Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters

G-protein coupled receptors (GPCRs) belong to biologically important and functionally diverse and largest super family of membrane proteins. GPCRs retain a characteristic membrane topology of seven alpha helices with three intracellular, three extracellular loops and flanking N' and C' terminal residues. Subtle differences do exist in the helix boundaries (TM-domain), loop lengths, sequence features such as conserved motifs, and substituting amino acid patterns and their physiochemical properties amongst these sequences (clusters) at intra-genomic and inter-genomic level (please re-phrase into 2 statements for clarity). In the current study, we employ prediction of helix boundaries and scores derived from amino acid substitution exchange matrices to identify the conserved amino acid residues (motifs) as consensus in aligned set of homologous GPCR sequences. Co-clustered GPCRs from human and other genomes, organized as 32 clusters, were employed to study the amino acid conservation patterns and species-specific or cluster-specific motifs. Critical analysis on sequence composition and properties provide clues to connect functional relevance within and across genome for vast practical applications such as design of mutations and understanding of disease-causing genetic abnormalities.     

Evaluation of Natural Attenuation of Benzene and Dichloroethanes at the KL Landfill

Natural attenuation of benzene and dichloroethanes in groundwater contaminated by leachate from the West KL Avenue landfill in Kalamazoo, Michigan, was evaluated in three phases. Existing data from the previous site investigations were used to locate a series of high-resolution vertical profile samples. By analyzing data from the discrete vertical profile samples, the rates of attenuation of benzene and dichloroethanes in the plume were forecasted. Permanent monitoring wells were installed over the depth intervals associated with high concentrations in the vertical profile sampling. These wells were monitored over time to extract independent estimates of the rates of degradation of benzene and dichloroethanes. Estimates of first-order attenuation rate constants were obtained using two methods: a method due to Buscheck and Alcantar (1995), which is based on a one-dimensional steady-state analytical solution, and the tracer correction method of Wiedemeier et al. (1996). The rates of attenuation predicted from the vertical profile sampling were found to be in good agreement with the rates obtained from the permanent monitoring well data, indicating that the long-term behavior of the contaminant plumes is consistent with the initial forecast. The results also indicated that the natural attenuation of benzene, 1,1-dichloroethane (DCA), and 1,2-DCA was statistically significant (at the 0.05 level).     

Reduced susceptibility of nonobese diabetic mice to TNF-alpha and D-galactosamine-mediated hepatocellular apoptosis and lethality

Nonobese diabetic (NOD/LtJ or NOD) mice are resistant to doses of LPS and D-galactosamine that uniformly produce lethality in C57BL/6J (B6) mice (p < 0.01). Liver caspase-3-like activity, serum transaminase levels (both p < 0.05), and the numbers of apoptotic liver nuclei were also reduced in NOD compared with B6 mice treated with LPS (100 ng) and D-galactosamine (8 mg). NOD mice were also at least 100-fold more resistant to recombinant human TNF-alpha and D-galactosamine treatment than B6 mice (p < 0.001). Binding of recombinant human TNF-alpha to splenocytes from NOD mice was similar to that seen in B6 mice, suggesting that the defect in responsiveness was not due to an inability of recombinant human TNF-alpha to bind the NOD TNF type 1 (p55) receptor. Because the TNF type 1 (p55) receptor shares a common signaling pathway with Fas (CD95), NOD and B6 mice were treated with the Fas agonist antibody, Jo-2. Surprisingly, NOD mice were as sensitive as B6 mice to Fas-induced lethality and hepatic injury. In addition, primary hepatocytes isolated from NOD mice and cultured in vitro in the presence of D-galactosamine with or without TNF-alpha were found to be resistant to apoptosis and cytotoxicity when compared with B6 mice. In contrast, Jo-2 treatment produced similar increases in caspase-3 activity and cytotoxicity in primary hepatocytes from NOD and B6 mice. The resistance to LPS- and TNF-alpha-mediated lethality and hepatic injury in D-galactosamine-sensitized NOD mice is apparently due to a post-TNFR binding defect, and independent of signaling pathways shared with Fas.     

TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences

Multiple sequence alignments become biologically meaningful only if conserved and functionally important residues and secondary structural elements preserved can be identified at equivalent positions. This is particularly important for transmembrane proteins like G-protein coupled receptors (GPCRs) with seven transmembrane helices. TM-MOTIF is a software package and an effective alignment viewer to identify and display conserved motifs and amino acid substitutions (AAS) at each position of the aligned set of homologous sequences of GPCRs. The key feature of the package is to display the predicted membrane topology for seven transmembrane helices in seven colours (VIBGYOR colouring scheme) and to map the identified motifs on its respective helices /loop regions. It is an interactive package which provides options to the user to submit query or pre-aligned set of GPCR sequences to align with a reference sequence, like rhodopsin, whose structure has been solved experimentally. It also provides the possibility to identify the nearest homologue from the available inbuilt GPCR or Olfactory Receptor cluster dataset whose association is already known for its receptor type. AVAILABILITY: The database is available for free at mini@ncbs.res.in.     

Oxidative protein damage is associated with poor grip strength among older women living in the community.

Grip strength, an indicator of muscle strength, has been shown to be a predictor of poor outcomes among older adults. Protein carbonylation, an indicator of oxidative damage to proteins, leads to cellular dysfunction and a decline in tissue function. Oxidative stress has been implicated in the pathogenesis of sarcopenia. The objective was to determine whether serum protein carbonyl concentrations are associated with grip strength in older women living in the community. A cross-sectional study was conducted in 672 women, aged 65 and older, from the Women's Health and Aging Study (WHAS) I, the one-third most disabled women residing in the community in Baltimore, MD. Protein carbonyl and grip strength were measured in each patient. In a multivariate analysis adjusting for age, race, body mass index, and Mini-Mental Status Examination score, protein carbonyls (nmol/mg) were associated with grip strength (beta = -6.77, P < 0.01). The statistical association was unchanged after the analysis adjusted for hypertension, congestive heart failure, and depression. Ordered logistic regression models adjusted for the above factors showed that protein carbonyls are associated with increased odds of being in the lower quartiles of grip strength (odds ratio 8.74, 95% confidence interval 1.06-71.89, P = 0.043). These results suggest oxidative protein damage is independently associated with low grip strength among older women living in the community. Increased oxidative stress may be contributing to loss of muscle strength in older adults.     

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2–8.6) and an average hydrogen concentration of 0.75% (range of 0.3–1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of iron metal may therefore be an effective technology for remediation of PCB-contaminated sediments.     

Low serum selenium concentrations are associated with poor grip strength among older women living in the community

Aging is associated with a loss of muscle strength, and, in turn, loss of muscle strength has been associated with increased risk of frailty, disability and mortality. The factors that contribute to loss of muscle strength with aging have not been well characterized. Selenium is important in normal muscle function because of its role in selenoenzymes that protect muscle against oxidative damage. We hypothesized that low serum selenium concentrations were associated with poor grip strength. We examined the association between serum selenium and hand grip strength among 676 moderately to severely disabled community-dwelling women in the Women's Health and Aging Study I in Baltimore, Maryland. After adjusting for age, race, body mass index, Mini-Mental Status Examination score, current smoking, hypertension, congestive heart failure and depression, serum selenium was associated with grip strength (P=0.04). This study supports the idea that selenium is important to muscle strength in older women.     

Over 17% Efficiency Stand‐Alone Solar Water Splitting Enabled by Perovskite‐Silicon Tandem Absorbers

Realizing solar‐to‐hydrogen (STH) efficiencies close to 20% using low‐cost semiconductors remains a major step toward accomplishing the practical viability of photoelectrochemical (PEC) hydrogen generation technologies. Dual‐absorber tandem cells combining inexpensive semiconductors are a promising strategy to achieve high STH efficiencies at a reasonable cost. Here, a perovskite photovoltaic biased silicon (Si) photoelectrode is demonstrated for highly efficient stand‐alone solar water splitting. A p⁺nn⁺ ‐Si/Ti/Pt photocathode is shown to present a remarkable photon‐to‐current efficiency of 14.1% under biased condition and stability over three days under continuous illumination. Upon pairing with a semitransparent mixed perovskite solar cell of an appropriate bandgap with state‐of‐the‐art performance, an unprecedented 17.6% STH efficiency is achieved for self‐driven solar water splitting. Modeling and analysis of the dual‐absorber PEC system reveal that further work into replacing the noble‐metal catalyst materials with earth‐abundant elements and improvement of perovskite fill factor will pave the way for the realization of a low‐cost high‐efficiency PEC system.