Integrated computational approaches to screen gene expression data to determine key genes and therapeutic targets for type-2 diabetes mellitus

There is a rapid rise in cases of Type-2-diabetes mellitus (T2DM) globally, irrespective of the geography, ethnicity or any other variable factors. The molecular mechanisms that could cause the condition of T2DM need to be more thoroughly analysed to understand the clinical manifestations and to derive better therapeutic regimes. Tools in bioinformatics are used to trace out key gene elements and to identify the key causative gene elements and their possible therapeutic agents. Microarray datasets were retrieved from the Gene expression omnibus database and studied using R to derive different expressed gene (DEG) elements. With the comparison of the expressed genes with disease specific genes in DisGeNET, the final annotated genes were taken for analysis. Gene Ontology studies, Protein–protein interaction (PPI), Co-expression analysis, Gene-drug interactions were performed to scale down the hub genes and to identify the novelty across the genes analysed so far. In vivo and invitro analysis of key genes and the trace of interaction pathway is crucial to better understand the unique outcomes from the novel genes, forming the basis to understand the pathway that ends up causing T2DM. Afterwards, docking was executed enabling recognition of interacting residues involved in inhibition. The complex CCL5-265 and CD8A-40585 thus docked showed best results as is evident from its PCA analysis and MMGBSA calculation. There is now scope for deriving candidate drugs that could possibly detect personalized therapies for T2DM.     

Mitotic checkpoint gene expression is tuned by codon usage bias

The mitotic checkpoint (also called spindle assembly checkpoint, SAC) is a signaling pathway that safeguards proper chromosome segregation. Correct functioning of the SAC depends on adequate protein concentrations and appropriate stoichiometries between SAC proteins. Yet very little is known about the regulation of SAC gene expression. Here, we show in the fission yeast Schizosaccharomyces pombe that a combination of short mRNA half‐lives and long protein half‐lives supports stable SAC protein levels. For the SAC genes mad2 ⁺ and mad3 ⁺, their short mRNA half‐lives are caused, in part, by a high frequency of nonoptimal codons. In contrast, mad1 ⁺ mRNA has a short half‐life despite a higher frequency of optimal codons, and despite the lack of known RNA‐destabilizing motifs. Hence, different SAC genes employ different strategies of expression. We further show that Mad1 homodimers form co‐translationally, which may necessitate a certain codon usage pattern. Taken together, we propose that the codon usage of SAC genes is fine‐tuned to ensure proper SAC function. Our work shines light on gene expression features that promote spindle assembly checkpoint function and suggests that synonymous mutations may weaken the checkpoint.     

Secretory and continuous expression of Aspergillus niger glucose oxidase gene in Pichia pastoris

We proposed a yeast transformant cell incorporating the Aspergillus niger glucose oxidase gene (GOX gene), which is capable of constitutively as well as secretory expression. The GOX gene has been cloned in this study. This conclusion is based on the following: first, the ligated DNA determined by electrophoresis, was a 1489-1882bp fragment, close to the size of glucose oxidase (GOD), which is 1818bp. Secondly, the single open reading frame encoded a protein of 605 amino acids. Thirdly, secreted GOD recombinant proteins in the culture supernatants of the GOX gene transformant migrated as a single band in SDS-PAGE with an apparent molecular mass of between 75,000 and 100,000 Da, which is glycosylated GOD by the Pichia pastoris X-33 host machinery during the secretion process. Finally, the clones were cultured and secreted a protein, which possessed the GOD activity of catalyzing beta-d-glucose oxidation. With regard to the pH characteristics, the activity was more than 80% of the maximum activity in the range between pH 5 and pH 7. As for the temperature characteristics, the activity was not less than 92% of the maximum in the temperature range between 10 and 45 degrees C. The GOX gene transformant was able to maintain the GOD enzyme activity and produce recombinant GOD continuously for at least 2 weeks.     

Long-term effects of hydropower installations and associated river regulation on River Shannon eel populations: mitigation and management

The Shannon, Ireland’s largest river, is used for hydroelectricity generation since 1929. Subsequently, the Electricity Supply Board assumed responsibility for management of its eel stocks, due to the impact of the hydro-dam on recruitment to the commercial fishery. In order to negate a decline in juvenile recruitment resulting from the installation of hydroelectric facilities, management was focused on stocking lakes with elvers and fingerling eels. These were trapped at the hydropower facilities and in estuarine tributaries during their up-stream migrations. Due to the decline of natural recruitment in more recent times, attempts have also been made to develop an estuarine glass eel fishery. Stock levels are then monitored through annual surveys of the population trends of juvenile (glass eel, elver), growing phase (yellow eel) and downstream migrating pre-spawners (silver eels). Survey results and fishery management programmes are reviewed in this article. In addition to the long-term effects the hydroelectric facilities have had on the stock levels, there is also an annual effect on the migratory patterns of downstream migratory silver eels. In the lower reaches of the river system flow rates are regulated by the hydroelectric stations. We review previous work that had highlighted the importance of flow in determining the timing of the silver eels migrations, and assess the relationship between flow and migration in more detail through the use of hydroacoustic and telemetric studies. Current research on seaward migrating silver eel populations, suggests that spawner escapement rates can most effectively be increased by trapping migrating eels at fishing weirs located up-stream of the power station and transporting them towards the estuary. Guest editors: R. L. Welcomme & G. Marmulla Hydropower, Flood Control and Water Abstraction: Implications for Fish and Fisheries     

Low seed availability may limit recruitment in grazed Atriplex vesicaria and contribute to its local extinction

Poor recruitment in Atriplex vesicaria Hewd exBenth (bladder saltbush) under sheep grazing in the chenopodshrublands of southern Australia contributes to a decline in the shrub'spopulation growth rate. This may lead to local extinction of the species overlarge areas around watering points. This study investigated whether low seedavailability may contribute to poor recruitment. It examined the incidence offlowering and seed bank size at sites distributed across a large grazedpaddock,and examined the longevity of seed in the soil. Grazing by sheep reduced theincidence of flowering and input to the seed bank. The proportion of shrubswithflowers increased with distance from water, showing the characteristicpiosphereresponse. Shrubs on grazed sites closer to water experienced extended periodswhen they failed to flower or flowered poorly. The seed bank was negligible atthree of the sites within 1650 m of water for all three years ofsampling. In contrast, the seed bank at the most distant site sampled (2800m from water) was small in 1990 (37 ± 5.1seeds/m²) but in 1991 and 1992 seed numberswere substantial (626 ± 315.2 seeds/m²and 318 ± 169.0, respectively). Soil seed was short-lived inthis study, with only 34% and 17% of the original seed remainingas viable ungerminated seed after 12 months for the under-canopy andexposed treatments respectively. Whilst recruitment may also be limited byaltered soil conditions due to grazing and trampling and the availability ofsafe sites, the results of this study suggest that low seed availability may bean important factor contributing to poor recruitment and may limit the abilityof the population to recover from the loss of established plants. Management ofgrazing must take into account the need for A. vesicariapopulations to flower and set seed on a regular basis.     

Representations of specific acoustic patterns in the auditory cortex and hippocampus

Previous behavioural studies have shown that repeated presentation of a randomly chosen acoustic pattern leads to the unsupervised learning of some of its specific acoustic features. The objective of our study was to determine the neural substrate for the representation of freshly learnt acoustic patterns. Subjects first performed a behavioural task that resulted in the incidental learning of three different noise-like acoustic patterns. During subsequent high-resolution functional magnetic resonance imaging scanning, subjects were then exposed again to these three learnt patterns and to others that had not been learned. Multi-voxel pattern analysis was used to test if the learnt acoustic patterns could be ‘decoded’ from the patterns of activity in the auditory cortex and medial temporal lobe. We found that activity in planum temporale and the hippocampus reliably distinguished between the learnt acoustic patterns. Our results demonstrate that these structures are involved in the neural representation of specific acoustic patterns after they have been learnt.     

Transcriptional and biochemical signatures of divergence in natural populations of two species of New Zealand alpine Pachycladon

New Zealand is diverse in alpine and subalpine environments, a consequence of Late Tertiary tectonic and climatic change. However, few studies have sought to evaluate the importance of these environments as abiotic drivers in the diversification of plant species. Of particular interest is the Late Tertiary radiation of Pachycladon, an endemic New Zealand genus of alpine cress. Here we report observations on genome-wide levels of differential expression measured in the habitats of two closely related species of Pachycladon with distinct altitudinal preferences. Using Arabidopsis microarrays, we have identified 310 predominantly hormone- and stress-response genes up-regulated in Pachycladon fastigiata and 324 genes up-regulated in Pachycladon enysii. Expression patterns for glucosinolate biosynthesis and hydrolysis genes (MAM1, MAM-I, MAM-D, AOP2, ESP, ESM1) as well as flavonoid biosynthesis genes (F3'H, FLS, FAH1) were found to be species specific. Predicted differences in flavonoid contents were partly confirmed by high performance liquid chromatography analysis. Differences in glucosinolate profiles and glucosinolate hydrolysis products obtained by high performance liquid chromatography and gas chromatography-mass spectrometry analysis, respectively, also supported inferences from expression analyses. Five glucosinolate chemotypes were matched to known Arabidopsis ecotypes, and the potential adaptive significance of these chemotypes has been discussed. Our findings, in contrast to expectations for evolution of the New Zealand flora, suggest that biotic drivers, such as plant-herbivore interactions, are likely to be as important as abiotic drivers in the diversification of Pachycladon.     

TRPV5 and TRPV6 calcium channels in human T cells

The recent cloning of the special calcium channels TRPV5 and TRPV6 (transient receptor potential vanilloid channels) has provided a molecular basis for studying previously unidentified calcium influx channels in electrically nonexcitable cells. In the present work using RT-PCR, we obtained the endogenous expression of mRNAs of genes trpv5 and trpv6 in lymphoblast leukemia Jurkat cells and in normal human T lymphocytes. Additionally, by immunoblotting, the presence of the channel-forming TRPV5 proteins has been shown both in the total lysate and in crude membrane fractions from Jurkat cells and normal T lymphocytes. The use of immunoprecipitation revealed TRPV6 proteins in Jurkat cells, whereas in normal T lymphocytes, this protein was not detected. The expression pattern and the selective Ca²⁺ permeation properties of TRPV5 and TRPV6 channels indicate the important role of these channels in Ca²⁺ homeostasis, as well as most likely in malignant transformation of blood cells.