Protein homology modeling and structure-function relationship of 2009 swine influenza virus hemagglutinin (HA1): more human than swine

The virulence and transmissibility of viruses are highly associated with their binding specificity to the host cell receptor. In influenza, this initial event of viral pathogenesis is mediated by a glycoprotein known as hemagglutinin (HA). In the present study we constructed homology models of the chain A of hemagglutinin (HA1) of 2009 swine influenza strain. The modeled proteins were compared with atomic coordinates of 1918 (Spanish flu strain) and 1930 HA1 (swine influenza strain). HA1 of recent swine influenza strain showed 84.83% and 93.14% homology with the same versions of 1918 and 1930 strains, respectively. Discrepancies in multiple sequence alignment particularly at the ligand-binding residues notified its receptor specificity to α-2,6 sialic acids in 1918 and 2009 viral strains in contrast to α-2,3 sialic acids as found in 1930 swine flu strain. This implicated the relatively closer relationship of 2009 strain with 1918 strain rather than swine origin strain of 1930. Similarly, the spatial orientations of receptor-binding residues, located in 190-helix, 130-loop and 220-loop, were found more aligned in 1918 and 2009 (RMSD 0.98 Å) than in 1930 and 2009 (RMSD 1.06 Å) strains HA1. More similarities were established between both human origin influenza viruses (1918 and 2009 strains) by the receptor-binding cavity architecture and the orientation of protease cleavage site (Arg327). Briefly, the present finding is expected to show molecular discrepancies and congruencies among the recent and past pandemic influenza strains and may also potentially illustrate the drug targets to rein the infection at earlier stages.     

New promising high yielding cotton Bt-Variety RH-647 adapted for specific agro-climatic zone

The Bt-cotton RH-647 was developed by Cotton Research Institute CRI, Khanpur has been acknowledged for its possesses superior plant characteristics and potential to yield out under harsh agro-climatic conditions of cotton productive district of Rahimyar Khan in Bahawalpur Division and southern Punjab in 2016. RH- 647 for its novel plant structure and improved fiber quality heat and drought tolerant to withstand successfully sustain yield out in harsh, highly variable hot and dry climatic conditions of and harsh seasoned. RH-647 was developed through one-way hybridization of elite parental genotypes accompanied by pedigree selection method through gene pyramiding technique for incorporation of excellent combinations of fiber traits and CLCuV disease tolerance with higher yield potential right from F1 population. The superior plant combinations were selected in F2-F6 generations were entirely based on phenotypic plant traits and progeny yield potential in field, plant shape, number of bolls per plant, average boll weight (g) and fiber quality traits over standard varieties. The single plant progenies were selected 56 sister lines were tested for Bt-gene (Cry1 Ac) were evaluated for high yielding performance for this superior cross and finally RH-647 as superior breeding line was bulked in year 2010. The strain was evaluated in Randomized Complete Block Design in preliminary yield trials (PYT) and two years in Advance Yield Trials (AYT) trials and Zonal Varietal trials for two years. The superior line 647/10 was ensued for performance in variety attestation tests as RH-647. RH-647 performed best in two years varietal trials (NCVT and PCCT and DUS) conducted for two successive growing seasons (2014–2015 and 2015–2016). RH-647 yielded out significantly compared with standard varieties MNH-886, FH-142 and CIM 602. After completion of mandatory trials in year 2016, RH-647 was approved as new Bt. cotton variety “RH-647”. RH-647 is early in maturity with high yield potential and best suited for wheat-cotton cropping pattern. It has fluffy opening and is easy to pick, strongly tolerant to CLCuV disease, high Ginning out turn GOT% (40.2%) with improved fiber traits; staple length (28.3 mm), fiber strength (4.2ug/inch) is duly capable to fulfill all industrial requisitions.     

Assessment of intraluminal impedance for the detection of pharyngeal bolus flow during swallowing in healthy adults

Intraluminal impedance, a nonradiological method for assessing bolus flow within the gut, may be suitable for investigating pharyngeal disorders. This study evaluated an impedance technique for the detection of pharyngeal bolus flow during swallowing. Patterns of pharyngoesophageal pressure and impedance were simultaneously recorded with videofluoroscopy in 10 healthy volunteers during swallowing of liquid, semisolid, and solid boluses. The timing of bolus head and tail passage recorded by fluoroscopy was correlated with the timing of impedance drop and recovery at each recording site. Bolus swallowing produced a drop in impedance from baseline followed by a recovery to at least 50% of baseline. The timing of the pharyngeal and esophageal impedance drop correlated with the timing of the arrival of the bolus head. In the pharynx, the timing of impedance recovery was delayed relative to the timing of clearance of the bolus tail. In contrast, in the upper esophageal sphincter (UES) and proximal esophagus, the timing of impedance recovery correlated well with the timing of clearance of the bolus tail. Impedance-based estimates of pharyngoesophageal bolus clearance time correlated with true pharyngoesophageal bolus clearance time. Patterns of intraluminal impedance recorded in the pharynx during bolus swallowing are therefore more complex than those in the esophagus. During swallowing, mucosal contact between the tongue base and posterior pharyngeal wall prolongs the duration of pharyngeal impedance drop, leading to overestimation of bolus tail timing. Therefore, we conclude that intraluminal impedance measurement does not accurately reflect the bolus transit in the pharynx but does accurately reflect bolus transit across the UES and below.     

Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY

Cation-coupled active transport is an essential cellular process found ubiquitously in all living organisms. Here, we present two novel ligand-free X-ray structures of the lactose permease (LacY) of Escherichia coli determined at acidic and neutral pH, and propose a model for the mechanism of coupling between lactose and H+ translocation. No sugar-binding site is observed in the absence of ligand, and deprotonation of the key residue Glu269 is associated with ligand binding. Thus, substrate induces formation of the sugar-binding site, as well as the initial step in H+ transduction.     

Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design

HTP (human thymidine phosphorylase), also known as PD-ECGF (platelet-derived endothelial cell growth factor) or gliostatin, has an important role in nucleoside metabolism. HTP is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose phosphate and product inhibition by both ligands. We have determined the structure of HTP from crystals grown in the presence of thymidine, which, surprisingly, resulted in bound thymine with HTP in a closed dead-end complex. Thus thymine appears to be able to reassociate with HTP after its initial ordered release before ribose phosphate and induces the closed conformation, hence explaining the mechanism of non-competitive product inhibition. In the active site in one of the four HTP molecules within the crystal asymmetric unit, additional electron density is present. This density has not been previously seen in any pyrimidine nucleoside phosphorylase and it defines a subsite that may be exploitable in drug design. Finally, because our crystals did not require proteolysed HTP to grow, the structure reveals a loop (residues 406-415), disordered in the previous HTP structure. This loop extends across the active-site cleft and appears to stabilize the dimer interface and the closed conformation by hydrogen-bonding. The present study will assist in the design of HTP inhibitors that could lead to drugs for anti-angiogenesis as well as for the potentiation of other nucleoside drugs.     

Ultrastructure and movements of cell organelles in the root cap of agravitropic mutants and normal seedlings of Arabidopsis thaliana

The root anatomy and ultrastructure of the agravitropic Arabidopsis thaliana L. mutants Dwf and aux-1 were compared with the gravitropic mutant aux-2 and the wild type (WT) in an attempt to find an explanation for the lack of response to gravity. No differences were found in the organization of the root cap. The central part of the cap (columella) contains 5 storeys of developing, functioning and degenerating statocytes. Their ultrastructure is very similar in all four types of plant. Particular attention was paid to the distribution of rough endoplasmie reticulum (ER). Both in the WT and the mutants the ER is concentrated in the distal part at the "floor" of the cell.
Light micrographs were used to compare the sedimentation rates of movable cell structures in normal and agravitropic root statocytes. A longitudinal movement of amyloplasts and nuclei was observed when the roots were inverted. In WT and aux-2 the rates were on average 6.3 μm h⁻¹ (amyloplasts) and 2.1 μm h⁻¹ (nucleus). In aux-1 the sedimentation rates were significantly lower: 2.4 and 0.6 μm h⁻¹, respectively. Based on magnified electron micrographs of normal and inverted statocytes a morphometrical analysis of the distribution and redistribution of amyloplasts, nuclei, mitochondria, vacuoles and ER was made. The only significant difference was found in the redistribution of amyloplasts between aux-1 and the gravitropical normal types.     

The effect of weak auxins on the growth of blue-green algae

Summary 5-Hydroxy indole-3-acetic acid promoted the growth (increase in dry weight) of Anacystis nidulans, Chlorogloea fritschii, Phormidium foveolarum, Nostoc muscorum and Tolypothrix tenuis. 5-Hydroxy tryptamine stimulated the growth of Chlorogloea fritschii and Nostoc muscorum. Phenyl-acetic acid promoted the growth of Nostoc muscorum and Tolypothrix tenuis. Tryptophol stimulated the growth of Chlorogloea fritschii, it failed to stimulate the growth of Nostoc muscorum. Isatin promoted the growth of Anacystis nidulans and Chlorogloea fritschii 2, 3, 5-triidobenzoic acid inhibited the growth of Anacystis nidulans, Chlorogloea fritschii, Phormidium foveolarum, Nostoc muscorum and Tolypothrix tenuis.     

Protein and lipid utilization during fasting with shallow and deep hypothermia in the European hedgehog (Erinaceus europaeus)

We investigated whether the relative contributions of body protein and lipid reserves differ according to the level of energy expenditure in fasting animals. Protein and lipid utilization was therefore quantified and compared in hedgehogs which fasted with shallow and deep hypothermia, i.e. by exposure at 5 or 20 °C ambient temperature. Body composition was determined for every 150-g decrease in mass throughout the experiment, allowing the calculation of regression lines between body mass (independent variable, x) and body composition (dependent variable, y: water, protein, neutral lipids, phospholipids and cholesterol). There were highly significant (P<0.001) linear decreases in all body components with decreasing body mass in both groups of hedgehogs. Neutral lipids were the main component of the total body mass loss (54%) in fasted animals with shallow and deep hypothermia, percentages of water (26–30%) and protein (10–11%) being lower, and those of phospholipid and cholesterol negligible (<0.5%). In spite of different levels in energy expenditure (2.54 and 1.07 W·kg^-1 in shallow-and deep-hypothermal fasting hedgehogs, respectively), the energy sources were identical in both groups, neutral lipid being the main fuel (91–92%) and body protein accounting for the remainder (8–9%). Prolonged fasting with shallow and deep hypothermia were marked by low alaninemia and glycemia, while plasma free fatty acids and -hydroxybutyrate were elevated. These data therefore indicate that the relative contribution of lipid and protein is similar during prolonged fasting with shallow and deep hypothermia, i.e. there is no specific effect of deep hypothermia on body fuel utilization. The tolerance of a much longer fast in deep-hypothermal hedgehogs can simply be attributed to the lower rates of lipid and protein utilization as a result of the lower level of energy expenditure.Abbreviations bm body mass     

PCR-amplified 16S rRNA sequence analysis to confirm nodulation of Datisca cannabina L. by the endophyte of Coriaria nepalensis Wall

Different Frankia strains and crushed nodule suspensions were tested for their ability to nodulate Coriaria nepalensis and Datisca cannabina. Datisca cannabina seedlings were nodulated effectively by both crushed nodule suspension from Coriaria nepalensis and Datisca cannabina. The origin of the endophyte in Datisca nodules induced by crushed nodules of Coriaria was confirmed by comparing partial PCR-amplified 16S rRNA sequences with those of the endophytes of both plants. Coriaria seedlings could only be nodulated by crushed nodule suspensions of Coriaria nepalensis. All pure cultures of Frankia used as a single inoculum source or in combinations with a nodule filtrate, failed to induce nodulation on Coriaria. Two atypical Frankia strains Cn3 and Cn7 isolated from Coriaria nodules showed no acetylene reduction activity and did not induce nodulation on the host seedlings.