Showing papers by "Stephen J. O'Brien published in 1994"

Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat.

Abstract: The mitochondrial DNA of plant and animal cells is a transcriptionally active genome that traces its origins to a symbiotic infection of eucaryotic cells by bacterial progenitors. As prescribed by the Serial Endosymbiosis Theory, symbiotic organelles have gradually transferred their genes to the eucaryotic genome, producing a functional interaction of nuclear and mitochondrial genes in organelle function. We report here a recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat. The integrated segment has subsequently become amplified 38–76 times and now occurs as a tandem repeat macrosatellite with multiple-length alleles resolved by pulse-field gel electrophoresis (PFGE) segregating in cat populations. Sequence determination of the nuclear mitochondrial DNA segment, Numt, revealed a d(CA)-rich 8-bp motif [ACACACGT] repeated imperfectly five times at the deletion junction that is a likely target for recombination. The extent and pattern of sequence divergence of Numt genes from the cytoplasmic mtDNA homologues plus the occurrence of Numt in other species of the family Felidae allowed an estimate for the origins of Numt at 1.8–2.0 million years ago in an ancestor of four modern species in the genus Felis. Numt genes do not function in cats; rather, the locus combines properties of nuclear minisatellites and pseudogenes. These observations provide an empirical glimpse of historic genomic events that may parallel the accommodation of organelles in eucaryotes.

A role for molecular genetics in biological conservation

Abstract: The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding, genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species.

Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines

Abstract: Certain human hereditary conditions, notably those with low penetrance and those which require an environmental event such as infectious disease exposure, are difficult to localize in pedigree analysis, because of uncertainty in the phenotype of an affected patient's relatives. An approach to locating these genes in human cohort studies would be to use association analysis, which depends on linkage disequilibrium of flanking polymorphic DNA markers. In theory, a high degree of linkage disequilibrium between genes separated by 10-20 cM will be generated and persist in populations that have a history of recent (3-20 generations ago) admixture between genetically differentiated racial groups, such as has occurred in African Americans and Hispanic populations. We have conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture. Our goal is to thoroughly explore the ranges of all relevant parameters or factors (e.g., sample size and degree of genetic differentiation between populations) that may be involved in gene localization studies, in hopes of prescribing guidelines for an efficient mapping strategy. The results provide reasonable limits on sample size (200-300 patients), marker number (200-300 in 20-cM intervals), and allele differentiation (loci with allele frequency difference of > or = .3 between admixed parent populations) to produce an efficient approach (> 95% ascertainment) for locating genes not easily tracked in human pedigrees.

Arthroscopic anatomy of the lateral elbow: a comparison of three portals.

Abstract: Summary Ten fresh cadaveric elbows were used to evaluate the proximity of the radial nerve and its branches to three anterolateral portals. A proximal anterolateral portal used routinely at our institution and located 2 cm proximal and 1 cm anterior to the lateral epicondyle was compared with the distal anterolateral portal described by Andrews and with a mid-anterolateral portal. The three portals were initially established without joint distention while the elbows were flexed 90°. Measurements were then obtained with and without joint distention at flexion angles of 0° and 90°. The radial nerve was found to be an average distance of 3.8 mm at extension and 7.2 mm at 90° of flexion from the distal anterolateral portal, located 3 cm distal and 1 cm anterior to the lateral epicondyle. Conversely, the distance between the proximal anterolateral portal cannula and the nerve was statistically greater (p 100 elbow anthroscopies without evidence of radial nerve injury, is recommended for use as the standard lateral access site, allowing excellent visualization while maximizing the distance from the radial nerve throughout the elbow's range of motion.

Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores.

Abstract: We describe a repetitive DNA region at the 3′ end of the mitochondrial DNA (mtDNA) control region and compare it in 21 carnivore species representing eight carnivore families. The sequence and organization of the repetitive motifs can differ extensively between arrays; however, all motifs appear to be derived from the core motif “ACGT.” Sequence data and Southern blot analysis demonstrate extensive heteroplasmy. The general form of the array is similar between heteroplasmic variants within an individual and between individuals within a species (varying primarily in the length of the array, though two clones from the northern elephant seal are exceptional). Within certain families, notably ursids, the array structure is also similar between species. Similarity between species was not apparent in other carnivore families, such as the mustelids, suggesting rapid changes in the organization and sequence of some arrays. The pattern of change seen within and between species suggests that a dominant mechanism involved in the evolution of these arrays is DNA slippage. A comparative analysis shows that the motifs that are being reiterated or deleted vary within and between arrays, suggesting a varying rate of DNA turnover. We discuss the evolutionary implications of the observed patterns of variation and extreme levels of heteroplasmy.

A lion lentivirus related to feline immunodeficiency virus : epidemiologic and phylogenetic aspects

Abstract: Feline immunodeficiency virus (FIV) is a novel lentivirus that is genetically homologous and functionally analogous to the human AIDS viruses, human immunodeficiency virus types 1 and 2. FIV causes immunosuppression in domestic cats by destroying the CD4 T-lymphocyte subsets in infected hosts. A serological survey of over 400 free-ranging African and Asian lions (Panthera leo) for antibodies to FIV revealed endemic lentivirus prevalence with an incidence of seropositivity as high as 90%. A lion lentivirus (FIV-Ple) was isolated by infection of lion lymphocytes in vitro. Seroconversion was documented in two Serengeti lions, and discordance of mother-cub serological status argues against maternal transmission (in favor of horizontal spread) as a major route of infection among lions. A phylogenetic analysis of cloned FIV-Ple pol gene sequences from 27 lions from four African populations (from the Serengeti reserve, Ngorongoro Crater, Lake Manyara, and Kruger Park) revealed remarkably high intra- and interindividual genetic diversity at the sequence level. Three FIV-Ple phylogenetic clusters or clades were resolved with phenetic, parsimony, and likelihood analytical procedures. The three clades, which occurred not only together in the same population but throughout Africa, were as divergent from each other as were homologous pol sequences of lentivirus isolated from distinct feline species, i.e., puma and domestic cat. The FIV-Ple clades, however, were more closely related to each other than to other feline lentiviruses (monophyletic for lion species), suggesting that the ancestors of FIV-Ple evolved in allopatric (geographically isolated) lion populations that converged recently. To date, there is no clear evidence of FIV-Ple-associated pathology, raising the possibility of a historic genetic accommodation of the lion lentivirus and its host leading to a coevolved host-parasite symbiosis (or commensalism) in the population similar to that hypothesized for endemic simian immunodeficiency virus without pathology in free-ranging African monkey species.

Linkage Disequilibrium in Admixed Populations: Applications in Gene Mapping

Abstract: A method to detect linkage of genetic traits to polymorphic DNA markers in outbred populations when pedigree analysis is not feasible is presented. The procedure takes advantage of increased linkage disequilibrium that occurs when isolated races or subspecies mate and interbreed. By selecting restriction fragment length polymorphism (RFLP) or microsatellite marker loci that have different allele frequencies in admixed populations, genetic associations produced de novo by hybridization will persist as a function of theta (map distance) for 10-20 generations after initial interbreeding. By careful selection of loci and study populations, the procedure detects linkage of traits otherwise refractory to linkage analysis.

Current Status of Allograft Meniscal Transplantation

Abstract: The meniscus has several roles that contribute to knee function. Many clinical studies have documented the detrimental effects of loss of meniscus function. Meniscal repair is recommended when technically and anatomically feasible to preserve meniscal function. Techniques for meniscal repair can be used to transplant meniscal allografts. Animal studies have documented that meniscal allografts can heal in the recipient. There are few clinical studies of meniscal allograft transplantation in humans. Indications, techniques, results, and complications of meniscal allograft transplantation in humans are described.

Genetic and phylogenetic analyses of endangered species

Abstract: INTRODUCTION 467 THE MATERIALS AND RESOURCES FOR CONSERVATION GENETICS ....... 469 SOME EXAMPLES 471 EACH POPULATION BOTTLENECK IS DIFFERENT AND QUALITATIVELY UNPREDICTABLE 475 SOME CRITIQUES OF THE BOTTLENECK HYPOTHESIS 478 MOLECULAR PHYLOGENY AND ENDANGERED SPECIES 480 CONCLUSIONS 483

Polymorphic admixture typing in human ethnic populations.

Abstract: A panel of 257 RFLP loci was selected on the basis of high heterozygosity in Caucasian DNA surveys and equivalent spacing throughout the human genome. Probes from each locus were used in a Southern blot survey of allele frequency distribution for four human ethnic groups: Caucasian, African American, Asian (Chinese), and American Indian (Cheyenne). Nearly all RFLP loci were polymorphic in each group, albeit with a broad range of differing allele frequencies ({delta}). The distribution of frequency differences ({delta} values) was used for three purposes: (1) to provide estimates for genetic distance (differentiation) among these ethnic groups, (2) to revisit with a large data set the proportion of human genetic variation attributable to differentiation within ethnic groups, and (3) to identify loci with high {delta} values between recently admixed populations of use in mapping by admixture linkage disequilibrium (MALD). Although most markers display significant allele frequency differences between ethnic groups, the overall genetic distances between ethnic groups were small (.066-.098), and <10% of the measured overall molecular genetic diversity in these human samples can be attributed to {open_quotes}racial{close_quotes} differentiation. The median {delta} values for pairwise comparisons between groups fell between .15 and .20, permitting identification of highly informative RFLP locimore » for MALD disease association studies. 43 refs., 5 figs., 5 tabs.« less

Evidence of natural bluetongue virus infection among African carnivores

Abstract: Bluetongue is an International Office of Epizootics List A disease described as the century's most economically devastating affliction of sheep. Bluetongue (BLU) viruses were thought to infect only ruminants, shrews, and some rodents, but recently, inadvertent administration of BLU virus-contaminated vaccine resulted in mortality and abortion among domestic dogs. We present evidence of natural BLU virus infection among African carnviores that dramatically widens the spectrum of susceptible hosts. We hypothesize that such infection occurred after ingestion of meat and organs from BLU virus-infected prey species. The effect of BLU virus on endangered carnivores such as the cheetah and African wild dog requires urgent investigation. Also, the role of carnivores in the epizootiology of this disease needs elucidation.

Pandas, people and policy

Abstract: Panda conservation in China has been plagued by controversy and cultural and political differences. But international cooperation, together with new studies identifying the main threats, offer renewed hope for the species' survival.

Phylogenetic Reconstruction of South American Felids Defined by Protein Electrophoresis

Abstract: Phylogenetic associations among six closely related South American felid species were defined by changes in protein-encoding gene loci. We analyzed proteins isolated from skin fibroblasts using two-dimensional electrophoresis and allozymes extracted from blood cells. Genotypes were determined for multiple individuals of ocelot, margay, tigrina, Geoffroy's cat, kodkod, and pampas cat at 548 loci resolved by two-dimensional electrophoresis and 44 allozyme loci. Phenograms were constructed using the methods of Fitch-Margoliash and neighbor-joining on a matrix of Nei's unbiased genetic distances for all pairs of species. Results of a relative-rate test indicate changes in two-dimensional electrophoresis data are constant among all South American felids with respect to a hyena outgroup. Allelic frequencies were transformed to discrete character states for maximum parsimony analysis. Phylogenetic reconstruction indicates a major split occurred approximately 5–6 million years ago, leading to three groups within the ocelot lineage. The earliest divergence led to Leopardus tigrina, followed by a split between an ancestor of an unresolved trichotomy of three species (Oncifelis guigna, O. geoffroyi, and Lynchaduris colocolo) and a recent common ancestor of Leopardus pardalis and L. wiedii. The results suggest that modern South American felids are monophyletic and evolved rapidly after the formation of the Panama land bridge between North and South America.

The Cheetah's Conservation Controversy

Abstract: The article by Merola (1994) reviews the extensive body of results that have been collected over the last decade relative to the population genetic structure of the Afi'ican cheetah and the implications for survival. The author attempts to synthesize the data in a critical manner that brings into question the relevance of previous observations that the cheetah has a remarkably reduced complement of genomic variation and is suffering a physiological fitness cost as a consequence. The article revives spurious and fallacious arguments that have been made earlier and concludes that \" . . . the genetic constitution of the cheetah does not appear to compromise the survival of the species.\" The end result is a rambling self-contradictory polemic that has so many misstatements, misinterpretations, disciplinary prejudices, and errors of omission as to be misleading (at best) and a disservice to the readers of Conservation Biology. In hopes of addressing the major points of disagreement in a lucid manner, I shall deal only with the primary arguments and refer to previously published discussions that cover the additional points. Merola's first point argues that the levels of genetic variation found in cheetahs is not really so low because \"more than 30% of compared carnivores exhibit levels of genetic diversity lower than that of cheetahs; eight of the carnivores show no polymorphism (Fig. 2).\" The author continues that \"rather than comparing cheetah with all other mammals, the more appropriate comparison may be other terrestrial members of Carnivora.\" There are several problems with this logic. First, the criticism deals only with allozyme estimates of genetic

The superolateral portal for arthroscopy of the shoulder

Abstract: With the advent of arthroscopic procedures for the treatment of a variety of clinical conditions affecting the shoulder has come the need for better techniques for visualization of structural pathology, and better techniques for visualization of intracapsular structures during operative procedures. We present a new portal for shoulder arthroscopy that is safe to insert, providing a panoramic view of the glenohumeral joint (especially anteriorly), and allowing unobstructed observation of large instruments passed through more traditional anterior portals nearby. The superolateral portal is particularly suited for use in anterior stabilization procedures of the shoulder, where it can be used for direct visualization of the anterior glenoid neck, thus permitting the surgeon to perform such tasks as debridement or mobilization of tissues, and placement of tacks or sutures.

Exchanges of short polymorphic DNA segments predating speciation in feline major histocompatibility complex class I genes.

Abstract: Sequence comparisons of 14 distinct MHC class I cDNA clones isolated from species representing the three major taxonomic lineages of Felidae (domestic cat lineage, ocelot lineage, and pantherine lineage) revealed that feline MHC class I alleles have highly mosaic structures with short polymorphic sequence motifs that are rearranged between alleles of individual MHC loci, between MHC class I genes within cat species, and between homologous MHC loci in different species. The pattern of sequence variation in felids supports the role of the following factors in production and maintenance of MHC variation: (1) gradual spontaneous mutation; (2) selective pressure to conserve certain residues but also to vary in hypervariable regions, notably residues that functionally participate in antigen recognition and presentation; and (3) recombination-mediated gene exchange between alleles and between related genes. The overall amount of genetic variation observed among MHC class I genes in the Felidae family is no greater than the amount of variation within any outbred cat species (i.e., domestic cat, ocelot). The occurrence of equivalent levels of polymorphism plus the simultaneous persistence of the same sequence motifs in divergent feline species suggest that most MHC class I nucleotide site polymorphism predated species divergences. Ancient polymorphisms have been transmitted through the speciation events and modern feline MHC class I alleles were derived by recombinational exchange of polymorphic sequence motifs. Moreover, some of these sequence motifs were found in other mammalian MHC class I genes, such as classical human HLA-B5, nonclassical human HLA-E class I genes, and bovine class I genes. These results raise the prospect of an ancient origin for some motifs, although the possibility of convergence in parallel mammalian radiations cannot be excluded.

Comparative genomics: The next generation

Abstract: Recent advances in human gene mapping technologies have led to increased emphasis in developing representative genetic maps for several species, particularly domestic plants and animals. These maps are being compiled with two distinct goals: to provide a resource for genetic analysis, and to help dissect the evolution of genome organization by comparing linkage relationships of homologous genes. We recently proposed a list of reference anchor loci suitable for comparative gene mapping in mammals and other vertebrate classes. The comparative anchors, which are Type I (coding gene) loci, provide a comparative framework, but the addition of Type II (microsatellite) loci is also necessary for mapping phenotypes in animal gene maps. Strategies for combining the advantages of Type I and Type II locus markers are presented with emphasis on application of these concepts to the construction of a gene map of the domestic cat.

Polymorphisms in the 3′ untranslated region of the IκB/MAD-3 (NFKBI) gene located on chromosome 14

Abstract: The NF-kappa B transcription factor regulates the expression of a number of genes, including immune function and growth control loci, and several viruses. For example, the long terminal repeat of the human immunodeficiency virus contains NF-kappa B binding sites. NF-kappa B activity in the nucleus is regulated by a cellular inhibitory protein I kappa B. To analyze the potential role of these genes in genetic disease we have mapped the NF-kappa B (NFKB2) and I kappa B/MAD-3 (NFKBI) loci in a panel of somatic cell hybrids to chromosomes 4 and 14, respectively. Amplification of the 3' untranslated region of NFKBI allows the detection of three independent polymorphisms within 410 bp. In combination these polymorphisms were informative in 27 of 36 CEPH families and allowed the gene to be placed onto the linkage map of chromosome 14, between the D14S32 and D14S42 markers.

Gene Mapping in the Spider Monkey (Ateles paniscus chamek)

Abstract: Sixteen isozyme markers have been assigned to the chromosome complement of the neotropical primate species Ateles paniscus chamek using three somatic cell hybrid panels. Several genetic associations were found to be common between humans and this species, despite the fact that Ateles is a karyologically rearranged taxon. Conversely, several human gene clusters were disrupted, resulting in gene associations not previously found in other primates. A comparison with other primates and mammalian orders, for which gene maps are available, was carried out for a comprehensive evaluation of genome evolution in these disparate taxa.

Perspective on conservation genetics

Abstract: Conservation genetics is an applied science. Much as electrical engineering is the application of principles of physics to building rockets, satellites and television stations, conservation genetics takes the methods and theories of molecular biology, genetics and evolution, and interprets the natural history of a threatened population, the hope being to provide useful clues about a population’s genetic structure that can be valuable in developing an effective management strategy. When combined with demographic, ecological, behavioral, and physiological characteristics of endangered species, genetic data has emerged as a unifying component for interpreting past history, present status, and future prospects for threatened populations facing extinction. A notable change has occurred in the last decade in developing conservation plans. Before 1980, endangered species protection emphasized ecological and demographic considerations. Today, genetics, reproductive physiology, clinical medicine, and infectious disease are agenda items on nearly all conservation management plans.