Publications by authors named "R W Debry"

40 Publications

DNA methylation and expression of estrogen receptor alpha in fathead minnows exposed to 17α-ethynylestradiol.

Aquat Toxicol 2021 Apr 23;233:105788. Epub 2021 Feb 23.

US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States. Electronic address:

The gene expression response thought to underlie the negative apical effects resulting from estrogen exposure have been thoroughly described in fish. Although epigenetics are believed to play a critical role translating environmental exposures into the development of adverse apical effects, they remain poorly characterized in fish species. This study investigated alterations of DNA methylation of estrogen receptor alpha (esr1) in brain and liver tissues from 8 to 10 month old male fathead minnows (Pimephales promelas) after a 2d exposure to either 2.5 ng/L or 10 ng/L 17α-ethynylestradiol (EE2). Changes in the patterns of methylation were evaluated using targeted deep sequencing of bisulfite treated DNA in the 5' region of esr1. Methylation and gene expression were assessed at 2d of exposure and after a 7 and 14d depuration period. After 2d EE2 exposure, males exhibited significant demethylation in the 5' upstream region of esr1 in liver tissue, which was inversely correlated to gene expression. This methylation pattern reflected what was seen in females. No gene body methylation (GBM) was observed for liver of exposed males. Differential methylation was observed for a single upstream CpG site in the liver after the 14d depuration. A less pronounced methylation response was observed in the upstream region in brain tissue, however, several CpGs were necessarily excluded from the analysis. In contrast to the liver, a significant GBM response was observed across the entire gene body, which was sustained until at least 7d post-exposure. No differential expression was observed in the brain, limiting functional interpretation of methylation changes. The identification of EE2-dependent changes in methylation levels strongly suggests the importance of epigenetic mechanisms as a mediator of the organismal response to environmental exposures and the need for further characterization of the epigenome. Further, differential methylation following depuration indicates estrogenic effects persist well after the active exposure, which has implications for the risk posed by repeated exposures..
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http://dx.doi.org/10.1016/j.aquatox.2021.105788DOI Listing
April 2021

Validating sonication as a DNA extraction method for use with carrion flies.

Forensic Sci Int 2017 Jun 20;275:171-177. Epub 2017 Mar 20.

Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA. Electronic address:

Entomological evidence can be critical in establishing a postmortem interval estimate. DNA-based species identification can be an extremely valuable tool for forensic entomology. The problem of processing samples in a consistent, cost-effective manner that retains the morphological attributes of the specimen for vouchering has led us to investigate sonication as a primary means of non-destructive DNA extraction from carrion flies. We analyze the efficacy of this technique and compare it to an established DNA extraction technique - the Qiagen DNeasy tissue kit. Our results indicate that sonication produces a significant reduction in the sequence length and lower PHRED quality scores when compared to sequences using DNA obtained using the DNeasy kit, but species identification and phylogenetic inferences between sonication and DNeasy extractions are equivalent.
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http://dx.doi.org/10.1016/j.forsciint.2017.02.014DOI Listing
June 2017

Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions.

PLoS One 2016 4;11(1):e0146375. Epub 2016 Jan 4.

Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America.

Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1) selection is weak; and 2) similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent) sites in the highly expressed Escherichia coli ribosomal protein gene rplQ from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAG mutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s| > 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146375PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699635PMC
July 2016

Sequencing human mitochondrial hypervariable region II as a molecular fingerprint for environmental waters.

Environ Sci Technol 2014 Sep 3;48(18):10648-55. Epub 2014 Sep 3.

Department of Biomedical, Chemical, and Environmental Engineering, University of Cincinnati , Cincinnati, Ohio 45221, United States.

To protect environmental water from human fecal contamination, authorities must be able to unambiguously identify the source of the contamination. Current identification methods focus on tracking fecal bacteria associated with the human gut, but many of these bacterial indicators also thrive in the environment and in other mammalian hosts. Mitochondrial DNA could solve this problem by serving as a human-specific marker for fecal contamination. Here we show that the human mitochondrial hypervariable region II can function as a molecular fingerprint for human contamination in an urban watershed impacted by combined sewer overflows. We present high-throughput sequencing analysis of hypervariable region II for spatial resolution of the contaminated sites and assessment of the population diversity of the impacting regions. We propose that human mitochondrial DNA from public waste streams may serve as a tool for identifying waste sources definitively, analyzing population diversity, and conducting other anthropological investigations.
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http://dx.doi.org/10.1021/es503189gDOI Listing
September 2014

Microbial survey of a full-scale, biologically active filter for treatment of drinking water.

Appl Environ Microbiol 2012 Sep 29;78(17):6390-4. Epub 2012 Jun 29.

University of Cincinnati, Department of Biological Sciences, Cincinnati, Ohio, USA.

The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.
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http://dx.doi.org/10.1128/AEM.00308-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416602PMC
September 2012

DNA-based identification of forensically important Lucilia (Diptera: Calliphoridae) in the continental United States.

J Forensic Sci 2013 Jan 4;58(1):73-8. Epub 2012 May 4.

Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, OH 45221-0006, USA.

Correct species identification is critical when dipteran larvae are used for inference of the postmortem interval. To facilitate DNA-based identification of forensically important flies of the genus Lucilia in the continental United States, we develop a vouchered reference collection and DNA sequence database. A total of 122 specimens were collected for nine of the 10 species of Lucilia reported to occur in the continental United States. Using the polymerase chain reaction and DNA sequencing, data were obtained for an 1100-bp region of the mitochondrial gene encoding cytochrome oxidase I (COI). We consider a species suitable for DNA-based identification if it is exclusively monophyletic in >95% of bootstrap pseudoreplicate phylogenetic analyses. Seven of the nine species meet that criterion. Two species (Lucilia coeruleiviridis and Lucilia mexicana) share COI sequence and cannot be distinguished using our reference database. We conclude that DNA-based identification is likely to be successful for the other seven species.
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http://dx.doi.org/10.1111/j.1556-4029.2012.02176.xDOI Listing
January 2013

mtDNA-based identification of Lucilia cuprina (Wiedemann) and Lucilia sericata (Meigen) (Diptera: Calliphoridae) in the continental United States.

Forensic Sci Int 2010 Oct 26;202(1-3):102-9. Epub 2010 May 26.

Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, OH 45221-0006, USA.

Existing data suggest that the forensically important dipteran species Lucilia cuprina (Wiedemann) and Lucilia sericata (Meigen) may be particularly difficult to discriminate using DNA sequence data. L. cuprina is paraphyletic with respect to L. sericata in mtDNA phylogenies, with some L. cuprina having mtDNA haplotypes that are very similar to those of L. sericata. We examine this problem by providing the first DNA data for L. cuprina from North America, including portions of both the mitochondrial COI gene and the nuclear 28S rRNA gene. With the new data, L. cuprina remains monophyletic for 28S but paraphyletic with respect to L. sericata for COI. However, we find that all flies that are identified as L. cuprina by morphology and have L. sericata-like mtDNA form a distinctly monophyletic mtDNA clade. This clade may possibly have originated by hybridization between L. cuprina and L. sericata, but its wide geographic distribution strongly suggests a singular origin as opposed to repeated incidents of hybridization. The phylogenetic results strongly support the hypothesis that L. cuprina and L. sericata can be discriminated using mtDNA sequence data. We find that a fragment of COI spanning approximately 1200 base pairs is sufficient to discriminate between the two species with greater than 95% bootstrap support.
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http://dx.doi.org/10.1016/j.forsciint.2010.04.038DOI Listing
October 2010

The nocturnal ovipositing behavior of carrion flies in Cincinnati, Ohio.

J Forensic Sci 2009 Nov 10;54(6):1450-2. Epub 2009 Oct 10.

Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA.

The behavioral patterns of nocturnal oviposition represent a window of time that potentially has a large impact on postmortem interval estimations. We investigated the behavioral patterns of carrion flies at night by exposing euthanized rats between sunset and sunrise to see if carrion flies oviposited upon the carrion over two consecutive summers. We investigated urban and rural locations, in both lit and unlit conditions with n = 125. We found that nocturnal ovipositing did not occur in the Cincinnati metropolitan area. We conclude that nocturnal oviposition is an unlikely event in the Cincinnati metropolitan area.
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http://dx.doi.org/10.1111/j.1556-4029.2009.01198.xDOI Listing
November 2009

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades.

BMC Evol Biol 2009 Apr 2;9:71. Epub 2009 Apr 2.

Department of Zoology, George S, Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.

Background: Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes.

Results: We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation.

Conclusion: Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.
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http://dx.doi.org/10.1186/1471-2148-9-71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674048PMC
April 2009

The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony.

Authors:
Ronald W Debry

Syst Biol 2005 Jun;54(3):432-40

Department of Biological Sciences, University of Cincinnati, Box 210006, Cincinnati, OH, 45221-0006, USA.

The effect of taxonomic sampling on phylogenetic accuracy under parsimony is examined by simulating nucleotide sequence evolution. Random error is minimized by using very large numbers of simulated characters. This allows estimation of the consistency behavior of parsimony, even for trees with up to 100 taxa. Data were simulated on 8 distinct 100-taxon model trees and analyzed as stratified subsets containing either 25 or 50 taxa, in addition to the full 100-taxon data set. Overall accuracy decreased in a majority of cases when taxa were added. However, the magnitude of change in the cases in which accuracy increased was larger than the magnitude of change in the cases in which accuracy decreased, so, on average, overall accuracy increased as more taxa were included. A stratified sampling scheme was used to assess accuracy for an initial subsample of 25 taxa. The 25-taxon analyses were compared to 50- and 100-taxon analyses that were pruned to include only the original 25 taxa. On average, accuracy for the 25 taxa was improved by taxon addition, but there was considerable variation in the degree of improvement among the model trees and across different rates of substitution.
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http://dx.doi.org/10.1080/10635150590946745DOI Listing
June 2005

Sonography in wrist tendon pathology.

J Clin Ultrasound 2004 Nov-Dec;32(9):462-9

Medical Imaging Department, Clinique Saint Joseph, Rue de Hesbaye, 75, B-4000 Liege, Belgium.

Wrist tendons may be affected by a variety of pathologic conditions, including those caused by trauma and overuse, inflammatory and metabolic disorders, or infection. Sonography is a very sensitive means of detecting tendinous pathology because of its spatial resolution and its comparative and dynamic capabilities. Its wide availability makes it the preferred first-line imaging modality in the case of wrist pain. This article reviews the pathologic conditions that may involve the wrist and their sonographic appearances.
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http://dx.doi.org/10.1002/jcu.20071DOI Listing
February 2005

Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: the phylogeny of Rodentia (Mammalia).

Authors:
Ronald W DeBry

Syst Biol 2003 Oct;52(5):604-17

Department of Biological Sciences, University of Cincinnati, Box 210006, Cincinnati, Ohio 45221-0006, USA.

Homoplasy among morphological characters has hindered inference of higher level rodent phylogeny for over 100 years. Initial molecular studies, based primarily on single genes, likewise produced little resolution of the deep relationships among rodent families. Two recent molecular studies (Huchon et al., 2002, Mol. Biol. Evol. 19:1053-1065; Adkins et al., 2003, Mol. Phylogenet. Evol. 26:409-420), using larger samples from the nuclear genome, have produced phylogenies that are generally concordant with each other, but many of the deep superfamilial nodes were still lacking substantial statistical support. Data are presented here for a total of approximately 3,600 base pairs from portions of three different nuclear protein-coding genes, CB1, IRBP, and RAG2, from 19 rodents and three outgroups. Separate analyses, with data partitioned according to both genes and codon position, produced conflicting results. Trees obtained from all partitions of CB1 and RAG2 and those obtained from the first- plus second-position sites of IRBP were generally concordant with each other and the trees from the two recent studies, whereas trees obtained from the third-position sites of IRBP were not. Although the IRBP third-position sites represent only 1/9 of the total data set, combined analyses using either parsimony or likelihood resulted in trees in agreement with the IRBP third-position sites and in disagreement with the remaining 8/9 of the sites from this data set and the two recent multigene studies. In contrast, maximum-likelihood analysis using a site-specific rates model did recover a tree that is highly congruent with the trees in the two recent studies. If the IRBP third-position sites are removed from the current data set, then combined likelihood analyses obtain a tree that is highly congruent with those of the two recent studies. This analysis also provides, for the first time in a study of rodent phylogeny, robust statistical support for every bipartition, with just one exception. This tree divides rodents into two major clades. The first contains Myodonta (Muroidea plus Dipodidae) and the only unresolved trichotomy, from which descend Geomyoidea, Pedetidae, and Castoridae. On the other side of the root is a clade containing Sciuroidea plus Gliridae, and Hystricognathi. Some uncertainty remains on the placement of the root. Trees on which the Hystricognathi are the basal sister group to Myodonta, Geomyoidea, Pedetidae, and Castoridae are also found within a Bayesian 95% credible set, as estimated by Metropolis-coupled Markov chain Monte Carlo sampling.
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http://dx.doi.org/10.1080/10635150390235403DOI Listing
October 2003

Improving interpretation of the decay index for DNA sequence data.

Authors:
R W DeBry

Syst Biol 2001 Sep-Oct;50(5):742-52

Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA.

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http://dx.doi.org/10.1080/106351501753328866DOI Listing
August 2002

A simulation study of reduced tree-search effort in bootstrap resampling analysis.

Syst Biol 2000 Mar;49(1):171-9

Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA.

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http://dx.doi.org/10.1080/10635150050207465DOI Listing
March 2000

Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes.

Authors:
R W DeBry

Syst Biol 1999 Jun;48(2):286-99

Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA.

Aligned protein-coding genes from 19 completely sequenced mammalian mitochondrial genomes were examined by parsimony and maximum likelihood analyses. Particular attention is given to a comparison between gene-based and structure-based data partitions. Because actual structures are not known for most of the mitochondrially encoded proteins, three different surrogate partitioning schemes were examined, each based on the identity of the consensus amino acid at a specific homologous position. One of the amino-acid-based partitioning schemes gave the highest likelihood, but that scheme was based on concordance with a well-corroborated phylogeny from an earlier parsimony analysis. The gene-based partitioning scheme gave a significantly higher likelihood compared to the only structure-based scheme examined that could be generated without prior assumptions about the phylogeny. Two contrasting phylogenetic inferences were supported by the analyses. Both unpartitioned analyses and analyses in which all partitions were constrained to have identical patterns of branch lengths supported ((Artiodactyla, Cetacea) (Perissodactyla, Carnivora)), whereas all analyses with that constraint relaxed supported (((Artiodactyla, Cetacea) Carnivora) Perissodactyla).
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http://dx.doi.org/10.1080/106351599260292DOI Listing
June 1999

Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP.

Authors:
R W DeBry R M Sagel

Mol Phylogenet Evol 2001 May;19(2):290-301

Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA.

The order Rodentia includes nearly half of all living mammalian species. Phylogenetic relationships among 22 species of rodents were investigated by use of a 1.2-kb region from exon 1 of the single-copy nuclear gene IRBP. IRBP has been extensively used for study of interordinal phylogeny in mammals, which allowed inclusion of 50 outgroup species, representing every eutherian order plus seven marsupials. Several clades were strongly supported, regardless of analytical method or inclusion/exclusion of data. These include a monophyletic Muroidea, with a clade including Spalax and Rhizomys as the first divergence; a clade uniting Zapus with Dipus, but excluding Sicista; a monophyletic Myodonta (Muroidea plus Dipodidae); and a clade including Aplodontidae as sister to Sciuridae. One bipartition, separating Hystricognathi and Geomyoidea from the remaining rodents, is strongly supported in all analyses that include third-position sites but almost completely absent from analyses that exclude third-position sites. A combination of nonstationary nucleotide composition and branch length effects may be causing all methods examined (including those using the LogDet distance) to support an incorrect conclusion when third-position sites are analyzed together with first- and second-position sites.
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http://dx.doi.org/10.1006/mpev.2001.0945DOI Listing
May 2001

Parallel adaptive radiations in two major clades of placental mammals.

Nature 2001 Feb;409(6820):610-4

Department of Biochemistry, University of Nijmegen, The Netherlands.

Higher level relationships among placental mammals, as well as the historical biogeography and morphological diversification of this group, remain unclear. Here we analyse independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, for all orders of placental mammals. Phylogenetic analyses resolve placental orders into four groups: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires. The first three groups are consistently monophyletic with different methods of analysis. Euarchonta plus Glires is monophyletic or paraphyletic depending on the phylogenetic method. A unique nine-base-pair deletion in exon 11 of the BRCA1 gene provides additional support for the monophyly of Afrotheria, which includes proboscideans, sirenians, hyracoids, tubulidentates, macroscelideans, chrysochlorids and tenrecids. Laurasiatheria contains cetartiodactyls, perissodactyls, carnivores, pangolins, bats and eulipotyphlan insectivores. Parallel adaptive radiations have occurred within Laurasiatheria and Afrotheria. In each group, there are aquatic, ungulate and insectivore-like forms.
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http://dx.doi.org/10.1038/35054544DOI Listing
February 2001

Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction.

Mol Biol Evol 2001 Feb;18(2):132-43

Department of Biology, University of California at Riverside, CA 92521, USA.

Both mitochondrial and nuclear gene sequences have been employed in efforts to reconstruct deep-level phylogenetic relationships. A fundamental question in molecular systematics concerns the efficacy of different types of sequences in recovering clades at different taxonomic levels. We compared the performance of four mitochondrial data sets (cytochrome b, cytochrome oxidase II, NADH dehydrogenase subunit I, 12S rRNA-tRNA-16S rRNA) and eight nuclear data sets (exonic regions of alpha-2B adrenergic receptor, aquaporin, ss-casein, gamma-fibrinogen, interphotoreceptor retinoid binding protein, kappa-casein, protamine, von Willebrand Factor) in recovering deep-level mammalian clades. We employed parsimony and minimum-evolution with a variety of distance corrections for superimposed substitutions. In 32 different pairwise comparisons between these mitochondrial and nuclear data sets, we used the maximum set of overlapping taxa. In each case, the variable-length bootstrap was used to resample at the size of the smaller data set. The nuclear exons consistently performed better than mitochondrial protein and rRNA-tRNA coding genes on a per-residue basis in recovering benchmark clades. We also concatenated nuclear genes for overlapping taxa and made comparisons with concatenated mitochondrial protein-coding genes from complete mitochondrial genomes. The variable-length bootstrap was used to score the recovery of benchmark clades as a function of the number of resampled base pairs. In every case, the nuclear concatenations were more efficient than the mitochondrial concatenations in recovering benchmark clades. Among genes included in our study, the nuclear genes were much less affected by superimposed substitutions. Nuclear genes having appropriate rates of substitution should receive strong consideration in efforts to reconstruct deep-level phylogenetic relationships.
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http://dx.doi.org/10.1093/oxfordjournals.molbev.a003787DOI Listing
February 2001

Comparative analysis of evolution in a rodent histone H2a pseudogene.

Authors:
R W DeBry

J Mol Evol 1998 Mar;46(3):355-60

Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA.

Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published sequence from M. musculus shows that this gene has likely been a pseudogene throughout the evolution of the genus Mus, while the gene from Rattus norvegicus is likely functional. Three large (> 20 bp) deletions were found among the Mus pseudogenes, a feature that is very unusual compared to surveys of processed pseudogenes. In addition, there are two single-base deletions and one 4-bp insertion among the Mus pseudogenes. The species distributions of one of the large deletions and the 4-bp insertion require either independent insertions of an identical sequence, independent deletions with identical boundaries, or a deletion followed by precise reintegration of the original sequence. The evidence favors the hypothesis of multiple deletions with identical boundaries. The "coding" regions of the Mus pseudogenes show a much reduced level of among-species variability in the 3' half of the pseudogene, compared both to the 5' half and to flanking sequences. This supports a hypothesis that the 3' end of the pseudogene is the target of frequent gene conversion by functional H2a genes.
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http://dx.doi.org/10.1007/pl00006312DOI Listing
March 1998

Characterization of the 55-kb mouse histone gene cluster on chromosome 3.

Genome Res 1996 Aug;6(8):702-14

Department of Biology, University of North Carolina (UNC) at Chapel Hill 27599-7100, USA.

The histone gene cluster on mouse chromosome 3 has been isolated as a series of overlapping P1 clones, covering 110-120 kb, by probing with the histone H3-614 gene that had been mapped previously to mouse chromosome 3. There are genes for 10 core histone proteins present in a 55-kb cluster within this contig. There are three histone H3 genes, two of which are identical; four histone H2a genes, two of which are identical, one histone H4 gene; and two histone H2b genes. These histone H3 and H2a genes encode approximately 40% of the total H3 and H2a mRNA, whereas the histone H4 and histone H2b genes encode < 10% of the total H4 and H2b mRNA. There are no histone H1 genes present in this cluster. All of the histone H2a genes encode histone H2a.2 proteins (or variants of H2a.2), and account for all the H2a.2 genes in the mouse genome. All three histone H3 genes encode the histone H3.2 protein. A 21-kb region containing the adjacent H3-614 and H2a-614 genes has been duplicated and is present in an inverted repeat separated by 4.5 kb. The other two H2a genes are adjacent, with the 3' ends of their mRNAs separated by only 49 nucleotides in the DNA and the U7 snRNP binding sites separated by only 20 nucleotides. One of the histone H2b genes has lost the stem-loop sequence characteristic of the replication-dependent histone mRNAs and encodes only polyadenylated mRNAs.
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http://dx.doi.org/10.1101/gr.6.8.702DOI Listing
August 1996

Human/mouse homology relationships.

Genomics 1996 May;33(3):337-51

Department of Medicine, Duke University Medical Center, Durham, North Carolina, 27710, USA.

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http://dx.doi.org/10.1006/geno.1996.0209DOI Listing
May 1996

[Hemi-arthroplasty of the shoulder: radiological, functional and dynamic studies].

Acta Orthop Belg 1995 ;61 Suppl 1:124-33

Centre hospitalier Saint-Joseph Espérance, Liège, Belgique.

From September 1973 to October 1992, forty-three shoulder arthroplasties were performed in forty-one patients with complicated fractures or degenerative disease. Radiological and functional assessment with a mean follow-up time of forty-five months permitted us to review twenty patients with fifteen Neer II prosthesis, three isoelastic prosthesis and two total shoulder replacements. Of these, eleven presented with traumatic injuries and four with degenerative disease. The mean age at operative time was 61 years. Radiological evaluation showed that all cases had a retroversion of about 30 degrees. Normal humeral length and lateral shifting were not achieved in most patients; in fact only one had a restored length and lateral shifting. The mean scapulothoracic range of motion was found to be half that of a normal gliding shoulder (angle 30 degrees instead of 60 degrees). The subacromial space was diminished by one third in all cases. Relief of shoulder pain was the most significant finding. Mobility was restored to a level of about 75% of normal according to Constant's Scale. Dynamometric measures showed an important loss of force (47% of normal) despite a normal external rotation force. Recent improvements in implant conception (modular prosthesis) and a better understanding of physiological shoulder mechanisms should improve the functional results of this arthroplasty in the future.
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June 1996

Selection on silent sites in the rodent H3 histone gene family.

Genetics 1994 Sep;138(1):191-202

Department of Biological Science, Florida State University, Tallahassee 32306-2043.

Selection promoting differential use of synonymous codons has been shown for several unicellular organisms and for Drosophila, but not for mammals. Selection coefficients operating on synonymous codons are likely to be extremely small, so that a very large effective population size is required for selection to overcome the effects of drift. In mammals, codon-usage bias is believed to be determined exclusively by mutation pressure, with differences between genes due to large-scale variation in base composition around the genome. The replication-dependent histone genes are expressed at extremely high levels during periods of DNA synthesis, and thus are among the most likely mammalian genes to be affected by selection on synonymous codon usage. We suggest that the extremely biased pattern of codon usage in the H3 genes is determined in part by selection. Silent site G + C content is much higher than expected based on flanking sequence G + C content, compared to other rodent genes with similar silent site base composition but lower levels of expression. Dinucleotide-mediated mutation bias does affect codon usage, but the affect is limited to the choice between G and C in some fourfold degenerate codons. Gene conversion between the two clusters of histone genes has not been an important force in the evolution of the H3 genes, but gene conversion appears to have had some effect within the cluster on chromosome 13.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1206130PMC
September 1994

BIOGEOGRAPHY OF NEW WORLD TAIGA-DWELLING MICROTUS (MAMMALIA: ARVICOLIDAE): A HYPOTHESIS TEST THAT ACCOUNTS FOR PHYLOGENETIC UNCERTAINTY.

Authors:
Ronald W DeBry

Evolution 1992 Oct;46(5):1347-1357

Department of Chemistry, Florida State University, Tallahassee, FL, 32306, USA.

If we adopt a statistical approach to systematics and recognize that phylogenies are estimated with error, then we can begin to explore statistically justified methods for testing a variety of comparative hypotheses, including those concerning the evolution of life-history characters and biogeography. In this paper I examine two biogeographic hypotheses concerning the rodent genus Microtus. Like many comparative hypotheses, these can be phrased so that each predicts the existence of a particular monophyletic group. Neither of the predicted groups appear on the single best phylogeny as determined by both Dollo parsimony and maximum likelihood analysis of restriction site maps of mitochondrial DNA. Simulation studies, however, suggest that often the best phylogeny from a single data set has only a low probability of being exactly correct. We must also examine those trees that, while not the single best-supported tree, are not rejected by the data. If we find the best phylogeny for which a hypothesis is satisfied, then likelihood methods can be used to test whether that phylogeny is significantly worse then the best tree overall. If that tree can be rejected, then so can the hypothesis. Computational constraints limit the use of likelihood methods for searching among topologies, so parsimony is used as a data exploratory tool. One of the predicted groups cannot be rejected, even though the most parsimonious tree which includes that group requires 11 more steps than does the most parsimonious tree.
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http://dx.doi.org/10.1111/j.1558-5646.1992.tb01128.xDOI Listing
October 1992

The consistency of several phylogeny-inference methods under varying evolutionary rates.

Authors:
R W DeBry

Mol Biol Evol 1992 May;9(3):537-51

Department of Chemistry, Florida State University, Tallahassee 32306.

A phylogenetic method is a consistent estimator of phylogeny if and only if it is guaranteed to give the correct tree, given that sufficient (possibly infinite) independent data are examined. The following methods are examined for consistency: UPGMA (unweighted pair-group method, averages), NJ (neighbor joining), MF (modified Farris), and P (parsimony). A two-parameter model of nucleotide sequence substitution is used, and the expected distribution of character states is calculated. Without perfect correction for superimposed substitutions, all four methods may be inconsistent if there is but one branch evolving at a faster rate than the other branches. Partial correction of observed distances improves the robustness of the NJ method to rate variation, and perfect correction makes the NJ method a consistent estimator for all combinations of rates that were examined. The sensitivity of all the methods to unequal rates varies over a wide range, so relative-rate tests are unlikely to be a reliable guide for accepting or rejecting phylogenies based on parsimony analysis.
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http://dx.doi.org/10.1093/oxfordjournals.molbev.a040740DOI Listing
May 1992

Florida dentist case: research affiliation and ethics.

Authors:
L G Abele R W DeBry

Science 1992 Feb;255(5047):903

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http://dx.doi.org/10.1126/science.1312252DOI Listing
February 1992

[Coxa vara. Isolated growth of the greater trochanter. Prevention-treatment].

Acta Orthop Belg 1990 ;56(1 Pt B):301-6

Clinique St Joseph, Liège, Belgique.

Prevention of avascular complications is a primary aim. The ischemic insult to the femoral head provokes different types of morphologic deformities depending on its location. When the lateral part of the growth plate is affected, the head will be in valgus with a short neck, on the contrary, when the medial part is affected, a coxa vara occurs. The sooner the growth is stopped, the shorter the neck will be. Nevertheless, the greater trochanter will continue its growth and under certain conditions, will extend beyond the head. The Articulo-Trochanteric Distance is a measurement of the deformity which may be checked regularly. Early recognition permits prevention and adequate treatment. Treatment options include epiphysiodesis of the greater trochanter before the age of 8 to 10 years, trochanteric repositioning with osteotomy, and valgus osteotomy (Pauwels' Y-osteotomy).
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September 1990

[Pathology of the anterior peroneus tendon and that of the intermetatarsal bone].

Acta Orthop Belg 1989 ;55(3):485-9

The inconstant peroneus tertius is the fourth muscle in the antero-lateral aspect of the leg. Its tendon crosses the fourth tendon of the extensor hallucis brevis on the dorsal aspect of the cuboïdo-metatarsal joint. If an impingement occurs it may provoke a painful condition and a typical synovial cyst. The anatomy and the pathology of the condition are described. The treatment is very simple: the inconstant tendon should be removed when it produces symptoms. An accessory bone, the intermetatarsal bone, located at the proximal part of the first intermetatarsal or intercuneiform space, may have various shapes. It can provoke pain in the first space when pressure is exerted on capsulo-ligamentous structures or on neuro-vascular elements. The treatment is excision of the accessory bone.
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February 1990