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Biomedical subjects

Pradeep Kumar

Publications and source records attributed to Pradeep Kumar.

At least 19 recordsLinked to original sources

Glass transition in biomolecules and the liquid-liquid critical point of water.

Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also coincides with the maxima of the isobaric specific heat C_{P} and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.

Computer Simulation↗

Binding site of a novel Kv1.5 blocker: a "foot in the door" against atrial fibrillation.

Kv1.5 channel blockers prolong atrial action potentials and may prevent atrial flutter or fibrillation without affecting ventricular repolarization. Here we characterize the mechanisms of action of 2'-{[2-(4-methoxy-phenyl)-acetylamino]-methyl}-biphenyl-2-carboxylic acid (2-pyridin-3-yl-ethyl)-amide (AVE0118) on Kv1.5 channels heterologously expressed in Xenopus laevis oocytes. Whole cell currents in oocytes were recorded using the two-microelectrode voltage clamp technique. AVE0118 blocked Kv1.5 current in oocytes with an IC50 of 5.6 microM. Block was enhanced by higher rates of stimulation, consistent with preferential binding of the drug to the open state of the channel. Ala-scanning mutagenesis of the pore domain of Kv1.5 identified the amino acids Thr479, Thr480, Val505, Ile508, Val512, and Val516 as important residues for block by AVE0118. A homology model of the pore region of Kv1.5 predicts that these six residues face toward the central cavity of the channel. In addition, mutation of two other S6 residues (Ile502 and Leu510) that are predicted to face away from the central cavity also diminished drug block. All these putative drug-binding residues are highly conserved in other Kv channels, explaining our finding that AVE0118 also blocked Kv1.3, Kv2.1, Kv3.1, and Kv4.3 channels with similar potency. Docking of AVE0118 into the inner cavity of a Kv1.5 pore homology model predicted an unusual binding mode. The drug aligned with the inner S6 alpha-helical domain in a manner predicted to block the putative activation gate. This "foot-in-the-door" binding mode is consistent with the observation that the drug slowed the rate of current deactivation, causing a crossover of tail current traces recorded before and after drug treatment.

Animals↗

Enantio- and diastereocontrolled total synthesis of (+)-boronolide.

An efficient stereoselective total synthesis of (+)-boronolide from valeraldehyde is described. The key steps include a Sharpless asymmetric hydroxylation, a chelation-controlled vinyl Grignard reaction followed by a Sharpless asymmetric epoxidation, hydrolytic kinetic resolution, and a ring-closing metathesis.

Lactones↗

Molecular dynamics study of orientational cooperativity in water.

Recent experiments on liquid water show collective dipole orientation fluctuations dramatically slower than expected (with relaxation time > 50 ns) [D.P. Shelton, Phys. Rev. B 72, 020201(R) (2005)]. Molecular dynamics simulations of extended simple point charge (SPC/E) water show a large vortexlike structure of the dipole field at ambient conditions surviving over [J. Higo, Proc. Natl. Acad. Sci. U.S.A. 98, 5961 (2001)]. Both results disagree with previous results on water dipoles in similar conditions, for which autocorrelation times are a few picoseconds. Motivated by these recent results, we study the water dipole reorientation using molecular dynamics simulations of the SPC/E model in bulk water for temperatures ranging from ambient 300 K down to the deep supercooled region of the phase diagram at 210 K. First, we calculate the dipole autocorrelation function and find that our simulations are well described by a stretched exponential decay, from which we calculate the orientational autocorrelation time t(alpha). Second, we define a second characteristic time, namely, the time required for the randomization of molecular dipole orientation, the self-dipole randomization time t(r), which is an upper limit on t(alpha); we find that t(r) is approximately equal to 5t(alpha). Third, to check if there are correlated domains of dipoles in water which have large relaxation times compared to the individual dipoles, we calculate the randomization time t(box) of the site-dipole field, the net dipole moment formed by a set of molecules belonging to a box of edge L(box). We find that the site-dipole randomization time t(box) is approximately equal to 2.5t(alpha) for L(box) approximately equal to 3 A, i.e., it is shorter than the same quantity calculated for the self-dipole. Finally, we find that the orientational correlation length is short even at low T.

Journal Article↗

Multifactorial day hospital intervention to reduce falls in high risk older people in primary care: a multi-centre randomised controlled trial [ISRCTN46584556].

Falls in older people are a major public health concern in terms of morbidity, mortality and cost. Previous studies suggest that multifactorial interventions can reduce falls, and many geriatric day hospitals are now offering falls intervention programmes. However, no studies have investigated whether these programmes, based in the day hospital are effective, nor whether they can be successfully applied to high-risk older people screened in primary care. The hypothesis is that a multidisciplinary falls assessment and intervention at Day hospitals can reduce the incidence of falls in older people identified within primary care as being at high risk of falling. This will be tested by a pragmatic parallel-group randomised controlled trial in which the participants, identified as at high risk of falling, will be randomised into either the intervention Day hospital arm or to a control (current practice) arm. Those participants preferring not to enter the full randomised study will be offered the opportunity to complete brief diaries only at monthly intervals. This data will be used to validate the screening questionnaire. Three day hospitals (2 Nottingham, 1 Derby) will provide the interventions, and the University of Nottingham's Departments of Primary Care, the Division of Rehabilitation and Ageing Unit, and the Trent Institute for Health Service Research will provide the methodological and statistical expertise. Four hundred subjects will be randomised into the two arms. The primary outcome measure will be the rate of falls over one year. Secondary outcome measures will include the proportion of people experiencing at least one fall, the proportion of people experiencing recurrent falls (>1), injuries, fear of falling, quality of life, institutionalisation rates, and use of health services. Cost-effectiveness analyses will be performed to inform health commissioners about resource allocation issues. The importance of this trial is that the results may be applicable to any UK day hospital setting. SITES: General practices across Nottinghamshire and Derbyshire. Day hospitals:Derbyshire Royal Infirmary (Southern Derbyshire Acute Hospitals NHS Trust)Sherwood Day Service (Nottingham City Hospital Trust)Leengate Day Hospital (Queen's Medical Centre Nottingham University Hospital NHS Trust).

Journal Article↗

A simple and efficient approach to 1,3-polyols: application to the synthesis of cryptocarya diacetate.

A highly enantio- and stereoselective synthetic strategy for both syn- and anti-1,3-polyols has been developed. The sequence involves iterative Jacobsen's hydrolytic kinetic resolution (HKR), diastereoselective iodine-induced electrophilic cyclization, and ring-closing metathesis (RCM). This protocol has subsequently been utilized for the synthesis of cryptocarya diacetate, a natural product with broad range of biological activity.

Cryptocarya↗

High ampicillin resistance in different biotypes and serotypes of Haemophilus influenzae colonizing the nasopharynx of healthy school-going Indian children.

Haemophilus influenzae is one of the main causes of otitis media, sinusitis, meningitis, pneumonia and septicaemia in children, and the development of ampicillin resistance in H. influenzae is a cause of serious concern. The aim of the present study was to determine the prevalence of ampicillin resistance in H. influenzae colonizing the nasopharynx of school-going healthy North Indian children, and to compare the distribution of different biotypes and serotype b in this population. A total of 2400 school-going healthy children from 45 rural and 45 urban schools were enrolled. Nasopharyngeal swabs were collected from the children and cultured. H. influenzae was isolated from 1001 (41.7 %) of the 2400 nasopharyngeal swabs collected. All these H. influenzae isolates were biotyped and serotyped, and their antibiotic susceptibility tested. All eight biotypes were present in this population. The most prevalent biotypes were I (19.6 %), II (16.8 %) and III (25.0 %). Of the 1001 isolates, 316 (31.6 %) were H. influenzae type b and 685 (68.4 %) were non-type b H. influenzae, and 22.9 % were resistant to ampicillin, 41.9 % to chloramphenicol, 27.5 % to erythromycin and 67.3 % to co-trimoxazole. Of the 316 H. influenzae type b isolates, 44.0 % were ampicillin resistant, while only 13.1 % non-type b H. influenzae isolates were ampicillin resistant. Of the 229 ampicillin-resistant H. influenzae isolates, 196 (85.6 %) were positive for beta-lactamase; 93.4 % (214/229) were biotypes I, II and III, of which 49 % were biotype I, 27.9 % were type II and 16.6 % were type III. Most of the strains belonging to biotypes III-VIII were ampicillin sensitive. Ampicillin resistance is significantly more common in biotype I and serotype b than in other biotypes and serotypes.

Ampicillin↗

Osteochondroma of the scapula associated with winging and large bursa formation.

OBJECTIVE: To report a case of scapular osteochondroma associated with pain and winging that is rarely reported in the medical literature. CASE PRESENTATION AND IDENTIFICATION: A 19-year-old male presented with pain and winging of the right scapula. CT scan revealed an osteochondroma of the medial border of the scapula with a large bursa between the chest wall and the tumour. Excision of the tumour relieved the symptoms. Pathological study showed osteochondroma of the scapula. In a follow-up 1 year later he was free of pain with no clinical or radiological sign of recurrence. CONCLUSION: A case of scapular osteochondroma associated with pain and winging treated by excision and follow-up showed no sign of clinical or radiological recurrence.

Adult↗

Role of TNF-alpha in prenatal alterations in dams of mice under thermal stress.

The possible involvement of cytokines such as tumour necrosis factor-alpha (TNF-alpha), interleukin-1 beta (IL-1 beta) and interferon-gamma (IFN-gamma) that are suspected of causing pregnancy loss and miscarriage has been investigated in dams of mice subjected to hyperthermia. Thermal stress was induced by exposing mice dams at 40+/-2 degrees C for 4 h every day during the different phases of the gestation period whereas the normothermic animals were housed at 22+/-2 degrees C. The effect of maternal thermal stress was measured in pregnant mice at different phases of the gestation period namely, blastogenesis-implantation phase (days 0-5 postconceptionem [p.c.]), organogenesis or embryogenesis phase (days 6-15 p.c.) and fetogenesis phase (days 16-20 p.c.). Uterine examination of dams subjected to hyperthermia on days 6-15 p.c. showed maximum reduction in live fetus number, gestational index and maximum pre and postimplantation loss in comparison with dams housed in normothermic environment and dams exposed to thermal stress between days 0-5 and 16-20 p.c. Maximum resorption rate and number of non-viable fetuses were observed in dams exposed to hyperthermia during days 6-15 p.c. Elevated levels of TNF-alpha and IL-1 beta were observed in the amniotic fluid of dams subjected to hyperthermia during days 6-15 p.c. but IFN-gamma levels remained unaltered. Single intraperitoneal (i.p.) administration of recombinant mouse TNF-alpha at a dose of 1 and 0.5 ng/mice in dams on day 6 in normothermic condition resulted in a reduced number of live fetuses. Administration of anti-TNF-alpha antibody i.p. at a dose of 10 microg/dam on day 6 p.c. and subjected to thermal stress between days 6-15 p.c. increased marginally the number of fetuses but failed to attain statistical significance in comparison with days 6-15 p.c. thermally stressed dams without antibody treatment. It is concluded that the induction of TNF-alpha, in the amniotic fluid is associated with thermal stress during pregnancy and may be linked to the reproductive performances of dams. This study will help in understanding the mechanism of thermal injury in pregnant subjects.

Amniotic Fluid↗

Air gun--a deadly toy?: A case report.

Air guns (air rifles) are used throughout the world as instruments of amusement such as toys in funfairs, for bird hunting and firearms training. In India and in many other countries, this instrument neither comes under the purview of the Arms Act, nor is there is any restriction on the user's age. This enables a person to gain access to this instrument quite easily. Sometimes serious and fatal injuries result when it is used by an ignorant person or by a criminal. There are reports which suggest that these 'toys' can cause painful injuries but only a few cases of death have been reported. There is no literature about the features of injuries that help to establish the range of fire by an air gun. Here we report a case where a boy was accidentally shot to death while watching bird shooting. We attempt to correlate the injury with the range of fire.

Autopsy↗

Polyethylenimine nanoparticles as efficient transfecting agents for mammalian cells.

Two cross-linkers based on polyethylene glycol (PEG) (MW=6 and 8 kDa), were synthesized for self-assembling and formation of nanoparticles of branched, high molecular weight polyethylenimine (PEI). Cross-linking was realized in two ways, viz., ionic as well as covalent. Ionic cross-linking was accomplished by using PEG-bis (phosphate) whereas, the covalent one was achieved by using PEG-bis (p-nitrophenylcarbonate). A range of nanoparticles of PEI was prepared by varying the degree of cross-linking (i.e. the amount of cross-linkers used). PEI-PEG nanoparticles were characterized by dynamic light scattering and transmission electron microscopy and found to be in the range of approximately 18-75 nm (hydrodynamic radii) with almost uniform population. Subsequently, these particles were used for DNA binding assay and zeta-potential measurements, taking native PEI-PEG nanoparticles as reference. As expected, the zeta potential values decreased, on increasing the percentage of cross-linking as well as on complexation with DNA. Further, PEI-PEG nanoparticles were investigated for their transfecting efficacy on COS-1 cells. It was found that PEI-PEG nanoparticles were 5- to 16-fold more efficient as transfecting agents compared to lipofectin and PEI itself. The toxicity of PEI-PEG nanoparticles was found to be reduced considerably in comparison to PEI polymer, as determined by MTT colorimetric assay. Out of the various systems prepared, PEI-PEG8000 (5% ionic) nanoparticles were found to be the most efficient transfecting agent for in vitro transfection.

Animals↗

Molluscicidal activity of Ferula asafoetida, Syzygium aromaticum and Carum carvi and their active components against the snail Lymnaea acuminata.

The molluscicidal activity of dried root latex powder of Ferula asafoetida, flower-bud powder of Syzygium aromaticum and seed powder of Carum carvi against the snail Lymnaea acuminata was studied. The molluscicidal activity of all the three plant products was found to be both time and concentration dependent. The toxicity of S. aromaticum flower-bud powder (96 h LC(50):51.98 mg/l) was more pronounced than that of root latex powder of F. asafoetida (96 h LC(50):82.71 mg/l) and seed powder of C. carvi (96 h LC(50):140.58 mg/l). Ethanol extract was more toxic than other organic extracts. The ethanol extract of S. aromaticum (24h LC(50):83.53 mg/l) was more effective than that of F. asafoetida (24h LC(50):132.31 mg/l) and C. carvi (24h LC(50):130.61 mg/l) in killing the test animals. The 96 h LC(50) of column purified fraction of seed powder of C. carvi was 5.40 mg/l whereas those of flower-bud powder of S. aromaticum and dried root latex powder of F. asafoetida were 7.87 and 9.67 mg/l, respectively. The product of F. asafoetida, S. aromaticum and C. carvi may be used as potent molluscicides.

Animals↗

Thermodynamics, structure, and dynamics of water confined between hydrophobic plates.

We perform molecular dynamics simulations of 512 waterlike molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic properties of water are shifted to lower temperatures relative to the bulk by approximately 40 K. The dynamics and structure of the confined water resemble bulk water at higher temperatures, consistent with the shift of thermodynamic anomalies to lower temperature. Because of this T shift, our confined water simulations (down to T=220 K) do not reach sufficiently low temperature to observe a liquid-liquid phase transition found for bulk water at T approximately 215 K using the TIP5P potential, but we see inflections in isotherms at lower temperatures presumably due to the presence of a liquid-liquid critical point. We find that the different crystalline structures that can form for two different separations of the plates, 0.7 and 1.10 nm, have no counterparts in the bulk system, and we discuss the relevance to experiments on confined water.

Journal Article↗

Relation between the Widom line and the dynamic crossover in systems with a liquid-liquid phase transition.

We investigate, for two water models displaying a liquid-liquid critical point, the relation between changes in dynamic and thermodynamic anomalies arising from the presence of the liquid-liquid critical point. We find a correlation between the dynamic crossover and the locus of specific heat maxima C(P)(max) ("Widom line") emanating from the critical point. Our findings are consistent with a possible relation between the previously hypothesized liquid-liquid phase transition and the transition in the dynamics recently observed in neutron scattering experiments on confined water. More generally, we argue that this connection between C(P)(max) and dynamic crossover is not limited to the case of water, a hydrogen bond network-forming liquid, but is a more general feature of crossing the Widom line. Specifically, we also study the Jagla potential, a spherically symmetric two-scale potential known to possess a liquid-liquid critical point, in which the competition between two liquid structures is generated by repulsive and attractive ramp interactions.

Journal Article↗

Static and dynamic anomalies in a repulsive spherical ramp liquid: theory and simulation.

We compare theoretical and simulation results for static and dynamic properties for a model of particles interacting via a spherically symmetric repulsive ramp potential. The model displays anomalies similar to those found in liquid water, namely, expansion upon cooling and an increase of diffusivity upon compression. In particular, we calculate the state points P (rho,T) from the simulation and successfully compare it with the state points P (rho,T) obtained using the Rogers-Young (RY) closure for the Ornstein-Zernike (OZ) equation. Both the theoretical and the numerical calculations confirm the presence of a line of isobaric density maxima, and lines of compressibility minima and maxima. Indirect evidence of a liquid-liquid critical point is found. Dynamic properties also show anomalies. Along constant temperature paths, as the density increases, the dynamics alternate between slowing down and speeding up, and we associate this behavior with the progressive structuring and destructuring of the liquid. Finally we confirm that mode coupling theory successfully predicts the nonmonotonic behavior of dynamics and the presence of multiple glass phases, providing strong evidence that structure (the only input of mode coupling theory) controls dynamics.

Journal Article↗

Structural basis for competition between drug binding and Kvbeta 1.3 accessory subunit-induced N-type inactivation of Kv1.5 channels.

Kvbeta subunits are accessory proteins that modify gating of Kv1 channels. Kvbeta1.3 subunits bind to the N termini of Kv1.5 alpha-subunits and induce fast N-type inactivation, slow the rate of deactivation, and alter the voltage dependence and kinetics of channel activation. The N terminus of a Kvbeta subunit and quaternary ammonium compounds bind to the inner pore of Kv1 channels; however, it is unknown to what extent the pore binding sites for drugs and Kvbeta subunits overlap. Here, we used site-directed Ala mutagenesis to scan residues of the Kv1.5 pore to define the binding site for Kvbeta1.3 subunits. Individual mutations of five residues in the S6 domain (Val505, Ile508, Leu510, Val512, and Val516) greatly retarded or prevented Kvbeta1.3 induced inactivation, and reduced effects on Kv1.5 deactivation. Mutation of Thr479 and Thr480 enhanced Kvbeta1.3-induced N-type inactivation. None of the Ala mutations prevented the Kvbeta1.3-induced negative shifts in the voltage dependence of activation or slow C-type inactivation, suggesting that these gating effects are mediated by an interaction other than the one for N-type inactivation. Thr479, Thr480, Val505, Ile508, and Val512, of Kv1.5 channels are also important interaction sites for the anthranilic acid S0100176 (N-benzyl-N-pyridin-3-ylmethyl-2-(toluene-4-sulfonylamino)-benzamide hydrochloride). Leu510 and V516A prevented Kvbeta1.3-induced inactivation but did not alter drug block. Block of Kv1.5 by S0100176 was reduced and voltage-dependent in the presence of Kvbeta1.3 but not in the presence of an N-truncated form of the Kvbeta subunit. Thus, residues in the pore of Kv1.5 required for N-type inactivation overlap with but are not identical to the drug binding site.

Amino Acid Sequence↗

Total synthesis of microcarpalide.

[reaction: see text] An efficient, convergent approach for the total synthesis of microcarpalide (1) is described. The synthetic strategy features the Sharpless asymmetric dihydroxylation, regioselective epoxide opening with various nucleophiles such as a lithium acetylide and cuprates derived from the vinyl stannane and the vinyl iodide for the construction of a C7-C8 trans-double bond and Yamaguchi macrolactonization as the key steps.

Alkanes↗