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  • PMC (PubMed Central)  (16,115)
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  • 1
    In: PLoS ONE, 2014, Vol.9(7)
    Description: Salicornia brachiata is an extreme halophyte that grows luxuriantly in coastal marshes. Previously, we have reported isolation and characterization of ESTs from Salicornia with large number of novel/unknown salt-responsive gene sequences. In this study, we have selected a novel salt-inducible gene SbSI-2 ( S alicornia b rachiata s alt- i nducible-2 ) for functional characterization. Bioinformatics analysis revealed that SbSI-2 protein has predicted nuclear localization signals and a strong protein-protein interaction domain. Transient expression of the RFP:SbSI2 fusion protein confirmed that SbSI-2 is a nuclear-localized protein. Genomic organization study showed that SbSI-2 is intronless and has a single copy in Salicornia genome. Quantitative RT-PCR analysis revealed higher SbSI-2 expression under salt stress and desiccation conditions. The SbSI-2 gene was transformed in E. coli and tobacco for functional characterization. pET28a-SbSI-2 recombinant E. coli cells showed higher tolerance to desiccation and salinity compared to vector alone. Transgenic tobacco plants overexpressing SbSI-2 have improved salt- and osmotic tolerance, accompanied by better growth parameters, higher relative water content, elevated accumulation of compatible osmolytes, lower Na + and ROS accumulation and lesser electrolyte leakage than the wild-type. Overexpression of the SbSI-2 also enhanced transcript levels of ROS-scavenging genes and some stress-related transcription factors under salt and osmotic stresses. Taken together, these results demonstrate that SbSI-2 might play an important positive modulation role in abiotic stress tolerance. This identifies SbSI-2 as a novel determinant of salt/osmotic tolerance and suggests that it could be a potential bioresource for engineering abiotic stress tolerance in crop plants.
    Keywords: Research Article ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 2
    In: Nature, 2011, Vol.476(7359), p.236
    Description: The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA (1). Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups (2), lack of a dependence on pH (3), and the dominant contribution of entropy to catalysis (4), it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2'-hydroxyl of the peptidyl-transfer RNA (5) and a Bronsted coefficient near zero (6) have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.
    Keywords: Catalysis -- Research ; Peptides -- Physiological Aspects ; Protein Synthesis -- Research ; Ribosomes -- Physiological Aspects;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 3
    In: PLoS ONE, 2014, Vol.9(8)
    Description: Tertiary structure prediction of a protein from its amino acid sequence is one of the major challenges in the field of bioinformatics. Hierarchical approach is one of the persuasive techniques used for predicting protein tertiary structure, especially in the absence of homologous protein structures. In hierarchical approach, intermediate states are predicted like secondary structure, dihedral angles, C α -C α distance bounds, etc. These intermediate states are used to restraint the protein backbone and assist its correct folding. In the recent years, several methods have been developed for predicting dihedral angles of a protein, but it is difficult to conclude which method is better than others. In this study, we benchmarked the performance of dihedral prediction methods ANGLOR and SPINE X on various datasets, including independent datasets. TANGLE dihedral prediction method was not benchmarked (due to unavailability of its standalone) and was compared with SPINE X and ANGLOR on only ANGLOR dataset on which TANGLE has reported its results. It was observed that SPINE X performed better than ANGLOR and TANGLE, especially in case of prediction of dihedral angles of glycine and proline residues. The analysis suggested that angle shifting was the foremost reason of better performance of SPINE X. We further evaluated the performance of the methods on independent ccPDB30 dataset and observed that SPINE X performed better than ANGLOR.
    Keywords: Research Article ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 4
    In: PLoS ONE, 2014, Vol.9(12)
    Description: Background Tobacco use in India is characterized by a high prevalence of smoking and smokeless tobacco use, with dual use also contributing a noticeable proportion. In the context of such a high burden of tobacco use, this study examines the regional variations, and socioeconomic, demographic and other correlates of smoking, smokeless tobacco and dual use of tobacco in India. Methods and Findings We analyzed a cross sectional, nationally representative sample of individuals from the Global Adult Tobacco Survey in India (2009–10), which covered 69,296 individuals aged 15 years and above. The current tobacco use in three forms, namely, smoking only, smokeless tobacco use only, and both smoking and smokeless tobacco use were considered as outcomes in this study. Descriptive statistics, cross tabulations and multinomial logistic regression analysis were adopted as analytical tools. Smokeless tobacco use was the major form of tobacco use in India followed by smoking and dual tobacco use. Tobacco use was higher among males, the less educated, the poor, and the rural population in India. Respondents lacking knowledge of health hazards of tobacco had higher prevalence of tobacco use in each form. The prevalence of different forms of tobacco use varies significantly by states. The prevalence of tobacco use increases concomitantly with age among females. Middle-aged adult males had higher prevalence of tobacco use. Age, education and region were found to be significant determinants of all forms of tobacco use. Adults from the poor household had significantly higher risk of consuming smokeless tobacco. Lack of awareness about the selected hazards of tobacco significantly affects tobacco use. Conclusions There is an urgent need to curb the use of tobacco among the sub-groups of population with higher prevalence. Tobacco control policies in India should adopt a targeted, population-based approach to control and reduce tobacco consumption in the country.
    Keywords: Research Article ; Medicine And Health Sciences ; People And Places
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: 2012, Vol.7(10), p.e46131
    Description: The amount and quality of nutrients consumed by organisms have a strong impact on stress resistance, life-history traits and reproduction. The balance between energy acquisition and expenditure is crucial to the survival and reproductive success of animals. The ability of organisms to adjust their development, physiology or behavior in response to environmental conditions, called phenotypic plasticity, is a defining property of life. One of the most familiar and important examples of phenotypic plasticity is the response of stress tolerance and reproduction to changes in developmental nutrition. Larval nutrition may affect a range of different life-history traits as well as responses to environmental stress in adult. ; Here we investigate the effect of larval nutrition on desiccation, starvation, chill-coma recovery, heat resistance as well as egg to adult viability, egg production and ovariole number in . We raised larvae on either protein rich diet or carbohydrate rich diet. We found that flies consuming protein rich diet have higher desiccation and heat shock resistance whereas flies developed on carbohydrate rich diet have higher starvation and cold resistance. Egg production was higher in females developed on protein rich diet and we also found trade-off between egg production and Egg to adult viability of the flies. Viability was higher in carbohydrate rich diet. However, sex specific viability was found in different nutritional regimes. Higher Egg production might be due to higher ovariole number in females of protein rich diet. ; Thus, adapts different stress tolerance and life-history strategies according to the quality of the available diet, which are correlated with phenotypic adjustment at anatomical and physiological levels.
    Keywords: Research Article ; Astronomical Sciences ; Biology ; Medicine ; Veterinary Science ; Physiology ; Developmental Biology ; Nutrition
    E-ISSN: 1932-6203
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  • 6
    In: PLoS ONE, 2013, Vol.8(1)
    Description: Microarrays have been widely used for various biological applications, such as, gene expression profiling, determination of SNPs, and disease profiling. However, quantification and analysis of microarray data have been a challenge. Previously, by taking into account translational and rotational diffusion of the target DNA, we have shown that the rate of hybridization depends on its size. Here, by mathematical modeling of surface diffusion of transcript, we show that the dynamics of hybridization on DNA microarray surface is inherently oscillatory and the amplitude of oscillation depends on fluid velocity. We found that high fluid velocity enhances the signal without affecting the background, and reduces the oscillation, thereby reducing likelihood of inter- and intra-experiment variability. We further show that a strong probe reduces dependence of signal-to-noise ratio on probe strength, decreasing inter-microarray variability. On the other hand, weaker probes are required for SNP detection. Therefore, we recommend high fluid velocity and strong probes for all microarray applications except determination of SNPs. For SNP detection, we recommend high fluid velocity with weak probe on the spot. We also recommend a surface with high adsorption and desorption rates of transcripts.
    Keywords: Research Article ; Biology
    E-ISSN: 1932-6203
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  • 7
    In: PLoS ONE, 2015, Vol.10(3)
    Description: A single transcription factor may interact with a multitude of targets on the genome, some of which are at gene promoters, others being part of DNA repeat elements. Being sequestered at binding sites, protein molecules can be prevented from partaking in other pathways, specifically, from regulating the expression of the very gene that encodes them. Acting as decoys at the expense of the autoregulatory loop, the binding sites can have a profound impact on protein abundance—on its mean as well as on its cell-to-cell variability. In order to quantify this impact, we study in this paper a mathematical model for pulsatile expression of a transcription factor that autoregulates its expression and interacts with decoys. We determine the exact stationary distribution for protein abundance at the single-cell level, showing that in the case of non-cooperative positive autoregulation, the distribution can be bimodal, possessing a basal expression mode and a distinct, up-regulated, mode. Bimodal protein distributions are more feasible if the rate of degradation is the same irrespective of whether protein is bound or not. Contrastingly, the presence of decoy binding sites which protect the protein from degradation reduces the availability of the bimodal scenario.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: PLoS ONE, March 3, 2017, Vol.12(3), p.e0173544
    Description: MLD and the decomposition process The decomposition procedure used for decomposing the overall inequality in immunization status into within-households and between-households (within-groups and between groups; each household is taken as a group) components is as follows: W is nothing but a weighted average...
    Keywords: Decomposition ; Inequality ; Children ; Immunization ; Immunization ; Elementary School Students ; Households ; Immunization ; Immunization;
    ISSN: 1932-6203
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  • 9
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 02 March 2018, Vol.115(12)
    Description: Efficient lignin valorization could add more than 10-fold the value gained from burning it for energy and is critical for economic viability of future biorefineries. However, lignin-derived aromatics from biomass pretreatment are known to be potent fermentation inhibitors in microbial production of fuels and other value-added chemicals. In addition, isopropyl-β-d-1-thiogalactopyranoside and other inducers are routinely added into fermentation broth to induce the expression of pathway enzymes, which further adds to the overall process cost. An autoregulatory system that can diminish the aromatics’ toxicity as well as be substrate-inducible can be the key for successful integration of lignin valorization into future lignocellulosic biorefineries. Toward that goal, in this study an autoregulatory system is demonstrated that alleviates the toxicity issue and eliminates the cost of an external inducer. Specifically, this system is composed of a catechol biosynthesis pathway coexpressed with an active aromatic transporter CouP under induction by a vanillin self-inducible promoter, ADH7, to effectively convert the lignin-derived aromatics into value-added chemicals using Escherichia coli as a host. The constructed autoregulatory system can efficiently transport vanillin across the cell membrane and convert it to catechol. Compared with the system without CouP expression, the expression of catechol biosynthesis pathway with transporter CouP significantly improved the catechol yields about 30% and 40% under promoter pTrc and ADH7, respectively. Furthermore, this study demonstrated an aromatic-induced autoregulatory system that enabled conversion of lignin-derived aromatics into catechol without the addition of any costly, external inducers, providing a promising and economically viable route for lignin valorization.
    Keywords: Basic Biological Sciences ; Lignin Valorization ; Vanillin-Inducible Promoter ; Aromatics Transporter ; Autoregulatory ; Catechol ; Sciences (General)
    ISSN: 0027-8424
    E-ISSN: 1091-6490
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  • 10
    Language: English
    In: PLoS ONE, 2012, Vol.7(4), p.e35045
    Description: Despite India's substantial economic growth in the past two decades, girls in India are discriminated against in access to preventive healthcare including immunizations. Surprisingly, no study has assessed the contribution of gender based within-household discrimination to the overall inequality in immunization status of Indian children. This study therefore has two objectives: to estimate the gender based within-household inequality (GWHI) in immunization status of Indian children and to examine the inter-regional and inter-temporal variations in the GWHI. ; The present study used households with a pair of male-female siblings (aged 1–5 years) from two rounds of National Family Health Survey (NFHS, 1992–93 and 2005–06). The overall inequality in the immunization status (after controlling for age and birth order) of children was decomposed into within-households and between-households components using Mean log deviation to obtain the GWHI component. The analysis was conducted at the all-India level as well as for six specified geographical regions and at two time points (1992–93 and 2005–06). Household fixed-effects models for immunization status of children were also estimated. ; Findings from household fixed effects analysis indicated that the immunization scores of girls were significantly lower than that of boys. The inequality decompositions revealed that, at the all-India level, the absolute level of GWHI in immunization status decreased from 0.035 in 1992–93 to 0.023 in 2005–06. However, as a percentage of total inequality, it increased marginally (15.5% to 16.5%). In absolute terms, GWHI decreased in all the regions except in the North-East. But, as a percentage of total inequality it increased in the North-Eastern, Western and Southern regions. The main conclusions are the following: GWHI contributes substantially to the overall inequality in immunization status of Indian children; and though the overall inequality in immunization status declined in all the regions, the changes in GWHI were mixed.
    Keywords: Research Article ; Biology ; Medicine ; Social And Behavioral Sciences ; Immunology ; Non-clinical Medicine
    E-ISSN: 1932-6203
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