Generation and analysis of 10 000 ESTs from the half‐smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers

Three normalized cDNA libraries were constructed, two of which were constructed from reproductive tissues ovary and testis, and the other one from pooled immune tissues including head kidney, intestine, liver and spleen. A total of 10 542 clones were sequenced generating 10 128 expressed sequence tags (ESTs). Cluster analysis indicated a total of 5808 unique sequences including 1712 contigs and 4096 singletons. A total of 4249 (73%) of the unique ESTs had significant hits to the non‐redundant protein database, 2253 of which were annotated using Gene Ontology (GO) terms. A total of 311 microsatellites (with 246 having sufficient flanking sequences for primer design) and 6294 putative SNPs were identified. These genome resources provide the material basis for future microarray development, marker validation and genetic linkage and QTL analysis.     

Detecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data

The detection of genetic segments of Identical by Descent (IBD) in Genome-Wide Association Studies has proven successful in pinpointing genetic relatedness between reportedly unrelated individuals and leveraging such regions to shortlist candidate genes. These techniques depend on high-density genotyping arrays and their effectiveness in diverse sequence data is largely unknown. Due to decreasing costs and increasing effectiveness of high throughput techniques for whole-exome sequencing, an influx of exome sequencing data has become available. Studies using exomes and IBD-detection methods within known pedigrees have shown that IBD can be useful in finding hidden genetic candidates where known relatives are available. We set out to examine the viability of using IBD-detection in whole exome sequencing data in population-wide studies. In doing so, we extend GERMLINE, a method to detect IBD from exome sequencing data by finding small slices of matching alleles between pairs of individuals and extending them into full IBD segments. This algorithm allows for efficient population-wide detection in dense data. We apply this algorithm to a cohort of Crohn''s Disease cases where whole-exome and GWAS array data is available. We confirm that GWAS-based detected segments are highly accurate and predictive of underlying shared variation. Where segments inferred from GWAS are expected to be of high accuracy, we compare exome-based detection accuracy of multiple detection strategies. We find detection accuracy to be prohibitively low in all assessments, both in terms of segment sensitivity and specificity. Even after isolating relatively long segments beyond 10cM, exome-based detection continued to offer poor specificity/sensitivity tradeoffs. We hypothesize that the variable coverage and platform biases of exome capture account for this decreased accuracy and look toward whole genome sequencing data as a higher quality source for detecting population-wide IBD.     

Peroxisome Proliferator-Activated Receptor γ Agonists Attenuate Hyperglycaemia-Induced Hyaluronan Secretion in Vascular Smooth Muscle Cells by Inhibiting PKCβ2

Changes in the composition and assembly of extracellular matrix (ECM) are the most prominent structure abnormalities of the vascular system encountered in early diabetes. Hyaluronan (HA) is a key biologically active element of ECM that plays a crucial role in vascular remodelling in atherosclerosis and restenosis following percutaneous coronary intervention. Hyperglycaemia led to significant increase in HA secretion by vascular smooth muscle cells. Hyperglycaemia also strongly induced HA synthase mRNA levels, notably HAS1–HAS3 mRNA. Remarkably, peroxisome proliferator-activated receptor (PPAR-γ) agonists pioglitazone (Pio) and rosiglitazone (Rosi), a class of anti-diabetic drugs, attenuated hyperglycaemia-induced HA secretion and reduced HAS2 mRNA expression. In vitro experiment with siRNA specific to PPAR-γ demonstrated that the attenuation of hyperglycaemia-induced HA secretion by Pio and Rosi was independent of PPAR-γ activity. Furthermore, hyperglycaemia-induced increase in HA secretion and HAS2 mRNA expression involved protein kinase Cβ2 (PKCβ2) activation, while Pio and Rosi exerted their attenuating effect on HA secretion by inhibiting PKCβ2.     

Hepatitis B Virus X Protein Sensitizes TRAIL-Induced Hepatocyte Apoptosis by Inhibiting the E3 Ubiquitin Ligase A20

Hepatitis B virus (HBV) infection causes hepatocyte death and liver damage, which may eventually lead to cirrhosis and liver cancer. Hepatitis B virus X protein (HBx) is a key antigen that is critically involved in HBV-associated liver diseases. However, the molecular basis for its pathogenesis, particularly in liver damage, has not been well defined. Herein, we report that HBx was able to enhance the susceptibility of hepatocytes to TNF-related apoptosis-inducing ligand (TRAIL)-induced apoptosis. Increased sensitivity to TRAIL was associated with HBx-induced upregulation of miR-125a, which, in turn, suppressed the expression of its putative target gene, A20 E3 ligase. Importantly, we demonstrate that the defective expression of A20 impaired the K63-linked polyubiquitination of caspase-8, which reciprocally enhanced the activation of caspase-8, the recruitment of Fas-associated death domain (FADD), and the formation of death-inducing signaling complex (DISC), thereby promoting HBx-mediated apoptotic signaling. Accordingly, antagonizing miR-125a or ectopically expressing A20 in hepatocytes abolished the pro-apoptotic effect of HBx. Conversely, the overexpression of miR-125a or knockdown of A20 mimicked HBx to enhance TRAIL susceptibility in hepatocytes. Thus, we establish, for the first time, a miR-125a/A20-initiated and caspase-8-targeted mechanism by which HBx modulates apoptotic signaling and increases hepatic susceptibility to the damaging agent, which might provide novel insight into HBV-related liver pathology.     

Helicobacter pylori-downregulated tumor necrosis factor receptor-associated protein 1 mediates apoptosis of human gastric epithelial cells

Heat shock proteins (HSPs) are crucial proteins in maintaining the homeostasis of human gastric epithelial cells. Tumor necrosis factor receptor-associated protein 1 (TRAP1), a member of the HSP90 family, has been shown to be involved in various crucial physiological processes, particularly against apoptosis. However, the regulation and function of TRAP1 in Helicobacter pylori infection is still unknown. Here, we found that TRAP1 expression was downregulated on human gastric epithelial cells during H. pylori infection by real-time polymerase chain reaction (PCR) and western blot analysis. Through virulence factors mutant H. pylori strains infection and inhibitors screening, we found that H. pylori vacuolating cytotoxin A ( vacA), but not cytotoxin-associated gene A ( cagA) protein, induced human gastric epithelial cells to downregulate TRAP1 via P38MAPK pathway by real-time PCR and western blot analysis. Furthermore, downregulation of TRAP1 with lentivirus carrying TRAP1 short hairpin RNA constructs impairs mitochondrial function, and increases apoptosis of gastric epithelial cells. The results indicate that H. pylori vacA downregulated TRAP1 is involved in the regulation of gastric epithelial cell apoptosis.     

Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy

The liver is the largest organ in the body, with many complex, essential functions, such as metabolism, deintoxication, and secretion, often regulated via post-translational modifications, especially phosphorylation. Thus, the detection of phosphoproteins and phosphorylation sites is important to comprehensively explore human liver biological function. The human Chang liver cell line is among the first derived from non-malignant tissue, and its phosphoproteome profile has never been globally analyzed. To develop the complete phosphoproteome and probe the roles of protein phosphorylation in normal human liver, we adopted a shotgun strategy based on strong cation exchange chromatograph, titanium dioxide and LC-MS/MS to isolate and identify phosphorylated proteins. Two types of MS approach, Q-TOF and IT, were used and compared to identify phosphosites from complex protein mixtures of these cells. A total of 1035 phosphorylation sites and 686 phosphorylated peptides were identified from 607 phosphoproteins. A search using the public database of PhosphoSite showed that approximately 344 phosphoproteins and 760 phosphorylation sites appeared to be novel. In addition, N-terminal phosphorylated peptides were a greater fraction of all identified phosphopeptides. With GOfact analysis, we found that most of the identified phosphoproteins are involved in regulating metabolism, consistent with the liver's role as a key metabolic organ.     

Comparative studies of LFA-1/ICAM-1 interaction by micropipette and flow chamber techniques

Interaction of lymphocyte function-associated antigen-1 (LFA-1) with intercellular adhesive molecule-1 (ICAM-1) is important in a number of cellular events, including inflammation, adhesion, transendothelial migration. The aim of this work was to study comparatively the adhesive interaction between LFA-1 and ICAM-1 by a micropipette technique and a flow chamber method, and also to explore the effects of tumor necrosis factor (TNF-alpha), phytohemagglutinin (PHA), and tetramethylpyrazine (TMP) on this interaction. The adhesion probability (Pa) between a lymphocyte cell line SKW-3 expressing LFA-1 and a red blood cell (RBC) coated with soluble ICAM-1 was approached by the micropipette technique, while the flow chamber allowed to observe the firm adhesion of SKW-3 on human umbilical vein endothelial cells (HUVECs). Experimental results show that PHA stimulation of lymphocytes resulted in significant increases in the adhesion probability (Pa) and in number of firmly adhered lymphocytes to HUVECs, but TMP treatment could significantly inhibit such increases.     

Study of correlation of se content in human hair and internal organs by INAA

The correlations of essential element Se between human hair and kidney-cortex, liver, and lung from the same subjects were investigated by instrumental neutron activation analysis, using the reaction⁷⁶Se (n, γ)^77mSe, for 24 Chinese autopsies. The concentration of Se is higher in kidney-cortex (2.04–5.36 mg/kg) than in liver (0.73–2.29), lung (0.50–1.85), and hair (0.37–1.43). It is important to know that there are significant relationships of Se concentration between hair and the other three internal organs. The correlation coefficient by linear regression analysis are 0.639, 0.570, and 0.635 for liver, lung, and kidney-cortex, respectively; and theP values are all less than 0.01 for the three tissues.     

Analysis of QTL×environment interaction for yield components and plant height in rice

 An F₂ and two equivalent F₃ populations of an indica-indica cross of rice, Tesanai 2/CB, were constructed and grown in different environments. The identification of quantitative trait loci (QTL) for yield components and plant height and an analysis of QTL×environment interaction were conducted for three trials. Interval mapping of QTL for eight traits was employed with a threshold of LOD=2 using the computer package MAPMAKER/QTL. A total of 44 QTL were detected in 18 intervals of nine chromosomes, including 3 for the number of panicles (NP), 5 for the number of filled grains (NFG), 6 for total number of spikelets (TNS), 3 for spikelet fertility (SF), 7 for 1000-grain weight (TGWT), 5 for grain weight per plant (GWT), 8 for plant height (PH) and 7 for panicle length (PL). The numbers of QTL detected in two or three trials were 1 for NP, 1 for NFG, 1 for TNS, none for SF, 4 for TGWT, 3 for GWT, 2 for PH and 5 for PL, making a total of 17. When a QTL was detected in more than one trial the direction and magnitude of its additive effect, the dominance effect and the degree of dominance were generally in good agreement. In all three trials, QTL were frequently detected for related traits in the same intervals. The directions of additive effect of QTL for related traits in a given interval were in agreement with few exceptions, no matter whether they were detected in the same trial or not. This result suggested that pleiotropism rather than close linkage of different QTL was the major reason why QTL for different traits were frequently detected in the same intervals. When gene pleiotropism was considered, 23 of the 29 QTL for yield and its components and 9 of the 15 QTL for plant stature were detected in more than one trial. This indicated that the detection of chromosomal segments harboring QTL was hardly affected by environmental factors. Received: 30 January 1997 / Accepted: 21 March 1997