Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome

Protein 3-nitrotyrosine is a post-translational modification that commonly arises from the nitration of tyrosine residues. This modification has been detected under a wide range of pathological conditions and has been shown to alter protein function. Whether 3-nitrotyrosine is important in normal cellular processes or is likely to affect specific biological pathways remains unclear. Using GPS-YNO2, a recently described 3-nitrotyrosine prediction algorithm, a set of predictions for nitrated residues in the human proteome was generated. In total, 9.27 per cent of the proteome was predicted to be nitratable (27 922/301 091). By matching the predictions against a set of curated and experimentally validated 3-nitrotyrosine sites in human proteins, it was found that GPS-YNO2 is able to predict 73.1 per cent (404/553) of these sites. Furthermore, of these sites, 42 have been shown to be nitrated endogenously, with 85.7 per cent (36/42) of these predicted to be nitrated. This demonstrates the feasibility of using the predicted dataset for a whole proteome analysis. A comprehensive bioinformatics analysis was subsequently performed on predicted and all experimentally validated nitrated tyrosine. This found mild but specific biophysical constraints that affect the susceptibility of tyrosine to nitration, and these may play a role in increasing the likelihood of 3-nitrotyrosine to affect processes, including phosphorylation and DNA binding. Furthermore, examining the evolutionary conservation of predicted 3-nitrotyrosine showed that, relative to non-nitrated tyrosine residues, 3-nitrotyrosine residues are generally less conserved. This suggests that, at least in the majority of cases, 3-nitrotyrosine is likely to have a deleterious effect on protein function and less likely to be important in normal cellular function. © 2013 The Authors.Link_to_subscribed_fulltex

Background heavy metal concentrations (Cd, Cu, Ni, Pb, Fe and Zn) in modiolus sp. collected from the coast waters of Peninsular Malaysia: A preliminary study.

The heavy metal concentrations in little black mussel Modiolus sp. have not been previously reported from Malaysia. In this study, the mussel species is widely distributed the coastal waters of Peninsular Malaysia and this mussel are found in Pantai Sri Tujuh [Kelantan], K. Kedah [Kedah], Kg. Sg. Berembang, Kg. Sg. Baru and Kuala Perlis [Perlis], and Bagan Tiang [Perak], Jeram and Sg. Janggut [Selangor]. From the 12 mussel populations collected in this study, the ranges of the metal concentrations (μg/g dry weight) in the total soft tissues and shells were 2.246.73 and 4.159.53 for Cd, 10.0231.94 and 6.2810.17 for Cu, 1.3549.38 and 22.2248.45 for Ni, 4.7556.27, and 54.86112.31 for Pb, 5985582 and 158 544 for Fe, and 43.8162 and 1.5025.4 for Zn. To our knowledge, this is the first report on the metal concentrations of Modiolus sp. collected from the coastal waters of Peninsular Malaysia. The present data are important for future ecotoxicological, genetic biochemical and molecular studies in establishing this marine mussel as a good biomonitor

Effects of organic fertilizers on growth and yield of Roselle (Hibiscus sabdariffa L.) on BRIS soil

The application of organic fertilizers on roselle has generated much interest among the researchers and farmers for the past two decades. However, little attention is given on the plantation quality in Beach Ridges Interspersed with Swales (BRIS) soil. Roselle is generally preferred because it is rich in ascorbic acid and anthocyanin that are very beneficial for health. This study determined the growth, yields and antioxidants of roselle on BRIS soils after application with different rate of organic fertilizers. Roselle was treated with five different rates of goat manure i.e. T1 (control), T2 (40 mt/ha), T3 (80 mt/ha), T4 (120 mt/ha) and T5 (160 mt/ha). Plant growth, yields and antioxidants of roselle calyxes were determined at three weeks interval for 21 weeks. Generally, organic fertilizer treated roselle showed significant increased (p<0.05) plant growth and plant yield. Higher rate of organic fertilizer, particularly T5 (160 mt/ha) increased the stem diameter and stem height, leaves number and leaves area as well as the biomass and number of calyx. Organic fertilizer treatments had no significant effect on ascorbic acid, carotenoids and anthocyanin production except for T3 treated plants whereas, chlorophyll content was significantly induced (p<0.05) in response to organic fertilizer treatments. In conclusion, application of organic fertilizers at higher rate showed positive effects on the growth, yield and antioxidant content of roselle. Therefore, organic fertilizer should be frequently applied in the farms to get the best growth and yields of the plant

Design and fabrication of indium phosphide air-bridge waveguides with MEMS functionality

We present the design and fabrication of a dual air-bridge waveguide structure integrated with MEMS functionality. The structure is designed to function as a tunable optical buffer for telecommunication application. The optical buffer structure is based on two parallel waveguides made of high refractive index material with subwavelength dimensions. They are suspended in air, and are separated by a sub-micron air gap. Due to the fact that the size of the waveguides is much smaller than the wavelength of light that propagates in the structure, a significant fraction of the optical mode is in the air gap between the waveguides. By changing the size of the air gap using MEMS techniques, we can vary this fraction and hence the effective refractive index of the waveguide structure, thus generating tunable optical delay.The optical buffer structure was grown on an InP substrate by molecular beam epitaxy, and the device layer was made of InGaP. An InGaAs layer was sandwiched between the device layer and the substrate to serve as a sacrificial layer. The sub-micron waveguides, their supports in the form of side pillars with tapered shapes in order to minimize optical losses, and the MEMS structures were patterned using electron beam lithography and plasma etching. Electrodes were integrated into the structure to provide electrostatic actuation. After the sample patterning, the waveguide structure was released using HF etch. Our simulations predict that by varying the waveguide separation from 50 nm to 500 nm, we could achieve a change in propagation delay by a factor of two

Investigation of plant growth and transpiration-induced matric suction under mixed grass-tree conditions

Although evapotranspiration-induced matric suction for single species has been widely studied, little is known about how mixed-species planting would affect the plant growth and induced matric suction. This study aims to explore the effects of grass-tree interaction on their growth and induced matric suction during evapotranspiration (ET) and rainfalls. Field monitoring was carried out to measure matric suction responses in compacted soil that was vegetated with (i) single tree species, Schefflera heptaphylla and (ii) mixed species of the trees and a grass species, Cynodon dactylon. In each condition, three tree spacings (120, 180 and 240 mm) were planted. When tree spacing increased from 120 to 240 mm, the peak tree root area index (RAI, for fine roots with diameterThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Quantifying the potential of pressure retarded osmosis advanced spacers for reducing specific energy consumption in hybrid desalination

A hypothetical PRO advanced spacer that delivers a 50 % mass transfer enhancement (i.e., 50 % higher Sherwood number) is simulated for a range of feed conditions and membrane properties, to shed insights into the effect of improved PRO spacer on the overall specific energy consumption (SEC) of RO-PRO hybrid desalination. Results show that a large increase in pressure drop in the PRO module has negligible impact on power density (PD) and SEC for RO-PRO. The analysis revealed that the PRO advanced spacer has marginal impact on SEC for a typical current PRO membrane. Even so, the PRO advanced spacer has an important impact in terms of PD, which can increase by 10 %, especially under severe external concentration polarization. The sensitivity analysis demonstrates that the extent of SEC reduction or power density enhancement related to the advanced spacer is most sensitive to the structural parameter. This is because internal concentration polarization is the major cause for osmotic pressure loss in PRO, which limits the potential PRO performance improvements from advanced spacers. Nevertheless, the benefits of PRO advanced spacers can be further exploited through the continuous development of new materials for novel membranes with a reduced structural parameter

Image-Guided Ablative Therapies for Lung Tumors

While the gold standard for early stage lung cancers is still surgical resection, many patients have comorbidities or suboptimal lung function making surgery unfavorable. At the same time, more and more small lung nodules are being incidentally discovered on computer tomography (CT), leading to the discovery of pre-malignant or very early stage lung cancers without regional spread, which could probably be eradicated without anatomical surgical resection. Various ablative energies and technologies are available on the market, including radiofrequency ablation, microwave ablation, cryoablation, and less commonly laser ablation and irreversible electroporation. For each technology, the mechanism of action, advantages, limitations, potential complications and evidence-based outcomes will be reviewed. Traditionally, these ablative therapies were done under CT guidance with percutaneous insertion of ablative probes. Recently, bronchoscopic ablation under ultrasound, CT, or electromagnetic navigation bronchoscopy guidance is gaining popularity due to improved navigation precision, reduced pleural-based complications, and providing a true “wound-less” option

A Real Time Quality Monitoring System for the Lighting Industry: A Practical and Rapid Approach Using Computer Vision and Image Processing (CVIP) Tools

In China, the manufacturing of lighting products is very labour intensive. The approach used to check quality and control production relies on operators who test using various types of fixtures. In order to increase the competitiveness of the manufacturer and the efficiency of production, the authors propose an integrated system. This system has two major elements: a computer vision system (CVS) and a real‐time monitoring system (RTMS). This model focuses not only on the rapid and practical application of modern technology to a traditional industry, but also represents a process innovation in the lighting industry. This paper describes the design and development of the prototyped lighting inspection system based on a practical and fast approach using computer vision and imaging processing (CVIP) tools. LabVIEW with IMAQ Vision Builder is the chosen tool for building the CVS. Experimental results show that this system produces a lower error rate than humans produce in the quality checking process. The whole integrated manufacturing strategy, aimed at achieving a better performance, is most suitable for a China and other labour intensive environments such as India.