Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847)

Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus, which is currently the only genus in the corynebacterial family Segniliparaceae. This family is of large interest because of a novel late-emerging genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300)

Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

A Locus on Chromosome 1p36 Is Associated with Thyrotropin and Thyroid Function as Identified by Genome-wide Association Study

Thyroid hormones are key regulators of cellular growth, development, and metabolism, and thyroid disorders are a common cause of ill health in the community. Circulating concentrations of thyrotropin (TSH), thyroxine (T4) and triiodothyronine (T3) have a strong heritable component and are thought to be under polygenic control, but the genes responsible are mostly unknown. In order to identify genetic loci associated with these metabolic phenotypes, we performed a genome-wide association study of 2,120,505 SNPs in 2014 female twins from the TwinsUK study and found a significant association between rs10917469 on chromosome 1p36.13 and serum TSH (p = 3.2 × 10⁻⁸). The association of rs10917469 with serum TSH was replicated (p = 2.0 × 10⁻⁴) in an independent community-based sample of 1154 participants in the Busselton Health Study. This SNP is located near CAPZB, which might be a regulator of TSH secretion and thus of pituitary-thyroid axis function. Twenty-nine percent of white individuals carry the variant, and the difference in mean TSH concentrations between wild-type individuals and those homozygous for the minor G allele was 0.5 mU/l, which is likely to be clinically relevant. We also provide evidence of suggestive association (p < 5.0 × 10⁻⁶) of other SNPs with serum TSH, free T4, and free T3 concentrations, and these SNPs might be good targets for further studies. These results advance understanding of the genetic basis of pituitary-thyroid axis function and metabolic regulation.     

Shoot regeneration from cotyledonary leaf explants of <Emphasis Type="Italic">Jatropha curcas</Emphasis>: a biodiesel plant

A simple, high frequency, and reproducible method for plant regeneration through direct organogenesis from cotyledonary leaf explants of Jatropha curcas was developed using Murashige and Skoog (MS) medium supplemented with different concentrations of thidiazuron (TDZ) or 6-benzyl aminopurine (BAP). Medium containing TDZ has greater influence on regeneration as compared to BAP. The induced shoot buds were transferred to MS medium containing 10 μM kinetin (Kn), 4.5 μM BAP, and 5.5 μM α-naphthaleneacetic acid (NAA) for shoot proliferation. The proliferated shoots could be elongated on MS medium supplemented with different concentrations and combinations of BAP, indole-3-acetic acid (IAA), NAA, and indole-3-butyric acid (IBA). MS medium with 2.25 μM BAP and 8.5 μM IAA was found to be the best combination for shoot elongation. However, significant differences in plant regeneration and shoot elongation were observed among the genotypes studied. Rooting was achieved when the basal cut end of elongated shoots were dipped in half strength MS liquid medium containing different concentrations and combinations of IBA, IAA, and NAA for 4 days, followed by transfer to growth regulators free half strength MS medium supplemented 0.25 mg l⁻¹ activated charcoal. Elongated shoot treated with 15 μM IBA, 5.7 μM IAA, and 11 μM NAA resulted in highest percent rooting. The rooted plants could be established in soil with more than 90% survival rate. The method developed may be useful in improvement of J. curcas through genetic modification.     

GA application induces alteration in sex ratio and cell death in <Emphasis Type="Italic">Jatropha curcas</Emphasis>

Jatropha curcas L. is a commercially important plant with biodiesel and medicinal potential. It is a monoecious plant with staminate and pistillate flowers in same inflorescence with number of staminate flowers being higher than pistillate ones resulting in very low fruit yield. Altering sex ratio to increase the number of female flowers would lead to better yield. Phytohormones are most important factors known to alter sex ratio in plants. The mechanism by which phytohormones alter sex ratio differs in different plant species. Among phytohormones, GA plays an important role in sex alteration. In this study, we report the effect of exogenous application of GA on sex modification in J. curcas. There was considerable increase in number of female flowers by application of GA. At lower concentrations (10 and 100 ppm), increase in number of female flowers and fruit yield was proportionate to the concentration of hormone used but at higher concentration (1,000 ppm) though there was an increase in number of female flowers, fruit yield decreased. This was due to an increased peduncle length and enhanced cell death as a consequence of endogenous release of hydrogen peroxide in response to increased GA, resulting in withering of fruits.     

Antibacterial activity of ZnO nanoparticles prepared via non-hydrolytic solution route

The antibacterial activity of ZnO nanoparticles has been investigated and presented in this paper. Nanoparticles were prepared via non-hydrolytic solution process using zinc acetate di-hydrate (Zn(CH₃COO)₂·2H₂O) and aniline (C₆H₅NH₂) in 6 h refluxing at ∼65 °C. In the presence of four pathogens such as Staphylococcus aureus, Escherichia coli, Salmonella typhimurium, and Klebsiella pneumoniae, the antibacterial study of zinc oxide nanoparticles were observed. The antibacterial activity of ZnO nanoparticles (ZnO-NPs) were studied by spectroscopic method taking different concentrations (5–45 μg/ml) of ZnO-NPs. Our investigation reveals that the lowest concentration of ZnO-NPs solution inhibiting the growth of microbial strain is found to be 5 μg/ml for K. pneumoniae, whereas for E. coli, S. aureus, and S. typhimurium, it was calculated to be 15 μg/ml. The diameter of each ZnO-NPs lies between “20 and 30 nm” as observed from FESEM and transmission electron microscopy images. The composition of synthesized material was analyzed by the Fourier transform infrared spectroscopy, and it shows the band of ZnO at 441 cm⁻¹. Additionally, on the basis of morphological and chemical observations, the chemical reaction mechanism of ZnO-NPs was also proposed.     

Evidence for Initial Non-specific Polypeptide Chain Collapse During the Refolding of the SH3 Domain of PI3 Kinase

Refolding of the SH3 domain of PI3 kinase from the guanidine hydrochloride (GdnHCl)-unfolded state has been probed with millisecond (stopped flow) and sub-millisecond (continuous flow) measurements of the change in fluorescence, circular dichroism, ANS fluorescence and three-site fluorescence resonance energy transfer (FRET) efficiency. Fluorescence measurements are unable to detect structural changes preceding the rate-limiting step of folding, whereas measurements of changes in ANS fluorescence and FRET efficiency indicate that polypeptide chain collapse precedes the major structural transition. The initial chain collapse reaction is complete within 150 μs. The collapsed form at this time possesses hydrophobic clusters to which ANS binds. Each of the three measured intra-molecular distances has contracted to an extent predicted by the dependence of the FRET signal in completely unfolded protein on denaturant concentration, indicating that contraction is non-specific. The extent of contraction of each intra-molecular distance in the collapsed product of sub-millisecond folding increases continuously with a decrease in [GdnHCl]. The gradual contraction is continuous with the gradual contraction seen in completely unfolded protein, and its dependence on [GdnHCl] is not indicative of an all-or-none collapse reaction. The dependence of the extent of contraction on [GdnHCl] was similar for the three distances, indicating that chain collapse occurs in a synchronous manner across different segments of the polypeptide chain. The sub-millisecond measurements of folding in GdnHCl were unable to determine whether hydrophobic cluster formation, probed by ANS fluorescence measurement, precedes chain contraction probed by FRET. To determine whether hydrogen bonding plays a role in initial chain collapse, folding was initiated by dilution of the urea-unfolded state. The extent of contraction of at least one intra-molecular distance in the collapsed product of sub-millisecond folding in urea is similar to that seen in GdnHCl, and the initial contraction in urea too appears to be gradual.