Riboswitch Detection Using Profile Hidden Markov Models

Background  

Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.     

Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins

Aromatic-aromatic hydrogen bonds are important in many areas of chemistry, biology and materials science. In this study we have analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π interactions and π-π networks play important roles in the structural stability of ILs and TNF proteins.     

Rural Clinician Scarcity and Job Preferences of Doctors and Nurses in India: A Discrete Choice Experiment

The scarcity of rural doctors has undermined the ability of health systems in low and middle-income countries like India to provide quality services to rural populations. This study examines job preferences of doctors and nurses to inform what works in terms of rural recruitment strategies. Job acceptance of different strategies was compared to identify policy options for increasing the availability of clinical providers in rural areas. In 2010 a Discrete Choice Experiment was conducted in India. The study sample included final year medical and nursing students, and in-service doctors and nurses serving at Primary Health Centers. Eight job attributes were identified and a D-efficient fractional factorial design was used to construct pairs of job choices. Respondent acceptance of job choices was analyzed using multi-level logistic regression. Location mattered; jobs in areas offering urban amenities had a high likelihood of being accepted. Higher salary had small effect on doctor, but large effect on nurse, acceptance of rural jobs. At five times current salary levels, 13% (31%) of medical students (doctors) were willing to accept rural jobs. At half this level, 61% (52%) of nursing students (nurses) accepted a rural job. The strategy of reserving seats for specialist training in exchange for rural service had a large effect on job acceptance among doctors, nurses and nursing students. For doctors and nurses, properly staffed and equipped health facilities, and housing had small effects on job acceptance. Rural upbringing was not associated with rural job acceptance. Incentivizing doctors for rural service is expensive. A broader strategy of substantial salary increases with improved living, working environment, and education incentives is necessary. For both doctors and nurses, the usual strategies of moderate salary increases, good facility infrastructure, and housing will not be effective. Non-physician clinicians like nurse-practitioners offer an affordable alternative for delivering rural health care.     

Numerical simulation of systemic O2 and CO2 exchange in a hyperbaric environment

The process of gas exchange in systemic capillaries and its surrounding tissue is simulated numerically in a hyperbaric environment, taking into account the molecular diffusion, convection, saturation of haemoglobin with O2 and CO2, and the metabolic activity in the tissue. Krogh tissue-cylinder is used as a geometrical representation of the capillary-tissue system. The resulting system of non-linear governing equations together with the physiologically relevant boundary conditions is solved numerically. It is found that the concentration of oxygen decreases from the axis of the capillary to the tissue periphery whereas the concentration of carbon dioxide increases. It is shown that very little CO2 is transported radially. The location of the vulnerable region from the point of view of CO2 accumulation is found to be the rim (r = R2, z = L) situated at the periphery of the tissue near the venous end of the capillary. It is also found that accumulation of O2 decreases whereas that of CO2 increases in a hyperbaric environment. Finally, it is surmised that one of the reasons in causing discomfort among divers could be excessive accumulation of CO2 in the tissue.     

Structural Basis for Allosteric Coupling at the Membrane-Protein Interface in Gloeobacter violaceus Ligand-gated Ion Channel (GLIC)

Ligand binding at the extracellular domain of pentameric ligand-gated ion channels initiates a relay of conformational changes that culminates at the gate within the transmembrane domain. The interface between the two domains is a key structural entity that governs gating. Molecular events in signal transduction at the interface are poorly defined because of its intrinsically dynamic nature combined with functional modulation by membrane lipid and water vestibules. Here we used electron paramagnetic resonance spectroscopy to delineate protein motions underlying Gloeobacter violaceus ligand-gated ion channel gating in a membrane environment and report the interface conformation in the closed and the desensitized states. Extensive intrasubunit interactions were observed in the closed state that are weakened upon desensitization and replaced by newer intersubunit contacts. Gating involves major rearrangements of the interfacial loops, accompanied by reorganization of the protein-lipid-water interface. These structural changes may serve as targets for modulation of gating by lipids, alcohols, and amphipathic drug molecules.     

Arginine metabolic pathways determine its therapeutic benefit in experimental heatstroke: Role of Th1/Th2 cytokine balance

We have demonstrated that therapeutic administration of L-arginine (L-arg) (120 mg/kg) at +2 h of whole body hyperthermia (WBH) could rescue the mice from heatstroke-induced death. Studies were undertaken to elucidate the role of L-arg in the immunomodulation of the heat-stressed mice. Administration of L-arginine (L-arg), (120 mg/kg, i.p.), at +2 h of WBH, rescued the mice from heat-induced death and reduced the hypothermia. At +4 and +24 h of WBH, levels of IL-1beta, IFN-gamma, nitrite, TNF-alpha, IL-4, TGF-beta1, inducible form of nitric oxide synthase (iNOS), and corticosterone significantly increased compared to the sham group. The elevated levels of Th(1) cytokines, namely TNF-alpha, IL-1beta, IFN-gamma, nitrite, and iNOS, decreased significantly both at +4 and +24 h of WBH, following L-arg administration. However, L-arg administration did not reduce the increased levels of Th(2) cytokines, namely IL-4 and TGF-beta1, in WBH mice at +4 h of WBH. L-arg administration significantly increased the levels of Th(2) cytokines at +24 h of WBH, compared to the saline-treated WBH mice. L-arg administration significantly increased both the splenic and hepatic arginase activity at +4 and +24 h of WBH compared to the saline-treated WBH mice. L-NAME treatment at +2 h of WBH and anti-TGF-beta antibody treatment at 0 h of WBH significantly increased the mortality compared to the saline-treated WBH mice. Altered liver histopathology was attenuated following the administration of L-arg at +2 h of WBH. These results suggest that therapeutic administration of L-arg at appropriate concentration and time attenuates the acute inflammatory response, leading to the rescue of mice from heatstroke.     

Characterization of a novel xylanase from Armillaria gemina and its immobilization onto SiO2 nanoparticles

Enhanced catalytic activities of different lignocellulases were obtained from Armillaria gemina under statistically optimized parameters using a jar fermenter. This strain showed maximum xylanase, endoglucanase, cellobiohydrolase, and β-glucosidase activities of 1,270, 146, 34, and 15 U mL^?1, respectively. Purified A. gemina xylanase (AgXyl) has the highest catalytic efficiency (k _cat/K _m?=?1,440 mg?mL^?1?s^?1) ever reported for any fungal xylanase, highlighting the significance of the current study. We covalently immobilized the crude xylanase preparation onto functionalized silicon oxide nanoparticles, achieving 117 % immobilization efficiency. Further immobilization caused a shift in the optimal pH and temperature, along with a fourfold improvement in the half-life of crude AgXyl. Immobilized AgXyl gave 37.8 % higher production of xylooligosaccharides compared to free enzyme. After 17 cycles, the immobilized enzyme retained 92 % of the original activity, demonstrating its potential for the synthesis of xylooligosaccharides in industrial applications.