A new tool for prioritization of sequence variants from whole exome sequencing data

Background

Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them.

Results

We designed a novel method for the filtration of WES data called TAPER? (Tool for Automated selection and Prioritization for Efficient Retrieval of sequence variants).

Conclusions

TAPER? implements a set of logical steps by which to prioritize candidate variants that could be associated with disease and this is aimed for implementation in biomedical laboratories with limited bioinformatics capacity. TAPER? is free, can be setup on a Windows operating system (from Windows 7 and above) and does not require any programming knowledge. In summary, we have developed a freely available tool that simplifies variant prioritization from WES data in order to facilitate discovery of disease-causing genes.

     

Combinatorial expression patterns of individual TLE proteins during cell determination and differentiation suggest non-redundant functions for mammalian homologs of Drosophila Groucho

The Drosophila protein Groucho is involved in the regulation of cell-determination events during insect neurogenesis and segmentation. A group of mammalian proteins, referred to as transducin-like Enhancer of split (TLE) 1 through 4, share with Groucho identical structures and molecular properties. The aim was to determine whether individual TLE proteins participate in the regulation of cell determination in mammals like their Drosophila counterpart. It is here reported that TLE family members are expressed in combinatorial ways during the in vitro differentiation of mouse P19 embryonic carcinoma cells (a model for neural determination) and rat CFK2 cells (a model for chondrocytic determination). TLE1 is up-regulated and TLE2 and TLE4 are down-regulated to different extents during early stages of differentiation. In contrast, later stages correlate with up-regulation of TLE2 and TLE4, and decreased expression of TLE1. Individual TLE proteins are also expressed in combinatorial as well as complementary patterns during the development of the cerebral cortex and spinal cord of mouse embryos. In particular, TLE1 is robustly expressed in both neural progenitor cells and postmitotic neurons of the outer layers of the cortical plate, whereas TLE4 expression marks preferentially postmitotic neurons of the inner layers. Taken together, these results strongly suggest non-redundant roles for individual TLE proteins during both cell-determination and cell-differentiation events.     

How Physical Disturbance and Nitrogen Addition Affect the Soil Carbon Decomposition?

The decomposition of soil organic carbon (SOC) plays a critical role in regulating atmospheric CO₂ concentrations and climate dynamics. However, the mechanisms and factors controlling SOC decomposition are still not fully understood. Here, we conducted a 60 days incubation experiment to test the effects of physical disturbance and nitrogen (N) addition on SOC decomposition. N addition increased the concentration of NO₃^- by 51% in the soil, but had little effect on the concentration of NH₄⁺. N addition inhibited SOC decomposition, but such an effect differed between disturbed and undisturbed soils. In disturbed and undisturbed soils, application of N decreased SOC decomposition by 37% and 15%, respectively. One possible explanation is that extra N input suppressed microbial N mining and/or increased the stability of soil organic matter by promoting the formation of soil aggregates and incorporating part of the inorganic N into organic matter, and consequently decreased microbial mineralization of soil organic matter. Physical disturbance intensified the inhibition of N on SOC decomposition, likely because physical disturbance allowed the added N to be better exposed to soil microbes and consequently increased the availability of added N. We conclude that physical disturbance and N play important roles in modulating the stability of SOC.     

Differential Expression of Small Heat Shock Protein 27 (Hsp27) in Ataxia telangiectasia Brains

Ataxia telangiectasia (A-T) is a progressive neurodegenerative disorder caused by disruption of the gene, ataxia telangiectasia mutated (ATM). Present study was aimed at identifying proteins that are present in abnormal levels in A-T brain that may identify alternative targets for therapeutic interventions. Proteomic and Western blot analysis have shown massive expression of the small heat shock protein 27 (Hsp27) in frontal cortices of A-T brains compared to negligible levels in controls. The expression of other stress proteins, Hsp70, αB-crystallin, and prohibitin remained unchanged in the A-T and control brains. Significant decreases in reactive oxygen species, protein carbonyl groups and lipid peroxidation products were observed in the A-T brains. There is no evidence of caspase 3 activation or DAXX mediated apoptosis. We propose that neurons in the frontal lobe are protected by the expression of Hsp27, which scavenges the oxidative stress molecules formed consequent to the primary loss of ATM function.     

Failure mechanism of the all-polyethylene glenoid implant

Fixation failure of glenoid components is the main cause of unsuccessful total shoulder arthroplasties. The characteristics of these failures are still not well understood, hence, attempts at improving the implant fixation are somewhat blind and the failure rate remains high. This lack of understanding is largely due to the fundamental problem that direct observations of failure are impossible as the fixation is inherently embedded within the bone.Twenty custom made implants, reflecting various common fixation designs, and a specimen set-up was prepared to enable direct observation of failure when the specimens were exposed to cyclic superior loads during laboratory experiments. Finite element analyses of the laboratory tests were also carried out to explain the observed failure scenarios.All implants, irrespective of the particular fixation design, failed at the implant–cement interface and failure initiated at the inferior part of the component fixation. Finite element analyses indicated that this failure scenario was caused by a weak and brittle implant–cement interface and tensile stresses in the inferior region possibly worsened by a stress raiser effect at the inferior rim.The results of this study indicate that glenoid failure can be delayed or prevented by improving the implant/cement interface strength. Also any design features that reduce the geometrical stress raiser and the inferior tensile stresses in general should delay implant loosening.     

Neurotoxic Potential of Three Structural Analogs of β-N-oxalyl-α,β-Diaminopropanoic Acid (β-ODAP)

Lathyrism is a non-progressive motor neuron disease produced by consumption of the excitatory amino acid, 3-N-oxalyl-L-2,3-diaminopropanoic acid (-ODAP). To learn more about the mechanisms underlying Lathyrism three structural analogs of -ODAP were synthesized. Carboxymethyl-,-diaminopropanoic acid (CMDAP) evoked inward currents which were antagonized by APV (30 M), but not by CNQX (10 M). N-acetyl-,-diaminopropanoic acid (ADAP) evoked no detectable ionic currents but potentiated N-methyl-D-aspartate (NMDA)-activated currents. The potentiation of NMDA currents by ADAP was blocked by 7-chlorokynurenic acid. Carboxymethylcysteine (CMC) did not activate any detectable ionic currents. None of the three -ODAP analogs produced visible symptoms of toxicity in day old chicks when administered for 2–3 consecutive days. Ligand binding studies demonstrated that all the three compounds were effective to in displacing [³H]glutamate. The maximum inhibition was 92% for CMDAP, 61% for ADAP, 65% for CMC and 99% for -ODAP. These data indicate that analogs of -ODAP may interact with glutamate receptors without producing neurotoxicity.     

Effect of feeding frequency as a rearing system on biological performance,survival, body chemical composition and economic efficiency of Asian seabass Lates calcarifer (Bloch, 1790) reared under controlled environmental conditions

A 70-day rearing trial was done to determine the optimal frequency of feeding on growth performance (GP), feed conversion rate (FCR), cannibalism, survival rate (SR), body chemical composition and economic efficiency of the Asian sea bass. This study tested four different treatments of feeding frequencies (FF), once (T1), twice (T2), three times (T3), and four times (T4) per day. An average initial weight of Asian sea bass fry was 0.2 g (SD = ±0.12) were stocked 10 individuals per m³ (9.14 m × 1.82 m × 1.22 m, L × W × H; water depth 0.61 m) with two replicates per treatment (4 × 2 = 8). Fry were fed a mixture of larval commercial feed and shrimp with a pellet diet containing (46% CP). Initially, the feeding rate of 8% biomass per day was further adjusted according to fish biomass on a weekly basis. Results showed that, the FF significantly affected (p < 0.05) on growth indictors and survival rate (SR). Specifically fry fed three times a day (T3) had the best FBW, FL, SGR, ADWG and FCR followed by T4 and T2 while fry fed one time a day was the lowest in these parameters. Also, VSI, HSI and CF (k) significantly differed among the treatments. The fish whole body content of protein, moisture and ash did not significantly (p < 0.05) be affected by feeding frequency, but lipid content differed and both T3, T4 were the highest. It could be concluded that, increasing FF up to three times a day had a positive effect on weight gain, survival rate and feed utilization of Lates calcarifer. The second degree polynomial regression indicates that fed three times a day is optimum for best growth performance and survival for Asian sea bass.