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  • 1
    Publication Date: 2018-03-15
    Description: The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.
    Print ISSN: 0233-111X
    Electronic ISSN: 1521-4028
    Topics: Biology
    Published by Wiley-Blackwell
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  • 2
    Publication Date: 2018-03-14
    Description: Mn-oxidizing potential of two metal-tolerant bacterial strains – Halomonas meridiana and Marinobacter algicola isolated from the South West Indian Ridge waters were compared at varying concentrations of Mn (II), i.e., 1, 10, and 100 μmol and mmol L −1 . Accompanying changes in their morphology and metabolism were also determined. At concentrations 〉1 mmol L −1 Mn (II), Mn-oxidizing potential of M. algicola was 2–7 times greater than that of H. meridiana . Scanning electron microscopy revealed that exposure to elevated metal content prompted bacterial cells especially those of M. algicola to been enveloped in exopolymeric material and form aggregates. Energy dispersive spectrometric analysis showed that exopolymeric material acts as a nucleation site for Mn deposition and oxide formation which occurs in the form of microspherical aggregates. These features show striking resemblance to biogenically produced Fe-Mn oxide deposits from Lau Basin. Surprisingly, diffractograms of auto-oxidized and bacterially formed Mn-oxide showed similarities to the hydrothermal vein mineral Rhodochrosite indicating that it can also be produced biotically. Elongation of cells by up to 4× the original size and distortion in cell shape were evident at Mn (II) concentrations 〉100 μmol L −1 . Marked differences in C-substrate utilization by the test strains were also observed in presence of Mn (II). A shift in use of substrates that are readily available in oceanic waters like N-acetyl- d -glucosamine to those that can be used under changing redox conditions ( d -cellobiose) or in the presence of metal ions ( d -arabinose, l -asparagine) were observed. These findings highlight the significant role of autochthonous bacteria in transforming reduced metal ions and aiding in the formation of metal oxides. Under natural or laboratory conditions, the mode of bacterially generated Mn-oxide tends to remain the same.
    Print ISSN: 0233-111X
    Electronic ISSN: 1521-4028
    Topics: Biology
    Published by Wiley-Blackwell
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  • 3
    Publication Date: 2018-03-14
    Description: Lyme disease, caused by Borrelia burgdorferi , is a focally endemic tick-transmitted zoonotic infection. In this study, the major factors underlying synonymous codon-related amino acid usage in the B. burgdorferi genome and bias in synonymous codon usage of the translation initiation region of coding sequences were analyzed. Additionally, adaptation of B. burgdorferi to several of its hosts was analyzed in the context of synonymous codon usage. Principal component analysis (PCA) revealed that nucleotide content at the third synonymous position of a codon influenced the synonymous codon usage pattern, but the strand-specific factor did not influence the synonymous codon usage pattern of B. burgdorferi . In terms of the low GC content of B. burgdorferi coding sequences, the effective number of codons (ENC) showed a significant correlation with GC 3 content (at the synonymous position). For the amino acid usage pattern for B. burgdorferi , PCA showed that the strand-specific factor did not contribute to this pattern, while the properties (aromaticity and hydrophobicity) of the amino acids themselves showed strong correlations with this pattern. Under-represented codons, which were frequently selected in the translation initiation region, possibly play roles in regulating gene expression in B. burgdorferi . In terms of co-evolution and synonymous codon usage patterns, adaptation of B. burgdorferi to different intermediate hosts was apparent to different degrees, and the degree of adaptation of this spirochete to wild animals was stronger than that of humans or mice.
    Print ISSN: 0233-111X
    Electronic ISSN: 1521-4028
    Topics: Biology
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  • 4
    Publication Date: 2018-03-06
    Description: Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers. Here, one EZ-Tn 5 transposon mutant of Xcc, altered in bacterial attachment, was isolated. Further analysis revealed that the transposon was inserted in the wxcX gene (encodes a hypothetical protein) of the transposon mutant. Sequence analysis revealed that WxcX is highly conserved in Xanthomonas , but none has been characterized. In this study, it was indicated that mutation of wxcX resulted in enhanced bacterial attachment, reduced virulence on the host cabbage, and increased sensitivity to sodium dodecyl sulfate. The affected phenotypes of the wxcX mutant could be complemented to wild-type levels by the intact wxcX gene. Site-directed mutagenesis revealed that E408 and E411 are critical amino acid residues for WxcX function in bacterial attachment. Taken together, our results demonstrate the roles of wxcX in attachment, virulence, and tolerance to sodium dodecyl sulfate in Xanthomonas for the first time.
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    Electronic ISSN: 1521-4028
    Topics: Biology
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  • 5
    Publication Date: 2018-03-06
    Description: The aim was to study the effect of artificially constructed consortia of microalgae-bacterial symbionts on growth and lipid production by Chlorella vulgaris ( C. vulgaris ), as well as the inter-relationship between microalgae and bacterial in a photoautotrophic system. The results showed that compared to an axenic culture of C. vulgaris , H1 co-culture system (axenic C. vulgaris - Stenotrophomona smaltophilia ) had the strongest effect on the C. vulgaris growth. The biomass, specific growth rate and maximum productivity of C. vulgaris were increased by 21.9, 20.4, and 18%, respectively. The bacteria in co-culture system had a significant effect on the accumulation of lipid and fatty acid components of C. vulgaris : the content of lipid was increased by 8.2–33.83%, and the components of the saturated fatty acids and oleic acids also had an obvious improvement. The results indicate that the microalgae-bacterial co-culture system can improve microalgal biomass and the quality of biodiesel.
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    Electronic ISSN: 1521-4028
    Topics: Biology
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  • 6
    Publication Date: 2018-03-06
    Print ISSN: 0233-111X
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    Topics: Biology
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  • 7
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    Wiley-Blackwell
    Publication Date: 2018-03-06
    Description: Cover illustration: The figure shows the presence of polyhydroxyalkanoates (PHA) granules in a bacterial cell that appears as white granules. These are carbon storage compounds. (Photo: Sajida Munir, University of the Punjab, Lahore, Pakistan, and Richard Webb, University of Queensland, Australia)
    Print ISSN: 0233-111X
    Electronic ISSN: 1521-4028
    Topics: Biology
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  • 8
    Publication Date: 2018-02-24
    Description: The aims of this study were to isolate and characterize N 2 -fixing bacteria from giant reed and switchgrass and evaluate their plant growth promotion and nutrient uptake potential for use as biofertilizers. A total of 190 bacteria were obtained from rhizosphere soil and inside stems and roots of giant reed and switchgrass. All the isolates were confirmed to have nitrogenase activity, 96.9% produced auxin, and 85% produced siderophores. Then the top six strains, including Sphingomonas trueperi NNA-14 , Sphingomonas trueperi NNA-19, Sphingomonas trueperi NNA-17, Sphingomonas trueperi NNA-20, Psychrobacillus psychrodurans NP-3, and Enterobacter oryzae NXU-38, based on nitrogenase activity, were inoculated on maize and wheat seeds in greenhouse tests to assess their potential benefits to plants. All the selected strains promoted plant growth by increasing at least one plant growth parameter or increasing the nutrient concentration of maize or wheat plants. NNA-14 outperformed others in promoting early growth and nutrient uptake by maize. Specifically, NNA-14 significantly increased root length, surface area, and fine roots of maize by 14%, 12%, and 17%, respectively, and enhanced N, Ca, S, B, Cu, and Zn in maize. NNA-19 and NXU-38 outperformed others in promoting both early growth and nutrient uptake by wheat. Specifically, NNA-19 significantly increased root dry weight and number of root tips of wheat by 25% and 96%, respectively, and enhanced Ca in wheat. NXU-38 significantly increased root length, surface area, and fine roots of wheat by 21%, 13%, and 26%, respectively, and enhanced levels of Ca and Mg in wheat. It is concluded that switchgrass and giant reed are colonized by N 2 -fixing bacteria that have the potential to contribute to plant growth and nutrient uptake by agricultural crops.
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    Topics: Biology
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  • 9
    Publication Date: 2018-02-15
    Description: Psychrotolerant yeast Rhodotorula sp. Y-23 was isolated from the sediment core sub-samples of Nella Lake, East Antarctica. Isolate was screened for lipase production using plate assay method followed by submerged fermentation. Production optimization revealed the maximum lipase production by using palmolein oil (5% v/v), pH 8.0 and inoculum size of 2.5% v/v at 15 °C. The potential inducers for lipase were 1% w/v of galactose and KNO 3 , and MnCl 2 (0.1% w/v). Final productions with optimized conditions gave 5.47-fold increase in lipase production. Dialyzed product gave a purification fold of 5.63 with specific activity of 26.83 U mg −1 and 15.67% yields. This lipase was more stable at pH 5.0 and −20 °C whereas more activity was found at pH 8.0 and 35 °C. Stability was more in 50 mM Fe 3+ , EDTA-Na (20 mM), sodium deoxycholate (20 mM), H 2 O 2 (1% v/v), and almost all organic solvents (50% v/v). Tolerance capacity at wider range of pH and temperature with having lower K m value i.e., 0.08 mg ml −1 and higher V max 385.68 U mg −1 at 15 °C make the studied lipase useful for industrial applications. Besides this, the lipase was compatible with commercially available detergents, and its addition to them increases lipid degradation performances making it a potential candidate in detergent formulation.
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    Topics: Biology
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  • 10
    Publication Date: 2018-02-13
    Description: In artisanal tanneries, the skins are immersed in cereals fermented by natural microbial flora in order to reduce the pH of the skin, an essential condition for carrying out the final step. The environmental thermal variation alters the fermentation process and affects the quality of the final product. The aim of this work was to isolate lactic acid bacteria from cereals mixture fermented in an artisanal tannery and to evaluate in vitro the acidifying activity of the strains as a first step for the formulation of a starter culture. In most samples, a prevalence of cocci (95%) was observed with respect to bacilli. The best acidifying strains were identified by phenotypic and genotypic techniques as Enterococcus faecium CRL 1943 (rapid acidification at 37 °C) and Leuconostoc citreum CRL 1945 (high acidifying activity at 18 °C). In addition, the biomass production of the selected strains was analyzed at free and controlled pH (bioreactors 1.5 L). The production of biomass was optimal at controlled pH, with a higher growth (0.5–1.1 log units). Both strains were compatible, allowing their inclusion in a mixed culture. These lactic strains could contribute to the systematization of the tanning process.
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    Topics: Biology
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