MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications

Post-translational modification (PTM) of a protein is an important event in regulating cellular functions. An algorithm, MAPRes, has been developed for mining associations among PTM sites and the preferred amino acids in their vicinity. The algorithm has been implemented to O-glycosylation and O-phosphorylation data (phosphorylated/glycosylated Ser/Thr/Tyr). The association patterns mined by MAPRes demonstrate significant correlations and the results are in conformity with the existing methods. These association rules/patterns will be helpful in predicting the sequences/motifs involved for specific PTMs in proteins.     

Health risk assessment of ‘tiger prawn seed’ collectors exposed to heavy metal pollution in the conserved mangrove forest of Indian Sundarbans: A socio-environmental perspective

Heavy metals contamination from anthropogenic sources in waterways of conserved mangrove ecosystem (Indian Sundarbans) poses serious health hazard to the economically marginalized ‘tiger prawn seed’ (TPS) collectors. Principal component analysis identifies Pb, Ni and Cd as anthropogenic pollutant in Indian Sundarbans. It is observed that Cu, Fe and Zn concentration increases in monsoon, whereas concentration of Cd and Pb decreases in comparison to pre-monsoon levels at all seven fishing villages. Economic status has been assessed using Wealth Rank Tool, which indicates 16–71% of population is in acute economic stress conditions and 5–70% of populations engaged in unsustainable TPS collection for their livelihood. Focus group discussion shows that collectors are exposed (exposure time (ET)) to contaminated water for 3–7 h/d, and lifetime exposure (exposure duration (ED)) varies from 5 to 20 yr. Using site-specific ET and ED results, cumulative hazard quotient (HQ) dermal is estimated to be higher in female than in male. HQ varies from medium (≥1 to <4) to high (>4) due to Cd pollution (0.1–0.26 mg L^-1). The study suggests that promoting alternative sustainable livelihood through group-based organizations (poultry, organic farming, entrepreneurship and transport) could be an effective solution to this problem.     

Effects of experimental hypothyroidism on myelin sheath structural organization

A previous study using the 2′3′cyclic nucleotide 3′phosphodiesterase (CNPase), an oligodendroglial marker that also stain ensheathed fibers, showed a decrease in the number of immunoreactive fibers and a change in the pattern of CNPase immunoreactivity (CNPase+) in hypothyroid animals. CNPase+ fibers, in mature hypothyroid animals, showed a continuous pattern of staining in contrast with a discontinuous one in controls. As CNPase, in adult animals, can be found only in regions in which oligodendrocyte cytoplasm remains as internal, external and paranodal loops, it was suggested that the reduction of thyroid hormone levels leads to a failure in myelin compaction. Previous data showed a higher frequency of some abnormalities in myelin sheath as multiple cytoplasmic loops and redundant myelin profiles in mutant animals that present a failure in myelin compaction. The increase in the frequency of these abnormalities (multiple internal and external loops and redundant myelin) indicates a failure in the interrelations between the axons and the oligodendroglial processes. To verify if the thyroid hormone deficiency during CNS development disturbs these interrelations, we evaluated the frequency of the morphological abnormalities (multiple internal and external loops and redundant myelin) in myelin sheath of corpus callosum (cc) in experimental hypothyroidism. Randomic fields were kept by electron microscopy and the analysis of the frequency of morphological abnormalities showed a significant difference in hypothyroid animals at 60-day-old (PND60), with no significant differences at 90-day-old (PND90) animals. The frequency of multiple internal loops is higher in hypothyroid animals at PND60 that indicates a disturbance in the wrapping by the oligodendroglial process. These findings showed that thyroid hormone might modulate the axon-oligodendroglial relationships that are important for the adequate temporal sequence of events that occur during myelinogenesis, with possible consequences on myelin compaction.     

Novel functional polymorphism on PADI-4 gene and its association with arthritis onset

BackgroundCitrullinated proteins formed by peptidyl arginine deiminases (PADIs) deimination of arginine residues in proteins are of particular interest in arthritis pathogenesis. Polymorphisms on the PADI-4 gene lead to the malfunctioning of PADIs leading to the onset of arthritis.ObjectiveThe present study was conducted to determine the polymorphisms on the PADI-4 gene and their association with rheumatoid arthritis (RA) as well as Osteoarthritis (OA).MethodologyTo achieve the above-mentioned objective a case-control study was conducted. Blood samples were collected from RA, OA, and control subjects. DNA was extracted from each blood sample by modified organic method and was quantified as well as qualified by DNA gel electrophoresis and Nanodrop. Patients were tested for rs874881, rs11203366, rs11203367, rs2240336, rs2240337, rs2240339, rs1748033 and rs2240340 polymorphic sites by amplifying targeted regions through PCR with site-specific primers. Genotyping was performed by Restriction Fragment Length Polymorphism and direct sequencing method. Mutations were identified by analyzing sequences on BioEdit software. Allelic, genetic, and multiple site analysis were performed by SHEsis and PLINK software. Change in the amino acid sequence was identified by MEGA 6.0 software.ResultsPolymorphisms were identified on all targeted polymorphic sites except rs2240337 in both RA and OA individuals. In addition, two novel mutations were also identified in exon 4 identified i-e SCV000804840: c.218T > C and SCV000807675: c.241G > T. All the SNPs except rs11203366 were found to be significantly associated with RA at an allelic level whereas all SNP’s have been significant risk factors in the onset of OA. At genotypic level rs874881, rs11203366, rs2240339, SCV000804840 and SCV000807675 were significantly associated to RA development whereas rs874881, rs11203366, rs11203367, rs2240339, SCV000804840 and SCV000807675 were genetic risk factors in OA onset. Haplotype analysis indicated that GACCACGCC and GACCACGCT were highly significant in disease development. Polymorphisms identified altered the functioning of PADIs by altering their amino acid sequence.ConclusionIn conclusion, it was found that PADI-4 gene polymorphism was not only involved in the onset of RA but was also found to be a significant risk factor in OA onset.     

Presence and possible role of C-ras and nuclear (c-fos and c-jun) proto-oncogene products in preimplantation embryonic development in mice

The presence and possible role of products of nuclear (c-fos and c-jun) and c-ras proto-oncogenes were investigated in preimplantation embryonic development in mice. Polyclonal antibodies to c-fos or c-jun proto-oncogene products did not affect development of in vitro-cultured embryos from two-cell to morula or from morula to late blastocyst stages. However, v-H-ras monoclonal antibody (mAb) to c-ras protein (p²¹), although it did not inhibit the development of in vitro-cultured embryos from two-cell to morula stages, it significantly (P < .001–.005) inhibited the development of morula to late blastocyst stages in a dose-dependent manner. The effects of v-H-ras mAb were specific, since immunoabsorption with synthetic ras peptide completely blocked inhibitory effects of v-H-ras mAb. Neither c-fos nor c-jun antibodies reacted with specific proteins corresponding to c-fos (62 kDa) and c-jun (39 kDa) products on the Western blots of various murine ova/embryos extracts. However, the c-fos and c-jun antibodies reacted with 62 and 39 kDa protein bands, respectively, on the blot of NIH 3T3 cells extract. The v-H-ras mAb specifically identified 21 ± 3 kDa protein corresponding to c-ras p²¹ on the blots of early as well as late blastocyst extracts. The rat control ascites IgG₁ did not react with any protein band on the blots of various ova/embryo extracts. The reactions of v-H-ras mAb on the Western blots of blastocyst extracts were specific, since immunoabsorbed antibody was unable to react with any specific band on blots of early or late blastocyst extract. These results were further confirmed by immunoprecipitation procedure utilizing v-H-ras mAb. Again, the v-H-ras mAb immunoprecipitated a 21 kDa band from early as well as late blastocyst extracts. The rat control ascites IgG₁ did not react with any band corresponding to p ²¹ in the immunoprecipitation procedure. These results suggest that the specific products of nuclear proto-oncogenes, the c-fos and c-jun, are not detected in murine ova and preimplantation embryos, and the respective antibodies do not inhibit embryogenesis, indicating that they may not play a major role in early embryonic development. On the other hand, the product of c-ras proto-oncogene is specifically expressed in the blastocyst-stage embryos and may have a possible role in preimplantation embryonic development in mice. © 1993 Wiley-Liss, Inc.     

Presence and role of c-myc proto-oncogene product in mammalian sperm cell function

The presence and role of c-myc protein was investigated in mature sperm cells of the human, mouse, and rabbit. The monoclonal antibodies against c-myc protein (c-myc) reacted with the acrosomal region of the sperm of these mammalian species in the indirect immunofluorescence technique. The c-myc monoclonal antibody (MCA) recognized c-myc protein of 62 and 64 kDa on Western blots of lithium diiodosalicylate-solubilized sperm preparations of these species. The c-myc MCA showed a dose-dependent inhibition of human sperm penetration of zona-free hamster eggs, inhibition of murine in vitro fertilization, and reduced in vivo fertilization in rabbits. There was no effect of the antibody on percent sperm motility, though the antibody significantly affected various motility characteristics such as mean and maximum amplitude of lateral head displacement and curvilinear velocity involved in hyperactivation phenomenon of human sperm cells. These results suggest that c-myc or c-myc-like protein is present in mature sperm cells and may have a role in sperm cell function especially in capacitation and/or acrosome reaction.     

Studies on Degradation of 7-ketocholesterol by Environmental Bacterial Isolates

Medical bioremediation is a unique strategy of targeting pathogenic compounds with an exogenous enzyme of microbial origin. The objective of this study was to isolate and screen the microorganisms from diverse environmental samples for their ability to catabolize 7-ketocholesterol. Isolation of bacterial strains was performed and molecular identification was carried out by amplification and sequencing of 16S rDNA for 4 the best degrader isolates. Degradation was confirmed on the basis of UV spectrophotometric and HPLC analysis. Four bacterial isolates, showing high catabolic activity towards 7-ketocholesterol were isolated: Alcanivorax jadensis IP4 (accession number KP309836; sea water sediment), Streptomyces auratus IP2 (accession number KP309837; soil), Serratia marcescens IP3 (accession number KP309838; soil) and Thermobifida fusca IP1 (accession number KM677184; manure piles). All the isolates were capable of utilizing 7-ketocholesterol as the sole organic substrate, resulting in its mineralisation. The most rapid degradation was observed with A. jadensis IP4 followed by T. fusca IP1. The degradation was followed and analyzed by HPLC. A. jadensis IP4 removed 7-ketocholesterol below detection levels within 8 days.     

A New Broad-Spectrum Peptide Antibiotic Produced by <Emphasis Type="Italic">Bacillus brevis</Emphasis> Strain MH9 Isolated from Margalla Hills of Islamabad,Pakistan

The antimicrobial peptide from a bacterial strain is isolated from soil sample of Margalla Hills of Islamabad, Pakistan. The peptide is found to significantly inhibit the growth of both Gram-positive (Staphylococcus aureus ATCC 6538 and Micrococcus luteus ATCC 10240) and Gram-negative (Escherichia coli ATCC 25922 and Salmonella typhi ATCC 14028) bacteria as compared to gramicidin as standard. The bacterium is identified as Bacillus brevis strain MH9 based on phenotype and phylogenetic analysis. The antibacterial polypeptide was produced optimally at 35 °C after 48 h of growth, precipitated by 50 % ammonium sulphate, and further purified using HPLC. The sequential steps of purification decrease the peptide contents with prominent antibacterial activity. The peptide composed of 11 amino acid was further characterized by FT-IR and NMR. Results suggested that the peptide molecule is a novel antibacterial agent that is effective against both Gram-positive and Gram-negative bacteria. This study may have important implications for new peptide antibiotic that could be a new addition to treat infections.     

Microwave treated Salvadora oleoides as an eco-friendly biosorbent for the removal of toxic methyl violet dye from aqueous solution—A green approach

In the present study, microwave treated Salvadora oleoides (MW-SO) has been investigated as a potential biosorbent for the removal of toxic methyl violet dye. A batch adsorption method was experimented for biosorptive removal of toxic methyl violet dye from the aqueous solution. The effect of various operating variables, viz., adsorbent dosage, pH, contact time and temperature on the removal of the dye was studied and it was found that nearly 99% removal of the dye was possible under optimum conditions. Kinetic study revealed that a pseudo-second-order mechanism was predominant and the overall process of the dye adsorption involved more than one step. Hence, in order to investigate the rate determining step, intra-particle diffusion model was applied. Adsorption equilibrium study was made by analyzing Langmuir, Freundlich, and Dubinin–Radushkevich (D–R) adsorption isotherm models and the biosorption data was found to be best represented by the Langmuir model. The biosorption efficiency of MW-SO was also compared with unmodified material, Salvadora oleoides (SO). It was found that the sorption capacity (q_max) increased from 58.5 mg/g to 219.7 mg/g on MW treatment. Determination of thermodynamic parameters such as free energy change (ΔG°), enthalpy change (ΔH°) and entropy change (ΔS°) confirmed the spontaneous, endothermic and feasible nature of the adsorption process. The preparation of MW-SO did not require any additional chemical treatment and a high percentage removal of methyl violet dye was obtained in much lesser time. Thus, it is in agreement with the principles of green chemistry. The results of the present research work suggest that MW-SO can be used as an environmentally friendly and economical alternative biosorbent for the removal of methyl violet dye from aqueous solutions.