Biomedical subjects

Vikas Kumar

Publications and source records attributed to Vikas Kumar.

At least 19 recordsLinked to original sources

PubMed2026

Ancient DNA unveils distinctive ancestries in the Bronze and Iron Ages of East Tianshan.

The East Tianshan Mountains occupy a key corridor between Central and East Asia, but their population history remains poorly understood. Here we report genome-wide data from 135 ancient individuals from 11 archaeological sites. We identify a previously unrecognized Bronze Age admixture between populations related to Yellow River millet farmers and steppe pastoralists associated with the Chemurchek culture. In contrast, we find little genetic contribution from contemporaneous middle-to-late Bronze Age steppe pastoralists, despite their eastward expansion across the Eurasian Steppe. By the Iron Age, regional populations had become more heterogeneous, incorporating additional eastern and steppe-related sources while retaining variable contributions from Early Bronze Age groups. These results reveal sustained demographic interactions in eastern Central Asia nearly 1800 years preceding the establishment of the historic Silk Road.

DNA, Ancient↗

PubMed2026

First complete mitochondrial genome of Uzelothrips scabrosus (Thysanoptera: Uzelothripidae) provides insights into gene rearrangements and phylogenetic position within Terebrantia.

The family Uzelothripidae is represented by a single genus Uzelothrips and can be distinguished from others by the presence of whip-like antennae, a circular ventral sensorium on antennal segment III, a well-developed tentorium, and a membranous ovipositor. Here, we generated the first complete mitochondrial genome of Uzelothrips scabrosus (15,674 bp) using next-generation sequencing to explore the gene rearrangements and phylogenetic relationships. It consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two putative control regions. The genome exhibits strong AT bias (71.35%) with negative AT and GC skew. Codon usage analyses indicate a strong bias towards A/U-ending codons and influenced by both natural selection and mutation pressure. All PCGs were under purifying selection, with cox1 being the most conserved and nad4L the most variable. The gene order of the family Uzelothripidae is highly rearranged compared to the ancestral insect gene order. Comparative analysis revealed that gene block B was the most widely conserved, whereas the remaining gene blocks exhibited family or lineage-specific conservation patterns, reflecting extensive mitochondrial gene rearrangements during the evolution of the Thysanoptera. Moreover, 228 synapomorphic and 68 autapomorphic gene boundaries were identified across thysanopteran mitogenomes. Phylogenies indicated that the family Uzelothripidae is in a sister relationship with Stenurothripidae, and the Uzelothripidae + Stenurothripidae clade is sister to Thripidae. This study provides the first mitogenomic insights into Uzelothripidae and highlights the need for broader taxon sampling and nuclear genomic data to resolve deep evolutionary relationships within Thysanoptera.

Comparative analysis↗

PubMed2006

Role of GABAergic antagonism in the neuroprotective effects of bilobalide.

Bilobalide, a constituent of Ginkgo biloba, has neuroprotective properties. Its mechanism of action is unknown but it was recently found to block GABA(A) receptors. The goal of this study was to test the potential role of a GABAergic mechanism for the neuroprotective activity of bilobalide. In rat hippocampal slices exposed to NMDA, release of choline indicates breakdown of membrane phospholipids. NMDA-induced choline release was almost completely blocked in the presence of bilobalide (10 microM) and under low-chloride conditions. Bicuculline (100 microM), a competitive antagonist at GABA(A) receptors, reduced NMDA-induced choline release to a small extent (-23%). GABA (100 microM) partially antagonized the inhibitory action of bilobalide. Exposure of hippocampal slices to NMDA also caused edema formation as measured by increases of tissue water content. NMDA-induced edema formation was suppressed by bilobalide and by low-chloride conditions. Bicuculline exerted partial protection (by 30%) while GABA reduced bilobalide's effect by about one third. To investigate bilobalide's interaction with GABA(A) receptors directly, we measured binding of [(35)S]-TBPS to rat cortical membranes. TBPS binding was competitively inhibited by bilobalide in the low micromolar range (IC(50)=3.7 microM). As a functional test, we determined (36)chloride flux in rat corticohippocampal synaptoneurosomes. GABA (100 microM) significantly increased (36)chloride flux (+65%), and this increase was blocked by bilobalide, but with low potency (IC(50): 39 microM). We conclude that, while antagonism of GABA(A) receptors may contribute to bilobalide's neuroprotective effects, additional mechanisms must be postulated to fully explain bilobalide's actions.

Animals↗

PubMed2006

Spontaneous intra-peritoneal bleeding secondary to warfarin, presenting as an acute appendicitis: a case report and review of literature.

BACKGROUND: Warfarin is a coumarin anti-coagulant, used widely for the therapeutic and prophylactic anticoagulation. Although, it is considered as a life saving medicine, it is associated with the significant adverse effects including intra-abdominal bleeding, which have been very well documented in literature. However, the presentation of warfarin induced intra-peritoneal bleeding as an acute appendicitis has not been reported in English literature. We report this rare, spontaneous intra-peritoneal bleeding secondary to warfarin therapy, mimicking the signs and symptoms of an acute appendicitis for the first time in English literature. CASE PRESENTATION: A 41 year-old female patient who was on warfarin for prophylaxis following the previous episode of pulmonary embolism, presented to the Casualty with the typical symptoms of an acute appendicitis. During operative intervention, we found it to be the spontaneous intra-peritoneal bleeding secondary to warfarin. The patient recovered well following the operation. CONCLUSION: We recommend the use of the radiological investigations in all the cases of acute abdomen who are on warfarin even if the INR is within the therapeutic range.

Journal Article↗

PubMed2006

Effects of chloride flux modulators in an in vitro model of brain edema formation.

Brain edema is a serious consequence of hemispheric stroke and traumatic brain injury and contributes significantly to patient mortality. In the present study, we measured water contents in hippocampal slices as an in vitro model of edema formation. Excitotoxic conditions induced by N-methyl-D-aspartate (NMDA, 300 microM), as well as ischemia induced by oxygen-glucose deprivation (OGD), caused cellular edema formation as indicated by an increase of slice water contents. In the presence of furosemide, an inhibitor of the Na,K,Cl-cotransporter, NMDA-induced edema were reduced by 64% while OGD-induced edema were unaffected. The same observation, i.e., reduction of excitotoxic edema formation but no effect on ischemia-induced edema, was made with chloride transport inhibitors such as DIDS and niflumic acid. Under ischemic conditions, modulation of GABAA receptors by bicuculline, a GABA antagonist, or by diazepam, a GABAergic agonist, did not significantly affect edema formation. Further experiments demonstrated that low chloride conditions prevented NMDA-induced, but not OGD-induced, water influx. Omission of calcium ions had no effect. Our results show that NMDA-induced edema formation is highly dependent on chloride influx as it was prevented by low-chloride conditions and by various compounds that interfere with chloride influx. In contrast, OGD-induced edema observed in brain slices was not affected by modulators of chloride fluxes. The results are discussed with reference to ionic changes occurring during tissue ischemia.

Animals↗

PubMed2006

CYP2C9 inhibition: impact of probe selection and pharmacogenetics on in vitro inhibition profiles.

Drug-drug interactions may cause serious adverse events in the clinical setting, and the cytochromes P450 are the enzyme system most often implicated in these interactions. Cytochrome P450 2C is the second most abundant subfamily of cytochrome P450 enzymes and is responsible for metabolism of almost 20% of currently marketed drugs. The most abundant isoform of this subfamily is CYP2C9, which is the major clearance pathway for the low therapeutic index drugs warfarin and phenytoin. Considering the importance of CYP2C9 to drug-drug interactions, the in vitro-in vivo extrapolation of drug-drug interactions for CYP2C9 may be confounded by the presence of polymorphic variants and the possibility of multiple binding regions within the CYP2C9 active site, leading to the potential for genotype- and substrate-dependent inhibition. To address the issues of genotype-dependent enzyme inhibition as well as probe substrate correlations, the inhibitory potency (Ki) of 28 effector molecules was assessed with five commonly used probes of CYP2C9 in both the CYP2C9.1 and CYP2C9.3 proteins. The inhibition of CYP2C9.1 and CYP2C9.3 by the battery of inhibitors with five substrate probes demonstrated differential inhibition potency not only between the two genotypes but also across substrate probes. Furthermore, the substrate probes fell into three distinct classes depending on genotype, suggesting that multiple probes may be needed to fully assess inhibition of CYP2C9 in vitro. Thus, both genotype and choice of probe substrate must be considered when attempting to predict potential CYP2C9 drug-drug interactions from in vitro data.

Aryl Hydrocarbon Hydroxylases↗

PubMed2006

NMDA receptor-antagonistic properties of hyperforin, a constituent of St. John's Wort.

Extracts of the medicinal plant St. John's wort (Hypericum perforatum) are widely used for the treatment of affective disorders. Hyperforin, a constituent of St. John's wort, is known to modulate the release and re-uptake of various neurotransmitters, an action that likely underlies its antidepressive activity. We now report that hyperforin also has N-methyl-D-aspartate (NMDA)-antagonistic effects. Hyperforin (10 microM) was found to inhibit the NMDA-induced calcium influx into cortical neurons. In rat hippocampal slices, hyperforin inhibited the NMDA-receptor-mediated release of choline from phospholipids. Hyperforin also antagonized the increase of water content in freshly isolated hippocampal slices, and it counteracted, at 3 and 10 microM, the increase of water content induced by NMDA. Hyperforin was inactive, however, in two in vivo models of brain edema formation, middle cerebral artery occlusion and water intoxication in mice. In conclusion, hyperforin has NMDA-receptor-antagonistic and potential neuroprotective effects in vitro. This effect may contribute to the therapeutic effectiveness of St. John's wort extracts in some situations, for example, for relapse prevention in alcoholism.

Animals↗

PubMed2006

Enzyme source effects on CYP2C9 kinetics and inhibition.

When choosing a recombinant cytochrome P450 (P450) enzyme system for in vitro studies, it is critical to understand the strengths, limitations, and applicability of the enzyme system to the study design. Although literature kinetic data may be available to assist in enzyme system selection, comparison of data from separate laboratories is often confounded by differences in experimental conditions and bioanalytical techniques. We measured the Michaelis-Menten kinetic parameters for four CYP2C9 substrates (diclofenac, (S)-warfarin, tolbutamide, and (S)-flurbiprofen) using four recombinant CYP2C9 enzyme systems (Supersomes, Baculosomes, RECO system, and in-house purified, reconstituted enzyme) to determine whether the enzyme systems exhibited kinetic differences in metabolic product formation rates under uniform experimental conditions. The purified, reconstituted enzyme systems exhibited higher K(m) values, reduced substrate affinity, and lower calculated intrinsic clearance values compared with baculovirus microsomal preparations. Six- to 25-fold differences in predicted intrinsic clearance values were calculated for each substrate depending on the enzyme system-substrate combination. Results suggest that P450 reductase interactions with the CYP2C9 protein and varying ratios of CYP2C9/P450 reductase in the enzyme preparations may play a role in these observed differences. In addition, when (S)-flurbiprofen was used as a substrate probe to determine CYP2C9 inhibition with a set of 12 inhibitors, decreased inhibition potency was observed across 11 of those inhibitors in the RECO purified, reconstituted enzyme compared with the Supersomes baculovirus microsomal preparation and pooled human liver microsomes. Considering these differences, consistent use of an enzyme source is an important component in producing comparable and reproducible kinetics and inhibition data with CYP2C9.

Aryl Hydrocarbon Hydroxylases↗

PubMed2006

A novel method of loading samples onto mini-gels for SDS-PAGE: increased sensitivity and Western blots using sub-microgram quantities of protein.

Commercially available mini-gels for sodium dodecyl sulphate (SDS)-PAGE and Western blotting are limited both by the number of lanes that can be loaded per gel and the minimum amount of protein per lane that must be loaded. Here we describe a method for loading protein samples onto existing commercially available mini-gels that allows loading of 50 or more lanes per gel. The enhanced sensitivity of the method allows Western blotting with sub-microgram quantities of protein. Samples are loaded onto filter paper strips mounted on a plastic backing sheet, and film-wrapped strips on a separate dummy loader interdigitate with the sample strips, creating a physical barrier to lateral diffusion. The sample loader sandwich is placed on top of the stacking gel, and is compatible with all commercially available SDS-PAGE systems. Comparison of 15-lane mini-gels with 30-lane micro-loader strips reveals up to a 10-fold increase in sensitivity with the new method. Using 50- and 66-lane micro-loaders, sub-microgram quantities of protein produce reliable and quantifiable signal by Western blotting. Manipulation of the ionic conditions within dummy loader strips provides a mechanism for enhancing lateral resolution, allowing for the possibility of further miniaturization.

Antibodies↗

PubMed2006

Amiodarone analog-dependent effects on CYP2C9-mediated metabolism and kinetic profiles.

CYP2C9 substrates can exhibit both hyperbolic and atypical kinetic profiles, and their metabolism can be activated or inhibited depending on the effector studied. CYP2C9 genetic variants can also affect both substrate turnover and kinetic profile. The present study assessed whether analogs of the effector amiodarone differentially altered the atypical kinetic profile of the substrate naproxen and whether this effect was genotype-dependent. Amiodarone, desethylamiodarone, benzbromarone, and its dimethyl analog (benz(meth)arone) were incubated with naproxen and either CYP2C9.1 or CYP2C9.3. Amiodarone activated naproxen demethylation at lower concentrations, regardless of the CYP2C9 allele, and inhibited metabolism at higher concentrations without altering the kinetic profile. Desethylamiodarone was a potent inhibitor of naproxen demethylation, irrespective of the CYP2C9 allele. Benzbromarone altered naproxen demethylation kinetics from a biphasic profile to that of a hyperbolic form in CYP2C9.1 and CYP2C9.3, resulting in inhibition and activation, respectively. In contrast, benz(meth)arone activated naproxen demethylation in both CYP2C9.1 and CYP2C9.3. In addition, the kinetic profile of naproxen demethylation became more hyperbolic at lower concentrations of benz(meth)arone and then reverted back to biphasic as the benz(meth)arone was increased further. Equilibrium binding and multiple-ligand docking studies were used to propose how such similar compounds exerted very different effects on naproxen metabolism. In summary, effectors of CYP2C9 metabolism can alter not only the degree of substrate turnover (activation or inhibition) but also the kinetic profile of metabolism of CYP2C9 substrates through effects on substrate binding and orientation. In addition, these kinetics effects are concentration- and genotype-dependent.

Amiodarone↗

PubMed2006

Definition and GIS-based characterization of an integral risk index applied to a chemical/petrochemical area.

A risk map of the chemical/petrochemical industrial area of Tarragona (Catalonia, Spain) was designed following a two-stage procedure. The first step was the creation of a ranking system (Hazard Index) for a number of different inorganic and organic pollutants: heavy metals, polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and polychlorinated aromatic hydrocarbons (PAHs) by applying self-organizing maps (SOM) to persistence, bioaccumulation and toxicity properties of the chemicals. PCBs seemed to be the most hazardous compounds, while the light PAHs showed the minimum values. Subsequently, an Integral Risk Index was developed taking into account the Hazard Index and the concentrations of all pollutants in soil samples collected in the assessed area of Tarragona. Finally, a risk map was elaborated by representing the spatial distribution of the Integral Risk Index with a geographic information system (GIS). The results of the present study seem to indicate that the development of an integral risk map might be useful to help in making-decision processes concerning environmental pollutants.

Chemical Industry↗

PubMed2006

Potential medicinal plants for CNS disorders: an overview.

Although very few drugs are currently approved by regulatory authorities for treating multi-factorial ailments and disorders of cognition such as Alzheimer's disease, certain plant-derived agents, including, for example, galantamine and rivastigmine (a semi-synthetic derivative of physostigmine) are finding an application in modern medicine. However, in Ayurveda, the Indian traditional system of medicine which is more than 5000 years old, selected plants have long been classified as 'medhya rasayanas', from the Sanskrit words 'medhya', meaning intellect or cognition, and 'rasayana', meaning 'rejuvenation'. These plants are used both in herbal and conventional medicine and offer benefits that pharmaceutical drugs lack. In the present article, an attempt has been made to review the most important medicinal plants, including Ginkgo biloba, St John's wort, Kava-kava, Valerian, Bacopa monniera and Convolvulus pluricaulis, which are widely used for their reputed effectiveness in CNS disorders.

Central Nervous System Diseases↗

PubMed2006

Meckel's diverticulum: a systematic review.

Meckel's diverticulum is the most common congenital malformation of gastrointestinal tract. It can cause complications in the form of ulceration, haemorrhage, intussusception, intestinal obstruction, perforation and, very rarely, vesicodiverticular fistulae and tumours. These complications, especially bleeding, are more common in the paediatric age group than in adults; however it is not uncommon to miss the diagnosis of Meckel's diverticulum in adults. Here, we reviewed the literature regarding the complications of this forgotten clinical entity in adults with potential diagnostic difficulties and management strategies.

Child↗

PubMed2005

Regulation of dendritic morphogenesis by Ras-PI3K-Akt-mTOR and Ras-MAPK signaling pathways.

Dendritic arborization and spine formation are critical for the functioning of neurons. Although many proteins have been identified recently as regulators of dendritic morphogenesis, the intracellular signaling pathways that control these processes are not well understood. Here we report that the Ras-phosphatidylinositol 3-kinase (PI3K)-Akt-mammalian target of rapamycin (mTOR) signaling pathway plays pivotal roles in the regulation of many aspects of dendrite formation. Whereas the PI3K-Akt-mTOR pathway alone controlled soma and dendrite size, a coordinated activation together with the Ras-mitogen-activated protein kinase signaling pathway was required for increasing dendritic complexity. Chronic inhibition of PI3K or mTOR reduced soma and dendrite size and dendritic complexity, as well as density of dendritic filopodia and spines, whereas a short-term inhibition promoted the formation of mushroom-shaped spines on cells expressing constitutively active mutants of Ras, PI3K, or Akt, or treated with the upstream activator BDNF. Together, our data underscore the central role of a spatiotemporally regulated key cell survival and growth pathway on trophic regulation of the coordinated development of dendrite size and shape.

Animals↗

PubMed2005

Functional metabotropic glutamate receptors on nuclei from brain and primary cultured striatal neurons. Role of transporters in delivering ligand.

G-protein-coupled receptors are well known for converting an extracellular signal into an intracellular response. Here we showed that the metabotropic glutamate receptor 5 (mGlu5) plays a dynamic intracellular role in signal transduction. Activation of endogenously expressed mGlu5 on striatal nuclear membranes leads to rapid, sustained calcium (Ca2+) responses within the nucleoplasm that can be blocked by receptor-specific antagonists. Extracellular ligands such as glutamate and quisqualate reach nuclear receptors via both sodium-dependent transporters and cystine glutamate exchangers. Inhibition of either transport system blocks radiolabeled agonist uptake as well as agonist-induced nuclear Ca2+ changes. Impermeable antagonists like LY393053 and LY367366 not only blocked [3H]quisqualate binding but also prevented nontransported agonists such as (RS)-3,5-dihydroxyphenylglycine from inducing intracellular Ca2+ changes in heterologous cells. In contrast, neither LY compound prevented quisqualate or glutamate from activating intracellular receptors leading to Ca2+ responses. Inasmuch as Ca2+ can enter the nucleoplasm via the nuclear pore complex or from the nuclear lumen, the presence of nuclear mGlu5 receptors appeared to amplify the latter process generating a faster nuclear response in heterologous cells. In isolated striatal nuclei, nuclear receptor activation results in the de novo appearance of phosphorylated CREB protein. Thus, activation of nuclear mGlu5 receptors initiates a signaling cascade that is known to alter gene transcription and regulate many paradigms of synaptic plasticity. These studies demonstrated that mGlu5 receptors play a dynamic role in signaling both on and off the plasma membrane.

Biological Transport↗

PubMed2005

The strength of receptor signaling is centrally controlled through a cooperative loop between Ca2+ and an oxidant signal.

Activation of cell-surface receptors stimulates generation of intracellular signals that, in turn, direct the cellular response. However, mechanisms that ensure combinatorial control of these signaling events are not well understood. We show here that the Ca2+ and reactive oxygen intermediates generated upon BCR activation rapidly engage in a cooperative interaction that acts in a feedback manner to amplify the early signal generated. This cooperativity acts by regulating the concentration of the oxidant produced. The latter exerts its influence through a pulsed inactivation of receptor-coupled phosphatases, where the amplitude of this pulse is determined by oxidant concentration. The extent of phosphatase inhibition, in turn, dictates what proportion of receptor-proximal kinases are activated and, as a result, the net strength of the initial signal. It is the strength of this initial signal that finally determines the eventual duration of BCR signaling and the rate of its transmission through downstream pathways.

Calcium↗

PubMed2005

Substrate specificity of glucose dehydrogenase (GDH) of Enterobacter asburiae PSI3 and rock phosphate solubilization with GDH substrates as C sources.

Enterobacter asburiae PSI3 is a rhizospheric isolate that solubilizes mineral phosphates by the action of a phosphate starvation-inducible GDH (EC 1.1.5.2). We report here that GDH activity of this isolate shows broad substrate range, being able to act on mono and disaccharides. Enterobacter asburiae PSI3 was proficient at bringing about a drop in pH and solubilization of RP with the use of 75 mmol/L of each of the GDH substrate sugars tested as the sole C source. It liberated amounts of P ranging from 450 micromol/L (on arabinose) to 890 micromol/L (on glucose). When grown on a mixture of 7 GDH substrates at concentrations of 15 mmol/L each, the bacterium solubilized RP equivalent to 46% of the value when 75 mmol glucose/L was the C source. HPLC analysis of the culture supernatant under these conditions showed that the acidification of the media is primarily due to the production of organic acids. The significance of these results on the efficacy of E. asburiae PSI3 at solubilizing phosphates under rhizospheric conditions is discussed.

Carbohydrates↗

PubMed2005

Port site tuberculosis following laparoscopic cholecystectomy.

Port site metastasis is being increasingly reported as a complication following laparoscopic surgery for malignant disorders. Various factors have been reported to be responsible and most are associated with either a high intra-peritoneal pressure due to pneumoperitoneum or the 'chimney effect' following sudden decompression of the abdomen. Direct implantation of the offending cells at the raw surface at the port has also been implicated and the use of retrieval bags is therefore recommended. We report on a rare case of port site seeding of tuberculosis in a 65-year-old woman following laparoscopic cholecystectomy.

Aged↗