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Background Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this study explored genome differentiation between a feral population of Andean horses introduced by the Spanish in the 1500s to the high Andes and their Iberian breed relatives. Results Using allelic genetic models and Fst analyses of∼50 K single nucleotide polymorphisms (SNPs) across the horse genome, 131 candidate genes for altitude adaptation were revealed (Bonferoni of p ≤ 2 × 10-7). Significant signals included the EPAS1 in the hypoxia-induction-pathway (HIF) that was previously discovered in human studies (p = 9.27 × 10-8); validating the approach and emphasizing the importance of this gene to hypoxia adaptation. Strong signals in the cytochrome P450 3A gene family (p = 1.5 ×10-8) indicate that other factors, such as highly endemic vegetation in altitude environments are also important in adaptation. Signals in tenuerin 2 (TENM2, p = 7.9 × 10-14) along with several other genes in the nervous system (gene categories representation p = 5.1 × 10-5) indicate the nervous system is important in altitude adaptation. Conclusions In this study of a large introduced herbivore, it becomes apparent that some gene pathways, such as the HIF pathway are universally important for high altitude adaptation in mammals, but several others may be selected upon based on the natural history of a species and the unique ecology of the altitude environment. [ABSTRACT FROM AUTHOR]

Background: The human mitochondrial genome includes only 13 coding genes while nuclear-encoded genes account for 99% of proteins responsible for mitochondrial morphology, redox regulation, and energetics. Mitochondrial pathogenesis occurs in HIV patients and genetically, mitochondrial DNA haplogroups with presumed functional differences have been associated with differential AIDS progression. Methodology/Principal Findings: Here we explore whether single nucleotide polymorphisms (SNPs) within 904 of the estimated 1,500 genes that specify nuclear-encoded mitochondrial proteins (NEMPs) influence AIDS progression among HIV-1 infected patients. We examined NEMPs for association with the rate of AIDS progression using genotypes generated by an Affymetrix 6.0 genotyping array of 1,455 European American patients from five US AIDS cohorts. Successfully genotyped SNPs gave 50% or better haplotype coverage for 679 of known NEMP genes. With a Bonferroni adjustment for the number of genes and tests examined, multiple SNPs within two NEMP genes showed significant association with AIDS progression: acyl-CoA synthetase medium-chain family member 4 (ACSM4) on chromosome 12 and peroxisomal D3,D2-enoyl- CoA isomerase (PECI) on chromosome 6. Conclusions: Our previous studies on mitochondrial DNA showed that European haplogroups with presumed functional differences were associated with AIDS progression and HAART mediated adverse events. The modest influences of nuclear-encoded mitochondrial genes found in the current study add support to the idea that mitochondrial function plays a role in AIDS pathogenesis. [ABSTRACT FROM AUTHOR]

The article presents a study on mitochondrial DNA variation as a risk factor of neuroretinal disorder (NRD) progression among HIV-positive patients. The study extracted DNA samples for genotyping and employed Cox proportional hazards model to determine the link between mitochondrial haplogroups and time to NRD. Results revealed that mitochondrial DNA variation was linked with 80% decrease in NRD progression, which implies that the genotype could influence the development of HIV-associated NRD.

The article presents a study which examines the association of mitochondrial DNA genotype with the severity of lipoatrophy in HIV-infected patients on highly active antiretroviral therapy (HAART) in the Multicenter AIDS Cohort Study (MACS). It mentions that the study was conducted through the analysis of 410 European American men with HIV. It was found out that the mitochondrial haplogroup is associated with the propensity of lipoatrophy.

The article studies the influence of AIDS restriction genes and haplotypes of the CCR5 P1 promoter and RANTES variants among HIV-1 infected patients on highly active antiretroviral therapy in the Multicenter AIDS Cohort Study and the Multicenter Hemophilia Cohort Study. It examines a range of genes that were predicted to influence HAART through various interactions with the HIV life cycle and drug metabolism.

We sequenced 912 bp of the cytochrome-b gene to examine phylogenetic relationships of the enigmatic Saw-billed Hermit (Ramphodon naevius), a large and distinctive hummingbird endemic to tropical forests of southeastern Brazil. Bootstrapped maximum parsimony and maximum likelihood analyses of sequence data from 11 hummingbirds and several outgroups (two swifts, one goatsucker) support: (a) monophyly of the traditional hermit (Phaethornithinae) and nonhermit (Trochilinae) subfamilies, (b) placement of Ramphodon among hermits, and (c) a sister relationship between Ramphodon and an exemplar of the widespread polytypic hermit genus Glaucis. The association of Ramphodon with derived hermit lineages is concordant with subfamilial patterns of wing anatomy and nest architecture. However, the unusual plumages (striped underparts) and male bills (long, serrated, hooked) shared by Ramphodon and the Tooth-billed Hummingbird (Androdon aequatorialis) appear to have evolved within separate hermit and nonhermit "tooth-billed" clades. Distal placement of the Ramphodon-Glaucis clade within hermits implies that even distinctive Brazilian endemics such as Ramphodon are derived forms that evolved relatively recently. [ABSTRACT FROM AUTHOR]

Presents a study which characterized DNA sequence variation in the mitochondrial control region and 12S ribosomal subunit for a sample of Andean Condors, or Vultur gryphus, representing populations distributed throughout the species' extensive geographic range, from Colombia to central Argentina and Chile. Details of the geographic distribution of haplotypes; Comparisons to other avian species; Discussion on the findings regarding genetic variability of the megafauna.

The article presents a study on the effect of host genetics on human immunodeficiency virus neuroretinal disorder (HIV-NRD) in patients with AIDS. It notes the loss of contrast sensitivity that is sufficient to impair reading speed. It mentions the validated AIDS restriction gene variants in evaluating the effect of host genes on HIV-NRD which has been implicated to influence HIV-1 infection, AIDS progression, therapy response, and antiviral drug metabolism.

The article discusses the highlights of the President's Symposium of the American Genetic Association (AGA) held in Guanajuato, Mexico from July 23 to 26, 2011. The theme focuses on genomics and biodiversity with topics including the reconstruction of the population history of Latin America, advances in the study of maize, and epigenetics of flowers. Resource speakers from various academies include Robert Wayne, Joshua Der and Rachel Mueller.

Robinson and colleagues respond to the points raised about their paper by Bakker et al. [ABSTRACT FROM AUTHOR]

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy facilitated by Epstein-Barr Virus infection. Here we resolve the major genetic influences for NPC incidence using a genome-wide association study (GWAS), independent cohort replication, and high-resolution molecular HLA class I gene typing including 4,055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. We detect and replicate strong association signals involving SNPs, HLA alleles, and amino acid (aa) variants across the major histocompatibility complex-HLA-A, HLA -B, and HLA -C class I genes (PHLA-A-aa-site-62 = 7.4 x10-29; PHLA-B-aa-site-116 = 6.56x10 ;PHLA-C-aa-site-156 = 6.8x10-8 respectively). Over 250 NPC-HLA associated variants within HLA were analyzed in concert to resolve separate and largely independent HLA-A, -B, and -C gene influences. Multivariate logistical regression analysis collapsed significant associations in adjacent genes spanning 500 kb (OR2H1, GABBR1, HLA-F, and HCG9) as proxies for peptide binding motifs carried by HLA- A*11:01. A similar analysis resolved an independent association signal driven by HLA-B*13:01, B*38:02, and B*55:02 alleles together. NPC resistance alleles carrying the strongly associated amino acid variants implicate specific class I peptide recognition motifs in HLA-A and -B peptide binding groove as conferring strong genetic influence on the development of NPC in China. [ABSTRACT FROM AUTHOR]

Background. Host genetic variation influences human immunodeficiency virus (HIV) infection and progression to AIDS. Here we used clinically well-characterized subjects from 5 pretreatment HIV/AIDS cohorts for a genome-wide association study to identify gene associations with rate of AIDS progression.Methods. European American HIV seroconverters (n = 755) were interrogated for single-nucleotide polymorphisms (SNPs) (n = 700,022) associated with progression to AIDS 1987 (Cox proportional hazards regression analysis, co-dominant model).Results. Association with slower progression was observed for SNPs in the gene PARD3B. One of these, rs11884476, reached genome-wide significance (relative hazard = 0.3; P =3. 370 × 10−9) after statistical correction for 700,022 SNPs and contributes 4.52% of the overall variance in AIDS progression in this study. Nine of the top-ranked SNPs define a PARD3B haplotype that also displays significant association with progression to AIDS (hazard ratio, 0.3; P = 3.220 × 10−8). One of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the expression profile of PARD3B splicing transcripts was observed in B cell lines with alternate rs10185378 genotypes. This SNP was typed in European cohorts of rapid progressors and was found to be protective for AIDS 1993 definition (odds ratio, 0.43, P = .025).Conclusions. These observations suggest a potential unsuspected pathway of host genetic influence on the dynamics of AIDS progression. [ABSTRACT FROM PUBLISHER]

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 European 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; 95% CI, 0.02-0.94; P = .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; 95% CI, 1.22- 31.54; P = .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. [ABSTRACT FROM AUTHOR]

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability. 1 During the latter half of the twentieth century, North America's largest soaring bird, 2 the California condor (Gymnogyps californianus ; Critically Endangered 3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented, 4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus ; Vulnerable 3) and the turkey vulture (Cathartes aura ; Least Concern 3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation. • The de novo California condor genome assembly is complete and contiguous • Runs of homozygosity in California condor genomes reveal inbreeding in the wild • Genome-wide diversity suggests California condors were historically abundant • Andean condor and turkey vulture genomes also reveal historic declines Robinson et al. sequence and analyze the genome of the Critically Endangered California condor. Genome-wide diversity in the California condor reveals evidence of historically high abundance followed by long-term decline, plus signs of recent inbreeding in the wild. Andean condor and turkey vulture genomes also show evidence of historical declines. [ABSTRACT FROM AUTHOR]

Nasopharyngeal carcinoma is a devastating epithelial malignancy facilitated by Epstein Barr Virus infection that claims over 50,000 lives each year, mostly in East Asia. Here we resolve the major genetic influences for NPC incidence using a genome wide association study (GWAS), independent cohort replication, and full molecular HLA Class I gene typing including 4055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. We detect and replicate strong association signals involving of 58 SNPs across the major histocompatibility complex-HLA-A, -B and -C Class I genes (Pcombined = 7.4 × 10-29; Pcombined = 6.5 × 10-19; Pcombined = 6.8 × 10-8 respectively). Approximately 300 SNP and amino acid variants driven by linkage disequilibrium within HLA were analyzed in concert to resolve separate and largely independent HLA-A, -B and -C gene influences. The exercise collapsed replicated associations in adjacent genes (HLA-A, OR2H1, GABBR1, HCG9 and HLA-F) as proxies for the HLA- A∗11:01 resistance phenotype and implicates specific Class I peptide recognition motifs in HLA-A and B peptide binding groove. Along with HLA we replicate 4 additional NPC associated loci, TNFRSF19 (CHR 13), MDS1-EVI1 (CHR 3) and CDNK2A/2B (CHR 9) and TMEM179 (CHR 14), to affirm the principal genetic influences on NPC onset in China. [ABSTRACT FROM AUTHOR]