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1.  Host genomic influences on HIV/AIDS 
Genome Biology  2013;14(1):201.
The AIDS era has seen multiple advances in the power of genetics research; scores of host genetic protective factors have been nominated and several have translated to the bedside. We discuss how genomics may inform HIV/AIDS prevention, treatment and eradication.
doi:10.1186/gb-2013-14-1-201
PMCID: PMC3663097  PMID: 23369251
2.  Needle Assisted Arthroscopic Clysis of the Medial Collateral Ligament of the Knee: a Simple Technique to Improve Exposure in Arthroscopic Knee Surgery 
Orthopedic Reviews  2013;5(4):e38.
During knee arthroscopy, narrowness and tightness maybe encountered in the medial compartment that does not allow sufficient visualization or instrumentation. When this occurs, our team has found it helpful to perform a percutaneous clysis of the deep portion of the medial collateral ligament with a spinal needle. With the knee positioned in 10° to 20° of flexion and a valgus stress is applied. A spinal needle (18 Gauge) is passed percutaneously through the medial collateral ligament between the tibial plateau and undersurface of the medial meniscus. Several passes are made with the spinal needle with the bevel of the needle angled to selectively divide the fibers while keeping the medial collateral ligament under tension. Then with controlled valgus force, the medial compartment will progressively open allowing improved visualization to the posteromedial corner of the knee. This increase in space gives an enhanced visual field and further allows more room for arthroscopic instrumentation.
doi:10.4081/or.2013.e38
PMCID: PMC3883079  PMID: 24416482
medial collateral ligament; knee arthroscopy; menisectomy; ligament release
3.  Fish Lateral Line Innovation: Insights into the Evolutionary Genomic Dynamics of a Unique Mechanosensory Organ 
Molecular Biology and Evolution  2012;29(12):3887-3898.
The mechanosensory lateral line, found only in fishes and amphibians, is an important sense organ associated with aquatic life. Lateral line patterns differ among teleost, the most diverse vertebrate taxa, hypothetically in response to selective pressures from different aquatic habitats. In this article, we conduct evolutionary genomic analyses of 34 genes associated with lateral line system development in teleosts to elucidate the significance of contrasting evolutionary rates and changes in the protein coding sequences. We find that duplicated copies of these genes are preferentially retained in the teleost genomes and that episodic events of positive selection have occurred in 22 of the 30 postduplication branches. In general, teleost genes evolved at a faster rate relative to their tetrapod counterparts, and the mutation rates of 26 of the 34 genes differed among teleosts and tetrapods. We conclude that following whole genome duplication, evolutionary rates and episodic events of positive selection on the lateral line system development genes might have been one of the factors favoring the subsequent adaptive radiation of teleosts into diverse habitats. These results provide the foundation for further detailed explorations into lateral line system genes and the evolution of diverse phenotypes and adaptations.
doi:10.1093/molbev/mss194
PMCID: PMC3494275  PMID: 22844072
lateral line; teleost; adaptive evolution; positive selection
4.  Molecular evidence for a recent demographic expansion in the puma (Puma concolor) (Mammalia, Felidae) 
Genetics and Molecular Biology  2013;36(4):586-597.
The puma is an iconic predator that ranges throughout the Americas, occupying diverse habitats. Previous phylogeographic analyses have revealed that it exhibits moderate levels of genetic structure across its range, with few of the classically recognized subspecies being supported as distinct demographic units. Moreover, most of the species’ molecular diversity was found to be in South America. To further investigate the phylogeographic structure and demographic history of pumas we analyzed mtDNA sequences from 186 individuals sampled throughout their range, with emphasis on South America. Our objectives were to refine the phylogeographic assessment within South America and to investigate the demographic history of pumas using a coalescent approach. Our results extend previous phylogeographic findings, reassessing the delimitation of historical population units in South America and demonstrating that this species experienced a considerable demographic expansion in the Holocene, ca. 8,000 years ago. Our analyses indicate that this expansion occurred in South America, prior to the hypothesized re-colonization of North America, which was therefore inferred to be even more recent. The estimated demographic history supports the interpretation that pumas suffered a severe demographic decline in the Late Pleistocene throughout their distribution, followed by population expansion and re-colonization of the range, initiating from South America.
doi:10.1590/S1415-47572013000400018
PMCID: PMC3873191  PMID: 24385863
conservation genetics; mammals; mitochondrial DNA; molecular time estimate; phylogeography
5.  A 1.5 Megabase Resolution Radiation Hybrid Map of the Cat Genome and Comparative Analysis with the Canine and Human Genomes 
Genomics  2006;89(2):189-196.
We report the construction of a 1.5 Mb resolution radiation hybrid map of the domestic cat genome. This new map includes novel microsatellite loci and markers derived from the 2X genome sequence that target previous gaps in the feline-human comparative map. Ninety-six percent of the 1793 cat markers we mapped have identifiable orthologues in the canine and human genome sequences. The updated autosomal and X chromosome comparative maps identify 152 cat-human and 134 cat-dog homologous synteny blocks. Comparative analysis shows the marked change in chromosomal evolution in the canid lineage relative to the felid lineage since divergence from their carnivoran ancestor. The canid lineage has a thirty-fold difference in the number of interchromosomal rearrangments relative to felids, while the felid lineage has primarily undergone intrachromosomal rearrangements. We have also refined the pseudoautosomal region and boundary in the cat and show that it is markedly longer than those of human or mouse. This improved RH comparative map provides a useful tool to facilitate positional cloning studies in the feline model.
doi:10.1016/j.ygeno.2006.08.007
PMCID: PMC3760348  PMID: 16997530
domestic cat; radiation hybrid map; canine genome; genome evolution; synteny; chromosome rearrangement
6.  Four Independent Mutations in the Feline Fibroblast Growth Factor 5 Gene Determine the Long-Haired Phenotype in Domestic Cats 
The Journal of heredity  2007;98(6):555-566.
To determine the genetic regulation of hair length in the domestic cat, a whole genome scan was performed in a multi-generational pedigree in which the long-haired phenotype was segregating. The two markers that demonstrated the greatest linkage to the long-haired trait (LOD≥6), flanked an estimated 10 Mb region on cat chromosome B1 containing the Fibroblast Growth Factor 5 gene (FGF5), a candidate gene implicated in regulating hair follicle growth cycle in other species. Sequence analyses of FGF5 in 26 cat breeds and two pedigrees of non-breed cats, revealed four separate mutations predicted to disrupt the biological activity of the FGF5 protein. Pedigree analyses demonstrated that different combinations of paired mutant FGF5 alleles segregated with the long-haired phenotype in an autosomal recessive manner. Association analyses of over 380 genotyped breed and non-breed cats were consistent with mutations in the FGF5 gene causing the long-haired phenotype in an autosomal recessive manner. In combination, these genomic approaches demonstrated that FGF5 is the major genetic determinant of hair length in the domestic cat.
doi:10.1093/jhered/esm072
PMCID: PMC3756544  PMID: 17767004
7.  How the Leopard Hides Its Spots: ASIP Mutations and Melanism in Wild Cats 
PLoS ONE  2012;7(12):e50386.
The occurrence of melanism (darkening of the background coloration) is documented in 13 felid species, in some cases reaching high frequencies at the population level. Recent analyses have indicated that it arose multiple times in the Felidae, with three different species exhibiting unique mutations associated with this trait. The causative mutations in the remaining species have so far not been identified, precluding a broader assessment of the evolutionary dynamics of melanism in the Felidae. Among these, the leopard (Panthera pardus) is a particularly important target for research, given the iconic status of the ‘black panther’ and the extremely high frequency of melanism observed in some Asian populations. Another felid species from the same region, the Asian golden cat (Pardofelis temminckii), also exhibits frequent records of melanism in some areas. We have sequenced the coding region of the Agouti Signaling Protein (ASIP) gene in multiple leopard and Asian golden cat individuals, and identified distinct mutations strongly associated with melanism in each of them. The single nucleotide polymorphism (SNP) detected among the P. pardus individuals was caused by a nonsense mutation predicted to completely ablate ASIP function. A different SNP was identified in P. temminckii, causing a predicted amino acid change that should also induce loss of function. Our results reveal two additional cases of species-specific mutations implicated in melanism in the Felidae, and indicate that ASIP mutations may play an important role in naturally-occurring coloration polymorphism.
doi:10.1371/journal.pone.0050386
PMCID: PMC3520955  PMID: 23251368
8.  Correction: Genome empowerment for the Puerto Rican parrot – Amazona vittata 
GigaScience  2012;1:17.
doi:10.1186/2047-217X-1-17
PMCID: PMC3626505  PMID: 23587100
9.  FIV diversity: FIVPle subtype composition may influence disease outcome in African lions 
Feline immunodeficiency virus (FIV) infects domestic cats and at least 20 additional species of non-domestic felids throughout the world. Strains specific to domestic cat (FIVFca) produce AIDS-like disease progression, sequelae and pathology providing an informative model for HIV infection in humans. Less is known about the immunological and pathological influence of FIV in other felid species although multiple distinct strains of FIV circulate in natural populations. As in HIV-1 and HIV-2, multiple diverse cross-species infections may have occurred. In the Serengeti National Park, Tanzania, three divergent subtypes of lion FIV (FIVPle) are endemic, whereby 100% of adult lions are infected with one or more of these strains. Herein, the relative distribution of these subtypes in the population are surveyed and, combined with observed differences in lion mortality due to secondary infections based on FIVPle subtypes, the data suggest that FIVPle subtypes may have different patterns of pathogenicity and transmissibility among wild lion populations.
doi:10.1016/j.vetimm.2011.06.013
PMCID: PMC3168974  PMID: 21723622
FIVPle; lions; CDV; Babesia
10.  Genome empowerment for the Puerto Rican parrot – Amazona vittata 
GigaScience  2012;1:13.
A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large sequencing centers.
doi:10.1186/2047-217X-1-13
PMCID: PMC3626504  PMID: 23587407
Puerto Rican parrot; Whole-genome sequencing; Genomics; Conservation; Education; Funding
11.  A Suite of Genetic Markers Useful in Assessing Wildcat (Felis silvestris ssp.)— Domestic Cat (Felis silvestris catus) Admixture 
Journal of Heredity  2011;102(Suppl 1):S87-S90.
The wildcat (Felis silvestris ssp.) is a conservation concern largely due to introgressive hybridization with its congener F. s. catus, the common domestic cat. Because of a recent divergence and entirely overlapping ranges, hybridization is common and pervasive between these taxa threatening the genetic integrity of remaining wildcat populations. Identifying pure wildcats for inclusion in conservation programs using current morphological discriminants is difficult because of gross similarity between them and the domestic, critically hampering conservation efforts. Here, we present a vetted panel of microsatellite loci and mitochondrial polymorphisms informative for each of the 5 naturally evolved wildcat subspecies and the derived domestic cat. We also present reference genotypes for each assignment class. Together, these marker sets and corresponding reference genotypes allow for the development of a genetic rational for defining “units of conservation” within a phylogenetically based taxonomy of the entire F. silvestris species complex. We anticipate this marker panel will allow conservators to assess genetic integrity and quantify admixture in managed wildcat populations and to be a starting point for more in-depth analysis of hybridization.
doi:10.1093/jhered/esr047
PMCID: PMC3157884  PMID: 21846752
captive breeding; conservation genetics; hybridization; introgression; reintroduction microsatellite
12.  Tissue sampling methods and standards for vertebrate genomics 
GigaScience  2012;1:8.
The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.
doi:10.1186/2047-217X-1-8
PMCID: PMC3626508  PMID: 23587255
Genome 10K; Sequencing; Vertebrates; Genomics; Tissue sampling; Tissue storage; Cell line; Tissue culture; RNA; DNA
13.  Thermal Shrinkage for Shoulder Instability 
HSS Journal  2010;7(2):108-114.
Thermal capsular shrinkage was popular for the treatment of shoulder instability, despite a paucity of outcomes data in the literature defining the indications for this procedure or supporting its long-term efficacy. The purpose of this study was to perform a clinical evaluation of radiofrequency thermal capsular shrinkage for the treatment of shoulder instability, with a minimum 2-year follow-up. From 1999 to 2001, 101 consecutive patients with mild to moderate shoulder instability underwent shoulder stabilization surgery with thermal capsular shrinkage using a monopolar radiofrequency device. Follow-up included a subjective outcome questionnaire, discussion of pain, instability, and activity level. Mean follow-up was 3.3 years (range 2.0–4.7 years). The thermal capsular shrinkage procedure failed due to instability and/or pain in 31% of shoulders at a mean time of 39 months. In patients with unidirectional anterior instability and those with concomitant labral repair, the procedure proved effective. Patients with multidirectional instability had moderate success. In contrast, four of five patients with isolated posterior instability failed. Thermal capsular shrinkage has been advocated for the treatment of shoulder instability, particularly mild to moderate capsular laxity. The ease of the procedure makes it attractive. However, our retrospective review revealed an overall failure rate of 31% in 80 patients with 2-year minimum follow-up. This mid- to long-term cohort study adds to the literature lacking support for thermal capsulorrhaphy in general, particularly posterior instability.
Electronic supplementary material
The online version of this article (doi:10.1007/s11420-010-9187-7) contains supplementary material, which is available to authorized users.
doi:10.1007/s11420-010-9187-7
PMCID: PMC3145864  PMID: 22754408
shoulder instability; arthroscopic shoulder stabilization; thermal capsulorrhaphy; outcomes
14.  Association of Host Genetic Risk Factors with the Course of Cytomegalovirus Retinitis in Patients Infected with HIV 
American journal of ophthalmology  2011;151(6):999-1006.e4.
Purpose
To evaluate the effects of previously reported host genetics factors that influence cytomegalovirus (CMV) retinitis incidence, progression to AIDS, and efficacy of highly active antiretroviral therapy (HAART) for mortality, retinitis progression, and retinal detachment in patients with CMV retinitis and AIDS in the era of HAART.
Design
Prospective, multicenter, observational study.
Methods
Cox proportional hazards model based genetic association tests examined the influence of IL-10R1_S420L, CCR5Δ32, CCR2-V64I, CCR5 P1, and SDF-3`A polymorphisms among patients with mortality, retinitis progression, and retinal detachment. Participants were 203 European American and 117 African American patients with AIDS and CMV retinitis.
Results
European American patients with the CCR5 +.P1.+ promoter haplotype showed increased risk for mortality (HR=1.83; 95% CI: 1.00–3.40; P=0.05). Although the same haplotype also trended for increased risk for mortality in African American patients, the result was not significant (HR=2.28; 95% CI: 0.93–5.60; P=0.07). However, this haplotype was associated with faster retinitis progression in African Americans (HR=5.22; 95% CI: 1.54–17.71; P=0.007). Increased risk of retinitis progression was also evident for African American patients with the SDF1-3′A variant (HR=3.89; 95% CI: 1.42–10.60; P=0.008). In addition, the SDF1-3′A variant increased the retinal detachment risk in this patient group (HR=3.05; 95% CI: 1.01–9.16; P=0.05).
Conclusion
Besides overall immune health, host genetic factors influence mortality, retinitis progression, and retinal detachment in patients with AIDS and CMV retinitis that are receiving HAART.
doi:10.1016/j.ajo.2010.11.029
PMCID: PMC3103625  PMID: 21396623
15.  Genetic Characterization of Feline Leukemia Virus from Florida Panthers 
Emerging Infectious Diseases  2008;14(2):252-259.
The emergent strain of FeLV, a novel subgroup A, was probably transmitted to panthers by a domestic cat.
From 2002 through 2005, an outbreak of feline leukemia virus (FeLV) occurred in Florida panthers (Puma concolor coryi). Clinical signs included lymphadenopathy, anemia, septicemia, and weight loss; 5 panthers died. Not associated with FeLV outcome were the genetic heritage of the panthers (pure Florida vs. Texas/Florida crosses) and co-infection with feline immunodeficiency virus. Genetic analysis of panther FeLV, designated FeLV-Pco, determined that the outbreak likely came from 1 cross-species transmission from a domestic cat. The FeLV-Pco virus was closely related to the domestic cat exogenous FeLV-A subgroup in lacking recombinant segments derived from endogenous FeLV. FeLV-Pco sequences were most similar to the well-characterized FeLV-945 strain, which is highly virulent and strongly pathogenic in domestic cats because of unique long terminal repeat and envelope sequences. These unique features may also account for the severity of the outbreak after cross-species transmission to the panther.
doi:10.3201/eid1402.070981
PMCID: PMC2600209  PMID: 18258118
Communicable diseases; emerging; leukemia virus; feline; molecular biology; immunodeficiency virus; research
16.  A Common HLA–DPA1 Variant is a Major Determinant of Hepatitis B Virus Clearance in Han Chinese 
The Journal of Infectious Diseases  2011;203(7):943-947.
A recent genome-wide study showed that the single nucleotide polymorphisms (SNPs) in the HLA-DP region were associated with chronic hepatitis B virus (HBV) infection in Japanese and Thai persons. We tested the effects of HLA-DP SNPs for all major HBV outcomes in Han Chinese (n = 1742): HBV resistance, clearance, chronic infection, cirrhosis, and hepatocellular carcinoma. HLA - DPA1 rs3077 T was strongly associated with decreased risk of chronic HBV infection (odds ratio, .62; P = .001), consistent with the previous report. We showed for the first time to our knowledge that it is a predictor for HBV clearance (odds ratio, 2.41; P < .001). However, rs3077 was not associated with the development of cirrhosis or hepatocellular carcinoma.
doi:10.1093/infdis/jiq154
PMCID: PMC3068033  PMID: 21402545
17.  Strong Influence of HLA-DP Gene Variants on Development of Persistent Chronic HBV Carriers in the Han Chinese Population 
Hepatology (Baltimore, Md.)  2011;53(2):422-428.
Chronic hepatitis B virus (HBV) infection is a major health issue, especially in Asia. A recent genome-wide association study (GWAS) has implicated genetic variants in the HLA-DP locus associated with chronic hepatitis B in Japanese and Thai populations. To confirm whether the polymorphisms at the HLA-DP genes are associated with persistent chronic hepatitis B virus infection in Han Chinese, we conducted an independent case-control study using 521 persistent chronic HBV carriers and 819 controls that included 571 persons with HBV natural clearance and 248 never HBV-infected (healthy) individuals. Eleven single nucleotide polymorphisms (SNPs) in a region including HLA-DPA and HLA-DPB and an adjacent SNP in strong linkage disequilibrium (LD) with a neighboring HLA-DR13 locus were genotyped using TaqMan SNP genotyping assay. Eleven variants at HLA-DP showed a strong association with persistent chronic HBV carrier status (p = 1.82×10−12 to 0.01). We also stratified the analysis by HBV clearance status to test the association between these polymorphisms and HBV natural clearance; similar results were obtained (p = 2.70×10−11 to 0.003). Included SNPs define highly structured haplotypes which were also strongly associated with HBV chronic infection (Block 1: odds ratio (OR) = 0.54, p = 8.73×10−7; block 2: OR = 1.98, p = 1.37×10−10). These results further confirm that genetic variants in the HLA-DP locus are strongly associated with persistent HBV infection in the Han Chinese population.
doi:10.1002/hep.24048
PMCID: PMC3056070  PMID: 21274863
Chronic hepatitis B; Haplotype association; GWAS; SNPs; Joint effects
18.  Emerging Viruses in the Felidae: Shifting Paradigms 
Viruses  2012;4(2):236-257.
The domestic cat is afflicted with multiple viruses that serve as powerful models for human disease including cancers, SARS and HIV/AIDS. Cat viruses that cause these diseases have been studied for decades revealing detailed insight concerning transmission, virulence, origins and pathogenesis. Here we review recent genetic advances that have questioned traditional wisdom regarding the origins of virulent Feline infectious peritonitis (FIP) diseases, the pathogenic potential of Feline Immunodeficiency Virus (FIV) in wild non-domestic Felidae species, and the restriction of Feline Leukemia Virus (FeLV) mediated immune impairment to domestic cats rather than other Felidae species. The most recent interpretations indicate important new evolutionary conclusions implicating these deadly infectious agents in domestic and non-domestic felids.
doi:10.3390/v4020236
PMCID: PMC3315214  PMID: 22470834
FIV; FCoV; FeLV; Felidae
19.  Genetic Associations of Variants in Genes Encoding HIV-Dependency Factors Required for HIV-1 Infection 
The Journal of Infectious Diseases  2010;202(12):1836-1845.
Background. High-throughput genome-wide techniques have facilitated the identification of previously unknown host proteins involved in cellular human immunodeficiency virus (HIV) infection. Recently, 3 independent studies have used small interfering RNA technology to silence each gene in the human genome to determine the importance of each in HIV infection. Genes conferring a significant effect were termed HIV-dependency factors (HDFs).
Methods. We assembled high-density panels of 6380 single-nucleotide polymorphisms (SNPs) in 278 HDF genes and tested for genotype associations with HIV infection and AIDS progression in 1633 individuals from clinical AIDS cohorts.
Results. After statistical correction for multiple tests, significant associations with HIV acquisition were found for SNPs in 2 genes, NCOR2 and IDH1. Weaker associations with AIDS progression were revealed for SNPs within the TM9SF2 and EGFR genes.
Conclusions. This study independently verifies the influence of NCOR2 and IDH1 on HIV transmission, and its findings suggest that variation in these genes affects susceptibility to HIV infection in exposed individuals.
doi:10.1086/657322
PMCID: PMC3107555  PMID: 21083371
20.  Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals 
Background
Matrix extracellular phosphoglycoprotein (MEPE) belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs) that play a key role in skeleton development, particularly in mineralization, phosphate regulation and osteogenesis. MEPE associated disorders cause various physiological effects, such as loss of bone mass, tumors and disruption of renal function (hypophosphatemia). The study of this developmental gene from an evolutionary perspective could provide valuable insights on the adaptive diversification of morphological phenotypes in vertebrates.
Results
Here we studied the adaptive evolution of the MEPE gene in 26 Eutherian mammals and three birds. The comparative genomic analyses revealed a high degree of evolutionary conservation of some coding and non-coding regions of the MEPE gene across mammals indicating a possible regulatory or functional role likely related with mineralization and/or phosphate regulation. However, the majority of the coding region had a fast evolutionary rate, particularly within the largest exon (1467 bp). Rodentia and Scandentia had distinct substitution rates with an increased accumulation of both synonymous and non-synonymous mutations compared with other mammalian lineages. Characteristics of the gene (e.g. biochemical, evolutionary rate, and intronic conservation) differed greatly among lineages of the eight mammalian orders. We identified 20 sites with significant positive selection signatures (codon and protein level) outside the main regulatory motifs (dentonin and ASARM) suggestive of an adaptive role. Conversely, we find three sites under selection in the signal peptide and one in the ASARM motif that were supported by at least one selection model. The MEPE protein tends to accumulate amino acids promoting disorder and potential phosphorylation targets.
Conclusion
MEPE shows a high number of selection signatures, revealing the crucial role of positive selection in the evolution of this SIBLING member. The selection signatures were found mainly outside the functional motifs, reinforcing the idea that other regions outside the dentonin and the ASARM might be crucial for the function of the protein and future studies should be undertaken to understand its importance.
doi:10.1186/1471-2148-11-342
PMCID: PMC3250972  PMID: 22103247
21.  Genetic Introgression and the Survival of Florida Panther Kittens 
Biological conservation  2010;143(11):2789-2796.
Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982-2008 and a live recapture-dead recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0 – 1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.
doi:10.1016/j.biocon.2010.07.028
PMCID: PMC2989677  PMID: 21113436
Burnham model; carnivore; Florida panther; juvenile; model averaging; survival
22.  Role of Exonic Variation in Chemokine Receptor Genes on AIDS: CCRL2 F167Y Association with Pneumocystis Pneumonia 
PLoS Genetics  2011;7(10):e1002328.
Chromosome 3p21–22 harbors two clusters of chemokine receptor genes, several of which serve as major or minor coreceptors of HIV-1. Although the genetic association of CCR5 and CCR2 variants with HIV-1 pathogenesis is well known, the role of variation in other nearby chemokine receptor genes remain unresolved. We genotyped exonic single nucleotide polymorphisms (SNPs) in chemokine receptor genes: CCR3, CCRL2, and CXCR6 (at 3p21) and CCR8 and CX3CR1 (at 3p22), the majority of which were non-synonymous. The individual SNPs were tested for their effects on disease progression and outcomes in five treatment-naïve HIV-1/AIDS natural history cohorts. In addition to the known CCR5 and CCR2 associations, significant associations were identified for CCR3, CCR8, and CCRL2 on progression to AIDS. A multivariate survival analysis pointed to a previously undetected association of a non-conservative amino acid change F167Y in CCRL2 with AIDS progression: 167F is associated with accelerated progression to AIDS (RH = 1.90, P = 0.002, corrected). Further analysis indicated that CCRL2-167F was specifically associated with more rapid development of pneumocystis pneumonia (PCP) (RH = 2.84, 95% CI 1.28–6.31) among four major AIDS–defining conditions. Considering the newly defined role of CCRL2 in lung dendritic cell trafficking, this atypical chemokine receptor may affect PCP through immune regulation and inducing inflammation.
Author Summary
Human chemokine receptors are cell surface proteins that may be utilized by HIV-1 for entry into host cells. DNA variation in the HIV-1 major coreceptor CCR5 affects HIV-1 infection and progression. This study comprehensively assesses the role of genetic variation of multiple chemokine receptor genes clustered in the chromosome 3p21 and 3p22 on HIV-1 disease outcomes in HIV-1 natural history cohorts. The multivariate survival analyses identified functional variants that altered disease progression rate in CCRL2, CCR3, and CCR8. CCRL2-F167Y affects the rate to AIDS development through a specific protection against pneumocystis pneumonia (PCP), a common AIDS–defining condition. Our study identified this atypical chemokine receptor CCRL2 as a key factor involved in PCP, possibly through inducing inflammation in the lung.
doi:10.1371/journal.pgen.1002328
PMCID: PMC3203199  PMID: 22046140
23.  Genome-Wide and Differential Proteomic Analysis of Hepatitis B Virus and Aflatoxin B1 Related Hepatocellular Carcinoma in Guangxi, China 
PLoS ONE  2013;8(12):e83465.
Both hepatitis B virus (HBV) and aflatoxin B1 (AFB1) exposure can cause liver damage as well as increase the probability of hepatocellular carcinoma (HCC). To investigate the underlying genetic changes that may influence development of HCC associated with HBV infection and AFB1 exposure, HCC patients were subdivided into 4 groups depending upon HBV and AFB1 exposure status: (HBV(+)/AFB1(+), HBV(+)/AFB1(-), HBV(-)/AFB1(+), HBV(-)/AFB1(-)). Genetic abnormalities and protein expression profiles were analyzed by array-based comparative genomic hybridization and isobaric tagging for quantitation. A total of 573 chromosomal aberrations (CNAs) including 184 increased and 389 decreased were detected in our study population. Twenty-five recurrently altered regions (RARs; chromosomal alterations observed in ≥10 patients) in chromosomes were identified. Loss of 4q13.3-q35.2, 13q12.1-q21.2 and gain of 7q11.2-q35 were observed with a higher frequency in the HBV(+)/AFB1(+), HBV(+)/AFB1(-) and HBV(-)/AFB1(+) groups compared to the HBV(-)/AFB(-) group. Loss of 8p12-p23.2 was associated with high TNM stage tumors (P = 0.038) and was an unfavorable prognostic factor for tumor-free survival (P =0.045). A total of 133 differentially expressed proteins were identified in iTRAQ proteomics analysis, 69 (51.8%) of which mapped within identified RARs. The most common biological processes affected by HBV and AFB1 status in HCC tumorigenesis were detoxification and drug metabolism pathways, antigen processing and anti-apoptosis pathways. Expression of AKR1B10 was increased significantly in the HBV(+)/AFB1(+) and HBV(-)/AFB1(+) groups. A significant correlation between the expression of AKR1B10 mRNA and protein levels as well as AKR1B10 copy number was observered, which suggest that AKR1B10 may play a role in AFB1-related hepatocarcinogenesis. In summary, a number of genetic and gene expression alterations were found to be associated with HBV and AFB1- related HCC. The possible synergistic effects of HBV and AFB1 in hepatocarcinogenesis warrant further investigations.
doi:10.1371/journal.pone.0083465
PMCID: PMC3877066  PMID: 24391771
24.  EPIZOOTIOLOGY AND MANAGEMENT OF FELINE LEUKEMIA VIRUS IN THE FLORIDA PUMA 
Journal of wildlife diseases  2008;44(3):537-552.
Feline leukemia virus (FeLV) was not detected in Florida pumas (Puma concolor coryi) in almost 20 yr of surveillance; however, the finding of two FeLV antigen-positive pumas during the 2002–2003 capture season led to an investigation of FeLV in the population. Between January 1990 and April 2007, the proportion of pumas testing FeLV antibody positive increased, with antibody-positive pumas concentrated in the northern portion of puma range. Five of 131 (4%) pumas sampled between July 2000 and April 2007 were viremic, with all cases clustered in Okaloacoochee Slough (OKS). Clinical signs and clinical pathology at capture were absent or included lymphadenopathy, moderate-to-severe anemia, and lymphopenia. All viremic pumas died; causes of death were septicemia (n=2), intraspecific aggression (n=2), and anemia/dehydration (n=1). Outcome after FeLV exposure in pumas was similar to that in domestic cats, with evidence of regressive, latent, and persistent infections. Management of the epizootic included vaccination, and as of April 2007, 52 free-ranging pumas had received one or more inoculations. Vaccinations were concentrated in OKS and in a band between OKS and the remainder of the puma population. There have been no new cases since July 2004; however, the potential for reintroduction of the virus remains.
PMCID: PMC3167064  PMID: 18689639
Feline leukemia virus; Florida panther; infectious disease; Puma concolor coryi; retrovirus; vaccination
25.  Effect of host genetics on CMV retinitis occurrence in patients with AIDS 
The Journal of infectious diseases  2010;202(4):606-613.
Background
Cytomegalovirus (CMV) retinitis is a common opportunistic infection among patients with AIDS and still causes visual morbidity despite the wide spread usage of highly active antiretroviral therapy (HAART). The ubiquitous CMV pathogen contains a human interleukin-10 (IL-10) homolog in its genome and utilizes it to evade host immune reactions through an IL-10 receptor mediated immune-suppression pathway.
Methods
Effects of IL-10R1, IL-10 and previously described AIDS restriction gene variants are investigated on the development of CMV retinitis in the Longitudinal Study of the Ocular Complications of AIDS (LSOCA) cohort (n=1284).
Results
In Europen Americans (n=750), a haplotype carrying an amino acid changing variation in the cytoplasmic domain (S420L) of IL-10R1 can be protective (OR = 0.14, CI: 0.02–0.94, P = 0.04) against, whereas another haplotype carrying an amino acid changing variation in the extracellular domain (I224V) of IL-10R1 can be more susceptible (OR = 6.21, CI: 1.22–31.54, P = 0.03) to CMV retinitis. In African Americans (n=534), potential effects of IL-10 variants are observed.
Conclusion
Host genetics may have a role in the occurrence of CMV retinitis in patients infected with HIV.
doi:10.1086/654814
PMCID: PMC2932829  PMID: 20617924
AIDS; CMV retinitis; HIV-1; host genetics; interleukin-10 receptor

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