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81.
Hunter MK Broderick D Ovenden JR Tucker KP Bonde RK McGuire PM Lanyon JM 《Molecular ecology resources》2010,10(2):368-377
The Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) are threatened species of aquatic mammals in the order Sirenia. Sirenian conservation and management actions would benefit from a more complete understanding of genetic diversity and population structure. Generally, species-specific microsatellite markers are employed in conservation genetic studies; however, robust markers can be difficult and costly to isolate. To increase the number of available markers, dugong and manatee microsatellite primers were evaluated for cross-species amplification. Furthermore, one manatee and four dugong novel primers are reported. After polymerase chain reaction optimization, 23 (92%) manatee primers successfully amplified dugong DNA, of which 11 (48%) were polymorphic. Of the 32 dugong primers tested, 27 (84%) yielded product in the manatee, of which 17 (63%) were polymorphic. Dugong and manatee primers were compared and the most informative markers were selected to create robust and informative marker-panels for each species. These cross-species microsatellite marker-panels can be employed to assess other sirenian populations and can provide beneficial information for the protection and management of these unique mammals. 相似文献
82.
Vololoniaina R. Razakamaharavo Susie M. McGuire Natalie Vasey Edward E. LouisJr. Rick A. Brenneman 《Primates; journal of primatology》2010,51(1):53-61
The current range of the red ruffed lemur (Varecia rubra) population is primarily restricted to forests of the Masoala Peninsula on the northeastern coast of Madagascar. Whereas
much of the peninsula is protected as Masoala National Park, parts of the forest are at risk from anthropogenic pressures
and habitat fragmentation. We sampled 32 individual red ruffed lemur from two sites: Ambatoledama (DAMA), a narrow forest
corridor across an area of degraded habitat connecting larger blocks of forest in the northwestern reaches of the park, and
Masiaposa (MAS) forest, a largely pristine forest on the lower western side of the peninsula. Population genetic parameters
were estimated for these two populations employing 15 microsatellite loci derived from the V. variegata genome. We found that by exceeding the expected heterozygosity at mutation-drift equilibrium, the DAMA population has undergone
a recent population bottleneck. Population structure analysis detected individuals harboring genotypic admixture of the DAMA
genetic cluster in the MAS population, suggesting a possibility of unilateral gene flow or movement between these populations. 相似文献
83.
Yu‐Chiang Lai Chandana Kondapalli Ronny Lehneck James B Procter Brian D Dill Helen I Woodroof Robert Gourlay Mark Peggie Thomas J Macartney Olga Corti Jean‐Christophe Corvol David G Campbell Aymelt Itzen Matthias Trost Miratul MK Muqit 《The EMBO journal》2015,34(22):2840-2861
Mutations in the PTEN‐induced kinase 1 (PINK1) are causative of autosomal recessive Parkinson''s disease (PD). We have previously reported that PINK1 is activated by mitochondrial depolarisation and phosphorylates serine 65 (Ser65) of the ubiquitin ligase Parkin and ubiquitin to stimulate Parkin E3 ligase activity. Here, we have employed quantitative phosphoproteomics to search for novel PINK1‐dependent phosphorylation targets in HEK (human embryonic kidney) 293 cells stimulated by mitochondrial depolarisation. This led to the identification of 14,213 phosphosites from 4,499 gene products. Whilst most phosphosites were unaffected, we strikingly observed three members of a sub‐family of Rab GTPases namely Rab8A, 8B and 13 that are all phosphorylated at the highly conserved residue of serine 111 (Ser111) in response to PINK1 activation. Using phospho‐specific antibodies raised against Ser111 of each of the Rabs, we demonstrate that Rab Ser111 phosphorylation occurs specifically in response to PINK1 activation and is abolished in HeLa PINK1 knockout cells and mutant PINK1 PD patient‐derived fibroblasts stimulated by mitochondrial depolarisation. We provide evidence that Rab8A GTPase Ser111 phosphorylation is not directly regulated by PINK1 in vitro and demonstrate in cells the time course of Ser111 phosphorylation of Rab8A, 8B and 13 is markedly delayed compared to phosphorylation of Parkin at Ser65. We further show mechanistically that phosphorylation at Ser111 significantly impairs Rab8A activation by its cognate guanine nucleotide exchange factor (GEF), Rabin8 (by using the Ser111Glu phosphorylation mimic). These findings provide the first evidence that PINK1 is able to regulate the phosphorylation of Rab GTPases and indicate that monitoring phosphorylation of Rab8A/8B/13 at Ser111 may represent novel biomarkers of PINK1 activity in vivo. Our findings also suggest that disruption of Rab GTPase‐mediated signalling may represent a major mechanism in the neurodegenerative cascade of Parkinson''s disease. 相似文献
84.
85.
Kyle Lapham Mark N. Kvale Jue Lin Sheryl Connell Lisa A. Croen Brad P. Dispensa Lynn Fang Stephanie Hesselson Thomas J. Hoffmann Carlos Iribarren Eric Jorgenson Lawrence H. Kushi Dana Ludwig Tetsuya Matsuguchi William B. McGuire Sunita Miles Charles P. Quesenberry Jr. Sarah Rowell Marianne Sadler Lori C. Sakoda David Smethurst Carol P. Somkin Stephen K. Van Den Eeden Lawrence Walter Rachel A. Whitmer Pui-Yan Kwok Neil Risch Catherine Schaefer Elizabeth H. Blackburn 《Genetics》2015,200(4):1061-1072
The Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort includes DNA specimens extracted from saliva samples of 110,266 individuals. Because of its relationship to aging, telomere length measurement was considered an important biomarker to develop on these subjects. To assay relative telomere length (TL) on this large cohort over a short time period, we created a novel high throughput robotic system for TL analysis and informatics. Samples were run in triplicate, along with control samples, in a randomized design. As part of quality control, we determined the within-sample variability and employed thresholds for the elimination of outlying measurements. Of 106,902 samples assayed, 105,539 (98.7%) passed all quality control (QC) measures. As expected, TL in general showed a decline with age and a sex difference. While telomeres showed a negative correlation with age up to 75 years, in those older than 75 years, age positively correlated with longer telomeres, indicative of an association of longer telomeres with more years of survival in those older than 75. Furthermore, while females in general had longer telomeres than males, this difference was significant only for those older than age 50. An additional novel finding was that the variance of TL between individuals increased with age. This study establishes reliable assay and analysis methodologies for measurement of TL in large, population-based human studies. The GERA cohort represents the largest currently available such resource, linked to comprehensive electronic health and genotype data for analysis. 相似文献
86.
Hoffmann TJ Kvale MN Hesselson SE Zhan Y Aquino C Cao Y Cawley S Chung E Connell S Eshragh J Ewing M Gollub J Henderson M Hubbell E Iribarren C Kaufman J Lao RZ Lu Y Ludwig D Mathauda GK McGuire W Mei G Miles S Purdy MM Quesenberry C Ranatunga D Rowell S Sadler M Shapero MH Shen L Shenoy TR Smethurst D Van den Eeden SK Walter L Wan E Wearley R Webster T Wen CC Weng L Whitmer RA Williams A Wong SC Zau C Finn A Schaefer C Kwok PY Risch N 《Genomics》2011,98(2):79-89
The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies. 相似文献
87.
Since its discovery in the winter of 2005-2006, white-nose syndrome (WNS) has killed over one million little brown bats (Myotis lucifugus) in the American northeast. Although many studies have reported die-offs of bats at winter hibernacula, it is important to understand how bat mortality linked to WNS at winter hibernacula affects bat activity levels in their summer ranges. In the summer (May-August) of 2007, 2008 and 2009, we recorded echolocation calls to determine bat activity at sites along the Hudson River, NY (within approx. 100 km of where WNS was first reported). We documented a 78 per cent decline in the summer activity of M. lucifugus, coinciding with the arrival and spread of WNS. We suggest that mortality of M. lucifugus in winter hibernacula is reflected by reduced levels of activity in the summer and that WNS affects the entire bat population of an area, and not only individual hibernacula. 相似文献
88.
89.
McGuire IC Davis JE Double ML MacDonald WL Rauscher JT McCawley S Milgroom MG 《Molecular ecology》2005,14(12):3657-3669
Heterokaryosis was recently reported in the chestnut blight fungus, Cryphonectria parasitica, in which individuals contain nuclei that are isogenic except at the mating-type locus (MAT). MAT heterokaryons were found in several natural populations, including a putatively clonal population in West Salem, Wisconsin, providing an opportunity to address the question of how heterokaryons arise. We represented relationships among RFLP fingerprint haplotypes as networks in which loop formation is considered evidence of recombination. From 1990 to 1995, this population was clonal, as indicated by a simple haplotype network without loops, and the correlation of vegetative compatibility (vc) types and mating types with haplotype lineages. By 1999, we observed loops in the haplotype network involving isolates of two vc types (WS-2 and WS-3). Isolates with haplotypes in the loops were either MAT heterokaryons, carried the opposite mating type from other isolates of the same vc type, and/or had two alleles at two or more codominant SCAR (sequence-characterized amplified region) loci. Segregation of markers and recombination were evident among single-spore isolates from one heterokaryon; these single-spore isolates had novel fingerprint haplotypes, also within the loops. In contrast, vc type WS-1, which comprises 85% of the population, was represented by a simple network with no loops, indicating a clonal lineage varying only by mutation. Almost all isolates of WS-1 had the same mating type; the exceptions were five isolates that were MAT heterokaryons. These results are consistent with the hypothesis that heterokaryons formed between vegetatively incompatible individuals, and recombination occurred by a parasexual process. 相似文献
90.
Tooth replacement poses many questions about development, pattern formation, tooth attachment mechanisms, functional morphology and the evolution of vertebrate dentitions. Although most vertebrate species have polyphyodont dentitions, detailed knowledge of tooth structure and replacement is poor for most groups, particularly actinopterygians. We examined the oral dentition of the bluefish, Pomatomus saltatrix, a pelagic and coastal marine predator, using a sample of 50 individuals. The oral teeth are located on the dentary and premaxillary bones, and we scored each tooth locus in the dentary and premaxillary bones using a four-part functional classification: absent (A), incoming (I), functional (F=fully ankylosed) or eroding (E). The homodont oral teeth of Pomatomus are sharp, deeply socketed and firmly ankylosed to the bone of attachment. Replacement is intraosseus and occurs in alternate tooth loci with long waves of replacement passing from rear to front. The much higher percentage of functional as opposed to eroding teeth suggests that replacement rates are low but that individual teeth are quickly lost once erosion begins. Tooth number increases ontogenetically, ranging from 15–31 dentary teeth and 15–39 premaxillary teeth in the sample studied. Teeth increase in size with every replacement cycle. Remodeling of the attachment bone occurs continuously to accommodate growth. New tooth germs originate from a discontinuous dental lamina and migrate from the lingual (dentary) or labial (premaxillary) epithelium through pores in the bone of attachment into the resorption spaces beneath the existing teeth. Pomatomus shares unique aspects of tooth replacement with barracudas and other scombroids and this supports the interpretation that Pomatomus is more closely related to scombroids than to carangoids. 相似文献