Gene expression profile in immunologically injured liver cell of mice

To study the gene expression profiles between immunologically injured liver cell and normal liver cell of mice and to screen on a large scale the differentially expressed genes associated with the formation of liver injury, the experimental mice were randomly divided into the normal group for controlling and the immunologically liver-injured group induced by BCG and LPS. The liver mRNA of the two groups were extracted respectively and reversely-transcribed to cDNA with the incorporation of different fluorescence (Cy3, Cy5) labeled dUTP as the hybridization probes. The mixed probes were hybridized to the cDNA microarray chips. The fluorescent signal results were acquired by scanner ScanArray 4000 and analyzed with software GenePix Pro 3.0. Among the 14112 target genes, 293 genes were found to be significantly differentially expressed, in which 188 genes were up-regulated and 105 genes were down-regulated. Based on the analysis of biological functions of those differentially expressed genes, it was indicated that the occurrence and development of mouse liver damage induced by BCG and LPS were highly correlated with the processes of immune reactions, cell synthesis, metabolism, apoptosis and transportation in liver cell, which might be quite important for elucidating the regulatory network of gene expression associated with the liver damage, also important for finally discovering the pathogenic mechanisms of immunological liver damage.     

A single residue mutation of 5-enoylpyruvylshikimate-3-phosphate synthase in Pseudomonas stutzeri enhances resistance to the herbicide glyphosate

A novel class II 5-enoylpyruvylshikimate-3-phosphate synthase (EPSPS) was identified from Pseudomonas stutzeri A1501 by complementation of an Escherichia coli auxotrophic aroA mutant. The single amino acid substitution of serine (Ser) for asparagine (Asn)-130 of the A1501 EPSPS enhanced resistance to 200 mM glyphosate. The mutated EPSPS had a 2.5-fold increase for IC(50) [glyphosate] value, a 2-fold increase for K (i) [glyphosate] value, but a K (m) [PEP] value similar to that of wild type. The effect of the single residue mutation on glyphosate resistance was also analyzed using a computer-based three-dimensional model.     

Phylogeny of Snub-Nosed Monkeys Inferred from Mitochondrial DNA,Cytochrome B,and 12S rRNA Sequences

Snub-nosed monkeys (Rhinopithecus spp.) are confined to isolated mountainous regions in China and North Vietnam. Their systematic classification and phylogenetic relationship has been controversial. The structures of mitochondrial DNA cytochrome b and 12S rRNA show that the 4 species of Rhinopithecus are quite different from other colobines. It is reasonable to regard them as an independent genus, as determined by external features, morphometric characters and behavior. However, whether or not there should be a subdivision between the Vietnamese and Chinese species at the subgeneric level remains to be clarified; more evidence from a large range of Asian colobine species is needed. The Guizhou species, Rhinopithecus brelichi, is a valid species, which is more closely related to Pygathrix than the other species ( R. roxellana, R. bieti and R. avunculus) are. Results also indicate that 3 species—Rhinopithecus roxellana, R. bieti and R. avunculus—might have diverged from R. brelichi, but the phylogenetic relationship of R. avunculus is not clear.     

Characterization of Recombinant Human Cardiac KCNQ1/KCNE1 Channels (I Ks) Stably Expressed in HEK 293 Cells

The present study was designed to characterize pharmacological, biophysical and electrophysiological properties of the recombinant human cardiac I _Ks (KCNQ1/KCNE1) channels at physiological temperature. Human cardiac KCNQ1 and KCNE1 genes were cotransfected into HEK 293 cells, and a cell clone stably expressing both genes was selected. Membrane currents were recorded using a perforated patch-clamp technique. The typical I _Ks was slowly activated upon depolarization voltages in HEK 293 cells stably expressing human cardiac KCNQ1 and KCNE1 genes, and the current was inhibited by I _Ks blockers HMR 1556 and chromanol 293B, with 50% inhibitory concentrations (IC₅₀s) of 83.8 nM and 9.2 μM, respectively. I _Ks showed a significant temperature-dependent increase in its magnitude upon elevating bath temperature to 36°C from room temperature (21°C). The current was upregulated by the β-adrenoceptor agonist isoproterenol, and the effect was reversed by H89. In addition, I _Ks was inhibited by Ba²⁺ in a concentration-dependent manner (IC₅₀ = 1.4 mM). Action potential clamp revealed a “bell-shaped” time course of I _Ks during the action potential, and maximal peak current was seen at the plateau of the action potential. A significant use- and frequency-dependent increase of I _Ks was observed during a train of action potential clamp. These results indicate that the recombinant human cardiac I _Ks stably expressed in HEK 293 cells is similar to native I _Ks in drug sensitivity and regulated by Ba²⁺ and β-adrenoceptor via the cyclic adenosine monophosphate/protein kinase A pathway. Importantly, the current exhibits significant temperature dependence, a bell-shaped time course during action potential and prominent use- or frequency-dependent accumulation during a train of action potentials.     

Pentoxifylline attenuates cardiac dysfunction and reduces TNF-alpha level in ischemic-reperfused heart

Although pentoxifylline (PTXF), a phosphodiesterase inhibitor, has been reported to exert beneficial effects in cardiac bypass surgery, its effect and mechanisms against ischemia-reperfusion (I/R) injury in heart are poorly understood. Because I/R is known to increase the level of tumor necrosis factor (TNF)-alpha in myocardium and PTXF has been shown to depress the production of TNF-alpha in failing heart, this study examined the hypothesis that PTXF may attenuate cardiac dysfunction and reduce TNF-alpha content in I/R heart. For this purpose, isolated rat hearts were subjected to global ischemia for 30 min followed by reperfusion for 2-30 min. Although cardiac dysfunction due to ischemia was not affected, the recovery of heart function upon reperfusion was markedly improved by PTXF treatment. This cardioprotective effect of PTXF was dose dependent; maximal effect was seen at a concentration of 125 microM. TNF-alpha, nuclear factor-kappaB (NF-kappaB), and phosphorylated NF-kappaB contents were decreased in ischemic heart but were markedly increased within 2 min of starting reperfusion. The ratio of cytosolic-to-homogenate NF-kappaB was decreased, whereas the ratio of particulate-to-homogenate NF-kappaB was increased in I/R hearts. These changes in TNF-alpha and NF-kappaB protein contents as well as in NF-kappaB redistribution due to I/R were significantly attenuated by PTXF treatment. The results of this study indicate that the cardioprotective effects of PTXF against I/R injury may be due to reductions in the activation of NF-kappaB and the production of TNF-alpha content.     

High-throughput sex identification by melting curve analysis in blue-breasted quail and chicken

The objective was to develop a high-throughput method of identifying sex in both Coturnix chinensis and Gallus gallus, which would be useful for biomedical research and hatcheries. Because chromo-helicase-DNA binding protein (CHD)-based Griffiths P2/P8 primers do not produce polymerase chain reaction (PCR) products with distinguishable sex-specific curves in melting curve analysis (MCA), these primers are unsuitable for high throughput application in either species. Conserved regions were identified by basic local alignment search tool (BLAST) analyses of cloned CHD-Z and CHD-W genes of C. chinensis. Based on sequence alignment, a female-specific CHD-W primer (W-cot-F1) and a female/male (or CHD-W/CHD-Z)-common primer (ZW-cot-F1) were redesigned for use in combination with the Griffiths P2 primer for MCA-based PCR reaction. In C. chinensis and G. gallus, W-cot-F1/P2 and ZW-cot-F1/P2 had amplicon lengths of 315/318 and 114 base pairs and melting temperatures (Tm) of approximately 79.5 °C to 80 °C and approximately 78.5 °C to 79°C, respectively. Thus, MCA distinguished sex based on two distinct Tm peaks in females versus only one Tm peak in males. The MCA-based real-time PCR combined with the proposed primer redesign provided a high-throughput method of identifying sex in C. chinensis and G. gallus.     

dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data

MOTIVATION: Oligonucleotide microarrays allow genotyping of thousands of single-nucleotide polymorphisms (SNPs) in parallel. Recently, this technology has been applied to loss-of-heterozygosity (LOH) analysis of paired normal and tumor samples. However, methods and software for analyzing such data are not fully developed. RESULT: Here, we report automated methods for pooling SNP array replicates to make LOH calls, visualizing SNP and LOH data along chromosomes in the context of genes and cytobands, making statistical inference to identify shared LOH regions, clustering samples based on LOH profiles and correlating the clustering results to clinical variables. Application of these methods to prostate and breast cancer datasets generates biologically important results. AVAILABILITY: The software module dChipSNP implementing these methods is available at http://biosun1.harvard.edu/complab/dchip/snp/ SUPPLEMENTARY INFORMATION: The breast cancer data are provided by Andrea L. Richardson, Zhigang C. Wang and James D. Iglehart.     

Apoptosis is required during early stages of tail regeneration in Xenopus laevis

The Xenopus tadpole is able to regenerate its tail, including skin, muscle, notochord, spinal cord and neurons and blood vessels. This process requires rapid tissue growth and morphogenesis. Here we show that a focus of apoptotic cells appears in the regeneration bud within 12 h of amputation. Surprisingly, when caspase-3 activity is specifically inhibited, regeneration is abolished. This is true of tails both before and after the refractory period. Programmed cell death is only required during the first 24 h after amputation, as later inhibition has no effect on regeneration. Inhibition of caspase-dependent apoptosis results in a failure to induce proliferation in the growth zone, a mispatterning of axons in the regenerate, and the appearance of ectopic otoliths in the neural tube, in the context of otherwise normal continued development of the larva. Larvae amputated during the refractory stage exhibit a much broader domain of caspase-3-positive cells, suggesting a window for the amount of apoptosis that is compatible with normal regeneration. These data reveal novel roles for apoptosis in development and indicate that a degree of apoptosis is an early and obligate component of normal tail regeneration, suggesting the possibility of the existence of endogenous inhibitory cells that must be destroyed by programmed cell death for regeneration to occur.