Identification of quantitative trait locus (QTL) linked to dorsal fin length from preliminary linkage map of molly fish, Poecilia sp.

A preliminary linkage map was constructed by applying backcross and testcross strategy using microsatellite (SSR) markers developed for Xiphophorus and Poecilia reticulata in ornamental fish, molly Poecilia sp. The linkage map having 18 SSR loci consisted of four linkage groups that spanned a map size of 516.1 cM. Association between genotypes and phenotypes was tested in a random fashion and QTL for dorsal fin length was found to be linked to locus Msb069 on linkage group 2. Coincidentally, locus Msb069 was also reported as putative homologue primer pairs containing SSRs repeat motif which encoded hSMP-1, a sex determining locus. Dorsal fin length particularly in males of Poecilia latipinna is an important feature during courtship display. Therefore, we speculate that both dorsal fin length and putative hSMP-1 gene formed a close proximity to male sexual characteristics.     

Semisynthetic ‘acid-esterase’: Conformational modification of ribonuclease

Bovine pancreatic ribonuclease has been modified by exposure to acidic conditions, addition of indole propionic acid and crosslinking with glutaraldehyde. The ‘acid-esterase’ generated was purified up to 100-fold by ammonium sulphate fractionation and gel filtration on Biogel P-30. The partially purified acid-esterase hydrolysed tryptophan ethyl ester (TrEE) and $\text{N-}\text{benzoyl}\text{-}\text{l}\text{-}\text{arginine}$ ethyl ester (BAEE) effectively at pH 6.0–6.3, but it had very little activity towards glycine ethyl ester and lysine ethyl ester. Hydrolysis of TrEE was competitively inhibited by tryptophan. The acid-esterase exhibited amidase activity towards benzoyl-l-arginine p-nitroanilide.     

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone‐efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user‐friendly, standalone program package named PSN‐Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X‐ray structures. The novelty in network construction lies in the explicit consideration of side‐chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long‐range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross‐correlation/interaction energy in PSN‐Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN‐Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin‐conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN‐Ensemble for single‐static structures of active/inactive states of β2‐adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN‐Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN‐Ensemble/psn_index.html .     

Apolipoprotein B-related gene expression and ultrastructural characteristics of lipoprotein secretion in mouse yolk sac during embryonic development.

In mice, the yolk sac appears to play a crucial role in nourishing the developing embryo, especially during embryonic days (E) 7;-10. Lipoprotein synthesis and secretion may be essential for this function: embryos lacking apolipoprotein (apo) B or microsomal triglyceride transfer protein (MTP), both of which participate in the assembly of triglyceride-rich lipoproteins, are apparently defective in their ability to export lipoproteins from yolk sac endoderm cells and die during mid-gestation. We therefore analyzed the embryonic expression of apoB, MTP, and alpha-tocopherol transfer protein (alpha-TTP), which have been associated with the assembly and secretion of apoB-containing lipoproteins in the adult liver, at different developmental time points. MTP expression or activity was found in the yolk sac and fetal liver, and low levels of activity were detected in E18.5 placentas. alpha-TTP mRNA and protein were detectable in the fetal liver, but not in the yolk sac or placenta. Ultrastructural analysis of yolk sac visceral endoderm cells demonstrated nascent VLDL within the luminal spaces of the rough endoplasmic reticulum and Golgi apparatus at E7.5 and E8.5. The particles were reduced in diameter at E13.5 and reduced in number at E18.5;-19.The data support the hypothesis that the yolk sac plays a vital role in providing lipids and lipid-soluble nutrients to embryos during the early phases (E7;-10) of mouse development. secretion in mouse yolk sac during embryonic development.     

Differences in evolutionary pressure acting within highly conserved ortholog groups

Background  

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes).     

Role of galactose in bovine factor V.

Using galactose oxidase as well as beta-galactosidase to produce modifications of the galactose units, the functional significance of these carbohydrate residues on the coagulant activity of bovine Factor V glycoprotein was evaluated. Incubation of native Factor V with galactose oxidase or hydrolysis of asialo-Factor V with beta-galactosidase results in a loss of Factor V activity. The inactivation of Factor V by oxidation of galactose moieties is partially reversible upon reduction of the newly formed aldehyde groups with sodium borohydride. The extent of reversal depends upon the degree of inactivation achieved. Thus, Factor V which retained 30% of the original activity following galactose oxidation returns to 75% of the original coagulant activity upon borohydride reduction; but, after destruction of 85% of the original activity treatment with borohydride returns to about 30%. In the initial stages of the inactivation of Factor V by treatment with galactose oxidase, the loss of Factor V coagulant activity is directly proportional to the moles of galactose oxidized. However, as the reaction progresses, the rate of galactose oxidation exceeds the rate of loss of Factor V activity. Moreover, galactose oxidation continues even after complete inactivation of Factor V. These results suggest that the galactose residues most susceptible to attack by galactose oxidase are those necessary for the activity of this coagulant protein. Only 15 galactose residues/mol of Factor V are susceptible to galactose oxidase prior to removal of sialic acid. In contrast, 37 galactose residues/mol of Factor V are found after acid hydrolysis. These results suggest that Factor V glycoprotein contains more than one type of sialyl-galactose linkages, the C2,3 or C2,4 linkages susceptible to oxidation in the native protein and the C2,6 linkage which is resistant. Native Factor V binds with diarachidonyl lecithin forming an active complex of lower buoyant density, while the Factor V oxidized with galactose oxidase does not. The Factor V-phospholipid complex is protected from inactivation by galactose oxidase. Moreover, lipid binding diminishes the extent of oxidation of galactose residues. Certain galactose groups are essential for coagulant activity probably because they are required for binding to phospholipid, a prerequisite to Factor V action.