Genome-Wide Comparative in silico Analysis of Calcium Transporters of Rice and Sorghum

The mechanism of calcium uptake, translocation and accumulation in Poaceae has not yet been fully understood. To address this issue, we conducted genome-wide comparative in silico analysis of the calcium (Ca2+) transporter gene family of two crop species, rice and sorghum. Gene annotation, identification of upstream cis-acting ele- ments, phylogenetic tree construction and syntenic mapping of the gene family were performed using several bio- informatics tools. A total of 31 Ca2+ transporters, distributed on 9 out of 12 chromosomes, were predicted from rice genome, while 28 Ca2+ transporters predicted from sorghum are distributed on all the chromosomes except chromosome 10 (Chr 10). Interestingly, most of the genes on Chr 1 and Chr 3 show an inverse syntenic relation- ship between rice and sorghum. Multiple sequence alignment and motif analysis of these transporter proteins re- vealed high conservation between the two species. Phylogenetic tree could very well identify the subclasses of channels, ATPases and exchangers among the gene family. The in silico cis-regulatory element analysis suggested diverse functions associated with light, stress and hormone responsiveness as well as endosperm- and meris- tem-specific gene expression. Further experiments are warranted to validate the in silico analysis of the predicted transporter gene family and elucidate the functions of Ca2+ transporters in various biological processes.     

Municipal sludge leachate-induced genotoxicity in mice--a subacute study

Inappropriate disposal of municipal sludge (MS) results in the leaching of toxic metals and organic chemicals, which can contaminate the surface and ground water leading to the serious health hazards. In this study, the genotoxic potential of the leachate prepared from MS sample was examined in mouse bone marrow cells through chromosomal aberrations (CA), micronucleus test (MT) and comet assay. Analysis of metals and physicochemical parameters of the leachate was also carried out to correlate the genotoxic results. The dried sludge showed high concentrations of heavy metals, viz. Cr, Cu, Pb and Ni. However, in 10% leachate, concentrations of these metals were manifold lower than that of obtained in dried sludge. Male mice orally gavaged to leachates (0.1-0.4 ml/mouse/day) for 15 days revealed significant (P<0.01, P<0.001) inhibition of mitotic index (MI) and induction of chromatid/chromosome fragments and breaks in all the treatment groups. The effect was observed to be dose-dependent. Treatment of mice with leachates also induced significant (P<0.001) frequencies of micronucleated polychromatic erythrocytes (MNPCE). The results of comet assay revealed a statistically significant (P<0.05 and <0.01) DNA damage in bone marrow cells exposed to 0.2-0.4 ml/mouse/day. Findings of the present study indicate that the constant exposure of MS leachate can cause genotoxic effects in mammals and suggest risks in human population.     

Crystal structure of the hypothetical protein TA1238 from <Emphasis Type="Italic">Thermoplasma acidophilum</Emphasis>: A new type of helical super-bundle

The crystal structure of the hypothetical protein TA1238 from Thermoplasma acidophilum was solved with multiple-wavelength anomalous diffraction and refined at 2.0 resolution. The molecule consists of a typical four-helix antiparallel bundle with overhand connection. However, its oligomerization into a trimer leads to a coiled super-helix which is novel for such bundles. Its central feature, a six-stranded coiled coil, is also novel for proteins. TA1238 does not have strong sequence homologues in databases, but shows strong structural similarity with some proteins in the Protein Data Bank. The function could not be inferred from the sequence but the structure, with some rearrangement, bears some resemblance to the active site region of cobalamin adenosyltransferase (TA1434). Specifically, TA1238 retains Arg104, which is structurally equivalent to functionally critical Arg119 of TA1434. For such conformational change, the overhand connection of TA1238 might need to be involved in a gating mechanism that might be modulated by ligands and/or by interactions with the physiological partners. This allowed us to hypothesize that TA1238 could be involved in cobalamin biosyntheses     

A chemical-genetic approach to studying neurotrophin signaling

Trk tyrosine kinases are receptors for members of the neurotrophin family and are crucial for growth and survival of specific populations of neurons. Yet, the functions of neurotrophin-Trk signaling in postnatal development as well as maintenance and plasticity of the adult nervous system are less clear. We report here the generation of mice harboring Trk knockin alleles that allow for pharmacological control of Trk kinase activity. Nanomolar concentrations of either 1NMPP1 or 1NaPP1, derivatives of the general kinase inhibitor PP1, inhibit NGF and BDNF signaling in TrkA(F592A) and TrkB(F616A) neurons, respectively, while no such Trk inhibition is observed in wild-type neurons. Moreover, oral administration of 1NMPP1 leads to specific inhibition of TrkA(F592A), TrkB(F616A), and TrkC(F167A) signaling in vivo. Thus, Trk knockin mice provide valuable tools for selective, rapid, and reversible inhibition of neurotrophin signaling in vitro and in vivo.     

Worldwide distribution of Pseudomonas aeruginosa clone C strains in the aquatic environment and cystic fibrosis patients

Highly successful bacterial clones have the ability to effectively colonize environmental niches and patients. However, the factors which determine the complex interplay between the colonization of environmental niches and patients are mainly unknown. In this study we show that Pseudomonas aeruginosa clone C strains are distributed worldwide and highly prone to infect cystic fibrosis (CF) patients in Canada, England, France and Germany. In Hanover, Germany and Vancouver, Canada, clone C strains are highly prevalent in the CF patient community, although the mechanisms of acquisition may have been different. All clone C strains showed highly related macrorestriction fragment pattern of the whole genome as visualized by pulsed-field gel electrophoresis and harboured the 102 kbp plasmid pKLC102. Comparison of three prevalent P. aeruginosa clones with different distribution between the environment and patients revealed that neither enhanced biofilm formation nor antibiotic resistance was responsible for the spread of clone C. Clone M, which was highly prevalent in the clinical environment such as sanitary facilities, lacked motility, which could explain its relatively low prevalence in CF patients. Elucidation of the mechanisms which lead to the prevalence of clone C strain in patients and the environment requires the investigation of additional phenotypes.     

Functional insights from the structure of the multifunctional C345C domain of C5 of complement

The complement protein C5 initiates assembly of the membrane attack complex. This remarkable process results in lysis of target cells and is fundamental to mammalian defense against infection. The 150-amino acid residue domain at the C terminus of C5 (C5-C345C) is pivotal to C5 function. It interacts with enzymes that convert C5 to C5b, the first step in the assembly of the membrane attack complex; it also binds to the membrane attack complex components C6 and C7 with high affinity. Here a recombinant version of this C5-C345C domain is shown to adopt the oligosaccharide/oligonucleotide binding fold, with two helices packed against a five-stranded beta-barrel. The structure is compared with those from the netrin-like module family that have a similar fold. Residues critical to the interaction with C5-convertase cluster on a mobile, hydrophobic inter-strand loop that protrudes from the open face of the beta-barrel. The opposite, helix-dominated face of C5-C345C carries a pair of exposed hydrophobic side chains adjacent to a striking negatively charged patch, consistent with affinity for positively charged factor I modules in C6 and C7. Modeling of homologous domains from complement proteins C3 and C4, which do not participate in membrane attack complex assembly, suggests that this provisionally identified C6/C7-interacting face is indeed specific to C5.