Abstract: Interleukin-2 (IL-2) gene regulation was investigated in primary cultures of highly purified human peripheral blood CD28+T cells. Two discrete mechanisms for induction of T-cell proliferation could be distinguished by examining cell cycle progression and the expression of the IL-2 gene. Stimulation of cells by CD3 MoAb induced only transiently expressed, small amounts of IL-2 mRNA that was completely suppressed by cyclosporine. Costimulation of T cells with CD3 MoAb and either CD28 MoAb or PMA, but not calcium ionophore, induced a 50-100-fold increased in IL-2 gene expression and secretion. High levels of IL-2 gene expression could also be achieved by stimulation with calcium ionophore and PMA or CD28 MoAb and PMA, but not by CD28 MoAb plus calcium ionophore. IL-2 gene expression and T-cell proliferation induced by CD3 MoAb plus PMA or calcium ionophore plus PMA were completely suppressible by cyclosporine. In contrast, IL-2 gene expression and T-cell proliferation induced by CD28 MoAb ...
Read "SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology, Genome Biology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
DNA actively 58-49-1 biological activity down-regulates the gene expression of LL37 in monocytes and epithelial cells. Nevertheless, due to the fact
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Effect of in vivo gene expression knockdown on neuroblast migration in the olfactory bulb. The RMS within the olfactory bulb (bRMS) is visible as more intensely
What is meant by gene expression? Gene expression refers to genes being turned on and producing a product. The product could be an enzyme, a structural protein, or a control molecule. Studies of gene expression typically measure the production of mRNA. Most mechanisms that control gene expression do so by controlling transcription, the synthesis of mRNA. However there are other mechanisms for controlling the rate of protein synthesis that occur downstream (between transcription and translation). Several of these are described in this animation. View the animation below, then complete the quiz to test your knowledge of the concept.. ...
Determining gene expression on a single pair of microarrays. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Genomes contain all the genetic information needed by an organism, regardless of the circumstance or environment. Generally, however, even single-cell organisms use only a fraction of their genome at any time; that is, cells generally express only a fraction of their genome at any given time. This is especially true among the individual cells that make up multicellular organisms, where cell specialization (differentiation) dictates that only certain genes be expressed in certain cells, and only at particular times during the organisms life span.. ...
Process of gene expression entails plasmid DNA or mRNA delivery to specific cells and is a technique routinely utilized in labs to study a gene of interest or a signaling pathway. Gene expression usually allows transient protein production, but in some cases stable integration into a genome and continuous protein production over time is required.
Gene Expression Macro Version 1.1 Instructions Rev B 1 Bio-Rad Gene Expression Macro Users Guide 2004 Bio-Rad Laboratories Table of Contents: Introduction Opening
Is a useful technique for acquiring the gene expression pattern of a number of selected genes due to its high sensitivity, specificity and broad quantification
The answer, though, is differences in gene expression in a cell. Clones have identical DNA, but the way the DNA is transcribed to RNA, and the way the RNA is translated to making a protein, can be specific to the cell. There are epigenetic factors - basically, chemicals that adhere to certain parts of the genome - that dictate NOT whether the DNA is there, but how often the DNA is read to make RNA and how efficiently that is made into functional proteins. Think about a fertilized egg. It divides into two cells, then 4 cells, then 8 cells, then 16 cells, then 32 cells, etc. Every time the cell divides, it has to make a perfect copy of its DNA. The cell machinery isnt always perfect and little changes in DNA can occur. Also, those chemicals that can affect gene expression can get added or subtracted as cells divide. Many of them, however, are passed on to the daughter cells. Thats how identical cells can have different levels of gene expression, and how people and horses and dogs with identical ...
Akhilesh Bajpai, Sravanthi Davuluri and Acharya KK* (*Correspondence: [email protected]), A comparative account of gene expression resources, feature-validations and application-based categorizations; In: Startbioinfo; 12 Oct 2011, http://www.startbioinfo.com/gene-expression/" ...
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An expression system refers to the factors that work together to yield a particular gene product such as a protein, ribozyme or RNA particle.
Effect of mannan-oligosaccharides (MOS) supplementation onperformance, immunity and HSP70 gene expression in broilerchicken during hot-dry summer
I am fascinated by a fundamental question in biology; How is regulation of gene expression as a response to external stimulus achieved? My laboratory
Chapter 18 Regulation of Gene Expression Gene Regulation Is Necessary By switching genes off when they are not needed, cells can prevent resources from being wasted. There should be natural selection
Im just not quite sure the answer to this. When we talk about epigenetics and gene expression, does it not matter if we have snps or not? For...
Genotyping & gene expression full services from Eurofins Genomics . Wide range of platforms and assays available ** Call +49 8092 8289-0
Telencephalic and diencephalic gene expression in the fgf16 morphants.The expression of emx1 (A, B), tbr1 (C, D), dlx2 (E, F), pax6a (G, H), and shh (I, J) in w
This function will fit smooth spline curves for the gene expression dynamics along pseudotime in a gene-wise manner and return the corresponding response matrix. This function is build on other functions (fit_models and responseMatrix) and used in calILRs and calABCs functions
C57BL/6 mice were injected with 400 mg of anti-CD4 (clone GK one.five BioXcell, NH, Usa) or anti-CD8 (clone 53,.seventy two BioXcell, NH, United states of
You need to make cDNA with random hexamers or oligo dT, then amplify the gene with specific primers after that by PCR. In my experience there isnt a whole lot of difference between random hexamers or oligo dT. They seem to work equally as well for cDNA generation.. Lately, I have been using the Invitrogen SuperScript III kit with random hexamers to amplify my cDNAs. Works great.. Rb. ...
I dont have a TV because it seems such a time sink. Nevertheless, over the past few years Ive felt the creep of media convergence. Now I found this site, not quite as bad as channel surfing...but its getting there ...
Sources tell TMZ the network has told the cast if they dont accept MTVs deal by the end of business Monday, they will be replaced. And, MTV has told them it does not have to be a package deal -- the cast members who accept the offer will stay ... those who do not can have a nice life ...
The Workshop on Evolutionary Tinkering in Gene Expression which was held at the end of August 1988. was planned to celebrate 20 successful Advanced Study Institutes (A. S. I.) in Molecular and Cell
BACKGROUND: Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro ...
Researchers use DNA microarrays, or gene chips, to distinguish among different types of tissues based on the expression patterns of thousands of genes. A new study says the technology can be modified to profile more tissue samples simultaneously and with greater efficiency. The innovation is called an array of arrays. Gene expression profiles are typically obtained one at a time by hybridizing a single tissue sample to a single array on an individual glass slide. The integrated device described in the study is a glass wafer that includes 49 individual oligonucleotide arrays arranged as a 7 × 7 array of arrays. David J. Lockhart and colleagues at the Genomics Institute of the Novartis Research Foundation, in San Diego, California, developed a way to hybridize many tissue samples to multiple arrays on a single glass slide, or wafer. Using this and other modifications, they completed a study of gene expression in ovarian cancer in a single experiment. This was done in a fraction of the time and ...
Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. So far, these assessments can only be performed at the population level. Therefore, they determine the average gene expression within a population, overlooking possible cell-to-cell heterogeneity that could lead to different cell behaviors/cell fates. Understanding individual cell behavior requires multiple gene expression analyses of single cells, and may be fundamental for the understanding of all types of biological events and/or differentiation processes. We here describe a new reverse transcription-polymerase chain reaction (RT-PCR) approach allowing the simultaneous quantification of the expression of 20 genes in the same single cell. This method has broad application, in different species and any type of gene combination. RT efficiency is evaluated. Uniform and maximized amplification conditions for all genes are provided. Abundance relationships are maintained, allowing the ...
Gene Expression Analysis Market-[By Technology (DNA Microarray, Real-Time PCR, Next Generation Sequencing), By Consumables (DNA chips, Reagents), By Services (Gene Profiling, Bioinformatics, Data Analysis Software) & Applications]-Global Forecast to 2018. The global gene expression analysis market is witnessing a significant growth and will continue to do so in the next five years. The factors contributing to this growth are increased funding scenario worldwide, increased government involvement, developments in research for diseases like cancer, and the use of gene expression in drug discovery and personalized medicine. The Asian region is projected to have the highest growth rate with growth hinged at China, India, and Japan. Apart from Asia, countries such as Turkey, Brazil, and South Africa too have a high projected growth.. In the Asian region, China is the genomic leader. China has cultivated a favorable condition to support gene expression analysis growth. From its humble beginning in 1999 ...
It is gene expression that defines a cells identity. Science, Sciences Science of Aging Knowledge Environment (SAGE KE), and Sciences STKE focus attention on the highly dynamic nature of gene expression. Mechanisms governing selective gene expression in multigene families, as well as those by which cis- and trans-acting factors contribute to regulation of gene expression, are topics under discussion. In addition, new methodologies allow researchers to gain insight into gene expression at the level of single cells and provide a glimpse at the real-time interactions among proteins and DNA.. ...
Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene expression levels increased markedly for several genes in the context of a reporter system. We propose that such splice sites represent a ...
The Gene Expression Metasignatures (GEMS) analysis tool was developed to allow researchers to determine a weighted consensus across multiple datasets for the regulation of a gene by acute (0-4 h) or chronic (24 h) treatment with 17beta-estradiol in MCF-7 cells. GEMS was retired in November 2012. In its place we have developed a broader, large-scale differential gene expression tool for the nuclear receptor signaling research community, Transcriptomine. Transcriptomine collates omics-scale differential gene expression studies across the nuclear receptor and coregulator signaling field into a single analysis tool, allowing researchers to detect patterns across multiple datasets. A large number of 17beta-estradiol MCF-7 datasets have been uploaded to the database, including all those originally in GEMS. These can currently be viewed as individual fold changes.. ...
The primary goal of the study is to measure in the intact human heart, the alterations in gene expression over time that are associated with reverse remodeling in response to β-blockade. The second goal is to investigate the signaling mechanisms which in turn are responsible for these changes in gene expression, and the third goal is to determine the relationship between intrinsic systolic dysfunction and remodeling of the left ventricle. This will be accomplished by measuring ventricular size, function, and gene expression in myocardial tissue samples obtained by percutaneous biopsy prior to initiation of β-blockade and at 3 and 12 months after start of therapy. The specific Aims and Hypotheses to be tested are:. ...
The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as snm, sva, and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.
Relative gene expression analysis requires precise, powerful and cutting edge technology called Real Time PCR, that is being utilized today by many research laboratories around the world.
Seker, H. (2004) A Multi-Fuzzy Filtering Approach to Reliable Gene Expression Profile Analysis. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, October 2004, pp. 37-40 ...
View Notes - Gene Expression from BIOL 101 at UNC. Gene Expression/Test 3 Tuesday, March 03, 2009 9:30 AM 1. Helicase molecule o Protein made on ribosome o In cytoplasm. Sometime cell needs sometime
An important new study has revealed the clearest picture yet of precisely how much measurement variation influences gene expression profiles of breast cancer.
Jurasek JV, Raposa LB, Gubicskóné Kisbenedek A et al.. Táplálkozástudományi és Dietetikai Intézet, Pécsi Tudományegyetem, Egészségtudományi Kar Pécs.. Orvosi hetilap. Mar 2017.. Nowadays, the food industry more often uses different type of additives during the food production.Our aim was to examine the monosodium-glutamates effect (in animal experiment) on DNA-methyltransferases in gene expression patterns of mRNA levels.In the investigation we used 24 (n=24) CD1 type female mice. The animals were fed with different equivalent human doses of the tested substance. After autopsy, mRNA was isolated from different tissues (lung, liver, kidney, spleen). DNMT1, DNMT3A and DNMT3B levels were determined by Quantitative Real-Time PCR.DNMT1 significantly suppressed the gene expression in all the three treated groups ( ...
The ability of cells to control the expression of genes is important for cell survival. Nutrients can alter the gene expression that controls levels of bioactive proteins. Herbs alter gene activity in various ways. Gene transcription, the most important, is the initial step in gene expression. The pregnane X receptor (PXR receptor) is the target […]. View Post ...
TimesVector is a triclustering tool for clustering time-series data that comprises multiple conditions, or phenotypes. It identifies gene clusters that exhibit distinctly similar or different gene expression patterns among the comparing sample conditions. For example, for a time-series data set of five different strains of yeast, each data sampled at 3 time points, TimesVector will search for gene clusters where a specific strain shows a distinctively different gene expression pattern from the others.. As an example result, 33 genes in cluster 25 were significantly induced at day 5 (D5) during fermentation, only in the DV10 yeast strain (data from GSE11651) ...
The secretory protein Reg3γ (also known as PAP III) is expressed in several tissues, and its expression is induced in various injuries and inflammatory conditions in gastrointestinal tract (Iovanna et al. 1992; Ogawa et al. 2003), skeletal muscle (Klasan et al. 2014) as well as in central and peripheral nervous system (Namikawa et al. 2005, 2006; Ampo et al. 2009; Kawahara et al. 2011; Klasan et al. 2014). However, almost nothing is known about cardiac Reg3γ gene expression, although increased Reg3γ expression has been repeatedly identified in cardiac gene expression profiling screens (Rysä et al. 2005; Tenhunen et al. 2006a; Watanabe et al. 2008; Liu et al. 2009). In this study, we are first to characterize the expression and regulation of Reg3γ in the heart. We found that Reg3γ gene expression is rapidly up‐regulated by post‐MI remodeling and Ang II in the adult rat heart in vivo. We showed that losartan treatment reduced left ventricular Reg3γ gene expression levels activated by ...
The general goal of the technique is similar to the DNA microarray. However, SAGE is a sequence-based sampling technique. Observations are not based on hybridization, which result in more qualitative, digital values. In addition, the mRNA sequences do not need to be known a priori, so genes or gene variants which are not known can be discovered. Microarray experiments are much cheaper to perform, so large-scale studies do not typically use SAGE. Quantifying gene expressions is more exact in SAGE because it involves directly counting the number of transcripts whereas spot intensities in microarrays fall in non-discrete gradients and are prone to background noise. ...
Renal Tissue Thawed for 30 Minutes Is Still Suitable for Gene Expression Analysis. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
BioXpedias Technologies for Gene Expression Profiling offers RNA analyses of samples, using technologies that are time-, cost-, and sample-effective.
Gene expression analysis market will surpass more than US$ 4,500 million revenues towards the end of the forecast period, 2017-2022.
Learn how to prepare RNA for gene expression analysis from cultured cells in 7 minutes. The Cells-to-CT 1-Step TaqMan Kit is a simple, quick alternative to traditional RNA extraction.
The RNAscope® and BaseScope™ ISH assays can both be applied as methods to detect gene expression with morphological context in a multitude of mouse models.
This package allows users to perform imputation on the HG-U133A platform so as to obtain estimated gene expression values for genes that are found on the HG-U133 Plus 2.0 platform.
Use tetracycline for reversible and efficient spatiotemporal control of gene expression. This on-demand gene induction mimics disease onset and progression.
The course Epigenetic Control of Gene Expression by Dr Marnie Blewitt from University of Melbourne will be offered free of charge to everyone on the Coursera platform. Sign up at http://www.coursera.org/course/epigenetics.
Another approach to delineating the pathophysiology of bipolar disorder involves studying changes in gene expression induced in rodent brains after administration of pharmacologic agents used to treat... more
Our dedicated gene expression workflow allows you to analyze any sample with the highest standards of sensitivity and specificity, so you can have confidence in your data. Our workflow offers you options for specific and sensitive quantification, regardless of the type of RNA you work with or transcript abundance, as well as streamlined procedures so you gain real insights faster ...
View Notes - Chapter 16 from BIO GENETIC at FAU. Chapter 16 Control of Gene Expression in Prokaryotes General Principles Bacterial cells respond to their environment Rapid changes in
Researchers have mapped primate gene expression throughout the day and discovered that the majority of critical gene activity is time dependent, which may aid the development of new treatments for many diseases.
A tumor-suppressing protein acts as a dimmer switch to dial down gene expression. It does this by reading a chemical message attached to another protein thats tightly intertwined with DNA, a team led by scientists at The ...
With the advent of more sophisticated methods of detecting changes in gene expression, it has become clear that many responses to plant hormones operate through up- and down-regulation of specific genes.
Modulation of "enhancer-directed RNAs" or "eRNAs" could provide a new way to alter gene expression in living cells, perhaps affecting the development or pathology of many diseases.
A schematic model composed of a basic signal transduction unit and one gene is presented. The regulation of the signaling pathway by gene expression patter
In gene expression when exposed to CO2 elevated to 560 mmolmol21. The expression of 4600 expressed sequence tags in poplar have been investigated by Gupta et
Browse Full Report @ https://www.reportsandmarkets.com/reports/1208329-global-gene-expression-analysis-market-growth-trends-forecasts-2017-2022 Gene expres
Tags: cancer, dna, gene, target, cell, enzyme, treatment, human, control, transcription, expression, cell nucleus, error, phosphorylation, code.
Looks at Alzheimers disease as a way to study modern molecular techniques applied to medicine. Covers human biology and cell functions.
From discovery to validation, targeting the most relevant cell types and biomarkers lets you accelerate your studies into actionable insights. With
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident. Read more > ...
A reader pointed me to an article, Aryan-Dravidian divide a myth: Study. Some of the authors of the paper I reviewed today (actually, I wrote the post yesterday and put it in schedule) had some interesting things to say: The great Indian divide along north-south lines now stands blurred. A pathbreaking study by Harvard and…. ...
In the 10 Questions for A.W.F. Edwards, a mathematical geneticist, he was asked: Like Fisher you have worked in both statistics and genetics. How do you see the relationship between them, both in your own work and more generally? Edwards responded in part: Genetical statistics has changed fundamentally too: our problem was the paucity of…. ...
In the present study, we examined the gene expression profile of 25 IGHV4-34 patients including subset #4, #16 and non-subset 4/16 cases. Initially, we compared the gene expression profiles between subset #4 and non-subset 4/16 patients and between subset #16 patients and non-subset 4/16 patients, and detected only few significant differences. This is probably because, overall, non-subset 4/16 IGHV4-34 cases exhibited a more heterogeneous gene expression profile, likely reflecting the structural heterogeneity of their BCR, which would be expected to be responsive to a far wider range of antigens than that recognized by stereotyped subsets. Interestingly, however, we detected distinct differences in gene expression patterns when comparing subset #4 and #16 cases, both of which can be reliably defined at the molecular level based on subset-specific VH CDR3 and subset-biased features of somatic hypermutation.8 This finding is supported by the recent observation that stereotyped subset cases have ...
Abstract: In this work, I focus on the development and testing of tools to explore differential gene expression as a molecular mechanism underlying the predisposition to complex disease. By definition, complex diseases (e.g. hypertension, diabetes, asthma) demonstrate both environmental and genetic factors in disease susceptibility, implicating genes that show both environmental response and genetic variability in predisposing disease. Differential gene expression is one important cellular response that reflects both of these factors in complex disease. Given their combined genetic and environmental influences, complex diseases are studied using a variety of analytical approaches. Consequently, the integration of data from diverse sources is a significant and important challenge in modern biomedical science. I demonstrate a statistical approach to integrating differential gene expression and genetic linkage data from multiple sources to reveal candidate genes, metabolic pathways, and DNA ...
... Future Conference: GENE EXPRESSION 2018; GENE EXPRESSION 2019; GENE EXPRESSION 2020;
The advent of experimental techniques for the time-course monitoring of gene expression at the single-cell level has paved the way to the model-based study of gene expression variability within- and across-cells. A number of approaches to the inference of models accounting for variability of gene expression over isogenic cell populations have been developed and applied to real-world scenarios. The development of a systematic approach for the validation of population models is however lagging behind, and accuracy of the models obtained is often assessed on a semi-empirical basis. In this paper we study the problem of validation of models of gene network dynamics for cell populations, providing statistical tools for qualitative and quantitative model validation and comparison, and guidelines for their application and interpretation based on a real biological case study.
NDSUs next Science Café will explore the topic of gene expression analysis. Megan Orr, assistant professor of statistics, is scheduled to present Increasing the power of the test: An introduction to gene expression analysis and false discovery rate Tuesday, March 10, at 7 p.m. in Stokers Basement, Hotel Donaldson in Fargo. Its free and open to the public. According to the abstract for Orrs presentation, the prevalence of high-dimensional data has skyrocketed in recent years because of advances in technology. This is especially true in experiments where mRNA transcripts, known as gene expressions, are measured for thousands of genes simultaneously. A goal in the analysis of these experiments is to identify genes that exhibit a change in mean expression levels across treatments. Orrs talk will focus on the analysis of gene expression data sets and illustrate why using traditional techniques is inappropriate. The false discovery rate, a common measure used to control for multiple testing ...
BACKGROUND: Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age.. RESULTS: Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential ...
TY - JOUR. T1 - Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs. AU - Jonker, Martijs J.. AU - Melis, Joost P.M.. AU - Kuiper, Raoul V.. AU - van der Hoeven, Tessa V.. AU - Wackers, Paul F.K.. AU - Robinson, Joke. AU - van der Horst, Gijsbertus T.J.. AU - Dollé, Martijn E.T.. AU - Vijg, Jan. AU - Breit, Timo M.. AU - Hoeijmakers, Jan H.J.. AU - Van Steeg, Harry. PY - 2013/10/1. Y1 - 2013/10/1. N2 - Aging and age-related pathology is a result of a still incompletely understood intricate web of molecular and cellular processes. We present a C57BL/6J female mice in vivo aging study of five organs (liver, kidney, spleen, lung, and brain), in which we compare genome-wide gene expression profiles during chronological aging with pathological changes throughout the entire murine life span (13, 26, 52, 78, 104, and 130 weeks). Relating gene expression changes to chronological aging revealed many differentially expressed genes (DEGs), ...
Diagnosis and prognosis of breast cancer are still mainly based on clinical, histological and immunohistochemical parameters, which are at best semi-quantitative [1, 2]. Recently, molecular characterization of breast cancer has greatly increased the understanding of biological pathways that are altered during neoplastic transformation. Molecular markers have a great impact on elucidating the biological variance within tumors, they allow new and more accurate classifications and they have the potential to improve diagnosis, estimation of prognosis and treatment decisions in individual patients [3-6].. Most gene expression studies are based on fresh frozen material which, in most instances, is not readily available, as surgical samples are usually fixed in formalin. Unfortunately, RNA derived from formalin-fixed, paraffin-embedded (FFPE) material is considerably fragmented and chemically modified, often impairing gene expression measurement using standard procedures. We developed a simple and ...
Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis. The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The relative mRNA proportions were
Fibroblasts play important roles in several cancers. It was hypothesized that cholangiocarcinoma (CCA)-associated fibroblasts (Cfs) differ from non-tumorigenic liver fibroblasts (Lfs) in their gene expression profiles resulting in the capability to promote cancer. Periostin (PN) is a multi-functional protein and has emerged as a promising marker for tumor progression. The role of PN in CCA, however, has not yet been explored. In this study, the gene expression profile of Cfs in comparison to Lfs was performed using oligonucleotide microarrays. The common- and unique-expressed genes in Cfs and the promising roles in cancer promotion and progression were determined. PN was markedly over-expressed in Cfs confirmed by real time RT-PCR and western blot analysis. Immunohistochemistry examination of a number of patients with intrahepatic CCA showed the expression of PN solely in stromal fibroblasts, but was expressed neither in cancer cells nor immune cells. Low to no expression of PN was observed in tissues
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA), and is informally termed gene regulation. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein.. Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Histone, DNA modifying enzymes and chromatin remodelling factors are major area to concentrate.. Relevant Conferences: Nucleic Acids Conferences , Biochemistry Conferences. 2ndInternational Conference on Transcriptomics, September 12-14, 2016 Philadelphia ...
Laboratory of Gene Expression (http://www.ibt.cas.cz/vyzkum/laboratore/laborator-genove-exprese/) is looking for two PhD and MSc candidates with an expected starting date for summer/autumn 2018. Students will participate on projects focused on molecular and developmental biology.. Laboratory: The Laboratory of Gene Expression is a well-funded research laboratory with an excellent publication track record and comprise of researchers with unique scientific expertise. We focus on gene expression studies using a combination of up-to date techniques such as single cell expression profiling and NGS. We also utilize good biological models to help explain aspects of embryonic development, neurodegenerative diseases and cancer progression. The laboratory is located in the new state-of-the-art BIOCEV research center.. Qualification: Applicants should have a background in biochemistry, physiology, molecular or cell biology and bioinformatics. We seek a highly motivated, creative person, with strong ...
Gene expression profiling, including quantitative RT-PCR (qPCR) and microarray experimentation, is invaluable for the molecular analysis of biological systems. The interpretation of results from such experiments (i.e., the determination of differential expression for a particular gene among datasets) is strongly influenced by the selection of reference genes for normalization across datasets [1]. Specifically, gene expression is normalized within a given dataset by calculating the transcript abundance of the gene of interest relative to a gene that is constantly expressed across independent datasets (termed a "housekeeping" or a "reference" gene), and differential expression between two datasets or samples is determined by calculating the ratio of the normalized expression levels for the gene of interest between the two datasets. Typically, housekeeping genes satisfy the following criteria: they are highly expressed in the cell, the variability in expression between samples is minimal, and the ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognise these limitations and addresses them. As such, it provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for clustering methods considered.
In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed (housekeeping) genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues. We measured whole genome expression in 31 human tissues, identifying 2374 housekeeping genes expressed in all tissues, and genes uniquely expressed in each tissue. Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism. Network topology of the housekeeping network was characterized by higher connectivity and shorter paths between the proteins than the global network. Ontology enrichment scoring
Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. So far, these assessments can only be performed at the population level. Therefore, they determine the average gene expression within a population, overlooking possible cell-to-cell heterogeneity that could lead to different cell behaviors/cell fates. Understanding individual cell behavior requires multiple gene expression analyses of single cells, and may be fundamental for the understanding of all types of biological events and/or differentiation processes. We here describe a new reverse transcription-polymerase chain reaction (RT-PCR) approach allowing the simultaneous quantification of the expression of 20 genes in the same single cell. This method has broad application, in different species and any type of gene combination. RT efficiency is evaluated. Uniform and maximized amplification conditions for all genes are provided. Abundance relationships are maintained, allowing the ...
Gene expression functions as a key pillar of the molecular biology market as multiple molecular biology techniques have been used extensively to study gene expression and gene quantification. Molecular biology techniques such as polymerase chain reaction (PCR); nucleotide sequencing, including next-
Total RNA was purified from the lungs of C57BL/6 mice that were sensitized and challenged with either PBS (2 mice) or CRA (3 mice). RNA was extracted using the RNeasy Mini Kit (Qiagen), and cDNA was synthesized from 1 µl of the extracted RNA using Superscript II RT enzyme (Invitrogen) according to the manufacturers protocol. Two microliters of the reverse transcription reaction (equivalent to 20 ng total RNA per 20 µl qPCR reaction) were used for qPCR with SYBR Premix Ex Taq II according to the recommended protocol. qPCR reactions were run in triplicate using probes for mouse IL-4 and GAPDH on an Applied Biosystems 7500 Real-Time PCR System. The relative gene expression level of IL-4 was determined using the delta/delta Ct method.. Buy SYBR Premix Ex Taq II (Tli RNaseH Plus) ,,. ...
Relapsed pediatric B-acute lymphoblastic leukemia (B-ALL) remains as the leading cause of cancer death among children. Other than stem cell transplantation and intensified chemotherapy, no other improved treatment strategies have been approved clinically. Gene expression profiling represents a powerful approach to identify potential biomarkers and new therapeutic targets for various diseases including leukemias. However, inadequate sample size in many individual experiments has failed to provide adequate study power to yield translatable findings. With the hope of getting new insights into the biological mechanisms underpinning relapsed ALL and identifying more promising biomarkers or therapeutic targets, we conducted a meta-analysis of gene expression studies involving ALL from 3 separate studies. By using the keywords
Is there a gene or genes that are activated at age 1 that signal to the other genes to perform gene expression appropriate for a one year old? Futhermore, is there a gene or genes that are activated at age 20 that signal to the other genes to perform gene expression appropriate for a twenty year old? Lastly, if there were a gene or genes that signals for twenty year old gene expression regulation, then if that gene were activated in an 80 year old, would the body of the 80 year old begin to exhibit the physiology of a 20 year old, thus increasing lifespan and healthspan? DE. ...
Discussion. Study design. In this study, we describe the analysis of 22K gene expression profiles of macular and peripheral RPE cells. There have been a number of other published studies that had a similar research question but employed different methodologies [8,17-21]. However, all of these studies suffered from one or more relative weaknesses in terms of sample selection, RPE cell handling, target selection, as well as microarray- or bioinformatics methods. Our aim was to avoid these limitations as much as possible (Table 5 and Table 6).. While the number of samples we used was limited, our entire strategy was focused on reduction of gene expression differences between individual eyes. In this study, we detected only consistent differences, more or less present in the RPE of each individual eye. We neither detected transient gene expression differences nor potential differences which co-occurred with high interindividual variation. The complexity of our material was greatly reduced by ...
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Large amounts of information generated by gene expression profiling will increase implementation of data management tools Gene expression profiling can...
The spatial information associated with gene expression is important for elucidating the context-dependent transcriptional regulation during development. Recently, high-resolution sampling approaches, such as RNA tomography or single-cell RNA-seq combined with fluorescence in situ hybridization (FISH), have provided indirect ways to view global gene expression patterns in three dimensions. Now in situ sequencing technologies, such as fluorescent in situ sequencing (FISSEQ), are attempting to visualize the genetic signature directly in microscope images. This article will examine the basic principle of modern in situ and single-cell genetic methods, hurdles in quantifying intrinsic and extrinsic forces that influence cell decision-making, and technological requirements for making a visual map of gene regulation, form, and function. Successfully addressing these challenges will be essential for investigating the functional evolution of regulatory sequences during growth, development, and cancer ...
We use RNA-seq technology to study transcriptome wide gene expression, while qPCR is applied for gene expression analysis of specific genes of interest.
Continuing on, Sams reference of gene atlases, both for non-coding RNA and protein encoding RNA in his videos is anything but irrelevant. A friend of mine who is a veterinarian and biologist explained to me exactly why this is, and so I will reword her response here. Simply put, gene expression charts show the default frequency at which a gene synthesizes proteins in different parts of the body. Gene expression levels are used by scientists as a means of accurately predicting how a particular gene affects the observable traits, or phenotypes, of whatever organism you are monitoring - the case in point being humans, although there is genomic expression data for rats and mice as well for MAO-A. Gene expression can offer predictions for what phenotypes are expressed as a result of protein synthesis from a particular gene, and to what extent. If this particular enzyme shows high gene expression in the liver, but low expression in the brain, then it is justifiable to say that the greatest appearance ...
Answering these questions is key to understanding the complex interaction between a pathogen and its host, as well as to the development of better treatments or vaccines. QIAGEN offers a range of solutions for profiling pathogen gene expression. Our tools provide efficient mechanical disruption of difficult-to-lyse microbes, optimized chemistry for high yields of nucleic acids, and accurate qPCR-based gene expression analysis to facilitate and advance your research ...
Spatiotemporal gene expression is the activation of genes within specific tissues of an organism at specific times during development. Gene activation patterns vary widely in complexity. Some are straightforward and static, such as the pattern of tubulin, which is expressed in all cells at all times in life. Some, on the other hand, are extraordinarily intricate and difficult to predict and model, with expression fluctuating wildly from minute to minute or from cell to cell. Spatiotemporal variation plays a key role in generating the diversity of cell types found in developed organisms; since the identity of a cell is specified by the collection of genes actively expressed within that cell, if gene expression was uniform spatially and temporally, there could be at most one kind of cell. Consider the gene wingless, a member of the wnt family of genes. In the early embryonic development of the model organism Drosophila melanogaster, or fruit fly, wingless is expressed across almost the entire ...
Eady, JJ, Wortley, GM, Wormstone, YM, Hughes, JC, Astley, SB, Foxall, RJ, Doleman, JF and Elliott, RM (2005) Variation in gene expression profiles of peripheral blood mononuclear cells from healthy volunteers ...