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Biomedical subjects

J L Oliver

Publications and source records attributed to J L Oliver.

At least 19 recordsLinked to original sources
PubMed2002

Study of statistical correlations in DNA sequences.

Here we present a study of statistical correlations among different positions in DNA sequences and their implications by directly using the autocorrelation function. Such an analysis is possible now because of the availability of large sequences or even complete genomes of many organisms. After describing the way in which the autocorrelation function can be applied to DNA-sequence analysis, we show that long-range correlations, implying scale independence, appear in several bacterial genomes as well as in long human chromosome contigs. The source for such correlations in bacteria, which may extend up to 60 kb in Bacillus subtilis, may be related to massive lateral transfer of compositionally biased genes from other genomes. In the human genome, correlations extend for more than five decades and may be related to the evolution of the 'neogenome', a modern evolutionary acquisition composed by GC-rich isochores displaying long-range correlations and scale invariance.

DNA↗
PubMed2002

A simple and species-independent coding measure.

We present a coding measure which is based on the statistical properties of the stop codons, and that is able to estimate accurately the variation of coding content along an anonymous sequence. As the stop codons play the same role in all the genomes (with very few exceptions) the measure turns out to be species-independent. We show results both for prokaryotic and for eukaryotic genomes, indicating, first, the accuracy of the measure, and, second, that better prediction is achieved if the measure is applied on homogeneous, isochore-like sequences than if it is applied following the standard moving window approach. Finally, we discuss on some of the possible applications of the measure.

Animals↗
PubMed2002

Daily treatment of growing foals with equine somatotropin: pathologic and endocrinologic assessments at necropsy and residual effects in live animals.

This experiment assessed the effects of 12 mo of daily treatment of young horses with recombinant equine somatotropin (eST) on 1) carcass and internal organ traits at necropsy and 2) residual effects in live horses for 60 d after cessation of treatment. Seven horses received eST daily at 20 microg/kg BW; seven others received vehicle (controls). Four horses from each group were killed at the end of treatment. There were few effects of eST treatment on hematologic assessments or histopathologic evaluations of internal organs. Treatment with eST increased the weights of the right adrenal gland (P = 0.090), left (P = 0.085) and right (P = 0.013) kidneys, liver (P = 0.012), tended to inrease the weights of pancreas (P = 0.082), spleen (P = 0.008), and heart (P = 0.102), and decreased (P = 0.032) somatotropin (ST) content in the adenohypophysis. Loin-eye area at the 10th rib was also greater (P = 0.01) in eST-treated horses than in controls. There was no difference (P > 0.15) between groups in left adrenal, brain, parathyroid glands, or thyroid gland weights or in 10th-rib fat thickness. In the remaining two control and three eST-treated horses (one control horse died), plasma IGF-I concentrations were higher (P = 0.001) in treated animals through d 6 after cessation of treatment and then dropped precipitously. Insulin concentrations in treated animals tended to be elevated (P = 0.08) only on d 0. There was a treatment x day interaction (P = 0.04) for plasma urea nitrogen levels, which increased in treated horses. A decrease (P < 0.05) in BW in the treated animals was observed by 21 d after treatment. There was no difference (P > 0.15) in insulin or glucose response to glucose tolerance tests given on d 0 through 60 after cessation of treatment. Overall ST response to secretagogue was reduced (P < 0.05) in eST-treated horses compared with controls. In summary, long-term treatment of growing horses with eST decreased endogenous ST response to secretagogue and increased plasma IGF-I concentrations and many internal organ weights but had little effect on hematologic or histopathologic characteristics at necropsy. The effects on IGF-I concentrations were lost within 6 d, and BW in treated horses decreased within 3 wk after cessation of treatment.

Animals↗
PubMed2001

Isochore chromosome maps of eukaryotic genomes.

Analytical DNA ultracentrifugation revealed that eukaryotic genomes are mosaics of isochores: long DNA segments (>>300 kb on average) relatively homogeneous in G+C. Important genome features are dependent on this isochore structure, e.g. genes are found predominantly in the GC-richest isochore classes. However, no reliable method is available to rigorously partition the genome sequence into relatively homogeneous regions of different composition, thereby revealing the isochore structure of chromosomes at the sequence level. Homogeneous regions are currently ascertained by plain statistics on moving windows of arbitrary length, or simply by eye on G+C plots. On the contrary, the entropic segmentation method is able to divide a DNA sequence into relatively homogeneous, statistically significant domains. An early version of this algorithm only produced domains having an average length far below the typical isochore size. Here we show that an improved segmentation method, specifically intended to determine the most statistically significant partition of the sequence at each scale, is able to identify the boundaries between long homogeneous genome regions displaying the typical features of isochores. The algorithm precisely locates classes II and III of the human major histocompatibility complex region, two well-characterized isochores at the sequence level, the boundary between them being the first isochore boundary experimentally characterized at the sequence level. The analysis is then extended to a collection of human large contigs. The relatively homogeneous regions we find show many of the features (G+C range, relative proportion of isochore classes, size distribution, and relationship with gene density) of the isochores identified through DNA centrifugation. Isochore chromosome maps, with many potential applications in genomics, are then drawn for all the completely sequenced eukaryotic genomes available.

Animals↗
PubMed2001

Plasma and bronchoalveolar fluid concentrations of nitric oxide and localization of nitric oxide synthesis in the lungs of horses with summer pasture-associated obstructive pulmonary disease.

OBJECTIVE: To determine concentrations of nitric oxide (NO) in plasma and bronchoalveolar lavage fluid (BALF) and localize nitric oxide synthesis in the lungs of horses with summer pasture-associated obstructive pulmonary disease (SPAOPD). ANIMALS: 7 adult horses with SPAOPD and 6 clinically normal adult horses. PROCEDURE: Severity of SPAOPD was determined by use of clinical scores, change in intrapleural pressure (APpl) during tidal breathing, cytologic analysis of BALF, and histologic evaluation of lung specimens obtained during necropsy. Nitric oxide concentrations in plasma, BALF and epithelial lining fluid (ELF) were determined by use of a chemiluminescent method. Inducible nitric oxide synthase (iNOS) and nitrotyrosine (NT) were localized in formalin-fixed lung specimens by use of immunohistochemical staining, and nicotinamide adenine dinucleotide phosphate diaphorase (NADPHd) activity was localized in cryopreserved specimens by use of histochemical staining. RESULTS: Plasma concentration of NO in affected horses was slightly but not significantly greater than concentration in nonaffected horses. Nitric oxide concentrations in BALF or ELF did not differ between groups. Immunoreactivity of iNOS in bronchial epithelial cells of 3 of 5 lung lobes was greater in horses with SPAOPD, compared with nonaffected horses. However, staining for NT and NADPHd activity did not differ between groups. CONCLUSIONS AND CLINICAL RELEVANCE: Expression of iNOS was greater in bronchial epithelial cells of horses with SPAOPD, compared with nonaffected horses, suggesting that NO may play a role in amplifying the inflammatory process in the airways of horses with this disease.

Animals↗
PubMed2000

Finding borders between coding and noncoding DNA regions by an entropic segmentation method.

We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method which uses only the general statistical properties of coding DNA. We find that this method is highly accurate in finding borders between coding and noncoding regions and requires no "prior training" on known data sets. Our results appear to be more accurate than those obtained with moving windows in the discrimination of coding from noncoding DNA.

DNA↗
PubMed2000

Effect of hyperbaric oxygen treatment on incorporation of an autogenous cancellous bone graft in a nonunion diaphyseal ulnar defect in cats.

OBJECTIVE: To determine whether hyperbaric oxygen treatment (HBOT) would affect incorporation of an autogenous cancellous bone graft in diaphyseal ulnar defects in cats. ANIMALS: 12 mature cats. PROCEDURE: Bilateral nonunion diaphyseal ulnar defects were created in each cat. An autogenous cancellous bone graft was implanted in 1 ulnar defect in each cat, with the contralateral ulnar defect serving as a nongrafted specimen. Six cats were treated by use of hyperbaric oxygen at 2 atmospheres absolute for 90 minutes once daily for 14 days, and 6 cats were not treated (control group). Bone labeling was performed, using fluorochrome markers. Cats were euthanatized 5 weeks after implanting, and barium sulfate was infused to evaluate vascularization of grafts. Ulnas were evaluated by use of radiography, microangiography, histologic examination, and histomorphometric examination. RESULTS: Radiographic scores did not differ between treatment groups. Microangiographic appearance of grafted defects was similar between groups, with all having adequate vascularization. Differences were not observed between treated and nontreated groups in the overall histologic appearance of decalcified samples of tissue in grafted defects. Mean distance between fluorescent labels was significantly greater in cats given HBOT than in nontreated cats. Median percentage of bone formation in grafted defects was significantly greater in cats given HBOT. CONCLUSIONS: Hyperbaric oxygen treatment increased the distance between fluorescent labels and percentage of bone formation when incorporating autogenous cancellous bone grafts in induced nonunion diaphyseal ulnar defects in cats, but HBOT did not affect revascularization, radiographic appearance, or qualitative histologic appearance of the grafts.

Animals↗
PubMed1999

Analysis of the effects of Perkinsus marinus proteases on plasma proteins of the Eastern oyster (Crassostrea virginica) and the Pacific oyster (Crassostrea gigas).

We employed two in vitro buffer systems to determine the potential pathogenic effects of Perkinsus marinus serine proteases on the plasma proteins of the eastern oyster (Crassostrea virginica) and the Pacific oyster (Crassostrea gigas). Specifically, this study characterized the oyster plasma protein targets of P. marinus proteases. Additionally, protease-specific inhibitory activity was revealed upon comparison of artificial (PBS) and endogenous (plasma-based) diluents employed during protease digestions. It was found that a C. virginica plasma protein of approximately 35 kDa was eliminated when a standard buffer (PBS) was used as a diluent; however, this protein was preserved when a low-molecular-weight, plasma-based, diluent was used. The results strongly indicate that low-molecular-weight inhibitors of P. marinus proteases are present in oyster plasma. A control (nonparasitic) serine protease, alpha-chymotrypsin, was employed to ascertain the specificity of the protease inhibitors. Although alpha-chymotrypsin possesses ample proteolytic activity for C. virginica plasma proteins, the anti-proteases could specifically inhibit only P. marinus proteases. Such specificity of anti-protease activity is not uncommon among low-molecular-weight serine proteases. The hemolymph target protein was isolated by 2D electrophoresis and isoelectrically isolated for further characterization by N-terminal amino acid sequencing.

Animals↗
PubMed1999

Compositional correlation between open reading frames with opposite transcriptional orientations in Escherichia coli.

This paper analyzes correlations in base composition between pairs of neighboring genes in Escherichia coli. The G + C contents of nearby, but convergently or divergently transcribed, genes show weak but significant correlations, and this is attributed to compositional variation among genomic regions. The finding that the base composition varies among intergenic regions, depending upon whether the adjacent genes are transcribed convergently, divergently, or in the same orientation, seems to indicate that transcription affects the patterns of mutation and, therefore, the overall base composition of the region.

Base Composition↗
PubMed1999

SEGMENT: identifying compositional domains in DNA sequences.

MOTIVATION: DNA sequences are formed by patches or domains of different nucleotide composition. In a few simple sequences, domains can simply be identified by eye; however, most DNA sequences show a complex compositional heterogeneity (fractal structure), which cannot be properly detected by current methods. Recently, a computationally efficient segmentation method to analyse such nonstationary sequence structures, based on the Jensen-Shannon entropic divergence, has been described. Specific algorithms implementing this method are now needed. RESULTS: Here we describe a heuristic segmentation algorithm for DNA sequences, which was implemented on a Windows program (SEGMENT). The program divides a DNA sequence into compositionally homogeneous domains by iterating a local optimization procedure at a given statistical significance. Once a sequence is partitioned into domains, a global measure of sequence compositional complexity (SCC), accounting for both the sizes and compositional biases of all the domains in the sequence, is derived. SEGMENT computes SCC as a function of the significance level, which provides a multiscale view of sequence complexity.

Algorithms↗
PubMed1999

Detection and comparison of nitric oxide in clinically normal horses and those with naturally acquired small intestinal strangulation obstruction.

The purpose of this study was to determine whether nitric oxide (NO) is present in clinically normal horses under basal conditions and if it increases secondary to naturally acquired small intestinal strangulation obstruction. Thirty-one horses were used; 20 horses with naturally acquired small intestinal strangulation obstruction and 11 clinically normal horses with no signs of gastrointestinal tract disease. Jugular venous blood, abdominal fluid, and urine were collected for NO quantification. Plasma, abdominal fluid, and urine were stored at -70 degrees C until analyzed for NO using a chemiluminescent method. Biopsy specimens collected from the affected jejunal segment, during anesthesia or after immediately after euthanasia, or from the midjejunum of control horses, were divided into subsections for fixation in zinc formalin and cryopreservation in OCT gel. Nicotinamide adenine dinucleotide phosphate (reduced) (NADPH) diaphorase histochemical stains were performed on cryopreserved tissues and inducible nitric oxide synthase (iNOS) and nitrotyrosine immunohistochemical stains were performed on formalin-fixed, paraffin-embedded tissues. There were significantly greater plasma and abdominal fluid NO concentrations in affected horses as compared with controls, but there were no significant differences between horses for urine NO concentrations. There was a significant decrease in NADPH diaphorase stain in mucosal epithelium, vasculature, and leukocytes, and in submucosal plexi in affected horses compared with control horses. There was a significant increase in iNOS staining in mucosal and submucosal leukocytes and in mucosal leukocyte nitrotyrosine staining of the affected compared with control horses. Endothelial NOS and neuronal NOS are present under basal conditions in the jejunum of horses and probably mediate physiologic or cytoprotective effects. Plasma and abdominal fluid, but not urine, NO concentrations increase subsequent to small intestinal strangulation obstruction; this may be associated with increased mucosal and submucosal iNOS staining in leukocytes, which was likely due to increased expression subsequent to stimuli associated with ischemia. The increased nitrotyrosine staining in mucosal leukocytes of affected horses likely reflects the presence of peroxynitrite subsequent to increased NO and superoxide production and may reflect a cytotoxic role of NO in small intestinal strangulation obstruction in horses.

Animals↗
PubMed1998

Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes.

The heterogeneity within, and similarities between, yeast chromosomes are studied. For the former, we show by the size distribution of domains, coding density, size distribution of open reading frames, spatial power spectra, and deviation from binomial distribution for C + G% in large moving windows that there is a strong deviation of the yeast sequences from random sequences. For the latter, not only do we graphically illustrate the similarity for the above mentioned statistics, but we also carry out a rigorous analysis of variance (ANOVA) test. The hypothesis that all yeast chromosomes are similar cannot be rejected by this test. We examine the two possible explanations of this interchromosomal uniformity: a common origin, such as genome-wide duplication (polyploidization), and a concerted evolutionary process.

Analysis of Variance↗
PubMed1997

Isolation and characterization of the canine melanoma antigen recognized by the murine monoclonal antibody IBF9 and its distribution in cultured canine melanoma cell lines.

OBJECTIVE: To characterize the canine melanoma antigen recognized by the murine monoclonal antibody IBF9 as to its cellular location, molecular size, protein and glycogen contents, and distribution in cell lines. SAMPLE POPULATION: 7 cultured canine melanoma cell lines. PROCEDURE: Molecular characteristics of the antigen were determined by western blotting, enzymatic digestion studies, and tunicamycin inhibition studies. Distribution of the antigen in the cultured melanoma cell lines was determined by flow cytometry. RESULTS: The antigen consists of 2 proteins with molecular mass of 89 and 85 kd. Tunicamycin and enzymatic digestion studies indicated that these proteins contained little glycosylation. Immunogold and immunofluorescence studies localized the antigen to the cell surface. Antigen expression was consistent within each cell line, with > 90% of the cells positive for all cell lines except 1 (80%). Percentage of positive cells and relative intensity of immunostaining were constant throughout all phases of the cell cycle. CONCLUSIONS: The antigen identified by MAB IBF9 is a well-conserved and highly expressed cell surface protein present during all phases of the cell cycle in all malignant canine melanoma cell lines examined. CLINICAL RELEVANCE: Because of consistency in expression, the antigen may have potential for use in dogs for melanoma immunodiagnostics and immunotherapy.

Animals↗
PubMed1996

Neurologic disease attributable to infection with Parelaphostrongylus tenuis in blackbuck antelope.

Substantial mortality attributable to infection with Parelaphostrongylus tenuis was reported in 2 herds of blackbuck antelope (Antelope cervicapra) in southwestern Louisiana. Both herds had outbreaks in which all affected antelope had neurologic disease and subsequently died. Affected antelope were anorectic and weak. They staggered, trembled, isolated themselves from the herd, became recumbent, and, possibly, were blind. In 1 herd, 6 of 27 antelope were affected, and in the second herd, 7 antelope were affected. Both herds were on farms that raised various native and imported ruminants, including white-tailed deer. None of the remaining ruminants was affected during these outbreaks, and subsequent outbreaks have not been reported. Four antelope and the brain of a fifth antelope were submitted for postmortem examination. Meningeal worms were identified grossly in only 1 antelope. Metastrongyloid nematodes were detected histologically in 3 antelope. The amount and extent of inflammation varied greatly among affected antelope.

Animals↗
PubMed1996

A relationship between GC content and coding-sequence length.

Since base composition of translational stop codons (TAG, TAA, and TGA) is biased toward a low G+C content, a differential density for these termination signals is expected in random DNA sequences of different base compositions. The expected length of reading frames (DNA segments of sense codons flanked by in-phase stop codons) in random sequences is thus a function of GC content. The analysis of DNA sequences from several genome databases stratified according to GC content reveals that the longest coding sequences-exons in vertebrates and genes in prokaryotes-are GC-rich, while the shortest ones are GC-poor. Exon lengthening in GC-rich vertebrate regions does not result, however, in longer vertebrate proteins, perhaps because of the lower number of exons in the genes located in these regions. The effects on coding-sequence lengths constitute a new evolutionary meaning for compositional variations in DNA GC content.

Animals↗
PubMed1996

Differences in the kinetics of T cell accumulations in C3H/HeN (Bcg-resistant) and C57BL/6 (Bcg-susceptible) mice infected with Mycobacterium paratuberculosis.

The accumulation of various T cell subsets in Bcg-susceptible (C57BL/6) and- resistant (C3H/HeN) strains of mice were compared following an intraperitoneal infection with Mycobacterium paratuberculosis. Groups of mice from both strains were killed at 3, 5, 10, 15, 30, and 150 days after infection and lymphocytes were harvested from the peritoneal exudate cells (PEC), spleen, intestinal epithelial lymphocytes (IEL), lamina propria lymphocytes (LPL), Peyer's patches, and mesenteric lymph node (MLN) and labelled with monoclonal antibodies to CD3, CD4, CD8, gamma delta TCR, CD25, and CD44 for flow cytometric analysis. Uninfected C3H/HeN mice had higher proportions of CD4+ cells in the spleen, MLN, LPL, IEL, and Peyer's patches, while uninfected C57BL/6 mice had higher proportions of CD8+ and/or gamma delta T cells. Significant increases in accumulation of CD8+ and gamma delta T cells were detected in the peritoneum and other tissues in both strains of mice after infection. Higher CD4/CD8 ratios were observed in most lymphoid tissues of C3H/HeN mice, while increased proportions of CD8+ and/or gamma delta T cells were present in C57BL/6 mice. These results indicate that significant differences in T cell profiles exist between these two strains of mice, both inherently and in response to infection with M. paratuberculosis. Innately lower levels of CD4+ cells and/or higher percentages of CD8+ and gamma delta T cells may play a role in the increased suspectibility of C57BL/6 mice to infection with M. paratuberculosis.

Animals↗