Biomedical subjects

Robert Friedman

Publications and source records attributed to Robert Friedman.

At least 37 records · Page 2Linked to original sources

PubMed2004

Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons.

It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum and P. yoelii, (2) the fungi Saccharomyces cerevisiae and S. paradoxus, and (3) the mammals mouse and rat. Codon volatility was not consistently associated with an elevated rate of nonsynonymous substitution, as would be expected under positive selection. Rather, the most consistent and powerful correlate of elevated codon volatility was nucleotide content at the second codon position, as expected, given the nature of the genetic code.

Animals↗

PubMed2004

How strong is the mutagenicity of recombination in mammals?

It is commonly believed that a high recombination rate such as that in a pseudoautosomal region (PAR) greatly increases the mutation rate because a 170-fold increase was estimated for the mouse PAR region. However, sequencing PAR and non-PAR introns of the Fxy gene in four Mus taxa, we found an increase of only twofold to fivefold. Furthermore, analyses of sequence data from human and orangutan PAR and X-linked regions and from autosomal regions showed a weak effect of recombination on mutation rate (a slope of less than 0.2% per cM/Mb), although a much stronger effect on GC content (1% to 2% per cM/Mb). Because typical recombination rates in mammals are much lower than those in PARs, the mutagenicity of recombination is weak or, at best, moderate, although its effect on GC% is much stronger. In addition, contrary to a previous study, we found no Fxy duplicate in Mus spretus.

Animals↗

PubMed2004

Dblox: a genome-wide test for ancient segmental duplication.

UNLABELLED: Dblox and RDblox provide a simple statistical test for duplicated genomic structure; the same programs can also be used to identify putatively duplicated regions. The method focuses on ancient duplication events involving protein-coding genes. AVAILABILITY: http://www.biol.sc.edu/~austin/

Algorithms↗

PubMed2004

Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse.

Gene duplication occurs repeatedly in the evolution of genomes, and the rearrangement of genomic segments has also occurred repeatedly over the evolution of eukaryotes. We studied the interaction of these two factors in mammalian evolution by comparing the chromosomal distribution of multigene families in human and mouse. In both species, gene families tended to be confined to a single chromosome to a greater extent than expected by chance. The average number of families shared between chromosomes was nearly 60% higher in mouse than in human, and human chromosomes rarely shared large numbers of gene families with more than one or two other chromosomes, whereas mouse chromosomes frequently did so. A higher proportion of duplicate gene pairs on the same chromosome originated from recent duplications in human than in mouse, whereas a higher proportion of duplicate gene pairs on separate chromosomes arose from ancient duplications in human than in mouse. These observations are most easily explained by the hypotheses that (1) most gene duplications arise in tandem and are subsequently separated by segmental rearrangement events, and (2) that the process of segmental rearrangement has occurred at a higher rate in the lineage of mouse than in that of human.

Animals↗

PubMed2004

Differential loss of ancestral gene families as a source of genomic divergence in animals.

A phylogenetic approach was used to reconstruct the pattern of an apparent loss of 2106 ancestral gene families in four animal genomes (Caenorhabditis elegans, Drosophila melanogaster, human and fugu). Substantially higher rates of loss of ancestral gene families were found in the invertebrates than in the vertebrates. These results indicate that the differential loss of ancestral gene families can be a significant factor in the evolutionary diversification of organisms.

Animals↗

PubMed2004

Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals.

Loss of ancestral gene families has played an important role in genomic specialization in animals. An examination of the pattern of gene family loss in completely sequenced animal genomes revealed that the same gene families have been lost independently in different lineages to a far greater extent than expected if gene loss occurred at random. This result implies that certain ancestral gene families-and thus the biological functions they encode-have been more expendable than others over the radiation of the animal phyla.

Animals↗

PubMed2004

Recent mammalian gene duplications: robust search for functionally divergent gene pairs.

Comparison of 317 gene pairs in human and mouse that were duplicated after the most recent common ancestor of the two species was used to search for candidates that may have undergone functional differentiation. Even when corrected for multiple tests, Tajima's relative rate test showed significant rate differences in 36% of cases for which the test was applicable. However, a significant result in this case was increasingly likely as the sequence length increased; thus, a statistically significant result of a relative rate test may not be biologically meaningful. We used regression methods to provide more robust methods of testing for functionally differentiated gene pairs, which take into account the variation in the entire data set by examination of residuals from regression-identified gene pairs with unusually high nonsynonymous divergence from a reference sequence and from each other. This approach identified six duplicate gene pairs that appeared to be candidates for functional differentiation as a result of positive Darwinian selection.

Amino Acid Sequence↗

PubMed2004

Pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish.

We used phylogenetic analyses of protein families containing two or more pairs of orthologues in the genomes of human and pufferfish (Takifugu rubripes) to test the hypothesis that these sequences show a strong signal of polyploidization events hypothesized to have occurred early in vertebrate history. In order to test for evidence of two distinct rounds of polyploidization (the 2R hypothesis), we compared the pattern of amino acid sequence divergence of proteins encoded by genes duplicated just prior to the most recent common ancestor of human and pufferfish with that of proteins encoded genes duplicated earlier. These sequence divergences were statistically indistinguishable, contrary to the prediction of the 2R hypothesis. The variance of amino acid sequence divergences between paralogues was significantly greater than expected from that of orthologues in the same families. Estimation of gene duplication times assuming a molecular clock provided earlier estimates than expected, suggesting that it may not be appropriate to time the duplication of paralogues using rate estimates derived from orthologous comparisons. Overall, the results indicate that amino acid sequences do not provide a strong signal supporting the hypothesis that gene duplications early in vertebrate history occurred by polyploidization. On the other hand, the data are easily explained under an alternative model that gene duplications occurred at different times in different vertebrate gene families.

Animals↗

PubMed2004

Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale.

Statistical analysis of the distribution of transposable elements (TEs) and tRNA genes in the genome of yeast Saccharomyces cerevisiae indicated that, although tRNA genes and other genes transcribed by RNA polymerase III are targets for TE insertion, the distribution of TEs was significantly more clumped than that of tRNAs. Genomic blocks putatively duplicated as the result of an ancient polyploidization event contained fewer TEs than expected by their length, and nearly two thirds of duplicated blocks lacked TEs altogether. In addition, the edges of duplicated blocks tended to be located in TE-poor genomic regions. These results can be explained by the hypotheses: (1) that transposition events have occurred well after block duplication; (2) that TEs have frequently played a role in genomic rearrangement events in yeast. According to this model, duplicated blocks identifiable as such in the present-day yeast genome are found largely in regions with low TE density because in such regions the duplicated structure has not been obscured by TE-mediated rearrangements.

DNA Transposable Elements↗

PubMed2004

A pilot trial of a telecommunications system in sleep apnea management.

BACKGROUND: Continuous positive airway pressure (CPAP) is an effective therapy for obstructive sleep apnea syndrome (OSAS), although many patients have difficulty adhering to this therapy. The purpose of this study was to investigate the effectiveness of totally automated telephone technology in improving adherence to prescribed CPAP therapy. RESEARCH DESIGN: This pilot study was a randomized clinical trial in 30 patients being started on CPAP therapy for OSAS. Patients were randomly assigned to use of a computer telephone system designed to improve CPAP adherence (telephone-linked communications for CPAP [TLC-CPAP]) in addition to usual care (n = 15) or to usual care alone (n = 15) for a period of 2 months. TLC-CPAP is a computer-based system that monitors patients' self-reported behavior and provides education and reinforcement through a structured dialogue. MEASURES: A sleep symptoms checklist and the Functional Outcomes of Sleep Questionnaire were administered at study entry and at 2-month follow up. Hours of CPAP use at effective mask pressure were measured by the CPAP device, stored in its memory, and retrieved at the 2-month visit. RESULTS: At 2 months, patients randomized to TLC-CPAP had fewer reported sleep-related symptoms (9.4 vs. 13.4, P = 0.047) than those receiving usual care. The average nightly CPAP use in the TLC-CPAP group was 4.4 hours compared with 2.9 hours (P = 0.076) in the usual-care group. CONCLUSIONS: This pilot study suggests that patients with OSAS started on CPAP and a concurrently administered automated education and counseling system had better CPAP adherence and better control of OSAS symptoms.

Adult↗

PubMed2004

Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles.

To test the hypothesis that the proteins of thermophilic prokaryotes are subject to unusually stringent functional constraints, we estimated the numbers of synonymous and nonsynonymous nucleotide substitutions per site between 17,957 pairs of orthologous genes from 22 pairs of closely related species of Archaea and Bacteria. The average ratio of nonsynonymous to synonymous substitutions was significantly lower in thermophiles than in nonthermophiles, and this effect was observed in both Archaea and Bacteria. There was no evidence that this difference could be explained by factors such as nucleotide content bias. Rather, the results support the hypothesis that proteins of thermophiles are subject to unusually strong purifying selection, leading to a reduced overall level of amino acid evolution per mutational event. The results show that genome-wide patterns of sequence evolution can be influenced by natural selection exerted by a species' environment and shed light on a previous observation that relatively few of the mutations arising in a thermophilic archaeon were nucleotide substitutions in contrast to indels.

Adaptation, Biological↗

PubMed2004

Patterns of sequence divergence in 5' intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories.

We compared the pattern of nucleotide difference in 8034 genes and in their 5' intergenic spacers between conspecific pairs of genomes from 10 species of pathogenic bacteria. Certain genes or spacers showed much greater sequence divergence between the genotypes compared to others; such divergent regions plausibly originated by recombinational events by which a gene and/or spacers was donated from a divergent genome. Different patterns of divergence in genes and spacers identified different recombinational patterns. For example, in Chlamydophila pneumoniae, there were examples of both unusually divergent spacers and unusually divergent genes, but there were no cases in which a gene and its spacer were both unusually divergent. This pattern suggests that, in C. pneumoniae, recombination events have broken up the linkage between genes and 5' spacers. By contrast, in Streptococcus agalactiae, there were a number of cases in which both spacer and gene were unusually divergent, indicating that a number of large-scale recombination events that included both genes and 5' spacers have occurred; there was evidence of at least two large-scale recombination events in the genomic region including the pur genes in S. agalactiae.

Bacteria↗

PubMed2004

Computer-based and live interviews on problem drinking: users' attitudes.

Some studies of computerized interviews particularly those that deal with personally sensitive topics demonstrate that people have a preference for automated interviews versus live interviews. To explore this phenomenon, we administered four open-ended questions after participants were screened for problem drinking by both an automated and a human telephone interviewer. Both interviews administered AUDIT (Alcohol Use Disorders Identification Test) for assessing problem drinking. Individuals were recruited into the study who responded to ads in daily papers. Sixty-two percent of the participants preferred the human interviewer and only 3% among these expressed a concern about confidentiality of the interview. Among the 22% who preferred the automated interview, 32% indicated confidentiality as a reason for their preference.

Alcohol Drinking↗

PubMed2003

The Group 3 LIM domain protein paxillin potentiates androgen receptor transactivation in prostate cancer cell lines.

Paxillin, a member of the group 3 subfamily of LIM domain proteins, is localized within focal adhesions and participates in a number of signal transduction pathways mobilized upon activation of cell surface receptors. In recent years, a number of group 3 LIM domain proteins have been found to also localize within the nucleus and exert direct effects on transcription. We show here that paxillin is present within nuclei and can target the nuclear matrix of CV-1 cells, cultured prostate cancer cell lines, and human prostate tissue. The increased targeting of androgen receptor to the nuclear matrix upon overexpression of paxillin may be brought about by direct interactions between paxillin and the receptor, which were detected in vitro. Paxillin functions as a coactivator for androgen receptor and glucocorticoid receptor, but not estrogen receptor alpha, similar to its close relative Hic-5/ARA55. Both paxillin and Hic-5/ARA55 use their COOH-terminal LIM domain to interact with steroid receptors. However, paxillin is distinguished from Hic-5/ARA55 by both the location of its receptor coactivation domain (i.e., COOH-terminal LIM domain) and by the dominant-negative activity of its NH(2)-terminal domain. Thus, highly related group 3 LIM domain proteins may use distinct mechanisms to modulate steroid hormone receptor transactivation.

Cytoskeletal Proteins↗

PubMed2003

Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses.

The phylogeny of 13 viral species in the genera Granulovirus and Nucleopolyhedrovirus (family Baculoviridae) was reconstructed on the basis of 22 conserved protein families shared by all species, and a comprehensive homology search and phylogenetic analysis of the complete genomes of these viruses was used to test for horizontal gene transfer from cellular organisms. Statistically significant evidence of horizontal transfer was found in the case of six protein families (DNA ligase, ribonucleotide reductase 1, SNF2 global transactivator, inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase). Three of these families are known to play key roles in the infection of insect hosts by these viruses. There was evidence that two of these (inhibitor of apoptosis and UDP-glucosyltransferase) were derived from the insect host. By contrast, the gene encoding chitinase in these viruses was evidently derived from a group of bacteria (the gamma subdivision of proteobacteria), which use chitinase to break down fungal chitins.

Animals↗

PubMed2003

Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana.

The genome of Arabidopsis thaliana is known to contain numerous open reading frames apparently encoding transposases. In order to test the hypothesis that transposable elements have played a role in segmental duplication in this species, we compared the distribution of transposable elements with that of genomic windows that shared gene families to a greater extent than expected by chance. Phylogenetic analyses indicated that duplication of these segments occurred after the monocot-dicot divergence and probably after the eurosid I-eurosid II divergence. Known transposable elements were found to occur in putatively duplicated segments to a far greater extent than expected on the basis of their genome-wide distribution, suggesting that transposition may have played a role in segmental duplication in this species.

Arabidopsis↗

PubMed2003

Severe intraoperative hypertension and opioid-resistant postoperative pain in a methadone-treated patient.

Patients who are treated with methadone present challenges for the anesthesiologist. We report the untoward effects of rapid preoperative methadone tapering on the operative and perioperative course of a patient who required emergency surgery. The patient's exaggerated stress response to surgery and severe intractable postoperative pain might have resulted from unrecognized methadone withdrawal. Continuation of methadone treatment in patients who have surgery may prevent exaggerated intraoperative hemodynamic responses to surgical stimuli and unnecessary postoperative suffering.

Adult↗

PubMed2003

Treating pain patients at risk: evaluation of a screening tool in opioid-treated pain patients with and without addiction.

Patients receiving opioid treatment for chronic pain, many of whom were hospitalized with medical complications of substance abuse, were asked to complete a screening questionnaire to help validate a simple self-administered survey. Questions relating to tobacco abuse and prior treatment for drug and alcohol abuse distinguished patients with addiction and pain from opioid-treated chronic pain patients.

Adult↗