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Biomedical subjects

S Kumar

Publications and source records attributed to S Kumar.

At least 1,117 records · Page 62Linked to original sources
PubMed1996

Expression and immunogenicity of the C-terminus of a major blood-stage surface protein of Plasmodium vivax, Pv200(19), secreted from Saccharomyces cerevisiae.

The carboxy-terminus of the major merozoite surface protein of Plasmodium has been shown to be the target of protective immunity in a number of non-vivax malaria parasite species. In an effort to develop a protective vaccine for Plasmodium vivax, the most prevalent form of human malaria, we expressed in Saccharomyces cerevisiae the 19-kDa a carboxy-terminus of Pv200 as a His6-tagged, secreted polypeptide. Five of seven H-2 congenic mouse strains elicited antibodies that recognized yeast produced PV200(19) by ELISA. The vaccine appears to be immunogenic and widely recognized, and to contain one or more helper T cell epitopes that may allow boosting with subsequent natural infections.

Amino Acid Sequence↗
PubMed1996

Spinal compression at peak isometric and isokinetic exertions in simulated lifting in symmetric and asymmetric planes.

OBJECTIVE: To determine if the spinal compression can be used as a criterion for the safety of the back. DESIGN: Various lifting strength activities were analysed using a 3-D biomechanical model to determine spinal compression forces. BACKGROUND: Despite many standards being set and the use of varied strategies, low-back injuries continue to be common in our society. Since the injuries occur to the tissues in the body, it may be more appropriate to investigate the effects of external loads on the tissues. Therefore it was decided to determine the spinal compression in standardized lifting tasks. METHODS: Twenty young adults (12 males and 8 females) performed maximal stoop and squat lifts in sagittal, 30 degrees lateral, and 60 degrees lateral planes at half, three-quarters, and full horizontal reach distances. The stoop lifts were performed in isokinetic and isometric modes; the isometric mode was performed with the hip at 60 degrees and 90 degrees. The squat lifts were also performed in isokinetic and isometric modes; the isometric mode consisted of postures with knee at 90 degrees and 135 degrees of flexion. In addition, the subjects also performed isometric lifts in stoop and squat postures at a self-selected optimum posture. During these activities the strength was measured using a static dynamic strength tester employing a load cell and force monitor. Three-dimensional postural recording was made using a 3-D Peak Performance Technologies imaging system. Using the postural and force data as input to a 3-D biomechanical model, the lumbosacral spinal compression was calculated. The values of strength and spinal compression were analysed and compared. RESULTS: The strength was significantly affected by the gender, the type of lift, plane of lift and reach of lift (P < 0.01); whereas the spinal compression was not affected by the reach at all. Two-way and three-way interactions were significant for strength (P < 0.02) but not for spinal compression. CONCLUSION: It was concluded that the spinal compression was the ultimate cost function in the safety of the back and as such preventative strategies should be based on this. RELEVANCE: The use of an appropriate cost function in a manner in which it can maximize the safety of the back will be of considerable value. Since injuries are biomechanical perturbation of the tissues, it is argued that the cost function be used in a manner where tissue load be considered as the primary factor.

Journal Article↗
PubMed1996

Perforated colorectal carcinomas.

BACKGROUND: Colorectal carcinomas that present with perforation are stated in the literature to carry a poor prognosis. This study is to verify or refute the dismal connotation associated with perforated colorectal carcinomas (PCCs). METHODS: A retrospective analysis of 1551 patients with colorectal carcinoma revealed that 51 (3.3%) patients presented with perforation. Mary Immaculate and St. John's Queens Hospital Divisions of the Catholic Medical Center of Brooklyn and Queens chart and tumor board data were retrieved for the period 1983 through 1993. RESULTS: Localized perforation with abscess formation occurred in 31 (61%) patients, and free perforation with generalized peritonitis in occurred 20 (39%) patients. Sixteen (31%) patients had distant metastasis at diagnosis with a mean survival of only 6 months. Overall operative mortality rate was 12%, and overall 5-year survival rate was 32%. By excluding 16 patients with documented Stage IV disease at diagnosis and 6 operative mortalities (3 of whom also had Stage IV disease at diagnosis), the remaining 32 patients had a mean survival of 59 months and a 5-year survival of 58%. CONCLUSION: In view of the 58% survival in our subset of patients, aggressive management is recommended. This includes management of sepsis and radical surgical resection of adjacent involved organs. A negative attitude associated with PCC is not substantiated in this retrospective 10-year study.

Carcinoma↗
PubMed1996

Structural and sequence characteristics of long alpha helices in globular proteins.

Elucidation of the detailed structural features and sequence requirements for alpha helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence, in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C(alpha) coordinates has been developed and used to analyze the structures of long alpha helices (number of residues > or = 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank. All long alpha helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins. The distribution and statistical propensities of individual amino acids to occur in long alpha helices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices. The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

Amino Acid Sequence↗
PubMed1996

Three-dimensional time-of-flight MR angiography of the arch of aorta and its major branches: a comparative study with contrast angiography.

The region of the arch of aorta and the intrathoracic course of its major branches was evaluated in 11 patients using three-dimensional time-of-flight magnetic resonance (MR) angiography. Abnormalities such as stenosis, occlusion, dilatation and aneurysm formation were documented in the innominate, both common carotid and both subclavian arteries. The results were compared with those of contrast angiography. There was a good correlation in 47 of the 55 arteries compared. There were five false positive results including overestimation of a stenosis, and three false negative results including underestimation of a stenosis. MR angiography had a sensitivity of 93% and a specificity of 89% for correctly detecting or excluding an abnormality. These results suggest that three-dimensional time-of-flight MR angiography demonstrates lesions in the major branches of the arch of aorta fairly accurately and will prove useful in the initial evaluation and in follow up studies.

Adolescent↗
PubMed1996

Micronucleus induction by diuron in mouse bone marrow.

Diuron, a widely used substituted urea herbicide, induced the formation of micronuclei in bone marrow cells of Swiss mice. A single i.p. dose of 340 mg/kg b.w. diuron which is maximum tolerated dose (MTD) increased significantly the number of micronuclei at 30 h and 48 h time period. The dose of 170 mg/kg b.w. also induced the micronuclei formation in the above time period. However, a dose of 85 mg/kg b.w. was ineffective at the time periods studied. No induction of micronuclei was observed at 72 h time period after all the doses of diuron studied as compared to the solvent control. The diuron-induced frequency of micronucleated erythrocytes was independent of the sex of the test animals.

Animals↗
PubMed1996

HHV-6 antigen and viral DNA detected in cervical cells from archived tissue using histochemical staining and hybridization.

BACKGROUND: Human herpesvirus type 6 (HHV-6), an ubiquitous virus, is the causative agent for exanthem subitum. The virus is frequently associated with lymphoproliferative disorders and other diseases. Recently, we have reported the frequent presence of HHV-6 in oral carcinoma and the present study extends the observation to cervical carcinoma. OBJECTIVE: To examine the presence of HHV-6 in cervical carcinoma. STUDY DESIGN: Formalin-fixed, paraffin-embedded cervical carcinoma tissues were examined for the presence of HHV-6 by immunohistochemistry using two monoclonal antibodies that react to HHV-6-encoded p41/38 and gp116/64/54. In situ hybridization with variant-specific probes were used to type the HHV-6 DNA sequences present. RESULTS: A total of 14/26 (53.9%) carcinoma tissue specimens and 5/8 (62.5%) normal tissue specimens were positive for viral antigens. In situ hybridization studies revealed the presence of HHV-6 DNA sequences in 10/26 (38.5%) carcinoma tissue specimens and 1/8 (12.5%) normal tissue specimens. In the normal tissue, the HHV-6 was present in the endocervical ciliated columnar-epithelial cells and some cells in the subepithelial mucosa but in the carcinoma, the transformed cells were positive for the virus. CONCLUSIONS: HHV-6 viral proteins and DNA were found in more than one third of the cervical tissue examined suggesting possible viral expression in these tumours. The significance of the distribution and role of the HHV-6 in cervical tissue remains unclear. Since HHV-6 has an oncogenic potential, the virus may cooperate with other transforming agents for the progression of the disease.

Antigens, Viral↗
PubMed1996

Cloning and expression of DiT33 from Dirofilaria immitis: a specific and early marker of heartworm infection.

Dirofilaria immitis is an important filarial parasite of dogs and cats, and a useful model for human filariasis. Current diagnostic tests for heartworm infection in animals rely on the presence of fecund female worms (usually found 6.5 months post-infection or later) and therefore fail to detect pre-patent infections. Putative pepsin inhibitors from 2 filarial parasites of humans namely Onchocerca volvulus (Ov33, Oc3.6, OvD5B) and Brugia malayi (Bm33), have been shown to be useful in diagnosis of onchocerciasis and lymphatic filariasis, respectively. Previous studies have suggested that a homologue exists in D. immitis (DiT33), which may have potential in diagnosis of heartworm infection. In this study, the isolation and characterization of a cDNA clone encoding DiT33 is described. This cDNA contains 12 bases of the nematode-specific 22 nucleotide spliced leader sequence and encodes a 26.4 kDa-protein with a high level of similarity (87-89%) to other filarial members of the family. DiT33 was over-expressed in E. coli as a fusion with the maltose-binding protein and serological analysis was performed using a panel of clinically defined dog sera. The findings of this study indicate that DiT33 is a promising antigen for the early detection of D. immitis and may be a valuable tool in the control and management of heartworm infection.

Amino Acid Sequence↗
PubMed1996

Processing of the Nedd2 precursor by ICE-like proteases and granzyme B.

BACKGROUND: The Nedd2/Ich-1 protein belongs to a growing family of mammalian cysteine proteases similar to interleukin-1 beta converting enzyme (ICE). Because of their similarity to the Cacnorhabditis elegans cell death protein CED-3, the ICE-like proteins are thought to play a key role in the execution of apoptosis. The active form of ICE is a tetramer consisting of two heterodimers (p20 + p10)2 derived from the cleavage of the pro-enzyme. RESULTS: In the present communication we show that the p51 Nedd2 precursor (pro-Nedd2) is also cleaved into p20-like (p19) and p10-like (p12) subunits by extracts prepared from cultured cell lines. Extracts from apoptotic NIH-3T3 cells but not normal growing NIH-3T3 cells also contained pro-Nedd2 cleaving activity. The processing of pro-Nedd2 by cell extracts was inhibited by characteristic inhibitors of ICE-like proteases. Additionally we show that pro-Nedd2 (p51) can be processed in vitro by active CPP32 and ICE, and to a lesser extent by Mch2 and Nedd2. Granzyme B, a serine protease required for cytotoxic T lymphocyte (CTL) mediated killing of target cells, also cleaved pro-Nedd2 to p19 + p12 subunits. CONCLUSIONS: Our observations suggest that Nedd2 activation requires cleavage by one or more ICE-like proteases that lie upstream in the proteolytic cascade. Cleavage of pro-Nedd2 by granzyme B indicates that Nedd2 may be one of the downstream effectors in the CTL-mediated killing of target cells.

3T3 Cells↗
PubMed1996

Hippocampal responses to corticosterone and stress, one of which is the 35,000 M(r) protein, glycerol phosphate dehydrogenase.

Previously, the synthesis of a hippocampal 35,000 M(r) protein increased in response to glucocorticoid treatment and a variety of stressors. We now show by immunoprecipitation that this cytosolic protein is glycerol 3-phosphate dehydrogenase (E.C.1.1.1.8; GPDH). In addition, four polypeptides encoded by glucocorticoid-induced mRNAs co-migrated with hippocampal protein synthetic products on two-dimensional polyacrylamide gels, including 35,000 M(r) protein of approximately pl 6.3, that had previously been identified as GPDH by hybrid-selection with a GPDH cDNA clone. The 35,000 M(r) in vitro translation product was also immunoprecipitated with the GPDH antibody. Using radiolabeled hippocampal slices and two-dimensional gel analysis, a 35,000 M(r) polypeptide of approximately pl 6.4 increased five-fold after 30 min of intermittent tail-shock. This protein was found predominantly in the 20,000 x g pellet and did not immunoprecipitate with the GPDH antibody. However, a 35,000 M(r) polypeptide was also found in the cytosol as a minor component after stress, which did immunoprecipitate with the GPDH antibody. Therefore, there are at least two shock-induced 35,000 M(r) proteins, one of which is GPDH. These results establish that increases in GPDH mRNA prevalence and protein synthesis occur in response to both glucocorticoids and stress in the adult rat hippocampus. Based on the increased enzyme activity seen in the nervous system in response to glucocorticoids, dietary restriction, and nerve injury, the induction of GPDH may have functional consequences in cellular adaptation to stress.

Animals↗
PubMed1996

Increased expression of ubiquitin during adenosine 3',5'-cyclic monophosphate-induced differentiation of neuroblastoma cells in culture.

The role of ubiquitin in proliferation and differentiation of nerve cells has not been studied. An elevation of the intracellular level of adenosine 3',5'-cyclic monophosphate (cAMP) in neuroblastoma cells induces terminal differentiation in these cells. Therefore, in this study we investigated the changes in the level and subcellular distribution of ubiquitin during proliferation and differentiation of neuroblastoma cells. Prostaglandin E1, a stimulator of adenylate cyclase, plus beta-carotene, and 4-(3-butoxy-4-methoxybenzyl)-2-imidazolidinone (Ro 20-1724), an inhibitor of cyclic nucleotide phosphodiesterase, plus beta-carotene were used to induce terminal differentiation in > 90% of neuroblastoma cells. Changes in ubiquitin level were studied by immunofluorescent staining using either a mouse monoclonal antibody or a rabbit polyvalent antibody to ubiquitin. Results showed that the dividing neuroblastoma cells contained very low levels of ubiquitin localized primarily in the cytoplasm. The intensity of cytoplasmic staining for ubiquitin markedly increased during cAMP-induced differentiation of neuroblastoma cells, being the highest at 4 days after treatment. The neurites of these differentiated cells were also stained, but the nuclei were not. We propose a hypothesis that higher levels of cytoplasmic ubiquitin are needed during cAMP-induced differentiation of neuroblastoma cells for the removal of proteins responsible for cell proliferation through rapid degradation and/or inhibition of transcription, later leading to terminal differentiation.

Animals↗
PubMed1996

Taxanes from in vitro cultures of the Himalayan yew Taxus wallichiana.

Culture conditions have been standardized for initiation of callus cultures of Himalayan yew (Taxus wallichiana) using young stem and needle explants from mature trees. Cultures were established on a modified Murashige and Skoog's medium supplemented with various levels of auxins (2.4-D, NAA) and cytokinin (kinetin). A medium containing 0.25 mg/l kinetin and 5.0 mg/l 2.4-D was optimal for stem callus growth whereas the presence of 0.25 mg/l kinetin along with 3.0 mg/l NAA in the medium supported optimal needle callus growth. Growth of stem callus was faster than needle callus growth. Supplementation of ascorbic acid (30 mg/l) amongst various anti-phenolic agents tested significantly reduced browning of initiated callus. Two taxanes (2-deacetoxytaxinine 1 and 2'-deacetoxyaustrospicatine) known to occur in stem bark, have also been isolated from undifferentiated tissue of T. wallichiana in equal or higher yields, for the first time.

Antineoplastic Agents, Phytogenic↗
PubMed1996

bc1-1 rearrangement and cyclin D1 protein expression in multiple lymphomatous polyposis.

Multiple lymphomatous polyposis (MLP), characterized by multiple polyps involving long segments of the gastrointestinal (GI) tract, is believed to represent GI involvement by mantle cell lymphoma (MCL), primarily based on its histologic and immunophenotypic similarities with MCL. However, rearrangement of the bcl-1 locus, the molecular lesion characteristic of MCL, has not been investigated in this group of patients. The authors evaluated the morphologic, immunophenotypic, and molecular features of 18 cases of MLP and 8 B-cell lymphomas involving the GI tract (including 6 MALT lymphomas). All MLP cases presented with GI disease, and were histologically similar to MCL. DNA extracted from formalin-fixed, paraffin-embedded tissue was analyzed for evidence of bcl-1 rearrangement by PCR, using chromosome 11 specific and consensus JH primers. Amplifiable DNA was obtained in 24 of 26 cases (16 of 18 MLP cases and 8 of 8 controls). bcl-1 rearrangement was detected in 6 of 16 cases (38%), subsequently confirmed by sequencing of the breakpoint region, and in 0 of 8 controls. Immunostaining for cyclin D1 was positive in 14 of 18 MLPs, including the 6 bcl-1 rearranged cases and negative in 6 of 6 evaluable controls. The detection of bcl-1 rearrangement and cyclin D1 expression in cases of MLP supports the view that MLP represents primary MCL, of the GI tract. These techniques may also be helpful in differentiating MLP from other GI lymphomas, particularly low grade lymphomas of MALT, when only small routinely fixed endoscopic biopsies are available.

Adult↗
PubMed1996

Evolution of the hedgehog gene family.

Effective intercellular communication is an important feature in the development of multicellular organisms. Secreted hedgehog (hh) protein is essential for both long- and short-range cellular signaling required for body pattern formation in animals. In a molecular evolutionary study, we find that the vertebrate homologs of the Drosophila hh gene arose by two gene duplications: the first gave rise to Desert hh, whereas the second produced the Indian and Sonic hh genes. Both duplications occurred before the emergence of vertebrates and probably before the evolution of chordates. The amino-terminal fragment of the hh precursor, crucial in long- and short-range intercellular communication, evolves two to four times slower than the carboxyl-terminal fragment in both Drosophila hh and its vertebrate homologues, suggesting conservation of mechanism of hh action in animals. A majority of amino acid substitutions in the amino- and carboxyl-terminal fragments are conservative, but the carboxyl-terminal domain has undergone extensive insertion-deletion events while maintaining its autocleavage protease activity. Our results point to similarity of evolutionary constraints among sites of Drosophila and vertebrate hh homologs and suggest some future directions for understanding the role of hh genes in the evolution of developmental complexity in animals.

Amino Acid Sequence↗
PubMed1996

Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates.

Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the 1st + 2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition/transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, alpha) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, alpha, and overall amount of evolution for 1st+2nd position data. It can also be used to estimate pairwise distances with appropriate values of alpha for a majority of genes.

Amino Acid Sequence↗
PubMed1996

A stepwise algorithm for finding minimum evolution trees.

A stepwise algorithm for reconstructing minimum evolution (ME) trees from evolutionary distance data is proposed. In each step, a taxon that potentially has a neighbor (another taxon connected to it with a single interior node) is first chosen and then its true neighbor searched iteratively. For m taxa, at most (m-1)!/2 trees are examined and the tree with the minimum sum of branch lengths (S) is chosen as the final tree. This algorithm provides simple strategies for restricting the tree space searched and allows us to implement efficient ways of dynamically computing the ordinary least squares estimates of S for the topologies examined. Using computer simulation, we found that the efficiency of the ME method in recovering the correct tree is similar to that of the neighbor-joining method (Saitou and Nei 1987). A more exhaustive search is unlikely to improve the efficiency of the ME method in finding the correct tree because the correct tree is almost always included in the tree space searched with this stepwise algorithm. The new algorithm finds trees for which S values may not be significantly different from that of the ME tree if the correct tree contains very small interior branches or if the pairwise distance estimates have large sampling errors. These topologies form a set of plausible alternatives to the ME tree and can be compared with each other using statistical tests based on the minimum evolution principle. The new algorithm makes it possible to use the ME method for large data sets.

Algorithms↗
PubMed1996

Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites.

We propose two approximate methods (one based on parsimony and one on pairwise sequence comparison) for estimating the pattern of nucleotide substitution and a parsimony-based method for estimating the gamma parameter for variable substitution rates among sites. The matrix of substitution rates that represents the substitution pattern can be recovered through its relationship with the observable matrix of site pattern frequences in pairwise sequence comparisons. In the parsimony approach, the ancestral sequences reconstructed by the parsimony algorithm were used, and the two sequences compared are those at the ends of a branch in the phylogenetic tree. The method for estimating the gamma parameter was based on a reinterpretation of the numbers of changes at sites inferred by parsimony. Three data sets were analyzed to examine the utility of the approximate methods compared with the more reliable likelihood methods. The new methods for estimating the substitution pattern were found to produce estimates quite similar to those obtained from the likelihood analyses. The new method for estimating the gamma parameter was effective in reducing the bias in conventional parsimony estimates, although it also overestimated the parameter. The approximate methods are computationally very fast and appear useful for analyzing large data sets, for which use of the likelihood method requires excessive computation.

Algorithms↗