Search PubMed⌕ Search

Biomedical subjects

M Bansal

Publications and source records attributed to M Bansal.

At least 37 records · Page 2Linked to original sources
PubMed2000

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study.

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

DNA↗
PubMed2000

Bilateral single-session percutaneous nephrolithotomy: a feasible and safe treatment.

BACKGROUND AND PURPOSE: The treatment of bilateral urinary calculus disease is often staged, irrespective of the modality of the treatment. Bilateral simultaneous percutaneous nephrolithotomy (PCNL) is still considered by many to be adventurous and risky. We carried out this prospective study of bilateral PCNL under a single anesthesia to study the feasibility, success rate, and complications if any. PATIENTS AND METHOD: From September 1996 to May 1999, 25 consecutive medically fit patients with bilateral renal calculi needing PCNL were subjected to bilateral PCNL under a single anesthesia. RESULTS: The PCNL could be accomplished bilaterally in 24 patients (96%). In one patient, the second-side PCNL was abandoned because of excessive bleeding on the first side. A total of 58 tracts and 27 sessions were required for complete treatment of the 48 renal units in the 24 successfully treated patients. The average operating time required for the procedure was 122 minutes. Nineteen patients were rendered stone free in one session, and two more patients were made stone free in a second session. Four renal units in three patients with residual calculi were cleared with double-J stenting and SWL. CONCLUSION: Bilateral PCNL in a single session is feasible and safe and can be carried out without increased morbidity. We advocate that an endourologist be prepared for bilateral PCNL in the patients in whom it is indicated. The opposite-side PCNL can be done if the first-side treatment is accomplished smoothly and in a reasonable time.

Adult↗
PubMed2000

Nephrostomy tube after percutaneous nephrolithotomy: large-bore or pigtail catheter?

BACKGROUND AND PURPOSE: A nephrostomy tube is an integral part of any percutaneous renal surgery. Commonly, a nephrostomy tube that is 2F to 3F smaller than the percutaneous tract is used after percutaneous nephrolithotomy (PCNL). In our experience, quite a few patients have pain at the nephrostomy tube site, and many patients complain of a prolonged urinary leak after tube removal when a large nephrostomy tube is used. This prospective study was planned to document whether these symptoms could be attributed to the size of the nephrostomy tube and whether a small pigtail catheter could reduce these problems without increasing complications. PATIENTS AND METHODS: Forty well-matched patients in whom a one-stage PCNL was done for calculus disease were studied prospectively. Alternate patients had a 28F nephrostomy tube or a 9F pigtail catheter placed at the end of the procedure. Patients were observed for the duration of hematuria, number of analgesic injections needed, and the duration of urinary leak after tube removal. RESULTS: The groups were comparable in the amount and duration of hematuria after PCNL. There was a statistically significant difference in the analgesic need and the duration of urinary leak after tube removal, both of which were less in patients having a pigtail catheter. CONCLUSIONS: A pigtail catheter nephrostomy tube after PCNL reduces the hospital stay by reducing the duration of the urinary leak. The postoperative course is smooth, as patient has less pain and needs less analgesic support. There is no statistically significant increase in the postoperative bleeding secondary to use of a pigtail catheter. Second-look nephroscopy was easy in the one patient with a pigtail nephrostomy catheter who needed the procedure.

Adult↗
PubMed2000

Safety and efficacy of pedicle screw placement for adult spinal deformity with a pedicle-probing conventional anatomic technique.

A prospective study of 50 adults treated with fusion, realignment, and segmental spinal instrumentation for spinal deformity was conducted to assess the safety, accuracy, and efficacy of the free-hand pedicle screw placement technique. Postoperative computed tomographic scans were performed to evaluate the placement of 282 screws and were correlated with patients' clinical outcomes. Five screws were placed at T12, 26 at L1, 39 at L2, 48 at L3, 73 at L4, 35 at L5, and 50 at S1. Nine screws (3%) were misplaced and included three screws (1.06%) that violated the medial wall with no clinical sequelae or revision surgery needed. There were no neurologic deficits related to screw placement. The free-hand technique is a safe and cost-effective method for pedicular screw placement during surgery for adult spine deformities.

Adult↗
PubMed1999

C-H.O hydrogen bonds in minor groove of A-tracts in DNA double helices.

Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 A) indicates that in both data sets, a majority of the (3'-Ade) H2..O2(3'-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3'-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as An.Tn and GAn.TnC tracts, which leads to a narrow minor groove in these regions.

Base Pairing↗
PubMed1999

Three-centre C-H---O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures.

AA.TT and GA.TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 A) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA.TT and GA.TC steps the electropositive C2-H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C-H---O hydrogen bonds in the DNA minor groove. The C2--H2---O2 hydrogen bonds in the A.T base pairs could be a natural consequence of Watson-Crick pairing. However, the cross-strand interactions between the bases at the 3'-end of the AA.TT and GA.TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2---O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 A) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A.T base pairs and the hydration of the minor groove, these C2-H---O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA).poly(dT).

Base Pairing↗
PubMed1999

Percutaneous cystolithotomy for vesical calculi: a better approach.

Vesical calculus is a common problem that is treated traditionally with open cystolithotomy or cystolithalopaxy. Open surgery has the inherent problems of a long scar, prolonged catheterization, extended hospitalization, and risk of infection. Transurethral cystolithalopaxy also requires special instruments that carry a risk of trauma, which could lead to urethral strictures. Thirty-eight patients (15 children and 23 adults) were treated for vesical calculi by percutaneous cystolithotomy (PCCL), a minimally invasive procedure. A fluoroscopic-guided tract was made to the bladder through a small suprapubic puncture (9-10 mm) and a nephroscope was inserted via an Amplatz sheath placed suprapubically. The calculus was fragmented with ultrasound or pneumatic energy before being flushed out. A suprapubic catheter was kept in place for 48 hours postsurgery; no urethral catheter was needed. Urethral instrumentation was kept to a minimum. After 48 hours, the suprapubic catheter was clamped and removed after the patient had two or three normal voids. No significant intraoperative or postoperative complication was encountered. Given that the urethra is spared, percutaneous cystolithotomy is a preferred approach in patients with vesical calculi.

Adult↗
PubMed1998

Dissecting alpha-helices: position-specific analysis of alpha-helices in globular proteins.

An analysis of the amino acid distributions at 15 positions, viz., N", N', Ncap, N1, N2, N3, N4, Mid, C4, C3, C2, C1, Ccap, C', and C" in 1,131 alpha-helices reveals that each position has its own unique characteristics. In general, natural helix sequences optimize by identifying the residues to be avoided at a given position and minimizing the occurrence of these avoided residues rather than by maximizing the preferred residues at various positions. Ncap is most selective in its choice of residues, with six amino acids (S, D, T, N, G, and P) being preferred at this position and another 11 (V, I, F, A, K, L, Y, R, E, M, and Q) being strongly avoided. Ser, Asp, and Thr are all more preferred at Ncap position than Asn, whose role at helix N-terminus has been highlighted by earlier analyses. Furthermore, Asn is also found to be almost equally preferred at helix C-terminus and a novel structural motif is identified, involving a hydrogen bond formed by N delta 2 of Asn at Ccap or C1 position, with the backbone carbonyl oxygen four residues inside the helix. His also forms a similar motif at the C-terminus. Pro is the most avoided residue in the main body (N4 to C4 positions) and at C-terminus, including Ccap of an alpha-helix. In 1,131 alpha-helices, no helix contains Pro at C3 or C2 positions. However, Pro is highly favoured at N1 and C'. The doublet X-Pro, with Pro at C' position and extended backbone conformation for the X residue at Ccap, appears to be a common structural motif for termination of alpha-helices, in addition to the Schellman motif. Main body of the helix shows a high preference for aliphatic residues Ala, Leu, Val, and Ile, while these are avoided at helix termini. A propensity scale for amino acids to occur in the middle of helices has been obtained. Comparison of this scale with several previously reported scales shows that this scale correlates best with the experimentally determined values.

Amino Acid Sequence↗
PubMed1998

Geometrical and sequence characteristics of alpha-helices in globular proteins.

Understanding the sequence-structure relationships in globular proteins is important for reliable protein structure prediction and de novo design. Using a database of 1131 alpha-helices with nonidentical sequences from 205 nonhomologous globular protein chains, we have analyzed structural and sequence characteristics of alpha-helices. We find that geometries of more than 99% of all the alpha-helices can be simply characterised as being linear, curved, or kinked. Only a small number of alpha-helices ( approximately 4%) show sharp localized bends in their middle regions, and thus are classified as kinked. Approximately three-fourths (approximately 73%) of the alpha-helices in globular proteins show varying degrees of smooth curvature, with a mean radius of curvature of 65 +/- 33 A; longer helices are less curved. Computation of helix accessibility to the solvent indicates that nearly two-thirds of the helices ( approximately 66%) are largely buried in the protein core, and the length and geometry of the helices are not correlated with their location in the protein globule. However, the amino acid compositions and propensities of individual amino acids to occur in alpha-helices vary with their location in the protein globule, their geometries, and their lengths. In particular, Gln, Glu, Lys, and Arg are found more often in helices near the surface of globular proteins. Interestingly, kinks often seem to occur in regions where amino acids with low helix propensities (e.g., beta-branched and aromatic residues) cluster together, in addition to those associated with the occurrence of proline residues. Hence the propensities of individual amino acids to occur in a given secondary structure depend not only on conformation but also on its length, geometry, and location in the protein globule.

Amino Acid Sequence↗
PubMed1998

Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes.

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen bonded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel triplex, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41--O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees , helical twist of the average structure from this simulation had a value of 36 degrees , while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel triplex, it was energetically comparable to the parallel triplex. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel triplex by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically. Together these results indicate that the parallel C.G*G triplex with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Carbohydrates↗
PubMed1998

Diagnosis of tuberculous meningitis by detection of antigen and antibodies in CSF and sera.

OBJECTIVE: To evaluate diagnostic potential of three immunological tests, namely, detection of H37Rv antigen of M. Tuberculosis in CSF, detection of antibodies (IgG) against H37Rv in CSF and detection of antibodies (IgG) against H37Rv in serum for diagnosis of tuberculous meningitis in children. SUBJECTS: 50 children diagnosed as patients of tuberculous meningitis were included as cases and 48 children with CNS diseases of nontubercular etiology [pyogenic meningitis (n = 31), encephalitis (n = 10), seizure disorder of unknown etiology (n = 5), brain tumor (n = 2)] served as controls. METHODS: H37Rv antigen of M. tuberculosis was detected in CSF by Dot ELISA, and antibodies (IgG) against H37Rv in CSF and serum were detected by Plate ELISA. RESULTS: Detection of H37Rv antigen in CSF was the most sensitive (90%) and specific (95.83%) with positive and negative predictive values of 95.74% and 90.19%, respectively, followed by detection of antibodies in CSF (sensitivity-74%, specificity-89.58%, positive predictive value-88.10%, negative predictive value-76.78%). Detection of antibodies in serum had low sensitivity (50%), specificity (91.67%), positive predictive value (86.21%) and negative predictive value (63.76%). CONCLUSIONS: Detection of antigen in CSF is a rapid, sensitive and specific test for diagnosis of tuberculous meningitis in children. Detection of antibody in CSF may be useful in some cases but needs further evaluation. Detection of antibody in serum does not appear to be useful for diagnosis of tuberculous meningitis.

Antigens, Bacterial↗
PubMed1997

MIC-1, a novel macrophage inhibitory cytokine, is a divergent member of the TGF-beta superfamily.

Macrophages play a key role in both normal and pathological processes involving immune and inflammatory responses, to a large extent through their capacity to secrete a wide range of biologically active molecules. To identify some of these as yet not characterized molecules, we have used a subtraction cloning approach designed to identify genes expressed in association with macrophage activation. One of these genes, designated macrophage inhibitory cytokine 1 (MIC-1), encodes a protein that bears the structural characteristics of a transforming growth factor beta (TGF-beta) superfamily cytokine. Although it belongs to this superfamily, it has no strong homology to existing families, indicating that it is a divergent member that may represent the first of a new family within this grouping. Expression of MIC-1 mRNA in monocytoid cells is up-regulated by a variety of stimuli associated with activation, including interleukin 1beta, tumor necrosis factor alpha (TNF-alpha), interleukin 2, and macrophage colony-stimulating factor but not interferon gamma, or lipopolysaccharide (LPS). Its expression is also increased by TGF-beta. Expression of MIC-1 in CHO cells results in the proteolytic cleavage of the propeptide and secretion of a cysteine-rich dimeric protein of Mr 25 kDa. Purified recombinant MIC-1 is able to inhibit lipopolysaccharide -induced macrophage TNF-alpha production, suggesting that MIC-1 acts in macrophages as an autocrine regulatory molecule. Its production in response to secreted proinflammatory cytokines and TGF-beta may serve to limit the later phases of macrophage activation.

Amino Acid Sequence↗
PubMed1997

Mechanistic analyses of site-specific degradation in DNA-RNA hybrids by prototypic DNA cleavers.

Bleomycin (BLM) binding and chemistry are apparently sensitive to differences in nucleic acid conformation and could conceivably be developed as a probe for sequence-dependent elements of conformation. We report on the development of a new methodology to synthesize heterogeneous DNA-RNA hybrids of defined sequence and present the results of our comparative studies on the cleavage of DNA and DNA-RNA hybrids by four drugs: BLM, neocarzinostatin and esperamicins A1 and C. In the case of BLM with duplex DNA, purine-pyrimidine steps such as GT and GC, are consistently hit, as previously observed. However, in heterogeneous sequence hybrids, not all GC sites are recognized by the drug, although all GT sites are. Suppressed GC sites are consistently flanked by pyrimidines on both the 3' and 5' sides, suggesting that the BLM binding site in hybrids spans at least four bases. Kinetic isotope studies with specifically deuterated substrates (kH/kD = 1.2-4.0) and the effect of oxygen on the product profile are presented in support of a mechanism consistent with 4'-hydrogen abstraction in hybrids. The powerful double-labeled probe technique was extended to study the mechanism of action of other DNA degrading drugs on DNA-RNA hybrids. For neocarzinostatin, the sequence specificity lies in the AT-rich region for hybrids and is similar to that of DNA, however, the overall cleavage pattern for the hybrid is significantly different from that for the same sequence of DNA. In the hybrid, a stretch of AT residues is essential and the A sites are damaged to a greater extent than they are in DNA. However, no kinetic isotope effects are observed and, based on the product profile, the mechanism of degradation of the DNA strand of hybrids seems to be limited to abstraction of the 5'-hydrogen. For esperamicin A1, damage on the DNA strand of hybrids occurs exclusively via 5'-hydrogen abstraction in a non-rate determining step and primarily at A and T sites. Esperamicin C behaves similarly, exhibiting no isotope effects at 1', 4' and 5' positions. Overall, the differences observed in site-specific cleavage between the two substrates is proposed to be a result of conformational differences between the DNA strand of duplex DNA and DNA-RNA hybrids.

Aminoglycosides↗
PubMed1997

Effects of hypoxanthine substitution on bleomycin-mediated DNA strand degradation in DNA-RNA hybrids.

We have reported on the differences in site-specific cleavage between DNA and DNA-RNA hybrids by various prototypic DNA cleavers (accompanying paper). In the case of bleomycin (BLM), degradation at 5'-GC-3'sites was suppressed relative to the same sequence in double-stranded DNA, while 5'-GT-3' damage remained constant. We now present results of our further investigation on the chemical and conformational factors that contribute to BLM-mediated DNA strand cleavage of DNA-RNA hybrids. Substitution of guanine by hypoxanthine on the RNA strand of hybrids resulted in a significant enhancement of 5'-GC-3' site damage on the DNA strand relative to double-stranded DNA, thus reversing the suppression noted at these sites. Additionally, 5'-AT-3' sites, which are damaged significantly more in the hybrid than in DNA, exhibit decreased product formation when hypoxanthine is present on the RNA strand of hybrids. However, when hypoxanthine is substituted for guanine on the DNA strand (a GC cleavage site becomes IC), 5'-IT-3' and 5'-IC-3' site cleavage is almost completely suppressed, whereas AT site cleavage is dramatically enhanced. The priority in metallobleomycin site-specific cleavage of hybrids changes with hypoxanthine substitution: the cleavage priority is AT > GT > GC in native hybrid; GC > GT > AT in hybrids substituted with hypoxanthine in the RNA strand; AT >> GT approximately GC in hybrids substituted with hypoxanthine in the DNA strand. The results of kinetic isotope effect studies on BLM cleavage are presented and, in most cases, the values are larger for the hypoxanthine-substituted hybrid. The results suggest that the 2-amino groups of guanine residues on both strands of the nucleic acid play an important role in modulation of the binding and cleavage specificity of BLM.

Bleomycin↗
PubMed1997

Effect of proteoglycan removal on solute mobility in articular cartilage.

Transport of nutrients, cytokines, pharmacologic agents, and matrix components through articular cartilage is critical for the viability and structural integrity of the tissue. To understand the role of the extracellular matrix in regulating this process, we measured the diffusivity of three uncharged solutes of different molecular size (glucose, MW 180; inulin, MW 5000; dextran, MW 70,000) into intact cartilage and cartilage that had its proteoglycan (PG) component removed. Solute diffusivity was measured by performing transient (nonsteady state) one-dimensional diffusion tests using radiolabelled solutes. Compared to intact cartilage, the diffusivity of glucose was unchanged after PG removal, inulin was unchanged but dextran increased by 1.7 times after 71% PG removal, and both inulin and dextran increased by 1.6 and 2.0 times, respectively, after 93% PG removal. The diffusivities of inulin and dextran were inversely proportional to the PG content. While no change was found in the tissue's bulk fluid content, PG depletion resulted in an increase in fluid content in the upper regions of the tissue and a decrease in the lower regions. These results indicate that in intact tissue small uncharged solutes have free mobility through the inter-molecular and intra-molecular PG volumes, larger molecules have limited intra-molecular mobility, and very large molecules are excluded from the intra-molecular space.

Animals↗
PubMed1997

Sequence-independent recombination triple helices: a molecular dynamics study.

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a triplex comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such triplex structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Base Sequence↗