Nucleic acid based detection technique for Ganoderma lucidum in coconut

Basal stem rot caused by Ganoderma lucidum is the most serious disease in coconut and arecanut gardens. Twenty-five Ganoderma isolates were collected from different parts of India and the pathogenicity of Ganoderma was proved on coconut seedlings. Mature sporophores developed within 10–13?weeks after inoculation of pathogen under in vivo. To detect the pathogen at early stage, DNA-based technology, polymerase chain reaction was used. In this, the primers Gan1 and Gan2 produced a product of 167?bp in size for all the Ganoderma isolates tested. Simultaneously, ITS 1 and ITS 4 primers amplified a fragment of 680?bp in the Ganoderma isolates. In addition, Ganoderma isolates showed polymorphism in the random amplified polymorphic DNA analysis.     

Chitosan-induced defence responses in tomato plants against early blight disease caused by Alternaria solani (Ellis and Martin) Sorauer

The in vitro antifungal properties of chitosan and its role in protection of tomato from early blight disease were evaluated. Chitosan inhibited the radial and submerged growth of Alternaria solani at 1 mg/ml, and controls tomato plants from blight pathogen. Chitosan induces the level of chitinase activity and new isoforms of chitinase resulting in the reduction of early blight disease severity in tomato leaves. These results suggested the role of chitosan in activation of defence responses as well as protecting tomato plants from A. solani infection.     

DISOselect: Disorder predictor selection at the protein level

The intense interest in the intrinsically disordered proteins in the life science community, together with the remarkable advancements in predictive technologies, have given rise to the development of a large number of computational predictors of intrinsic disorder from protein sequence. While the growing number of predictors is a positive trend, we have observed a considerable difference in predictive quality among predictors for individual proteins. Furthermore, variable predictor performance is often inconsistent between predictors for different proteins, and the predictor that shows the best predictive performance depends on the unique properties of each protein sequence. We propose a computational approach, DISOselect, to estimate the predictive performance of 12 selected predictors for individual proteins based on their unique sequence‐derived properties. This estimation informs the users about the expected predictive quality for a selected disorder predictor and can be used to recommend methods that are likely to provide the best quality predictions. Our solution does not depend on the results of any disorder predictor; the estimations are made based solely on the protein sequence. Our solution significantly improves predictive performance, as judged with a test set of 1,000 proteins, when compared to other alternatives. We have empirically shown that by using the recommended methods the overall predictive performance for a given set of proteins can be improved by a statistically significant margin. DISOselect is freely available for non‐commercial users through the webserver at http://biomine.cs.vcu.edu/servers/DISOselect/ .     

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.     

Glycosylation at Asn91 of H1N1 haemagglutinin affects binding to glycan receptors

The glycoprotein HA (haemagglutinin) on the surface of influenza A virus plays a central role in recognition and binding to specific host cell-surface glycan receptors and in fusion of viral membrane to the host nuclear membrane during viral replication. Given the abundance of HA on the viral surface, this protein is also the primary target for host innate and adaptive immune responses. Although addition of glycosylation sites on HA are a part of viral evolution to evade the host immune responses, there are specific glycosylation sites that are conserved during most of the evolution of the virus. In the present study, it was demonstrated that one such conserved glycosylation site at Asn(91) in H1N1 HA critically governs the glycan receptor-binding specificity and hence would potentially impinge on the host adaptation of the virus.     

A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets

The 2009 H1N1 influenza A virus continues to circulate among the human population as the predominant H1N1 subtype. Epidemiological studies and airborne transmission studies using the ferret model have shown that the transmission efficiency of 2009 H1N1 viruses is lower than that of previous seasonal strains and the 1918 pandemic H1N1 strain. We recently correlated this reduced transmission efficiency to the lower binding affinity of the 2009 H1N1 hemagglutinin (HA) to α2→6 sialylated glycan receptors (human receptors). Here we report that a single point mutation (Ile219→Lys; a base pair change) in the glycan receptor-binding site (RBS) of a representative 2009 H1N1 influenza A virus, A/California/04/09 or CA04/09, quantitatively increases its human receptor-binding affinity. The increased human receptor-affinity is in the same range as that of the HA from highly transmissible seasonal and 1918 pandemic H1N1 viruses. Moreover, a 2009 H1N1 virus carrying this mutation in the RBS (generated using reverse genetics) transmits efficiently in ferrets by respiratory droplets thereby reestablishing our previously observed correlation between human receptor-binding affinity and transmission efficiency. These findings are significant in the context of monitoring the evolution of the currently circulating 2009 H1N1 viruses.     

Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo

Human RNPS1 was originally purified and characterized as a pre-mRNA splicing activator, and its role in the postsplicing process has also been proposed recently. To search for factors that functionally interact with RNPS1, we performed a yeast two-hybrid screen with a human cDNA library. Four factors were identified: p54 (also called SRp54; a member of the SR protein family), human transformer 2β (hTra2β; an exonic splicing enhancer-binding protein), hLucA (a potential component of U1 snRNP), and pinin (also called DRS and MemA; a protein localized in nuclear speckles). The N-terminal region containing the serine-rich (S) domain, the central RNA recognition motif (RRM), and the C-terminal arginine/serine/proline-rich (RS/P) domain of RNPS1 interact with p54, pinin, and hTra2β, respectively. Protein-protein binding between RNPS1 and these factors was verified in vitro and in vivo. Overexpression of RNPS1 in HeLa cells induced exon skipping in a model β-globin pre-mRNA and a human tra-2β pre-mRNA. Coexpression of RNPS1 with p54 cooperatively stimulated exon inclusion in an ATP synthase γ-subunit pre-mRNA. The RS/P domain and RRM are necessary for the exon-skipping activity, whereas the S domain is important for the cooperative effect with p54. RNPS1 appears to be a versatile factor that regulates alternative splicing of a variety of pre-mRNAs.     

Fish Heat Shock Cognate 70 Derived AMPs <Emphasis Type="Italic">Cs</Emphasis>HSC70 A1 and <Emphasis Type="Italic">Cs</Emphasis>HSC70 A2

Heat shock cognate 70 (HSC70) is an important evolutionary conserved protein that plays a major role in maintaining the homeostasis and immunity of many organisms. In this study, a HSC70 from Channa striatus was identified from its cDNA library and characterized using bioinformatics and molecular biology tools. CsHSC70 cDNA was 1953 base pair (bp) in length along with an open reading frame which encoded a polypeptide of 650 amino acid residues. Tissue distribution results showed that CsHSC70 was considerably expressed in gill, to a lesser extent in head kidney, blood, spleen and liver and at low level in other tissues. Using C. striatus gill as cell model, effects of fungal, bacterial and poly I:C stimulant on the mRNA levels of CsHSC70 was examined. We also described the antimicrobial features of two peptides namely CsHSC70 A1and CsHSC70 A2 derived from the N-terminal of CsHSC70 protein. CsHSC70 A1 peptide (40 µg/ml) exhibited potent bactericidal activity against Micrococcus luteus cells. Flow cytometric analysis revealed that the M. luteus cells stained with propidium iodide, upon treated with CsHSC70 A1 at the concentration of 40 µM/ml showed 38% survival compared to its control (99.6%). It seems that CsHSC70 A1 peptide shows antimicrobial activity against M. luteus through membrane disruption. Additionally, scanning electron microscope (SEM) observation confirmed that CsHSC70 A1 peptide treatment completely damaged and destructed the M. luteus cells. Taken together, these findings suggest that CsHSC70 A1 peptide could be a safe and potential therapeutic molecule substitute to antibiotics in various clinical fields.