GENOTOXICITY IN CHIRONOMUS KIIENSIS (CHIRONOMIDAE: DIPTERA) AFTER EXPOSURE TO POLLUTED SEDIMENTS FROM RIVERS OF NORTH PENINSULAR MALAYSIA: IMPLICATION FOR ECOTOXICOLOGICAL MONITORING

Rapid industrialization and urbanization has led to increasing input of chemical contaminants into the aquatic environment of Malaysia. Despite the threat civilization poses to the biota, there are still very few relevant studies on ecotoxicological testing of river ecosystems. To overcome this knowledge gap, we examined lethal and genotoxic effects of sediments from different rivers of the northern Malaysia against Chironomus kiiensis, a group well represented in the aquatic fauna of this region. We exposed the larvae to sediments from Selama River (SR), Permatang Rawa River (PRR) and Kilang Ubi River (KUR) at various durations (0, 6, 12, 24 and 48 h). The larval mortality was monitored, whereas DNA damage in survivors' cells was determined using the comet assay. Pollution level indexed by the amounts of heavy metals and other organic contaminants in the sediment showed progressive increases from SR to PRR to KUR. Highly polluted sediments (PRR to KUR) were detrimental to C. kiiensis larvae, most of which did not survive following exposure for long periods. DNA analyses revealed greater damages in nuclei derived from larvae maintained on polluted sediments, in particular, those from KUR. The effects on the genomic material of C. kiiensis larvae occurred in a time‐dependent manner, with damage level increasing as exposure time progressed. Our results highlight the genotoxic properties of polluted sediments. More importantly, this study showed that C. kiiensis larvae could respond to different levels of pollution with respect to exposure time. It is concluded that C. kiiensis larvae is a potential candidate for river ecotoxicological monitoring. Copyright © 2012 John Wiley & Sons, Ltd.     

Does protein structure influence trypsin miscleavage?

In this article, a new database that relates structural information from proteins in protein data bank to closely related protein sequences in humans was developed. Because the match criteria are extremely stringent, the structure of proteins in other species to infer characteristics of the human proteins was used. As a demonstration of the approach, this database has been applied to the problem of identifying likely trypsin miscleavage sites, a significant problem in proteomics. However, the approach is very general, and can be used to answer many kinds of structural questions (including questions related to posttranslational modifications). The study found that both the surface area and the secondary structure of cleavage sites have highly statistically significant effects on trypsin cleavage. The results of this analysis do not, however, suggest that surface area or secondary structure properties of particular peptides can be used to predict miscleavage sites, at least at a global level. This analysis of cleavage sites demonstrates the general power of homology-based techniques, in which the characteristics of a single protein that has a structure that has been solved can be used to infer properties of other proteins. We expect that our database of related proteins, structures, and sequences and our ability to query experimentally determined sets of peptides against this database will allow us to answer many other questions relation to global protein expression and modification.     

A simulation of doping and trap effects on the spectral response of AlGaN ultraviolet detectors

We study, by means of numerical simulation, the impact of doping and traps on the performance of the “solar blind” ultraviolet Schottky detector based on AlGaN. We implemented physical models and AlGaN material properties taken from the literature, or from the interpolation between the binary materials (GaN and AlN) weighted by the mole fractions. We found that doping and traps highly impact the spectral response of the device, and in particular a compromise in the doping concentration must be reached in order to optimize the spectral response of the detector. These results give us a powerful tool to quantitatively understand the impact of elaboration and processing conditions on photodetector characteristics, and thus identify the key issues for the development of the technology.     

Evaluation of Low-Power Computing when Operating on Subsets of Multicore Processors

Given the accelerated growth in tablet devices, smartphones, and netbooks, designers are faced with serious challenges to meet the needs of mobility in terms of battery life and form factor. It is vital to investigate how to deliver the best mobile experience to users while ensuring adequate levels of performance. In this paper, we present a power management evaluation of multi-core processor systems by comparing thermal power, battery life, and performance when running different types of workloads under a limited number of cores. To show the potential gains from a system power management perspective, we have assessed a mobile platform featuring the Second Generation Intel Core i5 processor, and tested it on a wide selection of workloads and benchmarks. Experimental results show significant thermal power reduction (up to 40 %) in a variety of scenarios, while system performance was sustained in most cases but sacrificed in a few other uncommon situations.     

Intracranial arterial calcification is highly prevalent in hemodialysis patients but does not associate with acute ischemic stroke

Intracranial arterial calcification (IAC) is associated with ischemic stroke in the general population but this relationship has not been examined in hemodialysis patients. We examined the factors associated with IAC and its relationship with acute ischemic stroke in this population. We retrospectively studied 490 head computed tomographic scans from 2225 hemodialysis patients presenting with neurological symptoms at our center (October 2005-May 2009). Intracranial arterial calcification was graded using a validated scoring system. Multivariate regression was used to examine the factors associated with the presence of IAC, its severity, and its ability to predict acute ischemic stroke. Weibull's survival models analyzed the relationship between IAC severity and survival. Ninety-five percent of patients with ischemic stroke had IAC vs. 83% in the nonstroke group (P=0.02). Intracranial arterial calcification severity increased with age (P<0.001), hemodialysis vintage (P<0.001), serum phosphate (P<0.05), and major comorbidities. In patients with multiple computed tomographic scans during the study period, increased IAC severity at baseline was predictive of acute ischemic stroke (P=0.05) on logistic regression analysis. High-grade and not low-grade IAC was associated with worse survival (P=0.008). Intracranial arterial calcification is highly prevalent in hemodialysis patients, especially in those with acute ischemic stroke. Its severity is prognostically significant and associated with risk factors for vascular calcification and may confer a greater risk of acute ischemic stroke. The mechanisms underlying the high incidence of ischemic stroke in this patient group require further comprehensive study.     

Key challenges in proteomics and proteoinformatics

In this article, a survey on experimental and computational approaches related to proteomics is presented. Considered broadly, proteomics includes: techniques for identifying proteins in a sample, detecting posttranslational modifications (changes to proteins after translation), predicting the structure and function of proteins from sequence data, and integrating information about protein sequences from different databases. The paper focuses on the ways in which recent biological findings complicate the mapping from genes to RNA to protein. The authors argue that the challenges encountered in proteomics provide a valuable lesson on the complexity of life itself, as live organisms always contradict oversimplified models of biological information flow. In this overview, a snapshot of contemporary issues in proteomics is shown.