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Biomedical subjects

B Ramachandran

Publications and source records attributed to B Ramachandran.

At least 19 recordsLinked to original sources

Scaling dynamical correlation energy from density functional theory correlation functionals.

The scaling of dynamical correlation energy in molecules obtained by the correlation functionals of density functional theory (DFT) is examined. The approach taken is very similar to the scaled external correlation method of Brown and Truhlar but is based on the observation that DFT correlation functionals, especially the LYP, appear to represent the dynamical portion of the correlation energy in molecules. We examine whether higher accuracy in atomization energies can be gained by scaling without significant deterioration of the structural and spectroscopic properties of the molecules using four DFT functionals (BLYP, OLYP, B3LYP, and O3LYP) on 19 molecules including the six molecule AE6 database, the latter being representative of a much larger, 109 molecule training set. We show that, with molecule specific scale factors, nearly perfect agreement with experiment can be achieved in atomization energies without increasing the average errors in other molecular properties relative to the DFT calculation. We further show that it is possible to find optimal scale factors which reduce the mean unsigned error per bond to levels comparable to those of some multilevel multicoefficient methods.

Journal Article↗

A computational study of oxiranyllithium.

[reaction: see text] Computational methods were used to determine the structure, bonding, and aggregation states of oxiranyllithium in the gas phase and in THF solution, at 200 and 298 K. THF solvation was modeled by microsolvation with explicit THF ligands, forming a supermolecule that includes the oxiranyllithium aggregate and its first solvation shell. Because oxiranyllithium has a chiral center, two diastereomeric dimers were formed, the RR and the RS, along with their enantiomers. Similarly, three diastereomers of the tetramer were formed, the RRRR, RRRS, and RRSS and their enantiomers. Oxiranyllithium was found to exist predominantly as the tetramer in the gas phase, while the dimer was the dominant species in THF solution. The relative concentrations of the different stereoisomers were calculated from equilibrium constants.

Journal Article↗

Computational strategies for evaluating barrier heights for gas-phase reactions of lithium enolates.

Gas-phase activation energies were calculated for three lithium enolate reactions by using several different ab initio and density functional theory (DFT) methods to determine which levels of theory generate acceptable results. The reactions included an aldol-type addition of an enolate to an aldehyde, a proton transfer from an alcohol to a lithium enolate, and an S(N)2 reaction of an enolate with chloromethane. For each reaction, the calculations were performed for both the monomeric and dimeric forms of the lithium enolate. It was found that transition state geometry optimization with B3LYP followed by single point MP2 calculations generally provided acceptable results compared to higher level ab initio methods.

Journal Article↗

Quantum and quasiclassical studies of the O(3P)+HCl-->OH+Cl(2P) reaction using benchmark potential surfaces.

We have performed quantum mechanical (QM) dynamics calculations within the independent-state approximation with new benchmark triplet A" and A' surfaces [B. Ramachandran et al., J. Chem. Phys. 119, 9590 (2003)] for the rovibronic state-to-state measurements of the reaction O(3P)+HCl(v=2,j=1,6,9)-->OH(v'j')+Cl(2P) [Zhang et al., J. Chem. Phys. 94, 2704 (1991)]. The QM and experimental rotational distributions peak at similar OH(j') levels, but the QM distributions are significantly narrower than the measurements and previous quasiclassical dynamics studies. The OH(low j) populations observed in the measurements are nearly absent in the QM results. We have also performed quasiclassical trajectory with histogram binning (QCT-HB) calculations on these same benchmark surfaces. The QCT-HB rotational distributions, which are qualitatively consistent with measurements and classical dynamics studies using other surfaces, are much broader than the QM results. Application of a Gaussian binning correction (QCT-GB) dramatically narrows and shifts the QCT-HB rotational distributions to be in very good agreement with the QM results. The large QCT-GB correction stems from the special shape of the joint distribution of the classical rotational/vibrational action of OH products. We have also performed QM and QCT calculations for the transition, O+HCl(v=0,T=300 K)-->OH(v'j')+Cl from threshold to approximately 130 kcal mol(-1) collision energy as a guide for possible future hyperthermal O-atom measurements. We find in general a mixed energy release into translation and rotation consistent with a late barrier to reaction. Angular distributions at high collision energy are forward peaked, consistent with a stripping mechanism. Direct collisional excitation channel cross sections, O+HCl(v=0,T=300 K)-->O+HCl(v'=1), in the same energy range are large, comparable in magnitude to the reactive channel cross sections. Although the (3)A" state dominates most collision processes, above approximately 48 kcal mol(-1), the (3)A' state plays the major role in collisional excitation.

Journal Article↗

Diversity and divergence among the tribal populations of India.

Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (F(ST): 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.

Asia↗

Insulin mimetic effects of macrocyclic binuclear oxovanadium complexes on streptozotocin-induced experimental diabetes in rats.

AIM: The vanadium complexes so far tested for their insulin mimetic effects are either mono- or binuclear and contain only acyclic ligands. The leaching or hydrolysis of vanadyl ions from these complexes is much easier, and hence they elicit side effects. In the present study, a new binuclear macrocyclic oxovanadium complex was synthesized, and its efficacy was studied on streptozotocin (STZ)-induced diabetic rats over a period of 30 days. METHODS: The insulin mimetic effect of the complex was tested on the blood sugar level in the STZ-diabetic rats and on the activities of the carbohydrate-metabolizing enzymes present in the liver. RESULTS: Administration of vanadium complex to STZ-induced diabetic rats decreased blood glucose levels from hyperglycaemic to normoglycaemic when compared to diabetic rats. The activity of carbohydrate-metabolizing enzymes such as hexokinase, glucose-6-phosphate dehydrogenase, glycogen synthase and glycogen content were increased to near normal in vanadium complex-administered diabetic rats. The biochemical studies such as assay of blood urea and glutamate oxaloacetate transaminases revealed that the complex is not toxic to the system. CONCLUSION: The nontoxic nature of this complex may be due to the presence of the vanadyl ions in an intact macrocyclic form. Further, the vanadyl ions present in the macrocyclic binuclear oxovanadium complex are very close to each other, and this may enhance the insulin mimetic activity by synergic effect.

Animals↗

Zebra finch aromatase gene expression is regulated in the brain through an alternate promoter.

The learned singing behavior in songbirds is sex-steroid-dependent and sexually dimorphic. Estrogen plays a major role in masculinizing the song system in these songbirds. The songbird brain synthesizes large amounts of estrogen, which, in the case of zebra finches, have been found to enter the systemic circulation. Aromatase cytochrome P450 is the key enzyme catalyzing the conversion of androgens to estrogens. We have cloned a novel alternatively spliced form of aromatase cDNA expressed predominantly in the zebra finch brain. We have also isolated and characterized the gene coding for zebra finch aromatase which spans 20kb in length. The alternate forms of aromatase mRNA (ARO) differ in their 5'-untranslated regions encoded by either exon 1a or 1b. The putative promoter sequences controlling the regulation of the alternate forms of ARO in zebra finches contain consensus binding sites for various transcription factors. While both the promoters have binding sites for SRY-like transcription factor, a binding site for SF-1 is present only in the promoter 1b active in the ovary. Intriguingly, a 55bp segment within the promoter 1a sequence appears to be highly conserved among zebra finch, mouse and human aromatase promoters active in the brain.

5' Untranslated Regions↗

Adherence to combination antiretroviral therapies in HIV patients of low health literacy.

OBJECTIVE: To test the significance of health literacy relative to other predictors of adherence to treatment for HIV and AIDS. PARTICIPANTS: Community sample of HIV-seropositive men (n = 138) and women (n = 44) currently taking a triple-drug combination of antiretroviral therapies for HIV infection; 60% were ethnic minorities, and 73% had been diagnosed with AIDS. MEASUREMENTS: An adapted form of the Test of Health Literacy in Adults (TOFHLA), a comprehensive health and treatment interview that included 2-day recall of treatment adherence and reasons for nonadherence, and measures of substance abuse, social support, emotional distress, and attitudes toward primary care providers. MAIN RESULTS: Multiple logistic regression showed that education and health literacy were significant and independent predictors of 2-day treatment adherence after controlling for age, ethnicity, income, HIV symptoms, substance abuse, social support, emotional distress, and attitudes toward primary care providers. Persons of low literacy were more likely to miss treatment doses because of confusion, depression, and desire to cleanse their body than were participants with higher health literacy. CONCLUSIONS: Interventions are needed to help persons of low literacy adhere to antiretroviral therapies.

Acquired Immunodeficiency Syndrome↗

Barriers to HIV/AIDS treatment and treatment adherence among African-American adults with disadvantaged education.

African Americans are disproportionately affected by acquired immunodeficiency syndrome (AIDS). New treatments that slow the progression of human immunodeficiency virus (HIV) infection offer hope for individuals living with HIV/AIDS, but lack of access to care and poor treatment adherence remain significant obstacles to HIV treatment. This study investigated the association between education literacy to HIV treatment adherence and barriers to care among African Americans living with HIV/AIDS. A community-recruited sample of 85 African-American men and 53 women receiving HIV treatment completed measures of health literacy, health status, treatment adherence, emotional well-being, and barriers to care. Nearly one-third (29%) of the participants had < 12 years of education or were functionally illiterate, and those with low-education literacy were less likely to be adherent to HIV medications within the previous two days. Lower-education literacy also was related to reasons for missing medications and barriers to accessing medical care. Individuals of law-education literacy also were more emotionally distressed, lacked social support, and were less optimistic than those with higher education. These results indicate that education and health literacy are important factors in HIV-treatment adherence and access to medical care. Interventions are needed for improving treatment adherence among law-income minorities, and such interventions will need tailoring for individuals with limited reading ability.

Acquired Immunodeficiency Syndrome↗

Regulation of aromatase, 5 alpha- and 5 beta-reductase in primary cell cultures of developing zebra finch telencephalon.

Sex steroids act on the developing and adult telencephalon of songbirds to organize and activate the neural circuits required for the learning and production of song. Presumably, the availability of active androgens and estrogens to steroid-sensitive neural circuits controlling song is modulated by the local expression of androgen-metabolizing enzymes. Two enzymes, 5 alpha- and 5 beta-reductase, are expressed widely in the songbird telencephalon, as they are in the telencephalons of other avian species. These enzymes convert circulating testosterone (T) into the active and inactive metabolites, 5 alpha- and 5 beta-dihydrotestosterone (DHT), respectively. A third enzyme, aromatase, converts T into estradiol (E2) and is expressed at unusually high levels in several regions of the songbird telencephalon. In many tissues, including the brain, the regulation of expression of one or more of these enzymes can be a critical feature of their ability to control the production of active sex steroids. We have used primary cell cultures to examine factors that might regulate the expression of these enzymes in developing zebra finch telencephalon. Cultures were treated for 0-72 h with sex steroids (T, E2, 5 alpha-DHT, and 5 beta-DHT) or with dibutyryl cAMP. Afterward, activities of aromatase, 5 alpha- and 5 beta-reductase were determined or total RNA was extracted for Northern analysis. Treatments with cAMP increased both aromatase activity and aromatase mRNA levels by 220%. E2 significantly reduced aromatase activity by an average 65%, whereas 5 alpha- and 5 beta-DHT had no effect on aromatase activity. Compared to untreated controls, E2 treatment decreased aromatase mRNA levels by 56%. None of these treatments consistently affected either 5 alpha- and 5 beta-reductase activities. These results suggest that telencephalic E2 may regulate its own synthesis by repression of aromatase expression, whereas factors that upregulate cAMP in the telencephalon can increase the local concentrations of E2.

Aging↗

Infectious human herpesvirus 8 in a healthy North American blood donor.

BACKGROUND: Molecular studies have provided strong evidence for the association of human herpesvirus 8 (HHV-8) with Kaposi's sarcoma. These data have been supported by serological studies, which have also suggested that HHV-8 can be found in the healthy population. We report the presence of infectious HHV-8 in a healthy donor to a North American blood bank. METHODS: We examined the peripheral blood mononuclear cells or CD19 cells of blood donors by PCR for evidence of HHV-8 infection. The CD19 cells were separated from peripheral blood mononuclear cells by immunomagnetic-bead selection. To enhance detection of HHV-8, the CD19 cells from eleven unsystematically selected blood donors were activated with phorbol ester and recombinant interleukin-6; the culture fluid was filtered and inoculated onto HHV-8-negative target CD19 cells that had been prepared from phytohaemagglutinin-stimulated peripheral blood mononuclear cells. These inoculated target cells were cultured for 3 days and then analysed for HHV-8 sequences by PCR. Serum samples were tested for antibodies to HHV-8 by an indirect immunofluorescence assay. FINDINGS: One blood donor was consistently found to be infected with HHV-8 by PCR after the cell-culture activation procedure. He was seropositive for the virus. The HHV-8 recovered was infectious, as shown by a reverse-transcription-PCR technique that detected HHV-8 RNA in the inoculated target cells. INTERPRETATION: These data provide the first indication that HHV-8 can be recovered from the blood of a healthy individual, a blood donor, and that the virus is infectious. This observation suggests that HHV-8 could be transmitted by blood transfusion, a possibility that merits further study.

Adult↗

CD8+ cells from HIV-2-infected baboons control HIV replication.

OBJECTIVE: To analyze the CD8+ cell antiviral immune response in HIV-2-infected baboons. DESIGN: Baboons were infected with clinical isolates of HIV-2, CD8+ cells were isolated from phytohemagglutinin (PHA)-stimulated baboon peripheral blood mononuclear cells (PBMC). These cells were cultured with PHA-stimulated CD4+ cells acutely infected with HIV-2 at several CD8+:CD4+ cell ratios. Control of HIV-2 replication was determined by comparing peak levels of HIV-2 replication in fluids from CD8+:CD4+ cell cocultures with those in fluids from infected CD4+ cells cultured alone. RESULTS: CD8+ cells from HIV-2-infected baboons inhibited HIV-2 replication in acutely infected autologous CD4+ cells to a significantly greater extent than did CD8+ cells from uninfected baboons (P = 0.0001). At the beginning of the acute phase of HIV-2 infection, CD8+ cells showed either a transient reduction or loss in the antiviral activity. In some cases the CD8+ cell response enhanced HIV-2 replication. Subsequently, the strength of the CD8+ cell antiviral activity increased concomitant with a decrease in the HIV-2 load in the PBMC. Suppression of HIV replication could be demonstrated with filtered fluid from CD8+ cells. Other studies indicated that infected CD4+ cells are lost during coculture of CD8+ cells with infected CD4+ cells. CONCLUSIONS: CD8+ cells of HIV-2-infected baboons develop substantial anti-HIV-2 activity following HIV-2 infection, which may account in part for the low frequency of pathogenesis in HIV-2-infected baboons. Studies to elucidate the mechanism of this CD8+ cell antiviral activity suggest that it is mediated in part by a soluble antiviral factor, but primarily in association with the loss of infected CD4+ cells.

Animals↗

The induction of ret by Wnt-1 in PC12 cells is atypically dependent on continual Wnt-1 expression.

Wild type PC12 pheochromocytoma cells that had been infected with a Wnt-1-carrying virus and thus express Wnt-1 (PC12/Wnt-1) are known to acquire the same flat cell phenotype as that of spontaneously occurring PC12 flat cell variants except that the latter do not presently express Wnt-1. Flat cell variants of PC12 cells exhibit markedly altered morphology and gene expression. In order to assess the possibility that the spontaneously occurring flat cell variants could have been induced in wild type PC12 cells by previous transient expression of the cell's endogenous Wnt-1, we have isolated PC12/Wnt-1 cells expressing little or no Wnt-1. In spite of absent Wnt-1 expression, they retained their flat cell morphology, glutamate/aspartate transporter activity, increased neu mRNA levels and lack of both norepinephrine transporter activity and nerve growth factor-induced differentiation. Thus, Wnt-1 expression is not required to maintain the flat cell phenotype. However, we identified one gene, ret, whose mRNA level in PC12 was not only increased by Wnt-1 expression, but whose increased mRNA level was also dependent on continual Wnt-1 expression. This finding suggests that the induction of ret by Wnt-1 can be used to elucidate the Wnt-induced signalling pathway in mammalian cells.

ATP-Binding Cassette Transporters↗

Rat C6 and human astrocytic tumor cells express a neuronal type of glutamate transporter.

C6 glioma cells take up aspartate and glutamate by a Na(+)-dependent transporter. Using the polymerase chain reaction and degenerate oligonucleotide primers corresponding to conserved regions of previously cloned glutamate transporters, we isolated from these cells a partial cDNA clone with a sequence of the neuronal type EAAC1 glutamate transporter. The cells express a 4.4 kb message that hybridizes to this cDNA, and they do not express either of the previously described glial type glutamate transporters, GLT-1 or GLAST. The cells were sensitive to the toxic aspartate analog alanosine, which enters the cells by a glutamate transporter. Several human brain tumors examined, including some astrocytic tumors, expressed the EAAT3 glutamate transporter, which is the human homolog of the rodent EAAC1 transporter. Some of the tumors also expressed the other types of glutamate transporter.

ATP-Binding Cassette Transporters↗

Megakaryocyte-specific positive regulatory sequence 5' to the human PF4 gene.

Platelet factor 4 (PF4) is only expressed in platelets and is an appropriate marker for studying megakaryocytic differentiation. We previously characterized cDNA and genomic clones for human PF4 (hPF4) and now present transient expression studies defining the promoter of the gene. 12-O-tetradecanoyl-phorbol-13- acetate (TPA) induces megakaryocytic differentiation of human erythroleukemia (HEL) cells, providing an excellent model system for the study of megakaryocyte-specific promoter activity. Luciferase reporter-gene constructs containing sequences from -2074 to +49 were used to map regions that may regulate PF4 gene expression. The sequence in the region -239 to -107 increased basal promoter activity by four- to five-fold in TPA-induced HEL cells. The sequence between -239 and -107 contains 53 consecutive thymidine residues. Functional studies using constructs in this region show that poly(T) and the region -187 to -107 are necessary for the total increase in activity in TPA-induced HEL cells. Mobility-shift assays show that the poly(T) tract binds TPA-inducible proteins. The results suggest a complex promoter for the PF4 gene involving a basal nonspecific promoter element between -107 and +49, a positive promoter element between -239 and -107 binding specific nuclear proteins from megakaryocyte-lineage cells, and a silencer-like region between -2074 and -1653.

Base Sequence↗

Differential expression of transporters for norepinephrine and glutamate in wild type, variant, and WNT1-expressing PC12 cells.

Wild type PC12 pheochromocytoma cells express a Na(+)-dependent norepinephrine transporter that operates in the uptake of catecholamines, including dopamine. This transporter is not expressed in two spontaneously occurring flat cell variants of PC12 or in two other flat cell variants whose phenotype was induced by expression of the Wnt-1 oncogene. However, each of the flat cell variants, including those that express Wnt-1, exhibit a Na(+)-dependent, Cl(-)-independent glutamate/aspartate transporter activity that is not present in wild type PC12 cells. The flat cell variants took up glycine by a Na(+)-dependent process as well as did wild type cells. All of the flat cell variants have decreased levels of norepinephrine transporter mRNA but normal levels of glycine transporter mRNA. Glutamate/aspartate transporter mRNA was detected only in the variants that exhibited glutamate/aspartate transporter activity, and the nucleotide sequence of a partial glutamate/aspartate transporter cDNA from these cells demonstrated that it was the glial form of the transporter that was expressed. These variants were more sensitive than was wild type PC12 to alanosine, a toxic aspartate analog that enters cells by a transporter-mediated system such as the glutamate/aspartate transporter; however, these variants were as sensitive as wild type cells to another toxic aspartate analog, N-(phosphonacetyl)-L-aspartic acid, which is believed to enter cells by endocytosis. We suggest that the Wnt-1 gene product, or a homolog, may be involved in glial differentiation and that the mechanisms that alter the expression of the norepinephrine and glutamate/aspartate transporters in wild type and variant PC12 cells may also operate to regulate neurotransmitter transporter expression in vivo.

Alanine↗

Germ-cell deficient (gcd), an insertional mutation manifested as infertility in transgenic mice.

A genetic analysis is necessary to gain a greater understanding of the complex developmental processes in mammals. Toward this end, an insertional transgenic mouse mutant has been isolated that results in abnormal germ-cell development. This recessive mutation manifests as infertility in both males and females and is specific for the reproductive organs, since all other tissues examined were histologically normal. A developmental analysis of the gonadal tissues demonstrated that the germ cells were specifically depleted as early as day 11.5 of embryonic development, while the various somatic cells were apparently unaffected. Therefore, the mutated locus must play a critical role in the migration/proliferation of primordial germ cells to the genital ridges of developing embryos. In addition, females homozygous for the mutation could potentially be a valuable animal model of a human syndrome, premature ovarian failure. This mutation has been named germ-cell deficient, gcd.

Animals↗