Phytoplankton and nutrient dynamics of shallow coastal stations at Bay of Bengal,Eastern Indian coast

Phytoplankton dynamics of Eastern Indian coast was studied from surface water for a period of 24 months (April 2005–March 2007) in relation to environmental variables like, temperature, pH, dissolved oxygen, biochemical oxygen demand (BOD), salinity and nutrient contents—including nitrate, phosphate and silicate. Total 43 taxa were recorded during the study period. Phytoplankton density ranged from approximately 350–3,000 cells/ml and showed complete dominance of diatom genera namely, Asterionella japonica in winter and Odontella rhombus in summer. Other frequently occurring diatoms were Coscinodiscus perforatus, Actinocyclus normanii f. subsala, Thalassiothrix fraunfeldii, Ditylum brightwelli, Stephanodiscus hantzschoides, Cyclotella meneghiniana, Thalassionema nitzschoides etc. Seasonal changes in abundance and diversity of phytoplankton significantly differed showing maximum diversity in autumn with high diversity index (2.76-Oct, 05) and minimum in winter (0.326-January, 06). The species evenness varied from 0.137 (January 06) to 0.991 (August 06), which signifies minimum variation in percentage contribution of individual species to total phytoplankton population in monsoon and maximum in winter. Correlation studies of total cell count to physicochemical variables indicated significant positive relation with dissolved oxygen, salinity and pH but negative relation with nitrate, silicate and BOD of the water body. Multivariate procedures like ordination by principal component analysis and multi dimensional scaling of phytoplankton population based on their occurrence data and magnitude of abundance indicated that some genera (Biddulphia heteroceros, B. dubia, Odontella aurita, Gyrosigma acuminatum, Coscinodiscus granii, Paralia sulcata, etc.) have specific preference for water temperature and salinity and flourished maximally in particular season(s). While other genera (A. japonica, C. meneghiniana, C. perforatus, D. brightwelli, S. hantzschoides, etc.) appeared in wide range of temperature and salinity gradient.     

C-terminal region amino acid substitutions contribute to catalytic differences between murine class alpha glutathione transferases mGSTA1-1 and mGSTA2-2 toward anti-diol epoxide isomers of benzo[c]phenanthrene

The molecular basis for catalytic differences between structurally closely related murine class alpha glutathione (GSH) transferases mGSTA1-1 and mGSTA2-2 in the GSH conjugation of anti-diol epoxide isomers of benzo[c]phenanthrene (anti-B[c]PDE) was investigated. GSH conjugation of both (-)- and (+)-enantiomers of anti-B[c]PDE was observed in the presence of mGSTA1-1 (60 and 40% GSH conjugation, respectively), whereas mGSTA2-2 exhibited a preference for the (-)-anti-isomer (>97%). In addition, the specific activity of mGSTA2-2 toward the (-)-anti-B[c]PDE isomer was relatively higher than that of mGSTA1-1. The amino acid sequences of mGSTA1-1 and mGSTA2-2 differ at 10 positions that are distributed in three sections. Section I contains amino acid residues in positions 65 and 95; section II contains residues in positions 157, 162, and 169, and section III contains residues in positions 207, 213, 218, 221, and 222. Enzyme activity measurements with chimeras of mGSTA1-1 and mGSTA2-2 revealed that amino acid substitutions in section III account for their differential enantioselectivity and catalytic activity toward anti-B[c]PDE. Site-directed mutagenesis of amino acid residues in section III of mGSTA2-2 with corresponding residues of mGSTA1-1 followed by activity measurements of the wild type and mutated enzymes indicates that leucine 207 and phenylalanine 221 may be critical for the high catalytic activity of mGSTA2-2 toward (-)-anti-B[c]PDE. Molecular modeling studies demonstrated that the active site of mGSTA1-1 accommodates both enantiomers of anti-B[c]PDE, whereas the (-)-anti-isomer interacts more favorably with active site residues in mGSTA2-2. The results of this study clearly indicate that amino acid substitutions in the C-terminal region contribute to catalytic differences between mGSTA1-1 and mGSTA2-2 with respect to anti-B[c]PDE.     

Purification and properties of cis-aconitic decarboxylase

Summary Lyophilized and stored in a deep-freeze, the mycelial material was found to retain cis-aconitic decarboxylase activity unimpaired at the end of 2 months. Mycelia could be stored also in the frozen condition but after squeezing hard to remove as much of adherent water as possible. Extracts with maximum cis-aconitic decarboxylase activity were obtained when the frozen or better the lyophilized mycelia of Aspergillus terreus were ground in a mortar with phosphate buffer using pyrex glass powder as abrasive. Cis-aconitic decarboxylase was purified 25-fold by fractionation with ammonium sulfate, starting from extracts of the mycelia in phosphate buffer. The purified enzyme was considerably more stable than the crude extracts to storage and dialysis. The optimum pH was 5.8 using 0.2 m phosphate buffer; Km value was 5×10^-3 m at pH 5.8 and 37°C. EDTA and 8-hydroxyquinoline activated the enzyme; all metals tested inhibited the enzyme, Zn⁺⁺ and Cu⁺⁺ leading to complete inactivation. Fluoride, arsenite and azide also inhibited the enzyme activity.     

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding

Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify alpha-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi,psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding.     

Molecular recognition of a model globular protein apomyoglobin by synthetic receptor cyclodextrin: effect of fluorescence modification of the protein and cavity size of the receptor in the interaction

Labelling of proteins with some extrinsic probe is unavoidable in molecular biology research. Particularly, spectroscopic studies in the optical region require fluorescence modification of native proteins by attaching polycyclic aromatic fluoroprobe with the proteins under investigation. Our present study aims to address the consequence of the attachment of a fluoroprobe at the protein surface in the molecular recognition of the protein by selectively small model receptor. A spectroscopic study involving apomyoglobin (Apo‐Mb) and cyclodextrin (CyD) of various cavity sizes as model globular protein and synthetic receptors, respectively, using steady‐state and picosecond‐resolved techniques, is detailed here. A study involving Förster resonance energy transfer, between intrinsic amino acid tryptophan (donor) and N, N‐dimethyl naphthalene moiety of the extrinsic dansyl probes at the surface of Apo‐Mb, precisely monitor changes in donor acceptor distance as a consequence of interaction of the protein with CyD having different cavity sizes (β and γ variety). Molecular modelling studies on the interaction of tryptophan and dansyl probe with β‐CyD is reported here and found to be consistent with the experimental observations. In order to investigate structural aspects of the interacting protein, we have used circular dichroism spectroscopy. Temperature‐dependent circular dichroism studies explore the change in the secondary structure of Apo‐Mb in association with CyD, before and after fluorescence modification of the protein. Overall, the study well exemplifies approaches to protein recognition by CyD as a synthetic receptor and offers a cautionary note on the use of hydrophobic fluorescent labels for proteins in biochemical studies involving recognition of molecules. Copyright © 2013 John Wiley & Sons, Ltd.     

Descriptive epidemiology of intestinal helminth parasites from stray cat populations in Qatar

A total of 488 stray cats, 212 adult and 29 juvenile females plus 235 adult and 12 juvenile males, were examined post-mortem during the winter and summer months of 2006 from five sites in the vicinity of Doha and its outskirts. Five helminths, comprising three nematode and two cestode species were identified and the majority of cats harboured two of these species. The most prevalent was the cestode Taenia taeniaeformis (75.8%), followed by the cestode Diplopylidium sp. (42.8%), and the nematodes Ancylostoma tubaeforme (17.0%), Physaloptera sp. (6.6%) and Toxocara cati (0.8%). All five species were found to be typically overdispersed in their distribution. Using univariate and multivariate analyses, the prevalence and abundance of infections were primarily influenced by host gender and season, with females tending to harbour higher levels of infection during the summer. No significant differences were found relative to site except in the case of Physaloptera sp. Using bivariate Pearson product moment correlations, significant positive co-occurrences were identified between Diplopylidium sp. and T. taeniaeformis and also between A. tubaeforme and T. taeniaeformis. The results are discussed in relation to the effect of environmental conditions on the intestinal helminth infracommunities and their possible interactions in stray cat populations from such a harsh and arid region as Qatar.     

Role of arterial blood gas (ABG) as a valuable assessment tool of disease severity in SARS-CoV-2 patients

BackgroundCOVID-19 is caused by a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The foremost predominant complication of SARS-CoV-2 is arterial hypoxemia thereby disturbing lung compliance, requiring mechanical ventilation. The aim of the current research study is to analyze role of ABG as a valuable assessment tool of disease severity in SARS-CoV-2 patients.Methods170 arterial blood samples were collected from patients admitted in Intensive Care Unit (ICU) of Sri Guru Ram Das Charitable Hospital, Amritsar. They were analyzed for arterial blood gas using ABG analyzer. Parameters of ABG such as pH, pCO2, HCO3, O2 saturation, ionized calcium (iCa) and calculated ionized calcium (at pH 7.4) was calculated for all the samples.ResultsContinuous variables were described as medians with interquartile ranges (IQRs) and categorical variables as percentages and frequencies. Spearman correlation test was done for calculation of correlation between pH and other ABG parameters. Analysis of arterial blood gas revealed significant negative correlation (p<0.05) between pH and pCO2 and significant positive correlation (p<0.05) between pH and HCO3 and between pH and delta ionized calcium. Low levels (98.2%) of ionized calcium were observed while monitoring the ABG findings though weak negative correlation (p<0.05) was observed between pH and iCa.ConclusionsOur study suggests that ABG analysis acts as a momentous indicator for critically ill patients admitted in Intensive Care Unit (ICU). Estimation of iCa in this critical care setting acts as a distinctive biochemical feature of SARS-CoV-2 disease, as an initial assessment tool, for hypocalcemia.     

Sequence analysis of UTR and coding region of kappa-casein gene of Indian riverine buffalo (Bubalus bubalis).

In this study, complete nucleotide as well as derived amino acid sequence characterization of water buffalo (Bubalus bubalis) kappa-casein gene has been presented. Kappa-casein cDNA clones were identified and isolated from a buffalo lactating mammary gland cDNA library. Sequence analysis of kappa-casein cDNA revealed 850 nucleotides with an open reading frame (ORF) of 573 nucleotides, encoding mature peptide of 169 amino acids. The 5' untranslated region (UTR) comprised 71 nucleotides, while 3' UTR was of 206 nucleotides. A total of 11 nucleotide and seven amino acid changes were observed in, buffalo (Bubalus bubalis) as compared to cattle (Bos taurus), sheep (Ovis aries) and goat (Capra hircus). Among these nucleotide changes, eight were unique in buffalo as they were fully conserved in cattle, sheep and goat. Majority of the nucleotide changes and all the amino acid changes; 14 (Asp-Glu), 19(Asp/Ser-Asn), 96(Ala-Thr), 126(Ala-Val), 128(Ala/Gly-Val), 156(Ala/Pro-Val) and 168(Ala/Glu-Val) were limited to exon IV. Three glycosylation sites, Thr 131, Thr 133 and Thr 142 reported in cattle and goat kappa-casein gene were also conserved in buffalo, however, in sheep Thr 142 was replaced by Ala. Chymosin hydrolysis site, between amino acids Phe 105 and Met 106, important for rennet coagulation process, were found to be conserved across four bovid species. Buffalo kappa-casein with the presence of amino acids Thr 136 and Ala 148 seems to be an intermediate of "A" and "B" variants of cattle. Comparison with other livestock species revealed buffalo kappa-casein sharing maximum nucleotide (95.5%) and amino acid (92.6%) similarity with cattle, whereas with pig it showed least sequence similarity of 76.0% and 53.2%, respectively. Phylogenetic analysis based on both nucleotide and amino acid sequence indicated buffalo kappa-casein grouping with cattle, while sheep and goat forming a separate cluster close to them. The non-ruminant species viz. camel, horse and pig were distantly placed, in separate lineages.     

Seasonal distribution of Vibrio parahaemolyticus in freshwater environs and in association with freshwater fishes in Calcutta

The seasonal distribution of Vibrio parahaemolyticus in freshwater environs and in association with freshwater fishes was studied in 1982 and 1983. The occurrence of this organism in water and sediments at the three sites studied was very infrequent and was restricted to the summer months, although it was not always isolated during these months. The association of V. parahaemolyticus with plankton was chiefly confined to the summer months and progressively declined with the onset of monsoons, remaining below detectable levels during the postmonsoon and winter months. The incidence and counts of V. parahaemolyticus were consistently higher in association with plankton than with water and sediment samples. V. parahaemolyticus could be recovered throughout the period of investigation from freshly caught and market samples of freshwater fishes. The highest recovery rate of this halophile from fishes was invariably from fecal samples. Most of the strains isolated in this study were untypable, and those which could be typed were predominantly serotypes encountered in the environment. All the isolates were Kanagawa negative. From this study, it could be concluded that the survival of V. parahaemolyticus in freshwater ecosystems is transient and dependent on a biological host.