Reinvestigating the codon and amino acid usage of S. cerevisiae genome: a new insight from protein secondary structure analysis

Biased usage of synonymous codons has been elucidated under the perspective of cellular tRNA abundance for quite a long time now. Taking advantage of publicly available gene expression data for Saccharomyces cerevisiae, a systematic analysis of the codon and amino acid usages in two different coding regions corresponding to the regular (helix and strand) as well as the irregular (coil) protein secondary structures, have been performed. Our analyses suggest that apart from tRNA abundance, mRNA folding stability is another major evolutionary force in shaping the codon and amino acid usage differences between the highly and lowly expressed genes in S. cerevisiae genome and surprisingly it depends on the coding regions corresponding to the secondary structures of the encoded proteins. This is obviously a new paradigm in understanding the codon usage in S. cerevisiae. Differential amino acid usage between highly and lowly expressed genes in the regions coding for the irregular protein secondary structure in S. cerevisiae is expounded by the stability of the mRNA folded structure. Irrespective of the protein secondary structural type, the highly expressed genes always tend to encode cheaper amino acids in order to reduce the overall biosynthetic cost of production of the corresponding protein. This study supports the hypothesis that the tRNA abundance is a consequence of and not a reason for the biased usage of amino acid between highly and lowly expressed genes.     

A preliminary pharmacokinetic study of the enantiomers of the terfenadine acid metabolite in humans

A stereoselective and sensitive achiral/chiral method for the determination of terfenadine acid metabolite in human plasma was developed. The metabolite was separated and quantitated using an achiral chromatographic procedure with a cyano column. The mobile phase was 1 mM sodium acetate buffer (pH 4.0) and acetonitrile (25:75% v/v) at a flow rate of 2 ml/min, at ambient temperature. The stereospecific resolution was accomplished using a chiral-AGP column and a mobile phase consisting of sodium acetate (0.01 M): methanol (98.7:1.3% v/v), and 20 mM di-n-butylamine at a flow rate of 1.2 ml/min. The column temperature was maintained at 32°C. The eluent was monitored at 230 nm (excitation) and 300 nm (emission) with a cut-off filter at 270 nm. This assay was used for a pharmacokinetic study in five subjects after administration of a single dose of 60 mg of terfenadine. The t_½ values of the two enantiomers were similar, but the AUC values of the (+)-enantiomer were 2.05–2.35 times higher than those of (?)-enantiomer. © 1994 Wiley-Liss, Inc.     

Searching Biomarkers in the Sequenced Genomes of <Emphasis Type="Italic">Staphylococcus</Emphasis> for their Rapid Identification

Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5–6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-016-0565-9) contains supplementary material, which is available to authorized users.     

Design,Synthesis, and Antimycobacterial Evaluation of Novel Tetrahydroisoquinoline Hydrazide Analogs

A series of novel 2-substituted-5,7-dichloro-1,2,3,4-tetrahydroisoquinoline-6-carbohydrazide were designed, synthesized and structures were confirmed by analytical methods, viz., ¹H-NMR, ¹³C-NMR and Mass spectrometry. Synthesized derivatives were evaluated for their anti-mycobacterial activity against Mycobacterium tuberculosis (Mtb) H37Ra. Among all the evaluated compounds, 10A25 containing biphenyl moiety exhibited significant inhibition with IC₅₀ 4.7 μM. 10A19 , with an electron-withdrawing Iodo group in the ortho position of the phenyl exhibited significant anti-tubercular activity with IC₅₀ 8.8 μM. IC₅₀ values of the remaining compounds ranged from 9.2 to 73.6 μM. Molecular docking study of the significantly active compound 10A25 was performed to determine the putative binding position of the test ligand at the active site of the selected target proteins Mycobacterium tuberculosis enoyl reductase (InhA) PDB – 4TZK and peptide deformylase PDB – 3E3U. A suitable single crystal for one of the active compounds, 10A12 , was generated and analysed to further confirm the structure of the compounds.     

Polymorphism in chemokine receptor genes and risk of acute myocardial infarction in North Indian population

Chemokines regulates the trafficking of leukocytes to the site of inflammation hence may be implicated in cardiac events. Currently no consistent effects have been revealed their role in acute myocardial infarction (MI). The aim of current study was to investigate the impact of human chemokine receptor genetic variants, CCR5-Δ32 insertion/deletion, CCR5-59029-A/G, CX3CR1-V249I and CX3CR1-T280 M on acute MI. 230 acute MI and 300 controls were examined. Patients carrying CCR5-Δ32 genotype were at three times higher risk of developing MI odds ratio (OR, 3.24, CI 1.127–9.356, P = 0.04). Significant association was found with risk of acute MI in recipients who possessed homozygous 59029-A allele (OR 1.47, CI 1.03–2.09, P = 0.03). While CX3CR1-I249 and M280 were found to be protective in MI patients with OR 0.46, CI 0.32–0.66, P < 0.0001 and OR 0.36, CI 0.24–0.55, P < 0.0001, respectively. It might be possible that risk of acute MI is associated with genetic variation in chemokine receptors, i.e., CCR5 and CX3CR1.     

Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4–6 base cutters). Yersinia species have 6–7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences—carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0552-6) contains supplementary material, which is available to authorized users.     

Effect of potassium salts and distillery effluent on carbon mineralization in soil

Distillery effluent, a rich source of potassium, is used for irrigation at many places in the world. A laboratory experiment was conducted to study the influence of potassium salts present in post-methanation distillery effluent (PME) along with two other salts, KCl and K2SO4, on mineralization of carbon in soil. PME oxidized with H2O2, raw PME, KCl and K2SO4 solutions containing K equivalent to 10%, 20%, 40% and 100% of K present in PME were added to the soil separately, maintaining four replications for each treatment and control. Addition of salts up to a certain concentration stimulated C mineralization but a decline was noticed at higher concentrations. All the levels of salts caused higher CO2 evolution than the control suggesting that the presence of K salts enhanced the microbial activity resulting in increased CO2 evolution. The influence of K2SO4 was significantly higher than KCl in stimulating C mineralization in soil. Oxidized effluent had a higher stimulating effect than inorganic salts, showing the influence of other salts accompanying K in the PME. Raw PME, which contained excess organic C, increased CO2 evolution even at the highest salt level (100% PME) signifying the effect of added C on alleviating the salt stress on microbial activity.     

Quantification of the calcium-induced secondary structural changes in the regulatory domain of troponin-C.

The backbone resonance assignments have been completed for the apo (1H and 15N) and calcium-loaded (1H, 15N, and 13C) regulatory N-domain of chicken skeletal troponin-C (1-90), using multidimensional homonuclear and heteronuclear NMR spectroscopy. The chemical-shift information, along with detailed NOE analysis and 3JHNH alpha coupling constants, permitted the determination and quantification of the Ca(2+)-induced secondary structural change in the N-domain of TnC. For both structures, 5 helices and 2 short beta-strands were found, as was observed in the apo N-domain of the crystal structure of whole TnC (Herzberg O, James MNG, 1988, J Mol Biol 203:761-779). The NMR solution structure of the apo form is indistinguishable from the crystal structure, whereas some structural differences are evident when comparing the 2Ca2+ state solution structure with the apo one. The major conformational change observed is the straightening of helix-B upon Ca2+ binding. The possible importance and role of this conformational change is explored. Previous CD studies on the regulatory domain of TnC showed a significant Ca(2+)-induced increase in negative ellipticity, suggesting a significant increase in helical content upon Ca2+ binding. The present study shows that there is virtually no change in alpha-helical content associated with the transition from apo to the 2Ca2+ state of the N-domain of TnC. Therefore, the Ca(2+)-induced increase in ellipticity observed by CD does not relate to a change in helical content, but more likely to changes in spatial orientation of helices.     

Brinckochrysa scelestes [Neur.: Chrysopidae] as predator ofMyzus persicae [Hom.: Aphididae] on tobacco

Laboratory and field studies were conducted to study the suitability and efficacy ofBrinckochrysa scelestes Banks as a predator onMyzus persicae Sulzer in tobacco fields. Laboratory bred 2nd instar larvae ofB. scelestes at 6 per tobacco plant reduced the aphid population to the extent of 78% in 2 weeks. The movement of the predatory larvae on the tobacco plant and leaf was not at all hampered by the glandular trichomes and their secretions. The larvae moved freely and fed well and their pupae were recovered from all over the plant.

---

Résumé On étudie en laboratoire et en champ de tabac la valeur et l'efficacité deBrinckchrysa scelestes Banks comme agent de lutte biologique contreMyzus persicae Sulzer. Les larves du 2ème stade élevées en laboratoire de ce chrysope à raison de 6 par plante sont les plus actives et réduisent la population de pucerons de 78% en 2 semaines. Les sécrétions des trichomes des feuilles de tabac n'ont pas d'effet sur les larves ni sur leurs mouvements. Les larves se déplacent librement et se nourissent bien; des nymphes ont été trouvées sur tous les plants, ce qui indique que le prédateur est valable contreM. persicae et bien adapté à la culture de tabac.