Biomedical subjects

Nikhil Kumar

Publications and source records attributed to Nikhil Kumar.

9 recordsLinked to original sources

PubMed2026

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

The immunoregulatory architecture of human oral tissues remains poorly defined. We present an integrated single-cell and spatial proteotranscriptomic atlas profiling >250,000 single-cell transcriptomes and >4 million spatially resolved cells across 13 niches. Using our AI-enabled AstroSuite, we defined neighborhoods and interaction modules, revealing peri-epithelial fibroblast-centered hubs enriched in effector cytokines. We harmonized fibroblast subtypes (universal, immune, peri-epithelial, peri-vascular, peri-neural, antigen-presenting cell [APC]-like, stress responsive, and myofibroblasts) with stress-responsive subtypes partitioning between mucosae and glands (type I and II). Spatial multiomics mapped ligand-receptor programs and identified mucosal stress-responsive fibroblasts as putative immunoregulatory hubs. Niche-aware integration of healthy and diseased datasets revealed fibroblast rewiring into inflammatory and reparative niches. Disease neighborhoods exhibited expansion of major histocompatibility complex (MHC)-I+, MHC-II+, and programmed cell death ligand 1 (PD-L1)+ fibroblasts and predicted spatial engagement with T cells at tertiary lymphoid structures. Together, this atlas identifies fibroblasts as central regulators of structural immunity and provides a scalable framework to target stromal-immune interactions across barrier organs.

Journal Article↗

PubMed2006

Identification of novel cps locus polymorphisms in nontypable group B Streptococcus.

Group B Streptococcus (GBS) is an important pathogen responsible for a variety of diseases in newborns and the elderly. A clinical GBS isolate is considered nontypable (NT) when serological methods fail to identify it as one of nine known GBS serotypes. Eight clinical isolates (designated A1-A4, B1-B4) showed PFGE profiles similar to that of a GBS serotype V strain expressing R1, R4 surface proteins. These unique isolates were further characterized by immunologic and genetic methods. Rabbit sera to isolates A1 and A2 reacted weakly with concentrated HCl extracts of A1-A4 isolates, but not with those of B1-B4 isolates. In addition, a type V capsular polysaccharide (CPS) inhibition ELISA revealed that cell wall extracts from isolates A1-A4, but not from B1-B4, expressed low but measurable amounts of type V CPS. Molecular serotyping with PCR analysis showed that all eight isolates contained a type V-specific CPS gene (cpsO) and harboured the gene encoding the surface protein Alp3. Multilocus sequence typing identified isolate A1 as belonging to a new sequence type (ST) designated ST-173, whereas the other seven isolates keyed to ST-1. Sequencing of the 18 genes (17 736 bp) in the cps locus showed that each NT isolate harboured one to three unique polymorphisms, and also identified an IS1381 element in cpsE of the B4 isolate. Collectively, genetic and immunologic analyses revealed that these NT isolates expressing R1, R4 proteins have a genetic profile consistent with that of type V, an emergent, antigenically diverse and increasingly prevalent GBS serotype.

Animals↗

PubMed2006

Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.

To better understand Neisseria meningitidis genomes and virulence, microarray comparative genome hybridization (mCGH) data were collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491 and FAM18, and N. gonorrhoeae FA1090. By comparing hybridization data to genome sequences, the core N. meningitidis genome and insertions/deletions (e.g. capsule locus, type I secretion system) related to pathogenicity were identified, including further characterization of the capsule locus, bioinformatics analysis of a type I secretion system, and identification of some metabolic pathways associated with intracellular survival in pathogens. Hybridization data clustered meningococcal isolates from similar clonal complexes that were distinguished by the differential presence of six distinct islands of horizontal transfer. Several of these islands contained prophage or other mobile elements, including a novel prophage and a transposon carrying portions of a type I secretion system. Acquisition of some genetic islands appears to have occurred in multiple lineages, including transfer between N. lactamica and N. meningitidis. However, island acquisition occurs infrequently, such that the genomic-level relationship is not obscured within clonal complexes. The N. meningitidis genome is characterized by the horizontal acquisition of multiple genetic islands; the study of these islands reveals important sets of genes varying between isolates and likely to be related to pathogenicity.

Bacterial Capsules↗

PubMed2005

Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis.

Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering 283 Mb (0.44 x) of the estimated 650 Mb Brassica genome were searched against the Arabidopsis genome, and conserved Arabidopsis genome sequences (CAGSs) were identified. Of these 229,735 conserved regions, 167,357 fell within or intersected existing gene models, while 60,378 were located in previously unannotated regions. After removal of sequences matching known proteins, CAGSs that were close to one another were chained together as potentially comprising portions of the same functional unit. This resulted in 27,347 chains of which 15,686 were sufficiently distant from existing gene annotations to be considered a novel conserved unit. Of 192 conserved regions examined, 58 were found to be expressed in our cDNA populations. Rapid amplification of cDNA ends (RACE) was used to obtain potentially full-length transcripts from these 58 regions. The resulting sequences led to the creation of 21 gene models at 17 new Arabidopsis loci and the addition of splice variants or updates to another 19 gene structures. In addition, CAGSs overlapping already annotated genes in Arabidopsis can provide guidance for manual improvement of existing gene models. Published genome-wide expression data based on whole genome tiling arrays and massively parallel signature sequencing were overlaid on the Brassica-Arabidopsis conserved sequences, and 1399 regions of intersection were identified. Collectively our results and these data sets suggest that several thousand new Arabidopsis genes remain to be identified and annotated.

Arabidopsis↗

PubMed2004

Genetic diversity amongst landraces of a dioecious vegetatively propagated plant, betelvine (Piper betle L.).

Betelvine (Piper betle L., family Piperaceae) is an important, traditional and widely cultivated crop of India. The cultivators and consumers recognize more than 100 cultivars (landraces) based on regional and organoleptic considerations, while in terms of phytochemical constituents only five groups have been identified for all the landraces. Since betelvine is an obligate vegetatively propagated species, genomic changes, if any, may have become 'fixed' in the landraces. We carried out random amplified polymorphic DNA (RAPD) analysis in several landraces considered in four groups, namely, 'Kapoori', 'Bangla', 'Sanchi' and 'Others' in order to ascertain their genetic diversity. On the basis of the data from eleven RAPD primers, we distinguished genetic variation within and among the four groups of landraces. The results indicate the 'Kapoori' group is the most diverse. The neighbour joining (NJ) tree after a bootstrap (500 replicate) test of robustness clearly shows the four groups to be well separated. Interestingly, all known male or female betelvine landraces have separated in the NJ tree indicating an apparent gender-based distinction among the betelvines.

Algorithms↗

PubMed2004

Sympathetic ophthalmia following ciliary body laser cyclophotocoagulation for rubeotic glaucoma.

A 60-year-old Asian man presented with left rubeotic glaucoma secondary to a central retinal vein occlusion. He was successfully treated with laser diode cyclophotocoagulation of the ciliary body. Nine months later he developed right progressive visual loss, headache, corneal oedema, anterior chamber cells, flare, mutton fat keratic precipitates, a swollen disc, and a minimal inferior visual field defect. A diagnosis of sympathetic ophthalmia was made, which was confirmed by characteristic findings seen on fluorescein and indocyanine green angiography.

Ciliary Body↗

PubMed2004

Scleral buckle intrusion.

A case is reported of a 72-year-old man with an intruded scleral buckle presenting 30 years after retinal detachment repair. The lesion was noted incidentally and occupied the superotemporal retinal periphery. The diagnosis was confirmed by B-scan ultrasonography and external examination of the globe. The patient was treated conservatively. No clinical change was evident after 12 months follow up.

Aged↗

PubMed2003

Gunshot injury of the heart: an unusual cause of acute myocardial infarction.

A 30-year-old man had multiple pellet injuries after being shot. An asymptomatic, acute, inferior-wall myocardial infarction was detected on an electrocardiogram at the time of a pre-anesthetic evaluation for eye surgery. A computed tomographic scan of the chest confirmed the presence of an intracardiac foreign body. Coronary angiography showed occlusion of the distal right coronary artery by a pellet. The patient was managed conservatively with aspirin and metoprolol. In conclusion, a single coronary lesion, the absence of other cardiac complications, and a favorable outcome with conservative medical treatment after a gunshot injury contribute to the rarity of this case of myocardial infarction.

Adrenergic beta-Antagonists↗

PubMed2002

Stroke at high altitude: Indian experience.

UNLABELLED: Stroke is a common medical emergency. There is limited knowledge about stroke at high altitude. We present the clinical profile of 30 cases of stroke at high altitude seen at our center between November 1998 to July 2000. A detailed neurological and systemic examination was carried out. Cases were investigated with blood counts, lipid profile, cardiac evaluation, and CT scan/MRI. Coagulation parameters were studied in some cases. Strokes formed 13.7/1000 of hospital admissions from high altitude area, compared to 1.05/1000 in nonhigh altitude area. All our cases from high altitude area were males (serving soldiers of armed forces). Their mean high altitude stay was 10.2 months, and they were all located at heights greater than 4270 m. Age ranged from 22 to 48 years (mean 33.4 yr). Except for smoking (in four cases), they had no preexisting risk factors. Twenty-two cases were of ischemic stroke, 2 of intracerebral hemorrhage, 4 of TIA/RIND (transient ischemic attack/reversible ischemic neurological deficit), and 2 had cerebral venous thrombosis. Out of 30 cases, 28 were of "stroke in young" (<45 yr) and were compared with cases in the same age group from nonhigh altitude areas. Polycythemia with Hb ranging from 16.2 to 22 g.dL(-1) was seen in 21 of these 28 cases (75%). Protein C and S deficiency was found in 1 case in each group. CT scan showed massive infarcts involving at least 50% of one cerebral hemisphere in 12 cases. Multiple infarcts were seen in one case. CONCLUSION: Long-term stay at high altitude is associated with higher risk of stroke. Although all types of stroke were seen, ischemic stroke was the commonest. Massive infarcts were common. Polycythemia was an important risk factor.

Adult↗