iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

Translation is a key process for gene expression. Timely identification of the translation initiation site (TIS) is very important for conducting in-depth genome analysis. With the avalanche of genome sequences generated in the postgenomic age, it is highly desirable to develop automated methods for rapidly and effectively identifying TIS. Although some computational methods were proposed in this regard, none of them considered the global or long-range sequence-order effects of DNA, and hence their prediction quality was limited. To count this kind of effects, a new predictor, called “iTIS-PseTNC,” was developed by incorporating the physicochemical properties into the pseudo trinucleotide composition, quite similar to the PseAAC (pseudo amino acid composition) approach widely used in computational proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that the overall success rate achieved by the new predictor in identifying TIS locations was over 97%. As a web server, iTIS-PseTNC is freely accessible at http://lin.uestc.edu.cn/server/iTIS-PseTNC. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results without the need to go through detailed mathematical equations, which are presented in this paper just for the integrity of the new prection method.     

TargetCompare: A web interface to compare simultaneous miRNAs targets

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue.

Availability

http://lghm.ufpa.br/targetcompare     

施用缓释尿素对潮棕壤线虫营养类群产生的影响

本试验在中国科学院沈阳生态实验站(41°31′N,123°24′E)进行。该站位于下辽河平原,属于暖温带半湿润大陆性气候,年平均气温7～8℃,年降雨量650～700mm,≥10℃活动积温3300～3400℃,无霜期147～164d。供试土壤为潮棕壤,全氮0.69g·kg^-1,有机质15.52g·kg^-1,全磷0.67g·kg^-1,速效磷11.20mg·kg^-1,速效钾90.10mg·kg^-1,pH 6.7。     

Association study of AGER gene polymorphism and hypertension in Han Chinese population

Background

Advanced glycation end products (AGEs) are produced by non-enzymatic glycation or glycoxidation of proteins, lipids and nucleic acids. The bond of AGEs and the receptor of AGE (AGER) in a pro-oxidant environment could induce immune and inflammation reaction involved in progress of microvascular disease. Accumulated evidence warrant further study on AGE–AGER pathway and genetic susceptibility to hypertension (HT).

Methods

We designed a two-stage association study to evaluate the association of AGER polymorphism and HT. In stage 1, seven tagSNPs were tested in 524 cases and 531 controls and the significant SNPs (P < 0.05) would enter into stage 2 including 807 cases and 869 controls. Furthermore, joint analysis was performed for all 2731 subjects including 1331 cases and 1400 controls, and meta-analysis was applied to evaluate combined estimations from the subgroups of stage 1 and stage 2.

Results

In stage 1, rs204994 had significant association with HT (P < 0.05) and enter stage 2. Neither joint analysis nor meta-analysis found statistical association of rs204994 with HT after adjusted for the covariates in the whole population. However, further stratification analysis found that rs204994 was significantly associated with HT in < 50 years and ≥ 50 years groups, ORs (95%CI) of dominant model were 1.623 (1.054–2.500) and 0.721 (0.546–0.952) respectively. No significant correlation was found between blood pressure and the polymorphisms of rs204994.

Conclusions

Our data suggests that age might modulate the genetic effects of variation of rs204994 in AGER on HT and further replications in other populations and functional studies should be warranted.     

Preparation of lipid-free tissue extracts for chromatographic determination of thyroid hormones and metabolites

We have developed a new method of preparing tissues for analysis of thyroid hormones and metabolites which eliminates troublesome lipids and proteins. Frozen tissue is homogenized by grinding with dry ice in a Waring blender, and the moist powder obtained is extracted with chloroform:methanol (2:1). In a modification of the Folch procedure for the total separation of lipids, the filtered extracts then are partitioned into polar and nonpolar layers by the addition of 0.05% aqueous calcium chloride. The upper phase contains the iodocompounds of interest as well as all salts and small polar molecules. The lipids remain dissolved in the lower phase after it is back-extracted with pure upper phase. The combined upper or aqueous methanol layers are lyophilized and the residue is taken up in methanol to yield a concentrated solution ready for analysis of iodocompounds. The greater clarity of the extract permits application of larger samples for two-dimensional paper chromatography than has been customary. For gradient analysis by reverse-phase ion-pair high-performance liquid chromatography (HPLC), the nitrogen-evaporated methanol extract is dissolved in the initial mobile phase, 0.1% H₃PO₄, for injection onto the column. Using these methods we have achieved the first reported separation of ¹²⁵I-labeled tissue iodothyronine metabolites by HPLC. The new method of extraction is of general applicability to any biological sample which might be analyzed in thyroid hormone metabolism research.     

Predator perception of detritus and eggsac decorations spun by orb-web spiders Cyclosa octotuberculata: Do they function to camouflage the sniders?

Camouflage is one of the most widespread and powerful strategies that animals use to make detection/recognition more difficult. Many orb-web spiders of the genus Cyclosa add prey remains, plant debris, moults, and/or eggsacs to their webs called web decorations. Web decorations resembling spider body colour pattern have been considered to camouflage the spider from predators. While this camouflage is obvious from a human's perspective, it has rarely been investigated from a predator's perspective. In this study, we tested the visibility of web decorations by calculating chromatic and achromatic contrasts of detritus and eggsac decorations built by Cyclosa octotuberculata, against four different backgrounds viewed by both bird (e.g., blue tits) and hymenopteran (e.g. Wasps) predators. We showed that both juvenile and adult spiders on webs with detritus or egg-sac deco-rations were undetectable by both hymenopteran and bird predators over short and long distances. Our results thus suggest that decorating webs with detritus or eggsacs by C. Octotuberculata may camouflage the spiders from both hymenopteran and bird predators in their common habitats.     

Taxonomic identification of Amazonian tree crowns from aerial photography

Question: To what extent can aerial photography be used for taxonomic identification of Amazonian tree crowns? Objective: To investigate whether a combination of dichotomous keys and a web‐based interface is a suitable approach to identify tree crowns. Location: The fieldwork was conducted at Tiputini Biodiversity Station located in the Amazon, eastern Ecuador. Methods: High‐resolution imagery was taken from an airplane flying at a low altitude (600 m) above the ground. Imagery of the observable upper layer of the tree crowns was used for the analysis. Dichotomous identification keys for different types of crowns were produced and tested. The identification keys were designed to be web‐based interactive, using Google Earth as the main online platform. The taxa analysed were Iriartea, Astrocaryum, Inga, Parkia, Cecropia, Pourouma, Guarea, Otoba, Lauraceae and Pouteria. Results: This paper demonstrates that a combination of photo‐imagery, dichotomous keys and a web‐based interface can be useful for the taxonomic identification of Amazonian trees based on their crown characteristics. The keys tested with an overall identification accuracy of over 50% for five of the ten taxa with three of them showing accuracy greater than 70% (Iriartea, Astrocaryum and Cecropia). Conclusions: The application of dichotomous keys and a web‐based interface provides a new methodological approach for taxonomic identification of various Amazonian tree crowns. Overall, the study showed that crowns with a medium‐rough texture are less reliably identified than crowns with smoother or well‐defined surfaces.     

The role of ribose-binding protein in transport and chemotaxis in Escherichia coli K12.

The ribose-binding protein of Escherichia coli [Willis, R. C., and Furlong, C. E. (1974) J. Biol. Chem.249, 6926–6929] has been shown to be a required common receptor component for high-affinity ribose transport and for chemotaxis toward this attractant. Mutants devoid of the ribose-binding protein are missing high-affinity ribose transport and do not respond chemotactically to this sugar, whereas the response to other attractants is normal. Eight independently isolated ribose-positive revertant strains regained the binding protein, high-affinity ribose transport, and ribose chemotaxis. One revertant which grows slowly on ribose as a sole carbon source did not regain the binding protein, high-affinity transport, or ribose chemotaxis.     

The aggregating behaviour of <Emphasis Type="Italic">Argiope radon</Emphasis>, with special reference to web decorations

The existence of aggregations in taxa that are normally solitary poses questions regarding the costs and benefits of group living. Most orb-web spiders are solitary and are aggressive to conspecifics, but a few species aggregate in large numbers. These spiders benefit by enhancing the prey interception potential, but also suffer costs of increased predation and parasitism. In this study, we report on the natural history characteristics of the orb-web spider, Argiope radon, which not only lives in aggregations but also builds silk decorations. Our results show that A. radon aggregates facultatively and that the main benefit of aggregation that we could identify is enhanced mating potential. We also show that decorations built by A. radon are highly visible to both model prey and predator, and suggest that solitary individuals with longer and more frequent decorations may offset the foraging advantage of being in aggregations.