Vinayak Kapatral - Academia.edu (original) (raw)

Papers by Vinayak Kapatral

bioRxiv (Cold Spring Harbor Laboratory), Apr 7, 2023

Candida auris is an opportunistic fungal pathogen with high mortality rates that presents a clear... more Candida auris is an opportunistic fungal pathogen with high mortality rates that presents a clear and present threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not wellknown. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we found that B11220 was missing a 12.8 kb gene cluster encoding proteins related to alternative sugar utilization, possibly L-rhamnose. We show that B11221, which has the cluster, more readily assimilates and utilizes D-galactose and L-rhamnose. B11221 also exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both strains grown on glucose or galactose showed that genes associated with translation were upregulated in B11221, and the putative L-rhamnose gene cluster was upregulated when grown on D-galactose. These findings reinforce the growing evidence of a link between metabolism and tolerance. Since immune system evasion depends heavily on the cell surface, we characterized cell wall composition and macrophage evasion for the two strains. We found that B11221 has far less β-1,3-glucan exposure, a key determinant of immune system evasion, and resists phagocytosis by macrophages compared to B11220. In a transcriptomic analysis of both strains co-cultured with macrophages we found that B11221 upregulates genes associated with early stages of growth and transcription factors that regulate transport. These key differences in growth and membrane composition could explain the resistance to phagocytosis and increased stress tolerance in general of B11221, and indicates another connection between metabolism and immune system evasion. Taken together, these data show that membrane composition, metabolism, and transport all correlate with colonization, drug resistance, and immune system evasion in C. auris. .

Nature, May 1, 2003

Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or e... more Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes 1. It is closely related to the animal and human pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the former being used as a biological weapon and the latter as a pesticide. B. anthracis and B. thuringiensis are readily distinguished from B. cereus by the presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But phylogenetic studies based on the analysis of chromosomal genes bring controversial results, and it is unclear whether B. cereus, B. anthracis and B. thuringiensis are varieties of the same species 2 or different species 3,4. Here we report the sequencing and analysis of the type strain B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 5 enables us to perform comparative analysis, and hence to identify the genes that are conserved between B. cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers. The general features of the B. cereus ATCC 14579 genome are listed in Table 1. The region between 0.8 and 1.8 megabases (Mb) has G þ C content close to the average for the chromosome (35.3%); in the region between 3.7 and 0.8 Mb the G þ C content is higher than the average value, and in the region between 1.8 and 3.7 Mb it is lower than the average value (Fig. 1, circle 3). These regions are bordered with putative prophages (Fig. 1, circles 6 and 7), which could be indicative of the origin of the B. cereus ATCC

Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteoba... more Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia’s principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerab...

African Journal of Biotechnology, 2006

We present a comparative analysis of select insect mitochondrial DNA (mtDNA) representing four in... more We present a comparative analysis of select insect mitochondrial DNA (mtDNA) representing four insect orders (Diptera, Hymenoptera, Orthoptera and Coleoptera) consisting of 12 different species in an effort to study a common set of genes and to understand the evolution of mitochondrial genome. A functional analysis of mitochondrial genomes was carried out using ERGO bioinformatics suite. To compare the similarity between closely related insect mitochondrial genome sequences, dot-plot comparisons of sequences were performed. LSU and SSU rRNA sequences were used to construct a phylogenetic tree to determine the relationship among four insect orders. LSU rRNA sequences yielded a tree with branching patterns reflecting the expected pattern as insect species belonging to different orders were put into separate clades. Based on the sequence similarity, insect species belonging to four different orders in general appear to be closely related. However, a comparative and functional analysis ...

The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow trout... more The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow trout (Oncorhynchus mykiss), consists of a single circular genome of 2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has been used to select a line of rainbow trout with increased genetic resistance against bacterial cold water disease.

Biology and Fertility of Soils, 1992

We tested the response of the wetland rice cultivar Prakash to inoculation with ten vesicular-arb... more We tested the response of the wetland rice cultivar Prakash to inoculation with ten vesicular-arbucular mycorrhizal (VAM) fungi (three selected from the first screening and seven isolated from local paddy fields) in a pot experiment under flooded conditions, in order to select the most efficient mycorrhizal fungi to inoculate the rice nursery. A sandy clay loam soil was used as the substrate, fertilized with the recommended N and K levels (100 kg N ha-1 as ammonium sulphate and 50 kg K ha-1 as muriate of potash) and half the recommended level of P (25 kg ha-~ as super phosphate). The inoculation was made into dry nursery beds and the beds were flooded when the seedlings were about 25 cm high, in 15 days. Twenty-eight-day old seedlings were transferred to pots filled with well puddled soil flooded with 5 cm of standing water. Based on the increase in grain yield and total biomass, Glomus intraradices and Acaulospora sp. were considered efficient and suitable for inoculation into rice nurseries.

FEMS …

1. Editorial board • EDITORIAL BOARD Pages iii-vi ... 2. Comparative genome analysis of Bacillus ... more 1. Editorial board • EDITORIAL BOARD Pages iii-vi ... 2. Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis • SHORT COMMUNICATION Pages 175-184 Iain Anderson, Alexei Sorokin, Vinayak Kapatral, Gary Reznik, Anamitra Bhattacharya, Natalia ...

Alchornea cordifolia extract protects wistar albino rats against acetaminophen-induced liver damage

to contain 3,294,935 bp distributed over two circular chromosomes sv of 2,117,144 bp and 1,177,78... more to contain 3,294,935 bp distributed over two circular chromosomes sv of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the pE bioinformatics suite ERGO, 2,487 (78%) ORFs were assigned func- Bi tions. The origins of replication of the two chromosomes are similar to those of other a-proteobacteria. Housekeeping genes, including M those involved in DNA replication, transcription, translation, core Dl metabolism, and cell wall biosynthesis, are distributed on both 22 chromosomes. Type I, II, and III secretion systems are absent, but hi genes encoding sec-dependent, sec-independent, and flagella- ca specific type III, type IV, and type V secretion systems as well as ar adhesins, invasins, and hemolysins were identified. Several fea- ca tures of the B. melitensis genome are similar to those of the m symbiotic Sinorhizobium meliloti. fe fr

Journal of Industrial Microbiology and Biotechnology, 2020

Organic farming has become more prevalent in recent years as consumer demand for organic food and... more Organic farming has become more prevalent in recent years as consumer demand for organic food and fiber has rapidly grown. Until recently, organic fertilizers and soil amendments have largely been based on the practices of returning crop residues, manures and related agricultural wastes back to crop production areas. One rapidly growing segment in commercial organic fertilizer development is the use of spent microbial biomass (SMB) from industrial fermentation processes. While SMB is widely accepted in many organic farming systems (OFS), little is known concerning the effectiveness, environmental impact, and influence on prokaryotic communities in soils receiving this treatment. In this study, a comparative analysis of bacterial communities associated with OFS and conventional farming systems was performed over a growing season for a field containing yellow dent corn (Zea mays). A statistically significant increase in microbial population α-diversity, along with a strong recruitment...

Genome Biology, 2002

The entire Brucella melitensis genome sequence could pave the way to a vaccine against brucellosi... more The entire Brucella melitensis genome sequence could pave the way to a vaccine against brucellosis in humans Significance and context In 1887 the British army surgeon Sir David Bruce discovered the organism that caused Malta fever in humans. This organism is now better known as the facultative intracellular bacterial pathogen Brucella melitensis. Infection with B. melitensis causes abortion in goats and sheep and Malta fever in humans; it is still reported from Mediterranean regions and parts of Asia, Africa and Latin America. The symptoms are comparable with those at the start of influenza. Humans can get infected when they come into contact with unpasteurized milk or milk products, or infected animals. During the early stages of infection, B. melitensis enters macrophages, where it adapts to the acidic environment in vacuoles; it multiplies in the vacuolar compartment and prevents fusion of phagosomes with lysosomes. Brucellosis in humans spreads easily and no vaccines are yet available. This, together with the fact that Brucella pathogenesis is poorly understood, provided the impetus for an in-depth study of this bacterial pathogen, the entire genome sequence of which is now available for further research.

Journal of Pure and Applied Microbiology, 2016

Escherichia coli serotype O25b:H4 is involved in human urinary tract infections. In this study, w... more Escherichia coli serotype O25b:H4 is involved in human urinary tract infections. In this study, we sequenced and analyzed E. coli O25b:H4 isolated from a patient suffering from recurring UTI infections in an intensive care unit at Hera General Hospital in Makkah, Saudi Arabia. We aimed to determine the virulence genes for pathogenesis and drug resistance of this isolate compared to other E. coli strains. We sequenced and analyzed the E. coli O25b:H4 Saudi strain clinical isolate using next generation sequencing. Using the ERGO genome analysis platform, we performed annotations and identified virulence and antibiotic resistance determinants of this clinical isolate. The E. coli O25b:H4 genome was assembled into four contigs representing a total chromosome size of 5.28 Mb, and three contigs were identified, including a 130.9 kb (virulence plasmid) contig bearing the bla-CTX gene and 32 kb and 29 kb contigs. In comparing this genome to other uropathogenic E. coli genomes, we identified unique drug resistance and pathogenicity factors. In this work, whole-genome sequencing and targeted comparative analysis of a clinical isolate of uropathogenic Escherichia coli O25b:H4 was performed. This strain encodes virulence genes linked with extraintestinal pathogenic E. coli (ExPEC) that are expressed constitutively in E. coli ST131. We identified the genes responsible for pathogenesis and drug resistance and performed comparative analyses of the virulence and antibiotic resistance determinants with those of other E. coli UPEC isolates. This is the first report of genome sequencing and analysis of a UPEC strain from Saudi Arabia.

FEMS microbiology letters, 2015

We sequenced and analyzed Shigella dysenteriae strain Sd1617 serotype 1 that is widely used as mo... more We sequenced and analyzed Shigella dysenteriae strain Sd1617 serotype 1 that is widely used as model strain for vaccine design, trials and research. A combination of next-generation sequencing platforms and assembly yielded two contigs representing a chromosome size of 4.34 Mb and the large virulence plasmid of 177 kb. This genome sequence is compared with other Shigella genomes in order to understand gene complexity and pathogenic factors.

Photosynthesis Research, 2001

The genome of Rhodobacter capsulatus has been completely sequenced. It consists of a single chrom... more The genome of Rhodobacter capsulatus has been completely sequenced. It consists of a single chromosome containing 3.5 Mb and a circular plasmid of 134 kb. This effort, started in 1992, began with a fine-structure restriction map of an overlapping set of cosmids that covered the genome. Cosmid sequencing led to a gapped genome that was filled by primer walking on the chromosome and by using lambda clones. Methods had to be developed to handle strong stops in the high GC (68%) inserts. Annotation was done with the ERGO system at Integrated Genomics, as was the reconstruction of the cell&amp;#39;s metabolism. It was possible to recognize 3709 orfs of which functional assignments could be made with high confidence to 2392 (65%). Unusual features include the presence of numerous cryptic phage genomes embedded in the chromosome.