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V Ramakrishnan

Publications and source records attributed to V Ramakrishnan.

At least 145 records · Page 8Linked to original sources
PubMed1996

Univariate analysis of dichotomous or ordinal data from twin pairs: a simulation study comparing structural equation modeling and logistic regression.

The univariate analysis of categorical twin data can be performed using either structural equation modeling (SEM) or logistic regression. This paper presents a comparison between these two methods using a simulation study. Dichotomous and ordinal (three category) twin data are simulated under two different sample sizes (1,000 and 2,000 twin pairs) and according to different additive genetic and common environmental models of phenotypic variation. The two methods are found to be generally comparable in their ability to detect a "correct" model under the specifications of the simulation. Both methods lack power to detect the right model for dichotomous data when the additive genetic effect is low (between 10 and 20%) or medium (between 30 and 40%); the ordinal data simulations produce similar results except for the additive genetic model with medium or high heritability. Neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large and the sample size included 2,000 twin pairs. The SEM method was found to have better power than logistic regression when there is a medium (30%) or high (50%) additive genetic effect and a modest common environmental effect. Conversely, logistic regression performed better than SEM in correctly detecting additive genetic effects with simulated ordinal data (for both 1,000 and 2,000 pairs) that did not contain modest common environmental effects; in this case the SEM method incorrectly detected a common environmental effect that was not present.

Analysis of Variance↗
PubMed1996

Neutron scattering studies on chromatin higher-order structure.

We have been engaged in studies of the structure and condensation of chromatin into the 30 nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30 nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.

Animals↗
PubMed1996

Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S.

sigma S is an alternate sigma factor which functions with RNA polymerase to activate transcription of genes that are involved in a number of stress responses, including stationary-phase survival and osmoprotection. The similarity of the sigma S protein to sigma D (Escherichia coli's major sigma factor) in the regions thought to recognize and bind promoter sequences suggests that sigma S- and sigma D-associated RNA polymerases recognize promoter DNA in a similar manner. However, no promoter recognition sequence for sigma S holoenzyme (E sigma S) has been identified. An apparent conservation of cytosine nucleotides was noted in the -35 region of several sigma S-dependent promoters. Site-directed mutagenesis and reporter gene fusions were used to investigate the importance of the -35 cytosine nucleotides for sigma S-dependent transcription. Substitution of cytosine nucleotides for thymidine at the -35 site of the sigma D-dependent proU promoter effectively abolished transcription by E sigma D but allowed E sigma S to direct transcription from the mutant promoter. Inclusion of the sigma D consensus -10 hexamer strengthened transcription by E sigma S, demonstrating that both E sigma D and E sigma S can recognize the same -10 sequences. Conversely, replacement of -35 site cytosine nucleotides with thymidine in the sigma S-dependent osmY promoter reduced transcription by E sigma S and increased transcription by E sigma D. Our data suggest that DNA sequences in the -35 region function as part of a discriminator mechanism to shift transcription between E sigma D and E sigma S.

Amino Acid Transport Systems↗
PubMed1996

High-level expression and deuteration of sperm whale myoglobin. A study of its solvent structure by X-ray and neutron diffraction methods.

Neutron diffraction has become one of the best ways to study light atoms, such as hydrogens. Hydrogen however has a negative coherent scattering factor, and a large incoherent scattering factor, while deuterium has virtually no incoherent scattering, but a large positive coherent scattering factor. Beside causing high background due to its incoherent scattering, the negative coherent scattering of hydrogen tends to cancel out the positive contribution from other atoms in a neutron density map. Therefore a fully deuterated sample will yield better diffraction data with stronger density in the hydrogen position. On this basis, a sperm whale myoglobin gene modified to include part of the A c11 protein gene has been cloned into the T7 expression system. Milligram amounts of fully deuterated holo-myoglobin have been obtained and used for crystallization. The synthetic sperm whale myoglobin crystallized in P2(1) space group isomorphous with the native protein crystal. A complete X-ray diffraction dataset at 1.5A has been collected. This X-ray dataset, and a neutron data set collected previously on a protonated carbon-monoxymyoglobin crystal have been used for solvent structure studies. Both X-ray and neutron data have shown that there are ordered hydration layers around the protein surface. Solvent shell analysis on the neutron data further has shown that the first hydration layer behaves differently around polar and apolar regions of the protein surface. Finally, the structure of per-deuterated myoglobin has been refined using all reflections to a R factor of 17%.

Animals↗
PubMed1995

X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix.

The structures of the two domains of translational initiation factor IF3 from Bacillus stearothermophilus have been solved by X-ray crystallography using single wavelength anomalous scattering and multiwavelength anomalous diffraction. Each of the two domains has an alpha/beta topology, with an exposed beta-sheet that is reminiscent of several ribosomal and other RNA binding proteins. An alpha-helix that protrudes out from the body of the N-terminal domain towards the C-terminal domain suggests that IF3 consists of two RNA binding domains connected by an alpha-helix and that it may bridge two regions of the ribosome. This represents the first high resolution structural information on a translational initiation factor.

Amino Acid Sequence↗
PubMed1995

Prokaryotic translation initiation factor IF3 is an elongated protein consisting of two crystallizable domains.

We show that translation initiation factor IF3 can be split into two fragments of nearly equal size by the Escherichia coli outer membrane protease omptin. Circular dichroism and small-angle neutron scattering show that the two fragments are structured as domains. Each domain is relatively compact, and they are separated by about 45 A in intact IF3. Thus IF3 is an elongated protein that consists of two well-separated domains. We suggest that these two domains are involved in ribosome binding across the cleft of the 30S ribosome. We also report the crystallization of each domain of IF3.

Circular Dichroism↗
PubMed1995

Blood flow in colon anastomotic stricture formation.

PURPOSE: The influence of both blood flow and anastomotic technique on the development of anastomotic stricture formation was studied using a dog model. METHODS: Fifty-three dogs underwent distal colocolonic anastomosis with either an EEA (U.S. Surgical Corp., Norwalk, CT) circular stapler or a Czerny-Lembert two-layered, handsewn anastomosis. Blood flow was measured by Laser Doppler Velocimetry using the Laserflo BPM2 (Vasamedics Inc., St. Paul, MN). The animals were separated into three blood flow groups: greater than or equal to 62.5 percent of normal blood flow, between 37.5 percent and 62.5 percent of normal blood flow, and less than or equal to 37.5 percent of normal blood flow. Each blood flow group had an anastomosis performed by either stapling or by hand sewing techniques. At six weeks, the anastomoses were opened longitudinally and fixed to determine the anastomotic index (AI). AI is defined as two times the anastomotic circumference over the proximal circumference plus the distal circumference. Blood flow groups and anastomotic technique groups were compared with an interaction variable for the outcome, AI using a two-way analysis of variance. RESULTS: The AI of the stapled anastomoses was found to be significantly higher than handsewn anastomoses (P < 0.006). There was no difference in AI between different blood flow groups and no correlation of observed histologic findings with AI. CONCLUSION: Clinically relevant ischemia does not directly influence stricture formation in either handsewn or stapled distal colonic anastomoses.

Analysis of Variance↗
PubMed1995

Positive association between dietetics recommendations and achievement of enteral nutrition outcomes of care.

OBJECTIVE: To identify planned dietetics outcomes of care, dietitians activities performed an recommendations made, and outcome achievement and its relationship to recommendations followed. DESIGN: A multisite, single-group prospective pilot study was conducted to describe the care provided by dietitians to patients receiving enteral nutrition care. SUBJECTS/SETTING: Participants were 172 patients (16 of whom died during hospitalization) receiving at least 75% of nutrient requirements from enteral nutrition products. Subjects were from six acute-care facilities and one rehabilitation facility in the Chicago metropolitan area. MAIN OUTCOME MEASURES: Dietitians identified planned outcomes of care to be accomplished and documented activities performed during the provision of care. Data were collected to measure outcome achievement and to determine whether dietitians' recommendations were followed. STATISTICAL ANALYSES PERFORMED: Descriptive data are reported as frequencies or means +/- standard error. Odds ratios were constructed to estimate the association between dietitians' enteral care recommendations and the achievement of planned outcomes of care. RESULTS: Whether or not enteral nutrition outcomes of care were achieved was positively associated with dietitians' recommendations. The odds of patients' achieving the recommended energy intake goal (P < .001) or increasing (P < .01) or maintaining (P < .04) visceral protein stores were at least four times greater when dietitians' recommendations were followed than when they were not. In addition, dietetics activities performed at the local level were similar to established practices. APPLICATIONS: Dietitians can identify and measure outcomes of dietetics-related care that demonstrate positive contributions to the interdisciplinary enteral nutrition care process.

Dietary Services↗
PubMed1995

Correlates of physicians' decisions to refer children with cerebral palsy for physical therapy.

Videotapes of ten children with 'suspected' cerebral palsy were used as stimuli to elicit physicians' decisions regarding referral for physical therapy. Respondents were 99 developmental or general pediatricians, orthopaedists, neurologists or physiatrists who were members of the American Academy of Pediatrics or the American Academy of Cerebral Palsy. They rated their belief in the value of therapy; described their experience, training and practices relating to management of cerebral palsy; and responded to cases with their assessment of severity, diagnosis and referral decision. The decision to refer was significantly related to perceived severity of the condition, diagnostic certainty, and belief in the efficacy of physical therapy. Referral rates did not vary with tendency to use physical therapy for other types of patients, nor with training, experience or self-rated expertise in cerebral palsy.

Cerebral Palsy↗
PubMed1994

Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5.

The globular domain of chicken histone H1 (GH1) has been studied by 1H homonuclear and 1H-15N heteronuclear 2D NMR spectroscopy. After the full assignment of the proton and 15N resonances, the tertiary structure of GH1 was determined by an iterative procedure using distance geometry and restrained simulated annealing. The secondary structure elements of GH1, three helices (S5-A16, S24-A34, N42-K56) followed by a beta-hairpin (L59-L73), are folded in a manner very similar to the corresponding parts of the globular domain of chicken histone H5 (GH5) [Clore et al. (1987) EMBO J. 6, 1833-1842; Ramakrishnan et al. (1993) Nature 362, 219-223]. However, subtle differences are detected between the two structures and between the electrostatic potentials surrounding the molecules. The most important differences are located in the loop between the second and third helices, a region that could be responsible for the different affinity for DNA. The most positively charged regions are not found in exactly the same position in GH1 and GH5. Nevertheless, their location seems to agree with the model where nucleosome binding takes place through contact points located at one DNA terminus and close to the dyad axis of the nucleosome [Schwabe & Travers (1993) Curr. Biol. 3, 628-630].

Amino Acid Sequence↗
PubMed1994

Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14.

Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins. To verify this, the gene for Bacillus stearothermophilus L14 has been cloned, and the protein has been purified and crystallized. The crystals are in space group C2 with cell dimensions a = 67.0, b = 32.7, c = 49.4 A, and beta = 101.8 degrees, and there is one molecule in the asymmetric unit (V(m) = 2.0 A(3) Da(-1)). They are of high quality, and a native data set has been collected to a resolution of 1.6 A, with an R(merge) of 5.3%.

Journal Article↗
PubMed1994

Histone H1 is located in the interior of the chromatin 30-nm filament.

The linker histone H1 binds to the nucleosome and is essential for the organization of nucleosomes into the 30-nm filament of chromatin. It has been implicated in the repression of transcription, and phosphorylation of H1 may be involved in cell-cycle-dependent chromatin condensation and decondensation. A long-standing issue concerns the location of H1 in the chromatin filament. The original solenoidal model proposes that H1 is inside the 30-nm filament, but other models, also helical, suggest a variable or more accessible location for H1. Investigations to determine the location of the linker histone based on its accessibility to antibodies or immobilized proteases under various ionic conditions have yielded conflicting results. Here we use neutron scattering in a direct structural determination to show that H1 is located in the interior of the filament.

Chromatin↗
PubMed1994

Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein.

The crystal structure of protein L9 from the Bacillus stearothermophilus ribosome has been determined at 2.8 A resolution using X-ray diffraction methods. This primary RNA-binding protein has a highly elongated and unusual structure consisting of two separated domains joined by a long exposed alpha-helix. Conserved, positively charged and aromatic amino acids on the surfaces of both domains probably represent the sites of specific interactions with 23S rRNA. Comparisons with other prokaryotic L9 sequences show that while the length of the connecting alpha-helix is invariant, the sequence within the exposed central region is not conserved. This suggests that the alpha-helix has an architectural role and serves to fix the relative separation and orientation of the N- and C-terminal domains within the ribosome. The N-terminal domain has structural homology to the smaller ribosomal proteins L7/L12 and L30, and the eukaryotic RNA recognition motif (RRM).

Amino Acid Sequence↗
PubMed1994

Expression of chicken linker histones in E. coli: sources of problems and methods for overcoming some of the difficulties.

Expression of histones in Escherichia coli is important in structural studies on chromatin, because it allows isotopic labeling such as deuteration and replacement of methionines with selenomethionine as well as expression of specific domains of histones. We show that full-length H5 cannot be expressed in E. coli. We have determined that the problem is translational rather than transcriptional. Pulse-labeling studies show that protein turnover is not the reason for lack of accumulation. On dissecting the gene, we find that the problem lies in expressing the highly charged C-terminal tail of H5. We can make progressively increasing amounts of the tail, but at the point where over two-thirds of this region is transcribed, the protein ceases to be made. Surprisingly, full-length H1 is made. In vitro studies show that the H5 gene can be translated in a rabbit reticulocyte system but not in an E. coli system, suggesting that there may be a difference in the ability of eukaryotic and prokaryotic ribosomes to translate this message. The expression of the globular domains of H5 and H1 posed a different problem. There was little or no expression of some of the constructs, even though they were fragments of larger constructs that were well made. Replacement of the first five codons downstream of the initiating ATG codon with those optimized for E. coli, and which were AT rich, restored expression. This may have general implications for expression of eukaryotic proteins in E. coli.

Amino Acid Sequence↗
PubMed1994

Ultrasonographic detection of abnormal fetal growth with the gestational age-independent, transverse cerebellar diameter/abdominal circumference ratio.

OBJECTIVES: We prospectively evaluated the accuracy of a gestational age-independent method of detecting abnormal growth, the transverse cerebellar diameter/abdominal circumference ratio, and compared this with standard ultrasonographic methods of growth assessment. STUDY DESIGN: We prospectively studied 825 low-risk obstetric patients and 250 patients having risk factors for fetal macrosomia (n = 92) or growth retardation (n = 158). Measured fetal parameters included the biparietal diameter, head circumference, transverse cerebellar diameter, abdominal circumference, and femur length. The estimated fetal weight, head circumference/abdominal circumference, cerebellar diameter/abdominal circumference, and femur length/abdominal circumference ratios were calculated. Reference curves for these parameters were created from a cross-sectional analysis of the low-risk group. Univariate analysis was used to determine the sensitivity, specificity, predictive values, and odds ratios of each individual parameter in identifying a small- or large-for-gestational-age infant. A multivariate logistic regression model with a variable selection procedure was then used to determine whether significance remained when we controlled for other parameters. RESULTS: Within the low-risk group, the transverse cerebellar/abdominal circumference ratio was gestational age independent between 14 and 42 weeks with a mean of 13.68 +/- 0.96. A value exceeding 2 SD of the mean was significantly associated with birth or a small-for-gestational-age infant, being abnormal in 98% and 71% of asymmetrically and symmetrically growth-retarded infants, respectively. Significance was maintained in the multivariate regression model. The ratio was not helpful in detecting the large-for-gestational-age infant. CONCLUSION: The fetal transverse cerebellar diameter/abdominal circumference ratio is an accurate, gestational age-independent method of identifying the small-for-gestational-age but not the large-for-gestational-age infant.

Abdomen↗