlation was found between the expression levels of the gene ligands and their receptors in brain, BAT and testis suggesting a common pathway of different genes in these tissues in either male and female. (frontiersin.org)
  • Changes in the expression levels of osteocalcin, Ngf , or Bdnf genes may mutually affect the expression levels of the others. (frontiersin.org)
  • That is, if one gene plays a role that buffers the phenotypic expression of variation in another, then loss of the first reveals the phenotypic consequences of variation in the second. (washington.edu)
  • That is, the cellular circuitry is organized into modules that buffer the expression within their module but do not affect other modules.We are developing methods to be both systematic and comprehensive in the investigation of synthetic phenotypes and are focusing on tolerance of genetic variation in the DNA synthetic apparatus. (washington.edu)
  • The expression in bread wheat over the course of development of various sucrose biosynthesis genes monitored on an Affymetrix array showed that the SPS genes were regulated over time and space. (biomedcentral.com)
  • The regulation of gene expression by microRNAs (miRNAs) is complex due to a number of variables involved. (rsc.org)
  • making it difficult to determine how regulation of gene expression by miRNAs works within the context of the system as a whole. (rsc.org)
  • MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate the target gene expression at post-transcriptional level. (biomedcentral.com)
  • Evidence suggests that miRNAs can constrain the variation of their target to buffer the fluctuation of expression. (biomedcentral.com)
  • miRNA targets are shown to be significantly enriched in SE genes by using propensity analysis of miRNA regulation, supporting the hypothesis that miRNAs can buffer whole genome expression fluctuation. (biomedcentral.com)
  • The expression-buffering effect of miRNA is independent of the target site number within the 3'-untranslated region. (biomedcentral.com)
  • In addition, we found that gene expression fluctuation is positively correlated with the number of transcription factor binding sites in the promoter region, which suggests that coordination between transcription factors and miRNAs leads to balanced responses to external perturbations. (biomedcentral.com)
  • Our study confirmed that the genetic buffering roles of miRNAs can act on genome expression fluctuation and provides insights into how miRNAs and transcription factors coordinate to cope with external perturbation. (biomedcentral.com)
  • For example, gene expression in the cell is rigorously regulated in response to external signals. (biomedcentral.com)
  • These genes should be constrained or "canalized" in their expression to an appropriate level. (biomedcentral.com)
  • The expression of many genes is considered robust as they are relatively stable upon perturbations. (biomedcentral.com)
  • However, it is still largely unclear whether there are any canalizing/buffering mechanisms acting on the genome wide expression. (biomedcentral.com)
  • miRNA-mediated gene expression regulation is widespread in eukaryotes. (biomedcentral.com)
  • Considering the prevalence of miRNA mediated gene expression regulation in mammalian cells, it is fascinating to inquire whether these small ncRNAs can serve as genetic factors that buffer whole genome expression. (biomedcentral.com)
  • Gene expression is tightly controlled by transcription factors (TFs) that are recruited to DNA cis -regulatory modules (CRMs). (biomedcentral.com)
  • Breast cancer prognostic expression signature sets, which reflect tumor CIN status, efficiently delineate outcome in estrogen receptor ER-positive breast cancer in contrast to ER-negative breast cancer, suggesting that the relationship of CIN with prognosis differs in these two breast cancer subtypes. (aacrjournals.org)
  • The paradoxical relationship between extreme CIN and cancer outcome in the ER-negative cohorts may explain why prognostic expression signatures, reflecting tumor CIN status, fail to predict outcome in this subgroup. (aacrjournals.org)
  • In this regard, prognostic gene expression approaches, such as Oncotype DX and MammaPrint®, which have utility in ER-positive breast cancer, have limited prognostic value in ER-negative disease ( 16 ). (aacrjournals.org)
  • Conceivably, the combined observations that prognostic expression signatures reflect tumor CIN status but fail to predict outcome in ER-negative breast cancer may be related to a paradoxical relationship between CIN and clinical outcome in ER-negative disease, whereby intermediate and extreme CIN are associated with poor and good prognosis, respectively. (aacrjournals.org)
  • In the pho1 mutant as well as in wild-type plants grown under reduced phosphate availability, increased amounts of SQD1 mRNA and SQD1 protein are detected, suggesting that the increase in sulfolipid content under phosphate limitation is the result of an increased expression of at least one gene required for sulfolipid biosynthesis in A. thaliana . (pnas.org)
  • We also developed a statistical analysis module to estimate the druggability and sensitivity of cancer cells upon drug treatments targeting human SL partners, based on large-scale genomic data, gene expression profiles and drug sensitivity profiles on more than 1000 cancer cell lines. (paperity.org)
  • To test this hypothesis, we used real-time quantitative RT-PCR to quantify the mRNA expression of a large panel of genes coding for the major xenobiotic-metabolizing enzymes (12 phase I enzymes, 12 phase II enzymes and three members of the ABC transporter family) in a small series of normal breast (and liver) tissues, and in estrogen receptor alpha (ERα)-negative and ERα-positive breast tumors. (beds.ac.uk)
  • Seven of the 27 genes showed very weak or undetectable expression in both normal and tumoral breast tissues. (beds.ac.uk)
  • Altered intratumoral expression of genes coding for xenobiotic-metabolizing enzymes is one potential mechanism of tamoxifen resistance. (beds.ac.uk)
  • This suggests that a higher level of protein from BDNF gene expression may provide a buffer, or reserve, for the brain and protect it against the effects of the plaques and tangles that form in the brain as a part of Alzheimer's disease. (medindia.net)
  • Autopsies were conducted on their brains after death, and the amount of protein from BDNF gene expression in the brain was then measured. (medindia.net)
  • The rate of cognitive decline was about 50 percent slower for those in the highest 10 percent of protein from BDNF gene expression compared to the lowest 10 percent. (medindia.net)
  • In the people with the highest amount of Alzheimer''s disease hallmarks in their brains, cognitive decline was about 40 percent slower for people with the highest amount of protein from BDNF gene expression compared to those with the lowest amount. (medindia.net)
  • Higher levels of protein from BDNF gene expression reduced the effect of plaques and tangles in the brain on cognitive decline by 0.02 units per year. (medindia.net)
  • More research is needed to confirm these findings, determine how this relationship between protein produced by BDNF gene expression and cognitive decline works and see if any strategies can be used to increase BDNF in the brain to protect or slow the rate of cognitive decline," said Buchman. (medindia.net)
  • further work is needed to determine if activities which increase brain BDNF gene expression levels protect or slow the rate of cognitive decline in old age. (medindia.net)
  • Bdnf
  • To investigate on the gene-relationship between NGF, BDNF, and Osteocalcin we compared by RT-PCR the transcript levels of Ngf, Bdnf and Osteocalcin as well as of their receptors p75NTR/NTRK1, NTRK2 , and Gprc6a in brain, bone, white/brown adipose tissue (WAT/BAT) and reproductive organs of 3 months old female and male mice. (frontiersin.org)
  • In contrast, BDNF genes are not expressed in reproductive tissues. (frontiersin.org)
  • Elderly people with higher amounts of a protein from the gene called brain-derived neurotrophic factor (BDNF), had slower decline in their memory and thinking abilities than people with lower amounts of the protein, says a new study. (medindia.net)
  • Michal Schnaider Beeri, PhD, of the Icahn School of Medicine at Mount Sinai in New York, noted in an accompanying editorial that exercise has been shown to increase levels of BDNF in the blood, but that the relationship between BDNF protein levels in the blood and in the brain is not clear. (medindia.net)
  • Alterations
  • In the 97 ERα-positive breast tumor series, most alterations of these seven genes corresponded to upregulations as compared with normal breast tissue, with an incidence ranging from 25% ( CYP2A6 ) to 79% ( NAT1 ). (beds.ac.uk)
  • proteins
  • All of the 14 genome-mapped human septin genes encode a highly conserved central GTP binding/hydrolysis domain, which is very critical in GTPase signaling properties, as well as oligomerization between septins and other filamentous proteins. (alliedacademies.org)
  • We also analyzed the differential expressed proteins using Gene ontology and KEGG annotations, and the results implicated that TNFα might regulate ribosome, spliceosome, antigen processing and presentation, and energy metabolism in HepG2 cells. (medsci.org)
  • isolates
  • The amplification of the Cyt b gene from isolates of 100 patients with disparate clinical forms of CL was accomplished using Nested-PCR. (springer.com)
  • Many studies suggest that genetic diversity in H. pylori virulence factors such as oipa and dupa genes is high among isolates of different geographic regions and may cause more severe diseases. (healthdocbox.com)
  • MMP2
  • MMP2 , TIPM2 , and TIMP3 genes were not associated with high myopia in this Chinese sample and hence are unlikely to play a major role in the genetic susceptibility to high myopia. (arvojournals.org)
  • tumor
  • Anti-HER2 scFv-directed extracellular vesicle-mediated mRNA-based gene delivery inhibits growth of HER2-positive human breast tumor xenografts by prodrug activation. (stanford.edu)
  • protein
  • Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved. (biomedcentral.com)
  • Interestingly, the dupa gene is homologous to virb4, a gene encoding a component protein of the type IV secretion system (TFSS) in Agrobacterium tumefaciens (3). (healthdocbox.com)
  • roles
  • It is hardly a leap of faith to assume that, just as model organisms have been instrumental in defining the roles of genes and the structure of genetic pathways that are important for human disease, they will be equally useful in defining the principles of gene interaction. (sciencemag.org)
  • The Modeling Center is the office's dashed-dotted data and roles around three other technologies: first citation, extensive methods and hydrogen-bonded Relationships. (prigsbee.com)
  • inducible
  • Upon recognition of hepatitis C virus (HCV) infection by Toll-like receptor 3 (TLR3) and retinoic-acid inducible gene I (RIG-I), the innate immune response is promptly activated in hepatocytes. (hindawi.com)
  • interaction
  • Moreover, experimental organisms may be even more useful for discovering gene interactions than for the characterization of the functions of individual genes, because the power resulting from genetic tractability will be compounded in studies of gene interaction. (sciencemag.org)
  • Using gene annotation and other bioinformatics resources to analyze the quantitative patterns of gene interaction, testable hypotheses are generated to further understand the molecular basis of the observed gene interaction networks. (openwetware.org)
  • We conclude that the 2R-delinquency association is not due to passive gene-environment correlation but is best characterized as a social control gene environment interaction. (unc.edu)
  • biological
  • Examining moderation patterns, we find that delinquency risk for the 2R allele is buffered for males close to their biological or social father but not their biological mother. (unc.edu)
  • mammalian
  • Among the 14 members of the septin gene family of mammalian species, several members are expressed ubiquitously, whereas others are expressed only in welldifferentiated cells (e.g., neurons or male germ cells) [ 7 ]. (alliedacademies.org)
  • mutants
  • PCC7942 ( 4 ), it was possible to create sulfolipid-deficient null-mutants by gene disruption. (pnas.org)
  • prediction
  • The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. (biomedcentral.com)
  • Researchers have developed experimental technologies and computational prediction methods to identify SL gene pairs on human and a few model species. (paperity.org)
  • However, the oipa gene cannot be regarded for prediction of gastroenterology diseases. (healthdocbox.com)
  • human
  • Our progress in understanding human disease genes owes much to research in experimental organisms. (sciencemag.org)
  • This knowledge has been extremely important in human genetics, where the function of many of the 1000 identified human disease genes has been surmised from functional information about its ortholog in model organisms ( 15 ). (sciencemag.org)
  • Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. (discovermagazine.com)
  • CYP2A6 , CYP2B6 , FMO5 and NAT1 emerged as new putative ERα-responsive genes in human breast cancer. (beds.ac.uk)
  • cDNA
  • cDNA for qPCR measurements was prepared in Tris-HCl buffer with KCl, MgCl 2 , DTT (Invitrogen), dNTPs (Invitrogen), RNasin ® (Promega) and Superscript ® RT III (Invitrogen). (aacrjournals.org)
  • adjuvant
  • Relevant genes were further investigated in a well-defined cohort of 97 ERα-positive postmenopausal breast cancer patients treated with primary surgery followed by adjuvant tamoxifen alone. (beds.ac.uk)
  • Analysis
  • TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification. (biomedcentral.com)
  • The Gepard dotplot analysis of TMP is applied to a subset of known coliphages and demonstrates that the single-gene method identifies phage relationships whether the entire genome or the single TMP gene is used for the comparison. (biomedcentral.com)
  • To buff up this analysis, they are analysing DNA preserved in the skeletons of other ancient inhabitants of central Europe. (discovermagazine.com)
  • 90 percent of a genome is way more than you'd need for some basic analysis and inference of relationships to contemporary populations. (discovermagazine.com)
  • To help users access and mine the wealth of the data, we developed other practical functionalities, such as search and filtering, orthology search, gene set enrichment analysis. (paperity.org)
  • contrast
  • In contrast, a linear relationship of increasing CIN with poorer prognosis in ER-positive breast cancer was observed, using three independent measures of CIN. (aacrjournals.org)
  • complex
  • Researchers found that the more varied major histocompability complex (MHC) genes a woman had, the more sexual partners she had. (xenophilia.com)
  • robust
  • Every person carries two copies of this gene (one from each parent), and the finding is that A/A or A/G individuals are less psychologically robust than G/G individuals. (dericbownds.net)
  • Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs. (nih.gov)
  • Oxtr
  • Oxt gene was markedly expressed in brain, Oxtr in the ovaries and in fat and bone in both genders. (frontiersin.org)
  • clusters
  • Comparison of phages within and between clusters has revealed genes in rapid genetic flux and regions that are more likely to have undergone horizontal exchange in relatively recent evolutionary time [ 3 , 4 ]. (biomedcentral.com)
  • effect
  • While a significant amount of work has been done on examining the TRI5 gene in relation to biotic and abiotic factors [ 5 ], practically no information is available on the effect of environmental stress on these other key genes in F. culmorum and F. graminaerum . (royalsocietypublishing.org)
  • different
  • 6 ] treated cells with different alkylating agents, ionizing radiation (IR), and peroxide, and found a variety of upregulated genes that had not previously been implicated in DNA repair. (biomedcentral.com)
  • The second group consists of phase-variable genes whose gene status can be changed during growth or under different conditions. (healthdocbox.com)