TsDAF-21/Hsp90 is expressed in all examined stages of Trichinella spiralis

Trichinella is an important parasitic nematode of animals worldwide. Heat shock proteins are ubiquitous in nature and allow organisms to quickly respond to environmental stress. A portion of the Tsdaf-21 gene, a Caenorhabditis elegans daf-21 homologue encoding heat-shock protein 90 (Hsp90) was cloned from Trichinella spiralis. The partial nucleotide sequence resided near the 5′-end of the gene and encoded a polypeptide of 254 amino acid residues harboring a HATPase-c superfamily domain and Hsp90 protein domain. Phylogenetic analysis revealed that Tsdaf-21 is highly conserved and formed a monophyletic clade with other nematodes. The partial Tsdaf-21 transcript was subcloned and expressed for antibody production. Results using PCR primers specific for the Tsdaf-21 transcript, and mouse polyclonal antisera specific for the recombinant protein showed that both the RNA transcript and the corresponding protein were ubiquitously and consistently expressed in newborn larvae, muscle larvae and both male and female adult worms in the absence of any external stress or stimulation

FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium

<p>Abstract</p> <p>Background</p> <p>Human genome contains millions of common single nucleotide polymorphisms (SNPs) and these SNPs play an important role in understanding the association between genetic variations and human diseases. Many SNPs show correlated genotypes, or linkage disequilibrium (LD), thus it is not necessary to genotype all SNPs for association study. Many algorithms have been developed to find a small subset of SNPs called tag SNPs that are sufficient to infer all the other SNPs. Algorithms based on the <it>r</it>²LD statistic have gained popularity because <it>r</it>²is directly related to statistical power to detect disease associations. Most of existing <it>r</it>²based algorithms use pairwise LD. Recent studies show that multi-marker LD can help further reduce the number of tag SNPs. However, existing tag SNP selection algorithms based on multi-marker LD are both time-consuming and memory-consuming. They cannot work on chromosomes containing more than 100 k SNPs using length-3 tagging rules.</p> <p>Results</p> <p>We propose an efficient algorithm called FastTagger to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption. Our experiment results show that FastTagger is several times faster than existing multi-marker based tag SNP selection algorithms, and it consumes much less memory at the same time. As a result, FastTagger can work on chromosomes containing more than 100 k SNPs using length-3 tagging rules.</p> <p>FastTagger also produces smaller sets of tag SNPs than existing multi-marker based algorithms, and the reduction ratio ranges from 3%-9% when length-3 tagging rules are used. The generated tagging rules can also be used for genotype imputation. We studied the prediction accuracy of individual rules, and the average accuracy is above 96% when <it>r</it>²≥ 0.9.</p> <p>Conclusions</p> <p>Generating multi-marker tagging rules is a computation intensive task, and it is the bottleneck of existing multi-marker based tag SNP selection methods. FastTagger is a practical and scalable algorithm to solve this problem.</p

TsDAF-21/Hsp90 is expressed in all examined stages of Trichinella spiralis

Trichinella is an important parasitic nematode of animals worldwide. Heat shock proteins are ubiquitous in nature and allow organisms to quickly respond to environmental stress. A portion of the Tsdaf-21 gene, a Caenorhabditis elegans daf-21 homologue encoding heat-shock protein 90 (Hsp90) was cloned from Trichinella spiralis. The partial nucleotide sequence resided near the 5′-end of the gene and encoded a polypeptide of 254 amino acid residues harboring a HATPase-c superfamily domain and Hsp90 protein domain. Phylogenetic analysis revealed that Tsdaf-21 is highly conserved and formed a monophyletic clade with other nematodes. The partial Tsdaf-21 transcript was subcloned and expressed for antibody production. Results using PCR primers specific for the Tsdaf-21 transcript, and mouse polyclonal antisera specific for the recombinant protein showed that both the RNA transcript and the corresponding protein were ubiquitously and consistently expressed in newborn larvae, muscle larvae and both male and female adult worms in the absence of any external stress or stimulation

Super resolution DOA estimation with incomplete single snapshot data via matrix completion and compress sensing

A method of super resolution DOA estimation with incomplete single snapshot data via matrix completion (MC) and compress sensing (CS) is presented. First, the incomplete single snapshot data is reshaped into a low-rank Hankel matrix form and the complete data can be reconstructed through matrix completion. Then, super resolution DOA estimation can be got through CS algorithm using these constructed complete data. Numerical simulations demonstrate that this method can get high accuracy DOA estimation with less number of array elements

Epigenetic Silencing of the MLH1 Promoter in Relation to the Development of Gastric Cancer and its use as a Biomarker for Patients with Microsatellite Instability: a Systematic Analysis

Background/Aims: Human mutL homolog 1 (MLH1) promoter methylation was reported in gastric cancer (GC). This study determined the clinicopathological, prognostic, and diagnostic effects of MLH1 promoter methylation in GC. Methods: The combined odds ratio (OR) or hazard ratio (HR) and their corresponding 95% confidence intervals (95% CI) were calculated. The pooled sensitivity, specificity, and area under the curve (AUC) were analyzed. Results: A total of 4654 GC patients and 3669 non-malignant controls were identified in this systematic analysis. MLH1 promoter methylation was significantly higher in GC samples than in gastric adenomas, chronic gastritis, adjacent tissues, normal gastric mucosa, and normal healthy blood samples, but it exhibited a similar frequency in GC vs. intestinal metaplasia and dysplasia samples. MLH1 promoter methylation correlated with age and microsatellite instability (MSI), but it was not associated with gender, H. pylori infection, smoking, drinking behaviors, pathological histology, tumor differentiation, clinical stage, lymph node status, distant metastasis, or overall survival of GC. MLH1 promoter methylation exhibited a poor sensitivity value (&#x3c; 0.5) in patients with GC compared with adjacent tissues, gastric adenomas, chronic gastritis, normal gastric mucosa, and normal healthy blood samples. The pooled sensitivity, specificity, and AUC of MLH1 promoter methylation in GC with MSI vs. GC with microsatellite stability (MSS) samples were 0.64, 0.96, and 0.90, respectively. Conclusions: Our results suggest that the detection of MLH1 promoter methylation may be a potential prognostic biomarker for GC patients with MSI

Expression and functional characterization of a Rho-family small GTPase CDC42 from Trichinella spiralis

A full-length cDNA encoding a Rho-family small GTPase gene cdc42 of Trichinella spiralis was expressed in E. coli. The recombinant protein of TsCDC42 was purified and used to raise the polyclonal antibodies. The expression of TsCDC42 in different stages of parasite was investigated. The western blot showed that TsCDC42 was expressed in all stages of T. spiralis, including newborn larvae, muscle larvae and adult worms. The immuno-localization revealed that TsCDC42 was ubiquitously distributed in the newborn larvae, muscle larvae and adult worm. Cross-species RNAi was done by knockdown Tscdc42 RNAi in C. elegans. The results revealed that endogenous expression level of CDC42 was decreased by knockdown Tscdc42 RNAi in C. elegans, and this knockdown reduced the progeny of C. elegans. It suggested that Tscdc42 might play the same roles in the early development of T. spiralis.Xiamen Science Technology [3502Z20071077]; China National Nature Science Foundation [30972181]; Xiamen Universit

Structure Characterization and Otoprotective Effects of a New Endophytic Exopolysaccharide from Saffron

Saffron, a kind of rare medicinal herb with antioxidant, antitumor, and anti-inflammatory activities, is the dry stigma of Crocus sativus L. A new water-soluble endophytic exopolysaccharide (EPS-2) was isolated from saffron by anion exchange chromatography and gel filtration. The chemical structure was characterized by FT-IR, GC-MS, and 1D and 2D-NMR spectra, indicating that EPS-2 has a main backbone of (1&#8594;2)-linked &#945;-d-Manp, (1&#8594;2, 4)-linked &#945;-d-Manp, (1&#8594;4)-linked &#945;-d-Xylp, (1&#8594;2, 3, 5)-linked &#946;-d-Araf, (1&#8594;6)- linked &#945;-d-Glcp with &#945;-d-Glcp-(1&#8594; and &#945;-d-Galp-(1&#8594; as sidegroups. Furthermore, EPS-2 significantly attenuated gentamicin-induced cell damage in cultured HEI-OC1 cells and increased cell survival in zebrafish model. The results suggested that EPS-2 could protect cochlear hair cells from ototoxicity exposure. This study could provide new insights for studies on the pharmacological mechanisms of endophytic exopolysaccharides from saffron as otoprotective agent

The Spatially Separated Polarization Sensitive FDA-MIMO Radar: A New Antenna Structure for Unambiguous Parameter Estimation

Joint DOA-range-polarization estimation with a novel radar system, i.e., spatially separated polarization sensitive random frequency diverse array based on multiple-input multiple-output (SS-PSRFDA-MIMO) radar, is discussed. The proposed array can obtain not only unambiguous range estimation but also polarization parameter estimation. Firstly, the signal model of SS-PSRFDA-MIMO radar is constructed. Secondly, dimension reduction multiple signal classification (DR-MUSIC) algorithm is extended to parameter estimation with the proposed array. Last, simulations demonstrate the proposed algorithm is effective to estimate parameter, and the performance of proposed array is better than that of polarization sensitive frequency diverse array based on MIMO radar. It is worth mentioning that the Cramér–Rao lower bound (CRLB) of range estimation with the proposed array is much lower than that of PSFDA-MIMO radar

TsDAF-21/Hsp90 is expressed in all examined stages of Trichinella spiralis

Conference Name:13th International Conference on Trichinellosis. Conference Address: Changchun, PEOPLES R CHINA. Time:AUG 01-06, 2011.Natural Science Foundation of China [30972181]; Xiamen Science Technology program [3502Z20061098]Trichinella is an important parasitic nematode of animals worldwide. Heat shock proteins are ubiquitous in nature and allow organisms to quickly respond to environmental stress. A portion of the Tsdaf-21 gene, a Caenorhabditis elegans daf-21 homologue encoding heat-shock protein 90 (Hsp90) was cloned from Trichinella spiralis. The partial nucleotide sequence resided near the 5'-end of the gene and encoded a polypeptide of 254 amino acid residues harboring a HATPase-c superfamily domain and Hsp90 protein domain. Phylogenetic analysis revealed that Tsdaf-21 is highly conserved and formed a monophyletic clade with other nematodes. The partial Tsdaf-21 transcript was subcloned and expressed for antibody production. Results using PCR primers specific for the Tsdaf-21 transcript, and mouse polyclonal antisera specific for the recombinant protein showed that both the RNA transcript and the corresponding protein were ubiquitously and consistently expressed in newborn larvae, muscle larvae and both male and female adult worms in the absence of any external stress or stimulation. (C) 2013 Elsevier B.V. All rights reserved