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A Sanyal

Publications and source records attributed to A Sanyal.

At least 37 records · Page 2Linked to original sources
PubMed2004

Sequence variability in the structural protein-encoding region of foot-and-mouth disease virus serotype Asia1 field isolates.

A total of 30 field isolates of foot-and-mouth disease virus (FMDV) serotype Asia1 belonging to two different lineages and five isolates belonging to a divergent group as delineated earlier in 1D (encodingVP1 protein) gene-based phylogeny were sequenced in the structural protein (P1) coding region. Phylogenetic comparison of these isolates along with some of the published exotic sequences revealed the presence of five different lineages around the world. Similar grouping pattern was observed for the P1 region and 1D gene-based phylogeny, where the Indian isolates were clustered in two genetic lineages. The recently identified divergent group of virus falls into a separate sub-cluster. Similar grouping was also observed in L gene-based phylogeny. Comparison of amino acid sequences identified lineage-specific signature residues in all the structural proteins. Comparison of Asia1 field isolates at the identified key residues of other FMD viruses involved in the formation of the heparan sulfate-binding ligand confirmed many of them to be conserved and the presence of VP3(56) Arg suggested their cell culture adaptation. Although a considerable genetic variation was observed among the isolates of present study, all of them tested in micro-neutralization test were serologically related to the vaccine strain.

Amino Acid Sequence↗
PubMed2004

High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements.

The locus sun on the short arm of tomato chromosome 7 controls morphology of the fruit. Alleles from wild relatives impart a round shape, while alleles from certain cultivated varieties impart an oval shape typical of roma-type tomatoes. We fine mapped the locus in two populations and investigated the genome organization of the region spanning and flanking sun. The first high-resolution genetic map of the sun locus was constructed using a nearly isogenic F(2) population derived from a cross between Lycopersicon pennellii introgression line IL7-4 and L. esculentum cv Sun1642. The mapping combined with results from pachytene FISH experiments demonstrated that the top of chromosome 7 is inverted in L. pennellii accession LA716. sun was located close to the chromosomal breakpoint and within the inversion, thereby precluding map-based cloning of the gene using this population. The fruit-shape locus was subsequently fine mapped in a population derived from a cross between L. esculentum Sun1642 and L. pimpinellifolium LA1589. Chromosome walking using clones identified from several large genomic insert libraries resulted in two noncontiguous contigs flanking sun. Fiber-FISH analysis showed that distance between the two contigs measured 68 kb in L. esculentum Sun1642 and 38 kb in L. pimpinellifolium LA1589, respectively. The sun locus mapped between the two contigs, suggesting that allelic variation at this locus may be due to an insertion/deletion event. The results demonstrate that sun is located in a highly dynamic region of the tomato genome.

Chromosome Mapping↗
PubMed2004

Complete nucleotide sequence analysis of a vaccine strain and a field isolate of foot-and-mouth disease virus serotype Asia1 with an insertion in VP1 genomic region.

Complete nucleotide sequences except the poly (C) tract and poly (A) tail of a vaccine strain (IND 491/97) and an atypical field isolate (IND 321/01) of Foot-and-mouth disease virus (FMDV) serotype Asia1 are described. Amino acid (aa) sequence analysis of the VP1 protein of the field isolate revealed that the latter has 212 instead of 210 or 211 aa found in the so far available sequences of other FMDV isolates of Asia1 serotype. The insertion was localized in the hypervariable region of aa 130-160 of VP1 protein. Nucleotide sequencing of the entire genome was therefore carried out to detect changes in other parts of the genome, if any, besides VP1, which could contribute to its fitness. An 8.16 kb sequence of IND 491/97 and an 8.162 kb sequence of IND 321/01 were compared with each other and also with the known sequence of IND 63/72, another vaccine strain of serotype Asia1. Comparison of the entire polyprotein coding (L to 3D) region of IND 321/01 with those of the two Asia1 vaccine strains (IND 63/72 and IND 491/97) revealed no significant differences. A similar comparison of IND 491/97 with IND 63/72 revealed variability across the entire length of the genome. In addition to the capsid-coding region, sequence variability was also observed in non-structural proteins albeit to different extent. This study shows that in the gene pool of serotype Asia1 at least three groups of isolates/strains are present with respect to the length of VP1 protein.

Amino Acid Sequence↗
PubMed2003

Molecular phylogeny of leader proteinase gene of type A of Foot-and-mouth disease virus from India.

We previously demonstrated the presence of three genotypes (IV, VI and VII) of type A (subtype A22) of Foot-and-mouth disease virus (FMDV) in India based on 1D gene sequence analysis. In the present study, the leader proteinase (L(pro)) gene sequences of 35 type A FMDV field isolates sampled over a period of 24 years (1977-2000) have been analyzed. Maximum-likelihood (ML) phylogenetic analysis revealed four distinct genetic lineages (A-D), indicating high divergence in L gene of type A FMDV. Lineages A and D correspond to the earlier genotypes IV, and VII, respectively. The genotype VI isolates were divided into two separate lineages (B and C) in the tree with high confidence values (96-99%). One isolate (IND 21/90) showed incongruous grouping between the (1D and L) gene-based analyses, which could be due to intergenotypic recombination. The ML molecular clock hypothesis was easily rejected on the data set studied indicating the absence of clock-like evolution in the L gene. ML codon-substitution models identified positive selection in the amino acid site 194 of C-terminal extension of the Lb(pro) with high posterior probability (>99%). The catalytic triad of the L(pro) at C-51, H-148 and D-163 were conserved across all the Indian isolates studied. Finally, amino acid differences between the lineages have been discussed briefly.

Amino Acid Sequence↗
PubMed2003

Antigenic characterization of foot-and-mouth disease virus serotype Asia1 field isolates using polyclonal and monoclonal antibodies.

Foot-and-mouth disease virus (FMDV) serotype Asia1 field isolates (n = 100) were compared using a panel of 11 monoclonal antibodies (Mab) in sandwich ELISA. The majority (over 89%) of the isolates showed either homologous (76% and above reactivity) or reduced affinity (20-75% reactivity) for the Mabs 2A, 13, 40, 34 and 81, suggesting that these Mab binding epitopes are conserved, whereas a more variable reactivity was observed for the Mabs B3, 1A, 24, 72, 82 and 89. Polyclonal relationship ('r' value) of the field isolates in liquid phase blocking (LPB) ELISA was examined, and the mean 'r' value was 0.62 relative to vaccine virus IND 63/72. Some of the field isolates (n = 34) were tested in virus neutralization test (VNT) and showed an 'r' value of >0.40. Although a minor antigenic difference was observed in the Mab profiling study, there has not been large antigenic divergence between reference virus and field viruses, thereby providing evidence of wide antigenic coverage of the vaccine strain.

Animals↗
PubMed2003

Serotype C foot-and-mouth disease virus isolates from India belong to a separate so far not described lineage.

Complete 1D gene sequences of 13 Indian foot-and-mouth disease virus (FMDV) type C field isolates and a vaccine strain (C-Bombay/64) were determined. All the field isolates showed a greater genetic homogeneity (95-100%) among themselves and were 19.7-21.2% divergent from the vaccine strain. In the phylogenetic analysis, the Indian field isolates formed a separate lineage (lineage VII) different from the previously identified six lineages (lineage I-VI) in type C FMDV [J. Virol. 66 (1992) 3557]. The vaccine strain was grouped with European lineage (lineage II). Comparison of the deduced amino acid sequences of antigenic sites A and C of field isolates showed no significant variation from the vaccine strain. One-way serological relationship determined in ELISA showed antigenic closeness of the field isolates with C-Bombay/64.

Amino Acid Sequence↗
PubMed2003

Genetic and antigenic analysis of two recently circulating genotypes of type A foot-and-mouth disease virus in India: evidence for positive selection in the capsid-coding genes.

We have analyzed isolates of two recently circulating genotypes (genotypes VI and VII) of type A foot-and-mouth disease virus (FMDV) from India. Maximum-likelihood models provided support for the presence of positively selected sites in the capsid-coding (P1) region. Positive selection was detected at a number of amino acid positions behind a background of strong purifying selection. Among the positively selected sites, four were identified at known critical antigenic residues (VP2 79, VP3 59 and 70 and, VP1 83), suggesting that FMDVs are under pressure from the immune system. Two residues (VP2 134 and VP3 59) that are part of the heparan sulfate-binding pocket in subtype A22 FMDV are also inferred to be under positive selection. Antigenic divergence was observed between and within the genotypes in neutralization tests with sera raised against the representative isolates from genotypes VI and VII. The two vaccine strains showed one-way antigenic relationships (r value) of <0.2 with 64% of the isolates, whereas, with genotypes VI and VII an r value of >0.4 was observed with 24% and 64% of the isolates, respectively. No correlation could be deduced from the amino acid substitutions at specific critical residues and lower r values in the field isolates.

Amino Acid Sequence↗
PubMed2003

Mutation in the 1D gene (VP1) of Foot-and-mouth disease virus serotype Asia1 during serial cytolytic infections in cell culture.

Changes in the nucleotide sequence of the 1D gene of two vaccine strains (IND 63/72 and IND 491/97) of Foot-and-mouth disease virus (FMDV) serotype Asia1 during serial cytolytic infections in cell culture have been analyzed. Sequence comparisons revealed a majority of transition mutations in IND 491/97. The mutation frequency of the 1D gene of IND 491/97 was about 4.5 to 6.0 fold higher than that of IND 63/72. At the amino acids 40-60 and 140-160 regions the mutation frequency was higher compared to the whole VP1. Both viruses showed a constant change at certain residues of the G-H loop region with an accumulation of amino acid replacements during serial cytolytic passages in cell culture. The critical residues (145 and 153) identified previously using mAbs recognizing trypsin-sensitive epitopes were not substituted in the absence of immune selection but changes were observed at positions 142 and 148. Non-reactivity of IND 63/72 after 50(th) passage level onwards with a panel of mAbs indicated an alteration in the antigenic specificity of the virus. Comparison of amino acid sequences in the entire capsid coding region of the naturally occurring field isolates with that of the 50(th) and 100(th) passage level viruses of IND 63/72 revealed that the residues 56 and 74 of VP2 could be involved in mAb binding. The results suggest that fixation of amino acid replacements occurs in VP1 of Asia1 virus, which could play an important role in antigenic variation by modulating different antigenic epitopes located on the surface of the virus.

Amino Acid Sequence↗
PubMed2003

Combined effects of insulin-like growth factor-1 and transforming growth factor-beta1 on periosteal mesenchymal cells during chondrogenesis in vitro.

OBJECTIVE: Periosteum contains undifferentiated mesenchymal stem cells that have both chondrogenic and osteogenic potential, and has been used to repair articular cartilage defects. During this process, the role of growth factors that stimulate the periosteal mesenchymal cells toward chondrogenesis to regenerate articular cartilage and maintain its phenotype is not yet fully understood. In this study, we examined the effects of insulin-like growth factor-1 (IGF-1) and transforming growth factor-beta1 (TGF-beta1), alone and in combination, on periosteal chondrogenesis using an in vitro organ culture model. METHODS: Periosteal explants from the medial proximal tibia of 2-month-old rabbits were cultured in agarose under serum free conditions for up to 6 weeks. After culture the explants were weighed, assayed for cartilage production via Safranin O staining and histomorphometry, assessed for proliferation via proliferative cell nuclear antigen (PCNA) immunostaining, and assessed for type II collagen mRNA expression via in situ hybridization. RESULTS: IGF-1 significantly increased chondrogenesis in a dose-dependent manner when administered continuously throughout the culture period. Continuous IGF-1, in combination with TGF-beta1 for the first 2 days, further enhanced overall total cartilage growth. Immunohistochemistry for PCNA revealed that combining IGF-1 with TGF-beta1 gave the strongest proliferative stimulus early during chondrogenesis. In situ hybridization for type II collagen showed that continuous IGF-1 maintained type II collagen mRNA expression throughout the cambium layer from 2 to 6 weeks. CONCLUSION: The results of this study demonstrate that IGF-1 and TGF-beta1 can act in combination to regulate proliferation and differentiation of periosteal mesenchymal cells during chondrogenesis.

Animals↗
PubMed2002

Phylogenetic analysis of serotype A foot-and-mouth disease virus isolated in India between 1977 and 2000.

The genetic diversity among the Indian serotype A Foot-and-mouth disease virus (FMDV) isolates sampled over a period of 24 years (1977-2000) was studied by sequencing the VP1 gene. In the phylogenetic tree, constructed from 83 Indian and 37 other available sequences, the FMDV type A isolates were distributed into 10 major genotypes (designated as I-X). The Indian isolates were distributed in 4 genotypes (I, IV, VI and VII), and co-circulation of at least 2 genotypes (VI and VII) in different states of the country in recent years is evident from the result. The study also revealed differential geographic distribution of genotypes, for example, some (genotypes I and VII) were recovered from large geographical areas, some time even across the continents, suggesting the spread of the viruses beyond continental barriers. Localization of genotypes restricting to a particular country (genotypes III and X) was also observed in the study. The genetic diversity in the field isolates has been discussed in relation to the amino acid substitutions at the known antigenic sites. This work provides valuable insights into the epidemiological situation of type A FMDV in India and necessary information in the selection of suitable vaccine strain(s), if required, for the National FMD control program.

Amino Acid Sequence↗
PubMed2002

Genetic diversity in the VP1 gene of foot-and-mouth disease virus serotype Asia 1.

Complete nucleotide sequence of the 1D (VP1-encoding) gene of 61 foot-and-mouth disease (FMD) serotype Asia I virus isolates recovered from different outbreaks in India between 1985 and 1999 including two vaccine strains currently used were determined. The sequences were compared with each other and those from other Asian countries. On the basis of phylogenetic analysis the viruses could be grouped into four genotypes (genotypes I-IV). All the 61 isolates from India belong to a single genotype (genotype-II) which is further subdivided into three lineages (B1, B2 and B3) under the same genotype. The viruses of the lineage B1 and B3 were found to be more prevalent before 1996 while the viruses of lineage B2 appeared to be new variants responsible for most of the recent outbreaks. Most of the isolates of lineage B1 lack one amino acid in the VP1 protein (position 44) whereas most of the isolates of lineage B2 and B3 contain it which indicates the possibility of these lineages having evolved independently. The rate of evolution of FMDV Asia 1 virus was also estimated and found to be 2.7 x 10(-2) synonymous substitutions per nucleotide per year.

Amino Acid Sequence↗
PubMed2002

Expression of beta1 integrins during periosteal chondrogenesis.

OBJECTIVE: The interactions between integrins and extracellular matrix proteins are known to modulate cell behavior, and may be involved in regulating cartilage formation and repair. The purpose of this study was to determine the patterns and localization of expression of the beta1 integrins during cartilage formation by periosteum, which is used to repair articular cartilage. DESIGN: Periosteal explants from 2-month-old rabbit medial proximal tibiae were cultured in agarose suspension for 0 to 6 weeks, with 10 ng/ml transforming growth factor-beta1 added for the first 2 days of culture. Integrin expressions were measured by reverse transcriptase-polymerase chain reaction (RT-PCR) and localized by immunohistochemistry. RESULTS: Normal periosteum expressed the alpha1, alpha3, alpha5, beta1 subunits at low levels, and the proteins for all but the alpha3 subunits were identified by immunohistochemistry in the periosteum. Significant two- to five-fold up-regulation of the mRNA expression of the alpha1, alpha3, alpha5 and beta1 integrin subunits during the early proliferative stage of chondrogenesis was observed. The initial change was a five-fold increase in alpha5 expression on day 2 and a two-fold increase in alpha3 expression. On day 5, alpha1 expression was up-regulated (four-fold). beta1 expression was broadly up-regulated (three to four-fold) from day 5 to 14. In the early stage of chondrocyte differentiation, after day 14, alpha1 expression was down-regulated, while there was upregulation of alpha3 (three-fold), alpha5 (three-fold) and beta1 (four-fold) expressions. Thereafter, alpha1 expression was down-regulated, while alpha3, alpha5 and beta1 expressions were up-regulated again during matrix synthesis. Immunohistochemistry confirmed this late decrease in alpha1 levels and increase in alpha3, alpha5 and beta1 levels in chondrocytes. CONCLUSIONS: These observations indicate that the beta1 integrins play an important role in the process of chondrogenesis in periosteum.

Animals↗
PubMed2001

Histomorphological and proliferative characterization of developing periosteal neochondrocytes in vitro.

Periosteal chondrogenesis is relevant to cartilage repair and fracture healing. Cell proliferation is a limiting factor of cartilage production. We used an in vitro organ culture model to test the hypothesis that proliferative activity correlates with cell morphology. One hundred and four periosteal explants from 26 two-month old New Zealand rabbits were cultured for up to 42 days. They were analyzed histomorphologically, and immunohistochemically with proliferative cell nuclear antigen (PCNA). The periosteal neocartilage displayed a consistent zonal pattern of chondrocyte cell shapes. The flat cell zone from day 7 to 21, consisted of uniform-sized small spindle-shaped cells. The round cell zone, which appeared on day 14, consisted of variable-sized round cells averaging 510 +/- 250 microm2 in area. They were subdivided into small round (<510 microm2) and large round cells (>510 microm2). The proliferative index was highest in the small round cell group (32 +/- 6%), intermediate in the flat cell group (27 +/- 6%), and lowest in the large round cell group (20 +/- 7%) (P < 0.001). Furthermore, the proliferative indices in the round cell group were inversely proportional to cell size. Therefore, (1) there is a sequential progression of cell morphology during periosteal chondrogenesis, (2) cell differentiation is arrested prior to terminal differentiation for some cells and not for others, and (3) proliferative activity is strongly related to cell morphology. This organ culture model provides us with opportunities to study the regulation of terminal chondrocyte differentiation and the control of cell proliferation. This will contribute to our understanding of cartilage repair, fracture healing and growth plate physiology.

Animals↗
PubMed2001

Sequence analysis of the RNA polymerase gene of foot-and-mouth disease virus serotype Asia1.

The complete nucleotide (nt.) sequence of the RNA polymerase (3D) gene and 81 nt. in the 3'-untranslated region of foot-and-mouth disease virus (FMDV) serotype Asial (IND63/72) was determined and compared with the sequence of other FMDV serotypes. The 3D genomic region was 1410 nt. long encoding 470 amino acids with an inframe stop codon (TAA) at nt. position 1411-1413. The deduced amino acid sequence of the protein showed 8 conserved motifs as reported in other picornaviruses, 2 of which are 100% identical across the serotypes. Antigenic regions in the polymerase protein were predicted and found to be located at the N-terminus of the protein. The phylogenetic analysis showed that the FMD viruses were segregated into different clusters based on geographical origin; the Asia1 virus did not cluster tightly with any of the geographical groups.

Amino Acid Sequence↗
PubMed2001

Localization of chondrocyte precursors in periosteum.

OBJECTIVE: Periosteal chondrogenesis is relevant to cartilage repair and fracture healing. Periosteum contains two distinct layers: a thick, outer fibrous layer and a thin, inner cambium layer which is adjacent to the bone. Specific chondrocyte precursors are known to exist in periosteum but have not yet been identified. In this study, the location of the chondrocyte precursors in periosteum was determined. METHOD: One hundred and twenty periosteal explants from 30 2-month-old NZ rabbits were cultured for up to 42 days. Histomorphological changes and spatio-temporal localization of Col. II mRNA and protein were analysed. RESULTS: On day 7, chondrocyte differentiation appeared in the most juxtaosseous region in the cambium layer. Col. II mRNA and protein were also evident in the same region. By day 14, chondrocyte differentiation progressed further into the juxtaosseous cambium layer, as did Col. II mRNA and protein. With growth of the neocartilage, the cambium layer gradually diminished to the extent that by 21-28 days it was no longer evident. Cartilage growth was significant and followed an appositional pattern, growing away from the fibrous layer. The fibrous layer remained essentially unchanged from 0-42 days, without evidence of hypertrophy or atrophy. Col. II mRNA expression was never seen in the fibrous layer. CONCLUSION: From these data, three conclusions can be drawn concerning chondrogenesis from periosteum: (1) the chondrocyte precursors are located in the cambium layer of periosteum; (2) chondrogenesis commences in the juxtaosseous area in the cambium layer and progresses from the juxtaosseous region to the juxtafibrous region of the cambium layer; (3) neocartilage growth is appositional, which displaces the fibrous layer away from the cartilage already formed, as new cartilage is formed between these two layers. These findings suggest that the least differentiated (stem or reserve) cells are located in the cambium layer furthest from the bone. CLINICAL RELEVANCE: These findings show that the chondrocyte precursors are located in the cambium layer of periosteum. Preservation of this layer is essential for chondrogenesis. As neocartilage growth is appositional, away from the fibrous layer, it can be expected that the new cartilage deposited in and adjacent to a periosteal graft would be expected to be located on the side of the cambium layer, rather than on the side of the fibrous layer of the graft.

Animals↗
PubMed2001

Treatment of cholestasis and cholestatic disorders.

The future of therapy of chronic cholestatic disorders is bright given the large number of new drugs that are in the initial phases of study. UDCA is currently the mainstay of therapy.

Cholagogues and Choleretics↗