No abstract

India is endemic for foot-and-mouth disease (FMD) and in recent years a unique group within serotype A, carrying a codon deletion at an antigenically critical site in capsid protein VP3 has emerged (VP3(59)-deletion group). This tempted us to analyze the noncoding region, which is an under represented area, though critically associated with virus biology and pathogenesis. Analysis of the large fragment of 5' untranslated region (LF-5' UTR) of type A FMD virus revealed discrepancy in the overall tree topology between LF-5' UTR and 1D region possibly due to independent evolution of coding and noncoding regions. The VP3(59)-deletion group maintained its phylogenetic distinctness even at the LF-5' UTR. Eighteen lineage specific signatures detected here support independent evolutionary paths for the lineages. Extensive deletions of 45 and 89 nucleotides corresponding to the pseudoknot region were noticed. Conservation pattern in the 'A(253)AACA' motif in the cre/bus stem-loop indicates the importance of first three 'A' residues in VPg uridylylation. Of the three polypyrimidine tract binding protein (PTB) binding sites mapped on the internal ribosome entry site (IRES), the pyrimidine tract (Py tract) in the loop of domain 2 was found to be maximally conserved and it might be the major PTB binding site. Strikingly, a deletion group lineage specific transversion was noticed in the Py tract at the 3' end of IRES without significantly affecting its in vitro infectious titer. Hence, we presume that for efficient cap-independent viral translation, either a minimum number of pyrimidine residues rather than a complete Py tract or a Py tract tolerating transversions only at specific locations and a core motif 'CUUU' within the Py tract is essential.

We represent a simplified and rapid version of DNA extraction protocol from different mosquito species which is suitable for polymerase chain reaction(PCR) and other molecular biology works. The protocol involves three steps like lysis, phenol : chloroform (1:1) extraction and two fold isopropanol precipitation at-20 degree celcius using 1X STE buffer (50mM NaCl, 50mM Tris-Hcl,100mM EDTA,PH 8.0).The proposed extraction protocol has an advantage of DNA extraction from mosquitoes using 1X STE buffer at 37ºcelcius which prevent DNA degradation at higher temperature and kept DNA stability in long term storage. The protocol proved by three different mosquito species and removing for potential contamination showed that the protocol yields good quantity and quality DNA, typically better than commercial kits .The protocol was evaluated by polymerase chain reaction (PCR). The protocol of DNA extraction is a time saving as well as economies with available laboratory chemicals, consumables and basic equipments. The protocol is adoptable for laboratories in external and internal funded research projects with large numbers of mosquito samples in a small period .The protocol minimize the time for other DNA extraction protocols in two to three days and provides a workflow for mapping of malaria vectors ,their vectorial transmission in the area of translational research .

Background As plasma proteins were involved in drug metabolism, the aim of the study was to identify and characterize the plasma proteins of the drug resistant and drug respondent groups of HIV-1 infected first line ART patients with > 6 years in therapy. Methods Plasma proteomics analysis of the four drug-resistant (treatment failure) and four drug respondent (treatment responder) groups were conducted. High abundant plasma proteins like albumin and globulin were depleted from plasma through Aurum serum mini kit (Bio-Rad, USA). Plasma proteins were resolved using two-dimensional gel electrophoresis on IPG strips, pH range of 3–10. Eight protein spots were selected in the gel based on the density of staining which was common in the drug resistant and drug respondent groups separately. The fold change of each spot was calculated using image-J. Each protein spot was identified using the matrix assisted laser desorption/ionization-time of flight/time of flight (MALDI-TOF/TOF) after tryptic digestion. Peptide peaks were identified through flex analysis version 3.3, and a search against a protein database using the internal mascot search engine. Gene ontology study was completed through STRING v.11 and Panther 15.0. Results Out of eight spots from 2D gel of drug respondent and drug resistant samples analyzed by MALDI TOF/TOF, two proteins were found to have significant score (i;e > 56) after Flex analysis. These two proteins were identified to be apolipoproteinA1 and Serotransferrin. The fold change expression of these two proteins were analyzed in drug resistant and drug respondent group. ApolipoproteinA1and serotransferrin were observed to be expressed 1.76 and 1.13-fold more respectively in drug respondent group compared to drug resistant group. The gene ontology analysis revealed the involvement of these two proteins in various important physiological processes. Conclusion Apolipoprotein A-I and serotransferrin were found to be expressed more in drug respondent group compared to drug resistant group.