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Biomedical subjects

R Srinivasan

Publications and source records attributed to R Srinivasan.

At least 19 recordsLinked to original sources
PubMed1999

A physical basis for protein secondary structure.

A physical theory of protein secondary structure is proposed and tested by performing exceedingly simple Monte Carlo simulations. In essence, secondary structure propensities are predominantly a consequence of two competing local effects, one favoring hydrogen bond formation in helices and turns, the other opposing the attendant reduction in sidechain conformational entropy on helix and turn formation. These sequence specific biases are densely dispersed throughout the unfolded polypeptide chain, where they serve to preorganize the folding process and largely, but imperfectly, anticipate the native secondary structure.

Protein Conformation↗
PubMed1999

Coupling and uncoupling of tumor immunity and autoimmunity.

Self-antigens, in the form of differentiation antigens, are commonly recognized by the immune system on melanoma and other cancers. We have shown previously that active immunization of mice against the melanocyte differentiation antigen, a tyrosinase-related protein (TRP) gp75(TRP-1) (the brown locus protein) expressed by melanomas, could induce tumor immunity and autoimmunity manifested as depigmentation. In this system, tumor immunity and autoimmunity were mediated by autoantibodies. Here, we characterize immunity against another tyrosinase family glycoprotein TRP-2 (the slaty locus protein), using the same mouse model and method of immunization. As observed previously for gp75(TRP-1), immunity was induced by DNA immunization against a xenogeneic form of TRP-2, but not against the syngeneic gene, and depended on CD4(+) cells. Immunization against TRP-2 induced autoantibodies and autoreactive cytotoxic T cells. In contrast to immunization against gp75(TRP-1), both tumor immunity and autoimmunity required CD8(+) T cells, but not antibodies. Only autoimmunity required perforin, whereas tumor immunity proceeded in the absence of perforin. Thus, immunity induced against two closely related autoantigens that are highly conserved throughout vertebrate evolution involved qualitatively different mechanisms, i.e., antibody versus CD8(+) T cell. However, both pathways led to tumor immunity and identical phenotypic manifestations of autoimmunity.

Animals↗
PubMed1999

Quantitative structure-activity relationship (QSAR) analysis of surfactants influencing attachment of a Mycobacterium sp. to cellulose acetate and aromatic polyamide reverse osmosis membranes.

A series of 23 neutral, anionic, and zwitterionic surfactants were tested at a concentration of 0.1% wt/vol for their influence on attachment of a Mycobacterium sp. to cellulose acetate (CA) and polyamide (PA) reverse osmosis (RO) membranes. Four cell attachment bioassays were used: (1) semiconcurrent addition of surfactant and bacteria to RO coupons (standard assay); (2) surfactant pretreatment of RO membranes (membrane pretreatment assay); (3) surfactant treatment of adsorbed cells (detachment assay); and (4) surfactant pretreatment of mycobacteria (cell pretreatment assay). Seventeen surfactants inhibited attachment to PA membranes, whereas 15 inhibited attachment to CA in standard assays and, in 13 cases, the same surfactant inhibited attachment to both PA and CA. Despite greater cell attachment to PA than CA, surfactants were typically more effective in the former membrane system. More surfactants were effective in impairing cell attachment than in promoting detachment and a number enhanced attachment in membrane pretreatment assays, suggesting surface modification of RO membranes. Cell pretreatment inhibited attachment to CA membranes, suggesting the bacterial surface was also a target for detergent activity. Multivariate regression and cluster analyses indicated that critical micellar concentration (CMC) was positively correlated with Mycobacterium attachment in CA and PA standard assays. Surfactant dipole moment and octanol/water partitioning (LogP) also contributed to detergent activity in the PA system, whereas dipole moment, molecular topology (i.e., connectivity indices), and charge properties influenced activity in the CA system. Influential variables in membrane pretreatment assays included the LogP, topology indices, and charge properties, whereas CMC played a diminished role. Surfactant dipole moment was most influential in CA membrane detachment assays. Increasing system ionic strength by LiBr addition strengthened inhibition of cell attachment to CA membranes by dodecylbenzene sulfonic acid (DBSA) and promoted DBSA adsorption to CA surfaces as indicated by attenuated total reflection Fourier-transform infrared spectrometry. Results indicate that inhibition of bacterial attachment to RO membranes may be maximized by manipulating surfactant molecular structure to optimize surface adsorption behavior.

Bacterial Adhesion↗
PubMed1999

A complete conformational map for RNA.

A simple stereochemical framework for understanding RNA structure has remained elusive to date. We present a comprehensive conformational map for two nucleoside-5',3'-diphosphates and for a truncated dinucleotide derived from a grid search of all potential conformers using hard sphere steric exclusion criteria to define allowed conformers. The eight-dimensional conformational space is presented as a series of two-dimensional projections. These projections reveal several well-defined allowed and disallowed regions which correlate well with data obtained from X-ray crystallography of both large and small RNA molecules. Furthermore, the two-dimensional projections show that consecutive and ribose ring-proximal torsion angles are interdependent, while more distant torsion angles are not. Remarkably, using steric criteria alone, it is possible to generate a predictive conformational map for RNA.

Nucleic Acid Conformation↗
PubMed1999

Increased synchronization of neuromagnetic responses during conscious perception.

In binocular rivalry, the observer views two incongruent images, one through each eye, but is conscious of only one image at a time. The image that is perceptually dominant alternates every few seconds. We used this phenomenon to investigate neural correlates of conscious perception. We presented a red vertical grating to one eye and a blue horizontal grating to the other eye, with each grating continuously flickering at a distinct frequency (the frequency tag for that stimulus). Steady-state magnetic fields were recorded with a 148 sensor whole-head magnetometer while the subjects reported which grating was perceived. The power of the steady-state magnetic field at the frequency associated with a grating typically increased at multiple sensors when the grating was perceived. Changes in power related to perceptual dominance, presumably reflecting local neural synchronization, reached statistical significance at several sensors, including some positioned over occipital, temporal, and frontal cortices. To identify changes in synchronization between distinct brain areas that were related to perceptual dominance, we analyzed coherence between pairs of widely separated sensors. The results showed that when the stimulus was perceived there was a marked increase in both interhemispheric and intrahemispheric coherence at the stimulus frequency. This study demonstrates a direct correlation between the conscious perception of a visual stimulus and the synchronous activity of large populations of neocortical neurons as reflected by stimulus-evoked steady-state neuromagnetic fields.

Adult↗
PubMed1999

Gene identification in bacterial and organellar genomes using GeneScan.

The performance of the GeneScan algorithm for gene identification has been improved by incorporation of a directed iterative scanning procedure. Application is made here to the cases of bacterial and organnellar genomes. The sensitivity of gene identification was 100% in Plasmodium falciparum plastid-like genome (35 kb) and in 98% in the Mycoplasma genitalium genome (approximately 580 kb) and the Haemophilus influenzae Rd genome (approximately 1.8 Mb). Sensitivity was found to improve in both the Open Reading Frames (ORFs) which have been identified as genes (by homology or by other methods) and those that are classified as hypothetical. False positive assignments (at the nucleotide level) were 0.25% in H. influenzae genome and 0.3% in M. genitalium. There were no false positive assignments in the plastid-like genome. The agreement between the GeneScan predictions and GeneMark predictions of putative ORFs was 97% in M. genitalium genome and 86% in H. influenzae genome. In terms of an exact match between predicted genes/ORFs and the annotation in the databank, GeneScan performance was evaluated to be between 72% and 90% in different genomes. We predict five putative ORFs that were not annotated earlier in the GenBank files for both M. genitalium and H. influenzae genomes. Our preliminary analysis of the newly sequenced G + C rich genome of Mycobacterium tuberculosis H37Rv also shows comparable sensitivity (99%).

Algorithms↗
PubMed1999

EEG coherency II: experimental comparisons of multiple measures.

OBJECTIVE: A concentric spheres model was used in an earlier paper to estimate the effects of volume conduction, reference electrode and spatial filtering on different EEG coherence measures. EEG data are used here to verify theoretical predictions. METHODS: Three EEG data sets were: (1) 64 channel, recorded during 7 alternating periods of resting and mental calculation. (2) 128 channel, for comparison of eyes open versus eyes closed coherence. (3) 128 channel, recorded during deep sleep (stages 3 and 4) and REM. RESULTS: The directions of large scale (lobeal) coherency changes between brain states are relatively independent of coherence measure. However, coherence between specific electrode pairs is sensitive to method and frequency. Average reference and digitally linked mastoids provide reasonable semi-quantitative estimates of large-scale neocortical source coherence. Close bipolar, Laplacian, and dura image methods remove most reference electrode and volume conduction distortion, but may underestimate coherence by spatial filtering. CONCLUSION: Each EEG coherence method has its own potential sources of error and provides coherence estimates for different neural population sizes located in different locations. Thus, studies of coherence and brain state should include several different kinds of estimates to take full advantage of information in recorded signals.

Adolescent↗
PubMed1999

Spatial structure of the human alpha rhythm: global correlation in adults and local correlation in children.

OBJECTIVE: The maturation of the neocortex during childhood and adolescence involves dramatic increases in white-matter volume. EEG recordings from children and adults were examined to determine whether there are associated changes in spatial properties of dynamic processes in the neocortex. METHODS: Spontaneous eyes-closed and eyes-open EEG were recorded at 128 electrodes in 20 children aged 6-11 years and 23 adults aged 18-23 years. The surface Laplacian algorithm was applied to improve the spatial resolution of each electrode. Power and coherence were used to characterize the spatial structure of the alpha rhythm. A stochastic field model was used to eliminate coherences that are inflated due to volume conduction. RESULTS: In adults, the alpha rhythm is characterized by very high coherence between distant electrodes. The children demonstrated reduced anterior power and coherence between anterior and posterior electrodes at the peak alpha frequency in comparison to the adults. The Laplacian alpha rhythm demonstrated much higher power in the children at both anterior and posterior electrodes, but was weakly correlated between electrodes. CONCLUSIONS: The maturation of neocortex in late childhood involves increased global correlation by long-range corticocortical connections. The local correlation that contributes power to each electrode, independent of other electrodes, is reduced as the global correlation increases.

Adolescent↗
PubMed1999

Sessile polypoid gastric heterotopia of rectum: a report of 2 cases and review of the literature.

OBJECTIVE: The term heterotopia, a term derived from Greek, implies "other place." It refers to the finding of normal tissues at foreign sites. Heterotopic gastric tissue rarely involves the large bowel. We report 2 cases of this rare entity. DATA SOURCES: Case reports of 2 patients with sessile polypoid lesion in the rectum, with a review of the available literature, using both MEDLINE and relevant bibliographies of published articles. RESULTS: Biopsies of the rectal lesions in our 2 cases revealed the presence of gastric tissue. Only 27 other such cases have been reported in the English literature. CONCLUSIONS: Patients with rectal gastric heterotopia usually present with bleeding, but other presentations and complications are possible. Endoscopic or surgical excision is the treatment of choice, although the lesions also respond to histamine 2 receptor blockers.

Adult↗
PubMed1999

Expression of the c-erbB-3/HER-3 and c-erbB-4/HER-4 growth factor receptors and their ligands, neuregulin-1 alpha, neuregulin-1 beta, and betacellulin, in normal endometrium and endometrial cancer.

The objective of this study was to determine the immunohistochemical expression of the c-erbB-3 and c-erbB-4 growth factor receptors and their principal ligands, the neuregulins and betacellulin, in normal endometrium and determine whether there was evidence of under- or overexpression in endometrial adenocarcinoma. Immunohistochemistry was performed using well-characterized antibodies against each of the five proteins analyzed on formalin-fixed, paraffin-embedded archival material. Forty-three normal endometrial samples (16 proliferative, 19 secretory, and 8 hyperplastic) and 41 endometrial adenocarcinoma cases were analyzed. There was variable expression of the growth factor receptors and the ligands in the two principal phases of the menstrual cycle as well as in endometrial adenocarcinoma. In normal endometrium, the c-erbB-3 receptor was weakly expressed in both phases. The c-erbB-4 receptor and all of the ligands examined, neuregulin alpha, neuregulin beta, and betacellulin, were expressed at significantly higher levels in the secretory as compared with the proliferative phase of the menstrual cycle, suggesting a role for these proteins in endometrial maturation. In endometrial adenocarcinoma, overexpression of c-erbB-3, c-erbB-4, and betacellulin with underexpression of neuregulin a as compared with normal controls was observed. Neuregulin beta expression was not found to be significantly different in the two groups. These results suggest that signaling through the c-erbB-3 and c-erbB-4 receptors and the ligands neuregulin alpha, neuregulin beta, and betacellulin are important in endometrial carcinogenesis.

Amino Acid Sequence↗
PubMed1998

Tumor immunity and autoimmunity induced by immunization with homologous DNA.

The immune system can recognize self antigens expressed by cancer cells. Differentiation antigens are prototypes of these self antigens, being expressed by cancer cells and their normal cell counterparts. The tyrosinase family proteins are well characterized differentiation antigens recognized by antibodies and T cells of patients with melanoma. However, immune tolerance may prevent immunity directed against these antigens. Immunity to the brown locus protein, gp75/ tyrosinase-related protein-1, was investigated in a syngeneic mouse model. C57BL/6 mice, which are tolerant to gp75, generated autoantibodies against gp75 after immunization with DNA encoding human gp75 but not syngeneic mouse gp75. Priming with human gp75 DNA broke tolerance to mouse gp75. Immunity against mouse gp75 provided significant tumor protection. Manifestations of autoimmunity were observed, characterized by coat depigmentation. Rejection of tumor challenge required CD4(+) and NK1.1(+) cells and Fc receptor gamma-chain, but depigmentation did not require these components. Thus, immunization with homologous DNA broke tolerance against mouse gp75, possibly by providing help from CD4(+) T cells. Mechanisms required for tumor protection were not necessary for autoimmunity, demonstrating that tumor immunity can be uncoupled from autoimmune manifestations.

Animals↗
PubMed1998

Investigating neural correlates of conscious perception by frequency-tagged neuromagnetic responses.

In binocular rivalry, a subject views two incongruent stimuli through each eye but consciously perceives only one stimulus at a time, with a switch in perceptual dominance every few seconds. To investigate the neural correlates of perceptual dominance in humans, seven subjects were recorded with a 148-channel magnetoencephalography array while experiencing binocular rivalry. A red vertical grating flickering at one frequency was presented to one eye through a red filter and a blue horizontal grating flickering at a different frequency was presented to the other eye through a blue filter. Steady-state neuromagnetic responses at the two frequencies were used as tags for the two stimuli and analyzed with high-resolution power spectra. It was found that a large number of channels showed peaks at both frequencies, arranged in a horseshoe pattern from posterior to anterior regions, whether or not the subject was consciously perceiving the corresponding stimulus. However, the amount of power at the stimulus frequency was modulated in relation to perceptual dominance, being lower in many channels by 50-85% when the subject was not conscious of that stimulus. Such modulation by perceptual dominance, although not global, was distributed to a large subset of regions showing stimulus-related responses, including regions outside visual cortex. The results demonstrate a correlation between the conscious perception of a visual stimulus and the synchronous activity of large populations of neurons as reflected by steady-state neuromagnetic responses.

Adult↗
PubMed1998

Expression of the c-erbB-4/HER4 protein and mRNA in normal human fetal and adult tissues and in a survey of nine solid tumour types.

The c-erbB-4/HER4 receptor belongs to the family of the type I growth factor receptors. Mouse monoclonal antibodies have been raised to the cytoplasmic domain of the c-erbB-4 receptor and characterized; the antibody HFR-1 has been used to determine the pattern of expression of the c-erbB-4 protein immunohistochemically in formalin-fixed, paraffin-embedded adult and fetal tissues. The expression of c-erbB-4 mRNA was determined by using 35S-labelled riboprobes and tissue in situ hybridization. c-erbB-4 is widely expressed in many adult and fetal tissues, including the lining epithelia of the gastrointestinal, urinary, reproductive, and respiratory tracts, as well as the skin, skeletal muscle, circulatory, endocrine, and nervous systems. The developing brain and heart notably express high levels of this receptor. The pattern of c-erbB-4 protein expression is also reported in a survey of common solid human cancers. Loss of expression was noted in 40-80 per cent of adenocarcinomas and up to 100 per cent of squamous cell carcinomas, whereas overexpression was observed in about 10-20 per cent of adenocarcinomas and astrocytomas. In general, the pattern of c-erbB-4 expression in normal tissues and cancers suggests that it tends to be associated with the differentiated compartment.

Adenocarcinoma↗
PubMed1998

The type 1 growth factor receptor family: new ligands and receptors and their role in breast cancer.

The type 1 family of growth factor receptors, which consist of the epidermal growth factor receptor, c-erbB-2, c-erbB-3, and c-erbB-4, are expressed in normal breast ductal epithelial cells and in some breast cancers. Nine genes have now been identified which code for ligands. In some cases the genes are spliced into a series of proteins which differ in structure, but all retain an EGF-like element responsible for receptor recognition. The EGF receptor is expressed in normal breast and in some cancers, but is apparently reduced in expression in other cases. Cancers with EGF receptors appear to represent a greater threat to patients as in most studies they are associated with a shorter time to relapse and overall survival. The c-erbB-2 protein is overexpressed at very high levels in about one fifth of breast cancers and is indicative of poor prognosis. Other cancers may express lesser degrees of overexpression but it is not clear if this is biologically or clinically significant. The c-erbB-3 protein is expressed in normal breast epithelial cells and has been reported to be present at high levels in some cancers but at normal levels or at lower than normal levels in some others. The limited studies to date suggest that when measured on its own c-erbB-3 expression is not predictive. c-erbB-4 is also expressed in normal breast and in some cancers but no studies have yet been performed to address whether it is associated with disease behaviour. In the future it is likely that a greater understanding of the function of this complex family of interacting proteins will assist in gaining the maximum predictive power from measurement of their expression in human breast cancer.

Amino Acid Sequence↗