Muscling in on microarrays

2008 ◽  
Vol 33 (1) ◽  
pp. 124-129 ◽  
Author(s):  
Carl Virtanen ◽  
Mark Takahashi
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Dna Microarrays ◽  
Gene Expression Analysis ◽  
Exercise Physiology ◽  
Regulation Of Gene Expression ◽  
Enormous Amount ◽  
Potential Applications ◽  
New Generation ◽  
Affect Gene Expression

Adaptations that are the result of exercise require a multitude of changes at the level of gene expression. The mechanisms involved in regulating these changes are many, and can occur at various points in the pathways that affect gene expression. The completion of the human genome sequence, along with the genomes of related species, has provided an enormous amount of information to help dissect and understand these pathways. High-throughput methods, such as DNA microarrays, were the first on the scene to take advantage of this wealth of information. A new generation of microarrays has now taken the next step in revealing the mechanisms controlling gene expression. Analysis of the regulation of gene expression can now be profiled in a high-throughput fashion. However, the application of this technology has yet to be fully realized in the exercise physiology community. This review will highlight some of the latest advances in microarrays and briefly discuss some potential applications to the field of exercise physiology.

The application of DNA microarrays in gene expression analysis

2000 ◽  
Vol 78 (3) ◽  
pp. 271-280 ◽  
Author(s):  
Nicole L.W van Hal ◽  
Oscar Vorst ◽  
Adèle M.M.L van Houwelingen ◽  
Esther J Kok ◽  
Ad Peijnenburg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Dna Microarrays ◽  
Gene Expression Analysis

scholarly journals Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis

2014 ◽  
Vol 128 (10) ◽  
pp. 848-858 ◽  
Author(s):  
T J Ow ◽  
K Upadhyay ◽  
T J Belbin ◽  
M B Prystowsky ◽  
H Ostrer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Storage ◽  
Expression Analysis ◽  
High Throughput ◽  
Gene Expression Analysis ◽  
Biological Data ◽  
Biological Research ◽  
Nucleotide Sequencing ◽  
New Era ◽  
Crucial Component

AbstractBackground:Advances in high-throughput molecular biology, genomics and epigenetics, coupled with exponential increases in computing power and data storage, have led to a new era in biological research and information. Bioinformatics, the discipline devoted to storing, analysing and interpreting large volumes of biological data, has become a crucial component of modern biomedical research. Research in otolaryngology has evolved along with these advances.Objectives:This review highlights several modern high-throughput research methods, and focuses on the bioinformatics principles necessary to carry out such studies. Several examples from recent literature pertinent to otolaryngology are provided. The review is divided into two parts; this first part discusses the bioinformatics approaches applied in nucleotide sequencing and gene expression analysis.Conclusion:This paper demonstrates how high-throughput nucleotide sequencing and transcriptomics are changing biology and medicine, and describes how these changes are affecting otorhinolaryngology. Sound bioinformatics approaches are required to obtain useful information from the vast new sources of data.

scholarly journals Physiological Studies of Escherichia coli Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression

2003 ◽  
Vol 185 (18) ◽  
pp. 5611-5626 ◽  
Author(s):  
Eric Soupene ◽  
Wally C. van Heeswijk ◽  
Jacqueline Plumbridge ◽  
Valley Stewart ◽  
Daniel Bertenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Dna Microarrays ◽  
Degradation Products ◽  
Regulatory Gene ◽  
Regulation Of Gene Expression ◽  
Nitrate Respiration ◽  
Starch Degradation ◽  
Strain Mg1655 ◽  
Growth Defects

ABSTRACT Escherichia coli strain MG1655 was chosen for sequencing because the few mutations it carries (ilvG rfb-50 rph-1) were considered innocuous. However, it has a number of growth defects. Internal pyrimidine starvation due to polarity of the rph-1 allele on pyrE was problematic in continuous culture. Moreover, the isolate of MG1655 obtained from the E. coli Genetic Stock Center also carries a large deletion around the fnr (fumarate-nitrate respiration) regulatory gene. Although studies on DNA microarrays revealed apparent cross-regulation of gene expression between galactose and lactose metabolism in the Stock Center isolate of MG1655, this was due to the occurrence of mutations that increased lacY expression and suppressed slow growth on galactose. The explanation for apparent cross-regulation between galactose and N-acetylglucosamine metabolism was similar. By contrast, cross-regulation between lactose and maltose metabolism appeared to be due to generation of internal maltosaccharides in lactose-grown cells and may be physiologically significant. Lactose is of restricted distribution: it is normally found together with maltosaccharides, which are starch degradation products, in the mammalian intestine. Strains designated MG1655 and obtained from other sources differed from the Stock Center isolate and each other in several respects. We confirmed that use of other E. coli strains with MG1655-based DNA microarrays works well, and hence these arrays can be used to study any strain of interest. The responses to nitrogen limitation of two urinary tract isolates and an intestinal commensal strain isolated recently from humans were remarkably similar to those of MG1655.

scholarly journals Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

2013 ◽  
Vol 15 (4) ◽  
pp. 363-372 ◽  
Author(s):  
Victoria Moignard ◽  
Iain C. Macaulay ◽  
Gemma Swiers ◽  
Florian Buettner ◽  
Judith Schütte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Progenitor Cells ◽  
High Throughput ◽  
Gene Expression Analysis ◽  
Transcriptional Networks ◽  
Stem And Progenitor Cells ◽  
Cell Gene Expression ◽  
Cell Gene

scholarly journals Hepatic Gene Expression Changes in Hypothyroid Juvenile Mice: Characterization of a Novel Negative Thyroid-Responsive Element

Endocrinology ◽  
2007 ◽  
Vol 148 (8) ◽  
pp. 3932-3940 ◽  
Author(s):  
Hongyan Dong ◽  
Carole L. Yauk ◽  
Andrew Williams ◽  
Alice Lee ◽  
George R. Douglas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Transient Gene Expression ◽  
Early Response ◽  
Response Element ◽  
Gene Expression Studies ◽  
Maternal Thyroid ◽  
Responsive Element

The molecular mechanisms involved in the response of developing mice to disruptions in maternal thyroid hormone (TH) homeostasis are poorly characterized. We used DNA microarrays to examine a broad spectrum of genes from the livers of mice rendered hypothyroid by treating pregnant mice from gestational d 13 to postnatal d 15 with 6-propyl-2-thiouracil in drinking water. Twenty-four individuals (one male and one female pup from six litters of control or 6-propyl-2-thiouracil treatment groups, respectively) were profiled using Agilent oligonucleotide microarrays. MAANOVA identified 96 differentially expressed genes (false discovery rate adjusted P < 0.1 and fold change > 2 in at least one gender). Of these, 72 genes encode proteins of known function, 15 of which had previously been identified as regulated by TH. Pathway analysis revealed these genes are involved in metabolism, development, cell proliferation, apoptosis, and signal transduction. An immediate-early response gene, Nr4a1 (nuclear receptor subfamily 4, group A, member 1), was up-regulated by 3-fold in hypothyroid juvenile mouse liver; treatment of HepG2 cells with T3 resulted in down-regulation of Nr4a1. A potential thyroid response element −1218 to −1188 bp upstream of the promoter region of Nr4a1 was identified and demonstrated to bind TH receptor (TR)-α and TRβ. Point mutation or deletion of the sequence containing the potential Nr4a1-thyroid response element in transient gene expression studies resulted in both higher basal expression and loss of T3 regulatory capacity, suggesting that this site is responsible for the negative regulation of gene expression by TR and TH.

High-throughput gene expression analysis in bone healing around titanium implants by DNA microarray

2008 ◽  
Vol 19 (2) ◽  
pp. 173-181 ◽  
Author(s):  
Norinaga Kojima ◽  
Shogo Ozawa ◽  
Yasuhiro Miyata ◽  
Hideki Hasegawa ◽  
Yoshinobu Tanaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarray ◽  
Expression Analysis ◽  
High Throughput ◽  
Bone Healing ◽  
Gene Expression Analysis ◽  
Titanium Implants ◽  
High Throughput Gene Expression
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