Biomedical subjects

Abhijit Sarkar

Publications and source records attributed to Abhijit Sarkar.

6 recordsLinked to original sources

PubMed2006

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.

Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.

Azoarcus↗

PubMed2004

Two-peak and three-peak optimal complex networks.

A central issue in complex networks is tolerance of random failures and intentional attacks. Current literature emphasizes the dichotomy between networks with a power-law node connectivity distribution, which are robust to random failures but fragile to targeted attacks, versus networks with an exponentially decaying connectivity distribution, which are less tolerant to failures but more resilient to attacks. We prove analytically that the optimal network configuration under a classic measure of robustness is altogether different from both of the above: in all cases, failure and/or attack, there are no more than three distinct node connectivities in the optimal network.

Models, Biological↗

PubMed2003

Reduced models for the medium-frequency dynamics of stochastic systems.

In this paper, a frequency domain vibration analysis procedure of a randomly parametered structural system is described for the medium-frequency range. In this frequency range, both traditional modal analysis and statistical energy analysis (SEA) procedures well-suited for low- and high-frequency vibration analysis respectively, lead to computational and conceptual difficulties. The uncertainty in the structural system can be attributed to various reasons such as the coupling of the primary structure with a variety of secondary systems for which conventional modeling is not practical. The methodology presented in the paper consists of coupling probabilistic reduction methods with dynamical reduction methods. In particular, the Karhunen-Loeve and Polynomial Chaos decompositions of stochastic processes are coupled with an operator decomposition scheme based on the spectrum of an energy operator adapted to the frequency band of interest.

Journal Article↗

PubMed2003

Role of imprint cytology in the diagnosis of gastrointestinal tract malignancies.

Endoscopic biopsies obtained from 275 patients (180 from the upper gastrointestinal tract and 95 from the lower gastrointestinal tract) were studied to compare the accuracy of biopsy imprint cytology and histology in the diagnosis of gastrointestinal lesions, and also to establish the degree of reliability of imprint cytology alone for an early diagnosis of malignancy. Biopsy histology results were found to be correct in 100% cases. Imprint cytology had an overall accuracy of 100%, 96.7%, 95.8% and 95.8% for the diagnosis of malignancies of the oesophagus, stomach, duodenum and colorectum respectively. False negative results were obtained with lymphomas. Regenerative cellular atypia was an important cause for false positive results. It was concluded that imprint cytology can serve as a useful and simple tool for an immediate diagnosis of malignancy. This should be subsequently correlated with histopathology which facilitates exact tumour typing and assessment of tumour invasion.

Adult↗

PubMed2002

Dynamics of chromosome compaction during mitosis.

We have quantitatively studied the space-time dynamics of mitotic chromosome compaction in cultured amphibian cells. After collecting digital phase-contrast images we have done digital image analysis to study spatial correlations in density. We find a characteristic distance at which the strongest correlations occur, which provides a quantitative measure of the size of patches of dense chromatin during interphase and early prophase. Later in mitosis, this length corresponds to the thickness of prophase and metaphase chromosomes. We find that during interphase strong correlations exist at a few-micrometer length; during prophase this correlation length progressively drops as the chromosomes are compacted. Our data are explained by a model based on assembly of chromatin loops onto already fiberlike interphase chromosomes. To test this model we have microinjected cobalt hexamine trichloride into interphase nuclei and have observed the rapid condensation of the interphase chromatin into thick fibers with a spacing similar to the native-state interphase correlation length determined from our image analysis.

Animals↗

PubMed2002

Identification of a NifL-like protein in a diazotroph of the beta-subgroup of the Proteobacteria, Azoarcus sp. strain BH72.

NifA, the transcriptional activator of nitrogenase (nif) genes, has up to now been described to be regulated in its activity via the sensor NifL only for members of the gamma-subgroup of the PROTEOBACTERIA: This paper reports a functionally similar NifL-like protein outside this group in Azoarcus sp. strain BH72, a diazotrophic grass endophyte belonging to the beta-subgroup of the PROTEOBACTERIA: Its structural genes for nitrogenase (nifHDK) are regulated in response to combined nitrogen and O(2) and expressed endophytically inside rice roots. In order to characterize nitrogen-regulatory genes, an Azoarcus sp. BH72 genomic library was used to select cosmids that complemented a nifA mutation in Azotobacter vinelandii. Sequence analysis of the 3.4 kb genomic region complementing nifA showed two ORFs with sequence identities of 44% to NifL and 61% to NifA of Azotobacter vinelandii. According to Northern blot and reverse transcriptase PCR analysis, the nifLA transcript was more abundant at low combined nitrogen and O(2) levels, results which were corroborated by GUS (beta-glucuronidase) assays using a transcriptional nifL::gusA fusion. N(2) fixation was abolished in a NifLA(-) and a NifA(-) mutant, wild-type fixation being restored by nifLA in trans. The NifLA(-) mutant also failed to activate nifH::gus expression, indicating that NifA is the obligate transcriptional activator for nifHDK. A nifL mutant was diazotrophic and did not show repression of nifH::gusA by ammonium or O(2), suggesting that NifL of Azoarcus sp. strain BH72 has a similar role in inactivating NifA in response to O(2) and combined nitrogen as NifL in bacteria of the gamma-PROTEOBACTERIA:

Azoarcus↗