Operationally determined chemical speciation of barium and chromium in drilling fluid wastes by sequential extraction

ABSTRACT

A study has been conducted to determine the influence of pH on the speciation and distribution of barium and chromium in drilling mud. Samples in equilibrium under controlled conditions were subjected to sequential extraction procedure to fractionate the heavy metals into the designated forms of exchangeable, adsorbed, organically bound, carbonate and residual phases. This provides an insight into the potential availability of the heavy metals for possible release into groundwaters and/or surface waters. The major portion of both the metals studied was found in the carbonate and residual forms with the relative distribution depending on the pH. Generally, decreasing pH caused a shift from the residual form towards the carbonate or organic forms of metals. The occurrence of metals in more stable organic, carbonate and residual forms in drilling mud, coupled with no significant release to the aqueous phase upon varying the pH indicates the resistance of these metals to remobilisation from drilling mud.     

The Xerophyta viscosa Aldose Reductase (ALDRXV4) Confers Enhanced Drought and Salinity Tolerance to Transgenic Tobacco Plants by Scavenging Methylglyoxal and Reducing the Membrane Damage

We report the efficacy of an aldose reductase (ALDRXV4) enzyme from Xerophyta viscosa Baker in enhancing the prospects of plant’s survival under abiotic stress. Transgenic tobacco plants overexpressing ALDRXV4 cDNA showed alleviation of NaCl and mannitol-induced abiotic stress. The transgenic plants survived longer periods of water deficiency and salinity stress and exhibited improved recovery after rehydration as compared to the wild type plants. The increased synthesis of aldose reductase in transgenic plants correlated with reduced methylglyoxal and malondialdehyde accumulation and an elevated level of sorbitol under stress conditions. In addition, the transgenic lines showed better photosynthetic efficiency, less electrolyte damage, greater water retention, higher proline accumulation, and favorable ionic balance under stress conditions. Together, these findings suggest the potential of engineering aldose reductase levels for better performance of crop plants growing under drought and salt stress conditions.     

Genetic polymorphisms of CYP2E1 and DNA repair genes HOGG1 and XRCC1: Association with hepatitis B related advanced liver disease and cancer

A population based case–control study was designed to explore the genetic risk factors for hepatitis B virus (HBV) related liver disease susceptibility. A total of 424 subjects comprising 210 controls, 50 acute HBV (AVH), 84 chronic HBV (CHBV), 25 HBV related cirrhosis and 55 HBV related hepatocellular carcinoma (HCC) cases were included in the study. PCR-RFLP was used for the genotyping of Cyp2E1*5B, hOGG1 codon 326 and XRCC1 codon 399. Compared to controls, Cyp2E1 rsaI variant c2 genotype increased the risk of HBV related liver disease severity by 2.68 fold, the highest for HCC cases (3.981 folds, p = 0.106); and was associated with higher histology activity index (HAI) (p < 0.001) in CHBV patients. Cyp2E1 and hOGG1 variants were independently associated with a significantly higher fibrosis score in CHBV group. Analysis of gene–gene interaction studies showed an increased risk of HCC, cirrhosis and CHBV in a Cyp2E1 variant + XRCC1 variant combination (p < 0.001); and hOGG1 variants + XRCC1 variants. A mutually independent heterozygous hOGG1 and XRCC1 combination resulted in a decreased risk of HBV related liver disease. On the other hand, a wild-type hOGG1 and XRCC1 combination was associated with a significantly higher risk of AVH (p = 0.010) but a lower risk of CHBV (p = 0.032) and HCC (p = 0.006). The gene–gene interactions were also associated with a significant increase in HAI and fibrosis score in CHBV patients. Cyp2E1, hOGG1 and XRCC1 genotypes significantly alter the risk of HBV related liver disease susceptibility and severity, independently or through gene–gene interaction.     

Effects of wild-type and α-tocopherol-enriched transgenic Brassica juncea on the components of xenobiotic metabolism, antioxidant status, and oxidative stress in the liver of mice

Alpha (α)-tocopherol is the most biologically active and preferentially retained form of vitamin E in the human body and is known for its antioxidant and gene regulatory functions. Its increased intake is implicated in protection against diseases that involve an oxidative stress component. We have evaluated the chemopreventive potential of a diet supplemented with natural α-tocopherol-enriched transgenic (TR) Brassica juncea seeds. The modulation of phase I and phase II xenobiotic metabolism and of antioxidative enzymes was compared in the livers of mice fed on a control diet or on a diet supplemented with 2, 4, and 6 % (w/w) of wild-type (WT) or TR seeds. A dose-dependent increase in the specific activities of these enzymes was observed in those animals fed on diet supplemented with TR seeds. In comparison, an increase in the specific activities of antioxidative enzymes was substantial only at higher doses of WT seeds. Consequently, oxidative stress measured in terms of lipid peroxidation and lactate dehydrogenase activity was found to be lower in the case of mice fed with the supplemented diet. However, the chemopreventive potential of TR seeds was more pronounced than that of WT seeds. This study demonstrates the feasibility of fortifying diets with natural α-tocopherol for chemopreventive benefits by means of transgenic manipulation of a commonly used oilseed crop.     

Virulence and competitive ability in an obligately killing parasite

Mixed infections are thought to have a major influence on the evolution of parasite virulence. During a mixed infection, higher within‐host parasite growth is favored under the assumption that it is critical to the competitive success of the parasite. As within‐host parasite growth may also increase damage to the host, a positive correlation is predicted between virulence and competitive success. However, when parasites must kill their hosts in order be transmitted, parasites may spend energy on directly attacking their host, even at the cost of their within‐host growth. In such systems, a negative correlation between virulence and competitive success may arise. We examined virulence and competitive ability in three sympatric species of obligately killing nematode parasites in the genus Steinernema. These nematodes exist in a mutualistic symbiosis with bacteria in the genus Xenorhabdus. Together the nematodes and their bacteria kill the insect host soon after infection, with reproduction of both species occurring mainly after host death. We found significant differences among the three nematode species in the speed of host killing. The nematode species with the lowest and highest levels of virulence were associated with the same species of Xenorhabdus, indicating that nematode traits, rather than the bacterial symbionts, may be responsible for the differences in virulence. In mixed infections, host mortality rate closely matched that associated with the more virulent species, and the more virulent species was found to be exclusively transmitted from the majority of coinfected hosts. Thus, despite the requirement of rapid host death, virulence appears to be positively correlated with competitive success in this system. These findings support a mechanistic link between parasite growth and both anti‐competitor and anti‐host factors.     

Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations

Background

Massively parallel sequencing studies have led to the identification of a large number of mutations present in a minority of cancers of a given site. Hence, methods to identify the likely pathogenic mutations that are worth exploring experimentally and clinically are required. We sought to compare the performance of 15 mutation effect prediction algorithms and their agreement. As a hypothesis-generating aim, we sought to define whether combinations of prediction algorithms would improve the functional effect predictions of specific mutations.

Results

Literature and database mining of single nucleotide variants (SNVs) affecting 15 cancer genes was performed to identify mutations supported by functional evidence or hereditary disease association to be classified either as non-neutral (n = 849) or neutral (n = 140) with respect to their impact on protein function. These SNVs were employed to test the performance of 15 mutation effect prediction algorithms. The accuracy of the prediction algorithms varies considerably. Although all algorithms perform consistently well in terms of positive predictive value, their negative predictive value varies substantially. Cancer-specific mutation effect predictors display no-to-almost perfect agreement in their predictions of these SNVs, whereas the non-cancer-specific predictors showed no-to-moderate agreement. Combinations of predictors modestly improve accuracy and significantly improve negative predictive values.

Conclusions

The information provided by mutation effect predictors is not equivalent. No algorithm is able to predict sufficiently accurately SNVs that should be taken forward for experimental or clinical testing. Combining algorithms aggregates orthogonal information and may result in improvements in the negative predictive value of mutation effect predictions.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0484-1) contains supplementary material, which is available to authorized users.     

Satellite Tracking on the Flyways of Brown-Headed Gulls and Their Potential Role in the Spread of Highly Pathogenic Avian Influenza H5N1 Virus

Brown-headed gulls (Larus brunnicephalus), winter visitors of Thailand, were tracked by satellite telemetry during 2008–2011 for investigating their roles in the highly pathogenic avian influenza (HPAI) H5N1 virus spread. Eight gulls negative for influenza virus infection were marked with solar-powered satellite platform transmitters at Bang Poo study site in Samut Prakarn province, Thailand; their movements were monitored by the Argos satellite tracking system, and locations were mapped. Five gulls completed their migratory cycles, which spanned 7 countries (China, Bangladesh, India, Myanmar, Thailand, Cambodia, and Vietnam) affected by the HPAI H5N1 virus. Gulls migrated from their breeding grounds in China to stay overwinter in Thailand and Cambodia; while Bangladesh, India, Myanmar, and Vietnam were the places of stopovers during migration. Gulls traveled an average distance of about 2400 km between Thailand and China and spent 1–2 weeks on migration. Although AI surveillance among gulls was conducted at the study site, no AI virus was isolated and no H5N1 viral genome or specific antibody was detected in the 75 gulls tested, but 6.6% of blood samples were positive for pan-influenza A antibody. No AI outbreaks were reported in areas along flyways of gulls in Thailand during the study period. Distance and duration of migration, tolerability of the captive gulls to survive the HPAI H5N1 virus challenge and days at viral shedding after the virus challenging suggested that the Brown-headed gull could be a potential species for AI spread, especially among Southeast Asian countries, the epicenter of H5N1 AI outbreak.