PubMed Health⌕ Search

Biomedical subjects

A Sanyal

Publications and source records attributed to A Sanyal.

At least 19 recordsLinked to original sources
PubMed2006

Sequence analysis of the non-structural 3A and 3C protein-coding regions of foot-and-mouth disease virus serotype Asia1 field isolates from an endemic country.

A total of 18 foot-and-mouth disease virus (FMDV) serotype Asia1 field isolates belonging to two different lineages (including the divergent group) as delineated earlier in VP1-based phylogeny were sequenced in the non-structural 3A and 3C protein-coding regions. The phylogenetic trees representing the regions coding for the non-structural proteins were very similar to that of the structural VP1 protein-coding region. Phylogenetic comparison at 3C region revealed clustering of Asia1 viruses with the isolates of serotypes O, A and C in the previously identified clade. Comparison of amino acid sequences identified lineage-specific signature residues in both the non-structural proteins. Overall analysis of the amino acid substitutions revealed that the 3A coding region was more prone to amino acid alterations than 3C region.

Animals↗
PubMed2006

Sequence analysis of the nucleoprotein gene of Asian lineage peste des petits ruminants vaccine virus.

The complete nucleotide sequence of the nucleocapsid (N) protein of the peste-des-petits ruminants vaccine virus (PPRV Sungri/96) belonging to the Asian lineage was determined. The gene was 1692 nucleotides in length and encoded a polypeptide of 525 amino acids. The PPRV Sungri/96 N gene has a nucleotide homology of 92% for PPRV Nigeria 75/1 to 55.5% for canine distemper virus. At amino acid level the homology was 94.1% with PPRV Nigeria 75/1, while with other morbilliviruses, PPRV Sungri/96 had only 71.4-64.9% amino acid identity. The phosphorylation prediction reveals eight conserved sites across morbilliviruses, whereas in the C-terminal portion of the protein the sites are not conserved. Phylogenetic analysis of different N proteins of morbilliviruses revealed five well-defined clusters as observed previously. To the best of our knowledge this is the first report describing the nucleocapsid gene sequence of PPRV Indian isolate.

Amino Acid Sequence↗
PubMed2006

Sequence analysis of the haemagglutinin and fusion protein genes of peste-des-petits ruminants vaccine virus of Indian origin.

The amino acid composition of the two surface proteins of peste-des-petits ruminants vaccine virus belonging to lineage four from India were deduced from the nucleotide sequence. The fusion (F) protein gene of PPRV Sungri/96 is 2405 nucleotides long and in relation to the length, it is 80 nucleotides longer than that of PPRV Nigeria/75/1 which are found to be present at the 5'UTR of this virus. The complete F gene alignment with other morbillivirus reveals a homology of 89% with PPRV/Nigeria/75/1 and 48-51% with other morbilliviruses. The F protein of PPRV Sungri/96 exhibited characteristics similarity to those of other morbillivirus F proteins. The overall amino acid similarity with its counterpart PPRV Nigeria/75/1 was 96%; with other morbilliviruses it is 65-74%. The PPRV Sungri/96 haemagglutinin (H) protein gene is 1954 nucleotides long and showed a sequence homology of 90.7% with PPRV/Nigeria/75/1 and with other morbilliviruses it ranged from 33% to 45%. At amino acids level, PPRV Sungri/96 showed a homology of 92.3% with PPRV/Nigeria/75/1 and 34-49% with other morbilliviruses. The phylogenetic tree constructed for F and H gene reveals four separate groups which is very similar to that found in other genes. To the best of our knowledge this is the first report describing the F and H genes of an Indian isolate.

Amino Acid Sequence↗
PubMed2006

An unusual complication of oesophageal stent deployment.

Insertion of a self-expanding metal stent is commonly used to palliate dysphagia secondary to oesophageal carcinoma. Displacement of the stent itself is a recognized complication which can result in perforation of the upper gastrointestinal tract. We report the first case of bowel obstruction and perforation resulting from the olive of the deployment system. This was probably due to peritoneal deposits on the small intestine obstructing passage of the olive.

Adenocarcinoma↗
PubMed2005

A novel genetic lineage differentiating RT-PCR as a useful tool in molecular epidemiology of foot-and-mouth disease in India.

Comparison of nucleotide sequences at the VP1 coding region of foot-and-mouth disease serotype Asia1 viruses from India has revealed two genetic lineages with emergence of a genetically divergent group in recent years. In this study a simple, fast, relatively costeffective multi-primer RT-PCR assay to differentiate genetic lineages of type Asia1 viruses was developed. Efforts were made in the design of novel lineage-specific primers and in optimization of the multi-primer assay protocol in conjunction with the use of the serotype specific primer for confirmation of serotype Asia1 virus. This assay promises to be an effective tool in molecular epidemiological investigation of FMD in the country.

Capsid Proteins↗
PubMed2005

Analysis of the matrix protein gene sequence of the Asian lineage of peste-des-petits ruminants vaccine virus.

The M gene nucleotide sequence of an Indian peste-des-petits ruminants (PPRV) vaccine virus ("PPRV Sungri/96") belonging to Asian lineage was determined. The gene is 1476 nucleotides long with a single open reading frame (ORF). The nucleotide and predicted amino acid sequence was compared with the homologous region of the African Lineage Vaccine virus "PPRV/Nigeria/75/1". The nucleotide sequence of the "PPRV Sungri/96" was 86% identical to that of "PPRV/Nigeria/75/1", while a homology of 93% and 95% could be observed in the ORF and amino acids level, respectively. The M gene encodes a protein of 335 amino acids, with a predicted molecular weight (MW) of 37.8 kDa. The ORF is flanked by a 3' untranslated region of 436 nucleotides and a high level of sequence divergence (approximately 30%) could be observed in this region between the vaccine viruses of Asian and African lineages. A high degree of conservation of several amino acids of this protein observed previously was also confirmed in this study.

Amino Acid Sequence↗
PubMed2005

Comparative nucleotide sequence analysis of the phosphoprotein gene of peste des petits ruminants vaccine virus of Indian origin.

The nucleotide sequences of the phosphoprotein (P) gene of peste des petits ruminants (PPRV) vaccine virus (PPRV Sungri/96) belongs to Asian lineage have been determined and the deduced amino acid sequences were compared with another vaccine strain PPRV/Nigeria75/1 and with those of the other morbilliviruses. The 1652 nucleotides of the P gene encode a phosphoprotein of 509 amino acid residues (from nucleotide numbers 60 to 1587), which is 91% identical to that of PPRV/Nigeria75/1. The C protein consists of 177 amino acid residues and is 91% identical with that of PPRV/Nigeria75/1. The conserved mRNA editing site (5'TTAAAAGGGCACAG) was present at positions 742-756 in the P gene, which is conserved in all other morbilliviruses. The CTT trinucleotide sequence is present at the N/P and P/M intergenic region, which is totally conserved in morbilliviruses. This will be the third sequence for the P gene of PPRV since that of the vaccine strain and a wild-type Turkish isolate has been published already.

Amino Acid Sequence↗
PubMed2005

Comparative sequence analysis of the large polymerase protein (L) gene of peste-des-petits ruminants (PPR) vaccine virus of Indian origin.

The complete nucleotide sequence of the large polymerase (L) protein of the peste-des-petits ruminants (PPR) vaccine virus (PPRV Sungri/96) belonging to the Asian lineage was determined. The gene was 6643 nucleotides in length from the gene-start to the gene-end and encoded a polypeptide of 2183 amino acids. The PPRV Sungri/96 has a nucleotide homology of 94.1% for PPRV Nigeria 75/1 to 64.4% for Canine distemper virus. At amino acid level PPRV Sungri/96 has an amino acid identity of 96.2% with PPRV Nigeria 75/1 and 70.4% to 74.8% with other morbilliviruses. All the established domains in L protein characteristic of paramyxoviruses were also found to be present in PPRV Sungri/96. Phylogenetic analysis of different L proteins of morbilliviruses revealed five well-defined clusters as observed previously. The 3' trailer sequence of PPRV Sungri/96 is of 37 nucleotides long which is very similar to that of other morbilliviruses. To the best of our knowledge this is the first report describing the polymerase gene sequence of PPRV Indian isolate.

3' Untranslated Regions↗
PubMed2005

Genetic comparison of large fragment of the 5'untranslated region among foot-and-mouth disease viruses with special reference to serotype Asia1.

Foot-and-mouth disease (FMD), the most economically important disease of cloven-hoofed animals, is endemic in India. Sequence analysis revealed that phylogenetic grouping of type Asia1 field isolates on the basis of the large fragment of the 5'untranslated region (5'LF-UTR) was quite similar to that based on the sequences of the capsid-coding (VP1) region of the same viruses. The existence of two distinct lineages of type Asia1 suggested by the study on the VP1 region was further supported by the detection of a difference in length and predicted secondary structure of the 5'LF-UTR between the two lineages. Sequence variability between the isolates of the two lineages was also observed within the different domains of the internal ribosome entry site (IRES) around conserved motifs like the GNRA,- RAAA,- and the polypyrimidine tract. Certain group and lineage-specific signature nucleotides pertaining to FMDV type Asia1 in the 5'LF-UTR have been identified. The present study shows that the 5'LF-UTR of FMDV serotype Asia1 field isolates are variable in relation to the length and probable secondary structure of the IRES.

5' Untranslated Regions↗
PubMed2005

The formation of neural codes in the hippocampus: trace conditioning as a prototypical paradigm for studying the random recoding hypothesis.

The trace version of classical conditioning is used as a prototypical hippocampal-dependent task to study the recoding sequence prediction theory of hippocampal function. This theory conjectures that the hippocampus is a random recoder of sequences and that, once formed, the neuronal codes are suitable for prediction. As such, a trace conditioning paradigm, which requires a timely prediction, seems by far the simplest of the behaviorally-relevant paradigms for studying hippocampal recoding. Parameters that affect the formation of these random codes include the temporal aspects of the behavioral/cognitive paradigm and certain basic characteristics of hippocampal region CA3 anatomy and physiology such as connectivity and activity. Here we describe some of the dynamics of code formation and describe how biological and paradigmatic parameters affect the neural codes that are formed. In addition to a backward cascade of coding neurons, we point out, for the first time, a higher-order dynamic growing out of the backward cascade-a particular forward and backward stabilization of codes as training progresses. We also observe that there is a performance compromise involved in the setting of activity levels due to the existence of three behavioral failure modes. Each of these behavioral failure modes exists in the computational model and, presumably, natural selection produced the compromise performance observed by psychologists. Thus, examining the parametric sensitivities of the codes and their dynamic formation gives insight into the constraints on natural computation and into the computational compromises ensuing from these constraints.

Algorithms↗
PubMed2005

Phylogeny, genome evolution, and antigenic variability among endemic foot-and-mouth disease virus type A isolates from India.

The capsid-coding (P1) and 3A regions of foot-and-mouth disease virus (FMDV) type A field isolates including two vaccine strains collected during 1977-2000 were analyzed. In the phylogenies, the isolates were distributed into two previously identified genotypes VI and VII, with multiple sub-genotypes that are temporally clustered. Comparison of the antigenic relationships of field isolates with the two vaccine strains (IND 17/77 and IND 490/97) and the reference strains of the genotypes VI (IND 233/99) and VII (IND 40/00) indicated two broad antigenic groups that correlate with the phylogenetic groupings (genotypes VI and VII), and are highly divergent from the vaccine strains. The maximum likelihood method of selection analysis identified a number of amino acid sites within the P1 region to be under weak positive selection. Some of the positively selected sites were mapped at/near the antigenically critical amino acid sites of the P1 region, indicating host immune pressure as one of the important driving force behind the observed genetic and antigenic diversity in FMDV. A small number of selected sites are located in the heparan sulphate-binding pocket of the virus, suggesting a fitness advantage for cell entry of the virus. No positive selection was detected in the 3A dataset.

Amino Acid Sequence↗
PubMed2005

Bone marrow stromal cells express two distinct splice variants of ER-alpha that are regulated by estrogen.

Estrogen plays a critical role in bone metabolism in both sexes. While the major action of estrogen is to inhibit bone resorption, it is now clear that early osteoblastic (or stromal) cells are a target for estrogen action, mediating the effects of estrogen on bone formation as well as resorption. However, little is known about the expression or regulation of the estrogen receptor (ER)-alpha in these cells. The expression of ER-alpha is regulated by a complex set of promoters and ER-alpha splice variants are present in different tissues. Thus, we sought to define the ER-alpha splice variants and their regulation by estrogen in the mouse bone marrow stromal cell line, ST-2, which can be induced to differentiate into mature osteoblasts. ST-2 cells expressed the mRNAs and proteins for both the 66 and 46 kDa forms of ER-alpha; the latter lacks the AF-1 domain and can transduce estrogen signaling in some tissues, while serving as a dominant negative receptor in others. Using primers specific for each of the five 5'-untranslated exons of ER-alpha, we found that ST-2 cells utilized only the promoters upstream of exons F and C (in contrast to most reproductive tissues, which utilize promoters upstream of virtually all the five exons). Moreover, 17beta-estradiol (10(-8) M) treatment of ST-2 cells markedly diminished levels of the 66 kDa as well as the 46 kDa ER-alpha proteins, largely through suppression of the transcript arising from the F1 promoter. These data thus indicate that: (1) bone marrow stromal cells express at least two variants of ER-alpha and (2) estrogen down regulates the ER-alpha mRNA and protein in these cells.

Animals↗
PubMed2004

A fragment of the hypophosphatemic factor, MEPE, requires inducible cyclooxygenase-2 to exert potent anabolic effects on normal human marrow osteoblast precursors.

MEPE, 56.6 kDa protein isolated from tumors associated with hypophosphatemic osteomalacia, increases renal phosphate excretion and is expressed in normal human bone cells. AC-100, a central 23-amino acid fragment of MEPE, contains motifs that are important in regulating cellular activities in the bone microenvironment. Thus, we assessed in vitro effects of AC-100 on multipotential normal human marrow stromal (hMS) cells that have the capacity to differentiate into mature osteoblasts. Proliferation was quantified by [H3]thymidine uptake and cell counting and differentiation by the levels of mRNA for the alpha2-chain of type I procollagen (COL1A2), alkaline phosphatase (AP), and osteocalcin (OC) measured using real time reverse transcriptase PCR (RT-PCR) and by the formation of mineralized nodules. AC-100 increased proliferation by 257 +/- 89% (P < 0.005), increased gene expression of COL1A2 by 339 +/- 85% (P < 0.005), AP by 1,437 +/- 40% (P < 0.001), and OC by 1,962 +/- 337% (P < 0.001). In addition, it increased mineralized nodule formation by 81 +/- 14% (P < 0.001) in a dose- and time-dependent fashion. In equimolar dosages, the parent compound, MEPE, had the full activity of the AC-100 fragment. AC-100 elicited a comparable response to both IGF-I and BMP-2 with respect to proliferation and differentiation of hMS cells. Using gene expression microarray analysis, we demonstrated that AC-100 increased (by approximately 3-fold) the mRNA for cyclooxgenase-2 (COX-2), an inducible enzyme required for prostaglandin synthesis. Moreover, NS-398, a specific inhibitor of COX-2 action completely blocked AC-100-induced increases in proliferation and differentiation. Thus, AC-100 has potent anabolic activity on osteoblast precursor cells in vitro and these effects require the induction of COX-2.

Biomarkers↗
PubMed2004

Characterization of foot-and-mouth disease serotype asial viruses grown in the presence of polyclonal antisera in serology and nucleotide sequence analysis.

Foot-and-mouth disease viruses (FMDV) have a high rate of mutation and spontaneous mutants can be readily. isolated in the laboratory. In this study, plaque purified FMDV Asial vaccine strains (IND 63/72 and IND 491/97) were passaged in-vitro in Baby Hamster Kidney-21 cell monolayers in the presence of sub-neutralizing levels of antiviral polyclonal sera (APS), raised in guinea pigs against the purified and inactivated whole virus particles of IND 63/72, IND 491/97 and IND 13/01. After serial passages under selective immune pressure, the viruses starts growing in the presence of undiluted sera and showed certain characteristics like an increased resistance to neutralization by APS and reduction in plaque counts on titration in plaque assay. Cross-neutralization of these viruses with above-mentioned APS revealed selection of three complete and one partial polyclonal antibody resistant (PAR) viruses based on the 'r' value in micro neutralization test. Alterations were detected at several amino acid residues in the structural protein-coding P1 region. Many of the residues inferred to be positively selected sites in other serotypes of this virus were also prone to substitution under immune selection pressure in Asia1 virus. The present work extends the finding that selection exerted by host antibody also plays a major role in the rapid evolution of FMDV Asia1, as observed in other serotypes.

Amino Acid Sequence↗
PubMed2004

Emergence of a novel subgroup within the widely circulating lineage of foot-and-mouth disease virus serotype Asia 1 in India.

The complete VP1 encoding (1D) gene of 54 foot-and-mouth disease (FMD) virus serotype Asia1 field isolates, most of which were isolated during 2000 and 2001, was sequenced. The phylogenetic analysis identified a novel subgroup (>10% nucleotide divergence) within the widely circulating lineage of this serotype. The newly emerged viruses were responsible for disease outbreaks in both cattle and buffaloes and were present in six different states in the country. Amino acid sequence comparison of these isolates revealed significant sequence divergence at many of the amino acid positions in comparison to those of lineage VI-A and C. Emergence of such viruses may affect the efficacy of vaccine strain currently used for protection against FMD in India.

Amino Acid Sequence↗