Biomedical subjects

Charles C Berry

Publications and source records attributed to Charles C Berry.

At least 19 recordsLinked to original sources

PubMed2006

Retroviral DNA integration: viral and cellular determinants of target-site selection.

Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I-hypersensitive sites (i.e., +/- 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.

Attachment Sites, Microbiological↗

PubMed2006

Identification of genes whose expression is associated with cisplatin resistance in human ovarian carcinoma cells.

The goal of this study was to identify genes consistently differentially expressed in multiple pairs of isogenic cisplatin (DDP)-sensitive and resistant human ovarian carcinoma cell lines using microarray-based expression profiling. Expression profiling was carried out on six pairs of ovarian carcinoma cells lines growing under identical conditions; each cell expression profile was independently replicated six times. No genes were differentially expressed in all six pairs of cells or even in even in any five of the six pairs. Eighteen genes and 1 EST were upregulated, and four genes and 1 EST were downregulated, in at least four cell pairs. Of these, only metallothionein 2A has previously been implicated in DDP resistance. Among the genes identified on the basis of six replicates, an average of 24.8% would have been missed if only five replicates had been performed, and 38.3% would have been missed with only four replicates. The genes did not identify a dominant biochemical pathway or ontology category as being linked to DDP resistance; however, hierarchical clustering provided evidence for two classes DDP-resistant phenotypes within which there are additional cell pair-specific alterations. Many of the genes identified in this study play important roles in cell surface interactions and trafficking pathways not previously linked to DDP resistance. The genes discovered by this extensively replicated analysis are candidates for prediction of DDP responsiveness in ovarian cancer patients.

Antineoplastic Agents↗

PubMed2006

Assessing the trade-offs between crossover and parallel group designs in sleep research.

Sleep researchers invariably struggle with decisions regarding the optimal design for their studies. Whether such studies involve treatment for insomnia, obstructive sleep apnea, or any other sleep disorder, questions arise regarding the respective trade-offs between a parallel group and a crossover design. This study analyzed the variance structure of commonly measured polysomnographic variables in an effort to describe the statistical impact of these alternate designs. The study examined the effects of opioids on sleep and employed multiple crossovers between placebo, MS-contin, and methadone using a double-blind, randomized crossover design. Thirty-seven healthy subjects were studied. Four of the subjects were unable to complete the protocol for a variety of reasons, and polysomnogram data was unavailable for one subject. Data from 37 subjects provide the basis for this analysis. Despite dropouts, the crossover study was approximately four times as efficient as the parallel group design in terms of being able to recognize differences in deep sleep across these conditions. Other polysomnographic variables also favored the crossover design to varying extents. Despite the operational complexity of a crossover design, the statistical efficiency of this approach makes it a preferable approach for designing intervention studies in sleep research.

Adult↗

PubMed2005

Baseline topographic optic disc measurements are associated with the development of primary open-angle glaucoma: the Confocal Scanning Laser Ophthalmoscopy Ancillary Study to the Ocular Hypertension Treatment Study.

OBJECTIVE: To determine whether baseline confocal scanning laser ophthalmoscopy (CSLO) optic disc topographic measurements are associated with the development of primary open-angle glaucoma (POAG) in individuals with ocular hypertension. METHODS: Eight hundred sixty-five eyes from 438 participants in the CSLO Ancillary Study to the Ocular Hypertension Treatment Study with good-quality baseline CSLO images were included in this study. Each baseline CSLO parameter was assessed in univariate and multivariate proportional hazards models to determine its association with the development of POAG. RESULTS: Forty-one eyes from 36 CSLO Ancillary Study participants developed POAG. Several baseline topographic optic disc measurements were significantly associated with the development of POAG in both univariate and multivariate analyses, including larger cup-disc area ratio, mean cup depth, mean height contour, cup volume, reference plane height, and smaller rim area, rim area to disc area, and rim volume. In addition, classification as "outside normal limits" by the Heidelberg Retina Tomograph classification and the Moorfields Regression Analysis classifications (overall, global, temporal inferior, nasal inferior, and superior temporal regions) was significantly associated with the development of POAG. Within the follow-up period of this analysis, the positive predictive value of CSLO indexes ranged from 14% (Heidelberg Retina Tomograph classification and Moorfields Regression Analysis overall classification) to 40% for Moorfields Regression Analysis temporal superior classification. CONCLUSIONS: Several baseline topographic optic disc measurements alone or when combined with baseline clinical and demographic factors were significantly associated with the development of POAG among Ocular Hypertension Treatment Study participants. Longer follow-up is required to evaluate the true predictive accuracy of CSLO measures.

False Positive Reactions↗

PubMed2004

cDNA microarray-based identification of genes and pathways associated with oxaliplatin resistance.

In order to identify genes whose expression is associated with resistance to the chemotherapeutic agent oxaliplatin, transcripts differentially expressed between an oxaliplatin sensitive and a stably resistant subline were compared in six independent replicates using Stanford cDNA microarrays for five cell lines. "Significance analysis of microarrays" (SAM) was used to identify genes whose expression was statistically significantly different in the sensitive versus resistant members of each cell line pair. The biochemical pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were searched to identify those pathways in which the number of SAM-identified genes exceeded the number expected. This identified four pathways in which upregulated genes were significantly associated with resistance in two of the cell line pairs, and two pathways in which the association was found in three cell line pairs. The search also identified 12 pathways in which downregulated genes were associated with resistance in two cell line pairs and one pathway in which the association reached statistical significance in three cell line pairs. Pathways identified included the ribosome pathway, the Huntington's disease pathway that includes caspase 8, and the ATP synthesis pathways. Determination of the chromosomal location of each SAM-identified gene revealed several locales within which genes lay in close proximity, including three genes (APACD, IF-2, and REV1L) located on chromosome 2 that lie immediately adjacent to each other and were significantly upregulated in three of five cell line pairs. Biochemical pathway and chromosomal mapping of genes identified by SAM as differentially expressed in related cell line pairs points to mechanisms and chromosomal sites not previously suspected of association with the oxaliplatin-resistant phenotype.

Adenosine Triphosphate↗

PubMed2004

Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.

The completion of the human genome sequence has made possible genome-wide studies of retroviral DNA integration. Here we report an analysis of 3,127 integration site sequences from human cells. We compared retroviral vectors derived from human immunodeficiency virus (HIV), avian sarcoma-leukosis virus (ASLV), and murine leukemia virus (MLV). Effects of gene activity on integration targeting were assessed by transcriptional profiling of infected cells. Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection.

Avian Sarcoma Viruses↗

PubMed2004

In silico dissection of cell-type-associated patterns of gene expression in prostate cancer.

Prostate tumors are complex entities composed of malignant cells mixed and interacting with nonmalignant cells. However, molecular analyses by standard gene expression profiling are limited because spatial information and nontumor cell types are lost in sample preparation. We scored 88 prostate specimens for relative content of tumor, benign hyperplastic epithelium, stroma, and dilated cystic glands. The proportions of these cell types were then linked in silico to gene expression levels determined by microarray analysis, revealing unique cell-specific profiles. Gene expression differences for malignant and nonmalignant epithelial cells (tumor versus benign hyperplastic epithelium) could be identified without being confounded by contributions from stroma that dominate many samples or sacrificing possible paracrine influences. Cell-specific expression of selected genes was validated by immunohistochemistry and quantitative PCR. The results provide patterns of gene expression for these three lineages with relevance to pathogenetic, diagnostic, and therapeutic considerations.

Gene Expression Profiling↗

PubMed2004

Racial differences in optic disc topography: baseline results from the confocal scanning laser ophthalmoscopy ancillary study to the ocular hypertension treatment study.

OBJECTIVE: To examine racial differences in optic disc topography among ocular hypertensive participants in the Ocular Hypertension Treatment Study. METHODS: Four hundred thirty-nine participants from 7 Ocular Hypertension Treatment Study centers who had good-quality baseline images obtained using a quantitative 3-dimensional confocal scanning laser ophthalmoscope, the Heidelberg Retina Tomograph (Heidelberg Engineering, Dossenheim, Germany), were included in this study. The first 10 degrees- or 15 degrees-field of view mean topographic image acquired was included in all analyses. Differences in Heidelberg Retina Tomograph topographic optic disc parameter measurements by self-identified race were assessed using a mixed-effects linear model to control for confounders and for the use of both eyes in the model. RESULTS: By self-attribution, 74 (17%) of the 439 participants were of African origin, 329 (75%) were white, 24 (5%) were Hispanic, and 12 (3%) were Native American, Native Alaskan, Asian, Pacific Islander, or unknown. The African American participants had statistically significantly (P<.001) larger mean (SD) optic disc areas than the other participants, 2.17 (0.41) mm(2) vs 1.87 (0.38) mm(2), respectively. African American participants had a larger cup area, cup volume, cup depth, neuroretinal rim area, rim volume, and smaller rim-optic disc area ratios than the other participants. No difference between African American and the other participants was found for cup shape and retinal nerve fiber layer thickness. After controlling for optic disc area, none of the differences between African American and the other participants found in the univariate analysis remained statistically significant (P>.10). CONCLUSIONS: This study demonstrated in a large cohort of subjects with ocular hypertension, that African Americans have significantly larger optic discs, optic cups, neuroretinal rims, and cup-disc ratios than other racial groups. Furthermore, this study found that differences in topographic optic disc parameters between African Americans with ocular hypertension and other racial groups are largely explained by the larger optic disc area in the African Americans. These results highlight the need to consider race and optic disc size when evaluating the appearance of the optic disc in glaucoma.

Antihypertensive Agents↗

PubMed2004

The confocal scanning laser ophthalmoscopy ancillary study to the ocular hypertension treatment study: study design and baseline factors.

PURPOSE: To describe the study design of the Confocal Scanning Laser Ophthalmoscopy (CSLO) Ancillary Study to the Ocular Hypertension Treatment Study (OHTS) and to examine the associations between optic disk topography, and baseline demographic, clinical, and ocular factors at study entry. DESIGN: A randomized clinical trial. METHODS: Participants in this ancillary study were recruited from seven of the 22 OHTS clinical centers. Each participant completed imaging annually using a CSLO, the Heidelberg Retina Tomograph (HRT). Associations between HRT topographic optic disk measurements and intraocular pressure (IOP), baseline photographic estimates of horizontal and vertical cup-to-disk diameter ratios by the OHTS Optic Disk Reading Center, baseline visual field indices, and demographic and clinical factors were assessed using linear mixed effects models. RESULTS: Four hundred thirty-nine participants had good quality images and were included in this baseline analysis. No associations between HRT topographic optic disk measurements and diabetes, systemic hypertension, cardiovascular disease, IOP, or visual function were found. The HRT topographic optic disk measurements were associated with baseline stereophotographic estimates of horizontal and vertical cup-to-disk diameter ratios. The strongest associations were found between stereophotographic assessment of horizontal and vertical cup-to-disk diameter ratios, and HRT cup-to-disk area ratio (r =.85 and.84, respectively), rim-to-disk area ratio (r = -.85 and -.84, respectively), mean cup depth (r =.84 and.83, respectively), and cup area (r =.83 and.80, respectively). After adjusting for optic disk area, all HRT topographic optic disk measurements remained associated with stereophotographic assessment of horizontal and vertical cup-to-disk diameter ratios. CONCLUSIONS: The CSLO ancillary study to the OHTS is the first multicenter clinical trial to use CSLO imaging to monitor changes in the optic disk. At study entry, HRT topographic measurements corresponded well with both horizontal and vertical stereophotographic-based estimates of cup-to-disk diameter ratio in ocular hypertensive participants.

Female↗

PubMed2004

Automatic tracking, feature extraction and classification of C elegans phenotypes.

This paper presents a method for automatic tracking of the head, tail, and entire body movement of the nematode Caenorhabditis elegans (C. elegans) using computer vision and digital image analysis techniques. The characteristics of the worm's movement, posture and texture information were extracted from a 5-min image sequence. A Random Forests classifier was then used to identify the worm type, and the features that best describe the data. A total of 1597 individual worm video sequences, representing wild type and 15 different mutant types, were analyzed. The average correct classification ratio, measured by out-of-bag (OOB) error rate, was 90.9%. The features that have most discrimination ability were also studied. The algorithm developed will be an essential part of a completely automated C. elegans tracking and identification system.

Algorithms↗

PubMed2004

Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana.

Genetic analysis of natural variation in ecotypes of Arabidopsis thaliana can facilitate the discovery of new genes or of allelic variants of previously identified genes controlling physiological processes in plants. We mapped quantitative trait loci (QTL) for light response in recombinant inbred lines (RILs) derived from the Columbia and Kashmir accessions via two methods: composite interval mapping and eXtreme array mapping (XAM). After measuring seedling hypocotyl lengths in blue, red, far-red, and white light, and in darkness, eight QTL were identified by composite interval mapping and five localized near photoreceptor loci. Two QTL in blue light were associated with CRY1 and CRY2, two in red light were near PHYB and PHYC, and one in far-red light localized near PHYA. The RED2 and RED5 QTL were verified in segregating lines. XAM was tested for the identification of QTL in red light with pools of RILs selected for extreme phenotypes. Thousands of single feature polymorphisms detected by differential DNA hybridized to high-density oligo-nucleotide arrays were used to estimate allele frequency differences between the pools. The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simulations. The sensitivities of XAM to population type and size and genetic models were also determined by simulation analysis.

Arabidopsis↗

PubMed2003

Genome-wide insertional mutagenesis of Arabidopsis thaliana.

Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.

3' Untranslated Regions↗

PubMed2003

Evaluating several sources of variability for standard and SWAP visual fields in glaucoma patients, suspects, and normals.

PURPOSE: To quantify factors affecting test-retest variability of threshold measurements over a series of 3 serial visual fields (VF). DESIGN: Prospective comparative observational study. PARTICIPANTS: Forty-one normals, 10 suspects and 35 stable glaucoma patients. METHODS: All subjects performed 3 standard and 3 short-wavelength automated perimetry (SWAP) VFs. At each VF location, severity (defined as age-corrected total deviation) and test-retest variability (TRV), defined as the standard deviation of 3 serial threshold values, were calculated. A multiple regression model (constructed separately for standard VF and SWAP) incorporated 13 factors: severity, location, eccentricity, study group, diagnosis, superior versus inferior hemifield, nasal versus temporal hemifield, one-versus-two thresholds, age, mean pupil size, pupil size variability, between-subject variation, and residual variation. MAIN OUTCOME MEASURES: Variability in threshold sensitivity VF values. RESULTS: Mean TRV (+/- standard deviation) for normal, suspect and glaucoma eyes, respectively, was: 1.28 +/- 0.87, 1.53 +/- 1.04 and 2.20 +/- 1.79 dB for standard VF, and 1.87 +/- 1.35, 1.86 +/- 1.24 and 2.68 +/- 1.85 dB for SWAP. The contribution of each factor to the model for standard VF and SWAP (SWAP in parentheses) were: severity 15.5% (6.9%); location 2.7% (4.1%); eccentricity 1.1% (0.64%); diagnosis 2.9% (5.9%); "superior versus inferior" hemifield 0.17% (1.7%); "nasal versus temporal" hemifield 0.06% (0.02%); one-versus-two thresholds 0.04% (0.16%); age 0.1% (0.06%); mean pupil size 0.59% (0.1%); pupil size variability 3.2% (2.8%); between-subject 8.0% (13.5%) and residual variation 61.0% (66.6%). Excluding between-subject and residual variation, the 11-factor model was able to account for less than one third of the variability seen in both standard VF and SWAP. CONCLUSIONS: Severity of defect and between subject variation exerted the largest effect on TRV. However, even if all 11 factors could be adjusted for, it would reduce the magnitude of TRV by only 30%. More work is needed to reduce the remaining variability inherent in psychophysical testing and to better understand the intrinsic physiological variability present both in healthy and diseased eyes. It is possible that a larger number of VFs used for the calculation of TRV might further reduce the magnitude of the remaining variability found in this study.

Adult↗

PubMed2003

Immune cell CD62L and CD11a expression in response to a psychological stressor in human hypertension.

This study examined the effects of hypertension and an acute psychological stressor on white blood cells and their expression of CD62L and CD11a. Seventeen mild hypertensive and 23 normotensive volunteers were studied prior to and following a standardized laboratory public speech. In response to the speech, all subjects increased the number of circulating leukocyte populations (p's<.01). Patients with hypertension increased the number of circulating white blood cells more than normotensives (p<.01). Hypertensives also showed a greater increase in the number of circulating CD3(+)CD8(+) T cells (p<.02) in response to the speech. Only hypertensives increased the number of circulating CD8(+)CD62L(high) T cells (p=.001). The density of CD11a on lymphocytes was increased in all subjects following the speech (p<.001). Hypertensives showed a greater mean density of CD11a on lymphocytes (p<.01). Coupled with observations of increased expression of the endothelial CD11a ligand ICAM-1 in hypertension, these findings are consistent with the notion that patients with hypertension exhibit a circulatory environment conducive to increased leukocyte adhesion. Exposure to repeated psychological stressors may further augment this potentially adverse circulatory environment.

Adaptation, Physiological↗

PubMed2003

Quantitative classification and natural clustering of Caenorhabditis elegans behavioral phenotypes.

Genetic analysis of nervous system function relies on the rigorous description of behavioral phenotypes. However, standard methods for classifying the behavioral patterns of mutant Caenorhabditis elegans rely on human observation and are therefore subjective and imprecise. Here we describe the application of machine learning to quantitatively define and classify the behavioral patterns of C. elegans nervous system mutants. We have used an automated tracking and image processing system to obtain measurements of a wide range of morphological and behavioral features from recordings of representative mutant types. Using principal component analysis, we represented the behavioral patterns of eight mutant types as data clouds distributed in multidimensional feature space. Cluster analysis using the k-means algorithm made it possible to quantitatively assess the relative similarities between different behavioral phenotypes and to identify natural phenotypic clusters among the data. Since the patterns of phenotypic similarity identified in this study closely paralleled the functional similarities of the mutant gene products, the complex phenotypic signatures obtained from these image data appeared to represent an effective diagnostic of the mutants' underlying molecular defects.

Animals↗

PubMed2003

Hormone replacement therapy does not affect 24-h ambulatory blood pressure in healthy non-smoking postmenopausal women.

OBJECTIVE: Controversies surrounding the physiological effects of hormone replacement therapy (HRT) currently lie at the forefront of medicine. Important interindividual factors that affect blood pressure, such as smoking, body mass and sodium intake, may account for the conflicting findings seen in studies examining the effects of HRT on blood pressure. DESIGN: The study was a randomized, double-blind, placebo-controlled trial. METHODS: The effect of combination HRT and estrogen-only replacement therapy (ERT) on ambulatory blood pressure was examined in a sample of 46 healthy, normotensive, non-smoking, non-obese postmenopausal women between 45 and 65 years of age. Twenty-four hour urinary sodium excretion was examined prior to and following treatment. The women were randomized to 3 months' treatment with HRT, ERT or placebo. RESULTS: After treatment, there were no significant effects of either HRT or ERT on daytime or night-time systolic or diastolic blood pressure. Sodium excretion was similar across the groups. There were no effects of treatment on night-time blood pressure dipping. CONCLUSIONS: The findings from this prospective treatment study support the conclusion that HRT has no significant effect on daytime or night-time blood pressure in a sample of healthy, non-smoking postmenopausal women.

Aged↗

PubMed2003

Large-scale identification of single-feature polymorphisms in complex genomes.

We have developed a high-throughput genotyping platform by hybridizing genomic DNA from Arabidopsis thaliana accessions to an RNA expression GeneChip (AtGenome1). Using newly developed analytical tools, a large number of single-feature polymorphisms (SFPs) were identified. A comparison of two accessions, the reference strain Columbia (Col) and the strain Landsberg erecta (Ler), identified nearly 4000 SFPs, which could be reliably scored at a 5% error rate. Ler sequence was used to confirm 117 of 121 SFPs and to determine the sensitivity of array hybridization. Features containing sequence repeats, as well as those from high copy genes, showed greater polymorphism rates. A linear clustering algorithm was developed to identify clusters of SFPs representing potential deletions in 111 genes at a 5% false discovery rate (FDR). Among the potential deletions were transposons, disease resistance genes, and genes involved in secondary metabolism. The applicability of this technique was demonstrated by genotyping a recombinant inbred line. Recombination break points could be clearly defined, and in one case delimited to an interval of 29 kb. We further demonstrate that array hybridization can be combined with bulk segregant analysis to quickly map mutations. The extension of these tools to organisms with complex genomes, such as Arabidopsis, will greatly increase our ability to map and clone quantitative trait loci (QTL).

Arabidopsis↗

PubMed2003

Estimation of spontaneous mutation rates.

Spontaneous or randomly occurring mutations play a key role in cancer progression. Estimation of the mutation rate of cancer cells can provide useful information about the disease. To ascertain these mutation rates, we need mathematical models that describe the distribution of mutant cells. In this investigation, we develop a discrete time stochastic model for a mutational birth process. We assume that mutations occur concurrently with mitosis so that when a nonmutant parent cell splits into two progeny, one of these daughter cells could carry a mutation. We propose an estimator for the mutation rate and investigate its statistical properties via theory and simulations. A salient feature of this estimator is the ease with which it can be computed. The methods developed herein are applied to a human colorectal cancer cell line and compared to existing continuous time models.

Biometry↗