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Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Background The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression. Methodology/Principal Findings A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the ...

Reduction of protein sequence complexity by residue grouping

It is well known that there are some similarities among various naturally occurring amino acids. Thus, the complexity in protein systems could be reduced by sorting these amino acids with similarities into groups and then protein sequences can be simplified by reduced alphabets. This paper discusses how to group similar amino acids and whether there is a minimal amino acid alphabet ...

Genome Characterization of the Oleaginous Fungus Mortierella alpina

Mortierella alpina is an oleaginous fungus which can produce lipids accounting for up to 50% of its dry weight in the form of triacylglycerols. It is used commercially for the production of arachidonic acid. Using a combination of high throughput sequencing and lipid profiling, we have assembled the M. alpina genome, mapped its lipogenesis pathway and determined its major lipid ...

Proteomic analysis of human ovaries from normal and polycystic ovarian syndrome

Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility, affecting 5–10% of females of reproductive age. Currently, little is known about the changes in whole proteins between PCOS and normal ovaries. In the present study, a proteomic approach comprised two-dimensional gel electrophoresis (2DE) analysis and mass spectroscopy was used to identify ...

Clinical, Experimental, and Genomic Differences between Intermediately Pathogenic, Highly Pathogenic, and Epidemic Streptococcus suis

Background. Streptococcus suis emerged to cause an unusual outbreak of streptococcal toxic-shock-like syndrome (STSLS) in 2005. The mechanisms involved are unknown. Methods. Clinical, laboratory, and epidemiologic data on patients infected with culture-confirmed S. suis were analyzed. The strain involved in the outbreak, “epidemic” strain ST7, was compared with both a classical ...

A Recalibrated Molecular Clock and Independent Origins for the Cholera Pandemic Clones

Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6th (1899–1923) and 7th (1961–present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to ...

Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain

Protein-protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains, such as Src Homology 2 and 3 (SH2 and SH3) domains, which bind to specific sequence and structural motifs. It is important but challenging to determine the binding specificity of these domains accurately and to predict their physiological interacting partners. In ...

Antioxidant intervention of smoking-induced lung tumor in mice by vitamin E and quercetin

Background Epidemiological and in vitro studies suggest that antioxidants such as quercetin and vitamin E (VE) can prevent lung tumor caused by smoking; however, there is limited evidence from animal studies. Methods In the present study, Swiss mouse was used to examine the potential of quercetin and VE for prevention lung tumor induced by smoking. Results Our results suggest that ...

Glomerular filtration rate can be accurately predicted using lean mass measured by dual-energy X-ray absorptiometry

Background. Accurate assessment of renal function is important in the management of patients with kidney disease yet is often difficult to obtain. Formulae, designed for clinical use, have been developed to predict glomerular filtration rate (GFR) utilizing serum creatinine (Scr). Additional parameters are included in these formulae to account for variations in Scr due to ...

Mesenchymal stem cells are superior to angiogenic growth factor genes for improving myocardial performance in the mouse model of acute myocardial infarction

Both cell therapy and angiogenic growth factor gene therapy have been applied to animal studies and clinical trials. Little is known about the direct comparison between cell therapy and angiogenic growth factor gene therapy. The goal of this study was to compare the effects of human bone marrow-derived mesenchymal stem cells (hMSCs) transplantation and injection of angiogenic ...

Gcg-XTEN: An Improved Glucagon Capable of Preventing Hypoglycemia without Increasing Baseline Blood Glucose

Objective While the majority of current diabetes treatments focus on reducing blood glucose levels, hypoglycemia represents a significant risk associated with insulin treatment. Glucagon plays a major regulatory role in controlling hypoglycemia in vivo, but its short half-life and hyperglycemic effects prevent its therapeutic use for non-acute applications. The goal of this study ...

easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data

Background Alternative RNA splicing greatly increases proteome diversity and thereby contribute to species- or tissue-specific functions. The possibility to study alternative splicing (AS) events on a genomic scale using splicing-sensitive microarrays, including the Affymetrix GeneChip Exon 1.0 ST microarray (exon array), has appeared very recently. However, the application of this ...

Prevalence and persistence of chromosomal damage and susceptible genotypes of metabolic and DNA repair genes in Chinese vinyl chloride-exposed workers

Vinyl chloride (VC) was classified as a group 1 carcinogen by IARC in 1987. Although the relationship between VC exposure and liver cancer has been established, the mechanism of VC-related carcinogenesis remains largely unknown. Previous epidemiological studies have shown that VC exposure is associated with increased genotoxicity in humans. To explore chromosomal damage and its ...

DNA Hypomethylation Induced by Drinking Water Disinfection By-Products in Mouse and Rat Kidney

Bromodichloromethane (BDCM), chloroform, dibromoacetic acid (DBA), dichloroacetic acid (DCA), and trichloroacetic acid (TCA) are chlorine disinfection by-products (DBPs) found in drinking water that have indicated renal carcinogenic and/or tumor promoting activity. We have reported that the DBPs caused DNA hypomethylation in mouse liver, which correlated with their carcinogenic and ...

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome

Background Fig pollinating wasps form obligate symbioses with their fig hosts. This mutualism arose approximately 75 million years ago. Unlike many other intimate symbioses, which involve vertical transmission of symbionts to host offspring, female fig wasps fly great distances to transfer horizontally between hosts. In contrast, male wasps are wingless and cannot disperse. ...

Imaging and characterizing influenza A virus mRNA transport in living cells

The mechanisms of influenza A virus mRNA intracellular transport are still not clearly understood. Here, we visualized the distribution and transport of influenza A virus mRNA in living cells using molecular beacon (MB) technology. Confocal-FRAP measurements determined that the transport of influenza A virus intronless mRNA, in both nucleus and cytoplasm, was energy dependent, ...

Isoflurane indirectly depresses middle latency auditory evoked potentials by action in the spinal cord in the goat

Joseph F. Antognini Xiao Wei Wang Purpose: The auditory evoked potential (AEP) has been proposed as a method to determine depth of anesthesia, as AEPs are generated in the thalamus and cerebral

Boc5, a Non-Peptidic Glucagon-Like Peptide-1 Receptor Agonist, Invokes Sustained Glycemic Control and Weight Loss in Diabetic Mice

Ming-Wei Wang 0 1 Harald H. H. W. Schmidt, Monash University, Australia 0 a Current address: Department of Bioengineering, University of California, Riverside, California, United States of America b

An Exploratory Study of the Association between KCNB1 rs1051295 and Type 2 Diabetes and Its Related Traits in Chinese Han Population

Since the KCNB1 encoding Kv2.1 channel accounts for the majority of Kv currents modulating insulin secretion by pancreatic islet beta-cells, we postulated that KCNB1 is a plausible candidate gene for genetic variation contributing to the variable compensatory secretory function of beta-cells in type-2 diabetes (T2D). We conducted two studies, a case-control study and a ...