Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cervisiae and Escherichia coli.
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Animals↗
Biomedical subjects
J L Oliver
Publications and source records attributed to J L Oliver.
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↗
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↗
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↗
A possible relationship between VSP mismatch repair and gene expression level.
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Base Sequence↗
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↗
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↗
[Severe cellulitis in an immunocompetent patient].
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Aged↗
Comparison of the resistance of C57BL/6 and C3H/He mice to infection with Mycobacterium paratuberculosis.
Susceptibility of C57BL/6 (Bcgs) and C3H/HeN (Bcgr) mice to an intraperitoneal infection with Mycobacterium paratuberculosis strain 19698 was compared (by histopathology and the number of mycobacteria isolated from the spleen). Mycobacterial counts from the spleen of Bcgr mice progressively decreased over the course of infection but remained unchanged in Bcgs mice. Granulomatous lesions and acid-fast bacteria were consistently present in the liver and lymph nodes of Bcgs mice, whereas lesions were transient or absent in Bcgr mice. These results indicate that Bcgr mice are inherently resistant to M. paratuberculosis, whereas Bcgs mice are inherently susceptible. These differences may prove useful in elucidating the mechanisms of resistance and susceptibility to paratuberculosis and other mycobacterial infections.
Animals↗
Histopathology of C57BL/6 mice inoculated orally with Mycobacterium paratuberculosis.
The susceptibility of C57BL/6 mice to oral inoculation with Myobacterium paratuberculosis was evaluated histopathologically. Granulomatous lesions containing acid-fast bacteria developed in the mesenteric lymph nodes in over 50% of the mice by 11 months after inoculation. The results suggest that C57BL/6 mice may be useful for studying infection, pathogenesis, and other aspects of paratuberculosis.
Administration, Oral↗
On the origin of the periodicity of three in protein coding DNA sequences.
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Apolipoproteins↗
Compositional heterogeneity of the Escherichia coli genome: a role for VSP repair?
E. coli genes that contain a high frequency of the tetranucleotide CTAG are also rich in the tetramers CTTG, CCTA, CCAA, TTGG, TAGG, and CAAG (group-I tetramers). Conversely, E. coli genes lacking CTAG are rich in the tetranucleotides CCTG, CCAG, CTGG, and CAGG (group-II tetramers). These two gene samples differ also in codon usage, amino acid composition, frequency of Dcm sites, and contrast vocabularies. Group-I tetramers have in common that they are depleted by very-short-patch repair (VSP), while group-II tetramers are favored by VSP activity. The VSP system repairs G:T mismatches to G:C, thereby increasing the overall G+C content of the genome; for this reason the CTAG-rich sample has a lower G+C content than the CTAG-poor sample. This compositional heterogeneity can be tentatively explained by a low level of VSP activity on the CTAG-rich sample. A negative correlation is found between the frequency of group-I tetramers and the level of gene expression, as measured by the Codon Adaptation Index (CAI). A possible link between the rate of VSP activity and the level of gene expression is considered.
Base Sequence↗
Molecular characterization and transcription of the histone H2B gene from the protozoan parasite Trypanosoma cruzi.
The structure, genomic organization and transcription of the gene encoding histone H2B in the protozoan parasite Trypanosoma cruzi have been studied. This gene consists of a 746-nucleotide unit, tandemly repeated at least 18 times in each of two clusters. DNA probes corresponding to histones H2B and H3 hybridized to different chromosomes revealing that the genes coding for these two histones are not physically linked in the genome of T. cruzi. The primary transcription product of the H2B gene is processed by trans-splicing and polyadenylation. Inhibition of DNA synthesis with aphidicolin resulted in the reduction of histone H2B mRNA to undetectable levels in about two hours, suggesting that its abundance is regulated throughout the cell cycle as it occurs in other eukaryotes. In addition, a concomitant inhibition of translation by cycloheximide reverted this effect indicating that de novo protein synthesis is required for RNA instability. Histone mRNA abundance was dependent on the life-cycle stage of T. cruzi: abundant in amastigotes and epimastigotes, the dividing forms in the host cell and the insect vector, respectively, while undetected in trypomastigotes, the parasite's non-dividing life stage.
Amino Acid Sequence↗
Entropic profiles of DNA sequences through chaos-game-derived images.
A new method to determine entropic profiles in DNA sequences is presented. It is based on the chaos-game representation (CGR) of gene structure, a technique which produces a fractal-like picture of DNA sequences. First, the CGR image was divided into squares 4-m in size (m being the desired resolution), and the point density counted. Second, appropriate intervals were adjusted, and then a histogram of densities was prepared. Third, Shannon's formula was applied to the probability-distribution histogram, thus obtaining a new entropic estimate for DNA sequences, the histogram entropy, a measurement that goes with the level of constraints on the DNA sequence. Lastly, the entropic profile for the sequence was drawn, by considering the entropies at each resolution level, thus providing a way to summarize the complexity of large genomic regions or even entire genomes at different resolution levels. The application of the method to DNA sequences reveals that entropic profiles obtained in this way, as opposed to previously published ones, clearly discriminate between random and natural DNA sequences. Entropic profiles also show a different degree of variability within and between genomes. The results of these analyses are discussed in relation both to the genome compartmentalization in vertebrates and to the differential action of compositional and/or functional constraints on DNA sequences.
Animals↗
Dinucleotides and G+C content in human genes: opposite behavior of GpG, GpC, and TpC at II-III codon positions and in introns.
We have studied the behavior of the dinucleotide preferences under G+C content variation in human genes. The doublet preferences for each dinucleotide were compared between two functionally distinct zones in genes, the II-III codon positions, and the introns. The 16 dinucleotides have been tentatively classified in three groups: AA, AC, CC, CT, and GA, doublets showing no difference between introns and II-III codon positions in the full range of G+C variation TG and TA, which differ in the full range of G+C variation AT, AG, GT, TC, TT, GG, GC, CG, and CA, which show differences in regions over 50% G+C A remarkable pattern observed concerns the behavior of GG, GC, and TC, which showed opposite trends in II-III codon positions and in introns. If codon positions and introns are under the same structural requirements and the same mutational bias, our results indicate that the differences observed could be related to post-transcriptional constraints acting on mRNA.
Base Composition↗
Antigen expression in canine tissues, recognized by a monoclonal antibody generated against canine melanoma cells.
A murine hybridoma monoclonal antibody (MAB), IBF9, was generated by fusing myeloma cells (P3X63Ag8.653) with spleen cells from a BALB/c mouse immunized with the canine melanoma cell line CML-10c7. Initial screening of hybridoma antibodies was performed by use of an indirect immunoperoxidase assay on formalin-fixed CML-10c7 cells. The isotype of MAB IBF9 was IgG1 as determined by radial gel immunodiffusion. The antibody was tested for reactivity against a panel of formalin-fixed, paraffin-embedded normal and neoplastic canine tissues, using immunoperoxidase staining. Immunostaining was observed in melanomas (24 of 38), a few carcinomas, basal cell tumors, and cutaneous lymphosarcomas. Immunostaining was not observed in fibrosarcomas, hemangiosarcomas, hemangiopericytomas, or histiocytomas. Staining of normal adult canine tissues was limited to a few epithelial tissues and a small percentage of lymphocytes. Fetal tissues were not reactive with MAB IBF9. There were statistically significant differences in frequency of reactivity among melanomas with regard to oral vs non-oral, malignant vs benign, and mitotic indices greater than or equal to 1 vs mitotic indices less than 1. Differences were not significant when tumors were compared for degree of pigmentation or histologic type. On the basis of these findings, we suggest that MAB IBF9 may be of assistance in diagnosis of nonpigmented melanomas and in assessing the malignant potential of melanomas.
Animals↗
Isolation of Mycoplasma bovirhinis from the kidneys of a bull with urinary obstruction and subacute nephritis.
A bull with urethral obstruction secondary to urolithiasis died following exploratory laparotomy. Postmortem examination revealed renal, cystic, and urethral calculi. Gross and histologic findings were consistent with acute urethral and bilateral renal obstruction. Bacteriologic culture of renal tissue revealed Mycoplasma bovirhinis.
Animals↗
The general stochastic model of nucleotide substitution.
DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
Animals↗