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"Manly, Brian"
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Mitochondrial DNA Analysis Reveals Substantial Population Structure within the Endangered Black-Capped Petrel (Pterodroma hasitata)
by
Lee, Davis S.
,
Arbogast, Brian S.
,
Tuinen, Marcel Van
in
birds
,
Black-capped Petrel
,
body size
2013
Despite being listed as endangered, substantial morphological and behavioral variation exists within Black-capped Petrel (Pterodroma hasitata) populations. To examine the population genetic structure of the Black-capped Petrel, we amplified Cytochrome Oxidase 1 sequences from museum specimens collected during 1970–1980 off the coast of North Carolina, USA. These sequences revealed a 1.2% fixed genetic difference between dark and light morphs. Individuals with intermediate plumage all grouped phylogenetically with the light morph. Combined with significant differences in body size and phenology, our genetic results suggest breeding isolation of the dark and light morphs. Consistent with other Pterodroma species, our results imply that the Black-capped Petrel may comprise two distinct, reproductively isolated taxa. Further knowledge about the genetic identity of birds at specific nesting colonies will be valuable for geographic delineation of populations.
Journal Article
FOR THE RECORD
EDITOR: I am writing to clarify a story written about Mitsubishi Motors in the Washington Post, reprinted in The Press Democrat July 7. It is a story about a \"safety scandal\" at Mitsubishi Motors Corporation in Japan. First of all, the story is old news. Second, I am writing because I had to turn to page two of the article, seven paragraphs into the story, before a sentence appeared stating, \"none of the defective cars or trucks were sent to the United States.\"
Newspaper Article
Combined Expression Trait Correlations and Expression Quantitative Trait Locus Mapping
2006
Coordinated regulation of gene expression levels across a series of experimental conditions provides valuable information about the functions of correlated transcripts. The consideration of gene expression correlation over a time or tissue dimension has proved valuable in predicting gene function. Here, we consider correlations over a genetic dimension. In addition to identifying coregulated genes, the genetic dimension also supplies us with information about the genomic locations of putative regulatory loci. We calculated correlations among approximately 45,000 expression traits derived from 60 individuals in an F2 sample segregating for obesity and diabetes. By combining the correlation results with linkage mapping information, we were able to identify regulatory networks, make functional predictions for uncharacterized genes, and characterize novel members of known pathways. We found evidence of coordinate regulation of 174 G protein-coupled receptor protein signaling pathway expression traits. Of the 174 traits, 50 had their major LOD peak within 10 cM of a locus on Chromosome 2, and 81 others had a secondary peak in this region. We also characterized a Riken cDNA clone that showed strong correlation with stearoyl-CoA desaturase 1 expression. Experimental validation confirmed that this clone is involved in the regulation of lipid metabolism. We conclude that trait correlation combined with linkage mapping can reveal regulatory networks that would otherwise be missed if we studied only mRNA traits with statistically significant linkages in this small cross. The combined analysis is more sensitive compared with linkage mapping alone.
Journal Article
Rehabilitation of Executive Functioning in Patients with Frontal Lobe Brain Damage with Goal Management Training
by
O'Connor, Charlene
,
Stuss, Donald T.
,
Schweizer, Tom A.
in
Aging
,
Attention deficit hyperactivity disorder
,
Attention task
2011
Executive functioning deficits due to brain disease affecting frontal lobe functions cause significant real-life disability, yet solid evidence in support of executive functioning interventions is lacking. Goal Management Training (GMT), an executive functioning intervention that draws upon theories concerning goal processing and sustained attention, has received empirical support in studies of patients with traumatic brain injury, normal aging, and case studies. GMT promotes a mindful approach to complex real-life tasks that pose problems for patients with executive functioning deficits, with a main goal of periodically stopping ongoing behavior to monitor and adjust goals. In this controlled trial, an expanded version of GMT was compared to an alternative intervention, Brain Health Workshop that was matched to GMT on non-specific characteristics that can affect intervention outcome. Participants included 19 individuals in the chronic phase of recovery from brain disease (predominantly stroke) affecting frontal lobe function. Outcome data indicated specific effects of GMT on the Sustained Attention to Response Task as well as the Tower Test, a visuospatial problem-solving measure that reflected far transfer of training effects. There were no significant effects on self-report questionnaires, likely owing to the complexity of these measures in this heterogeneous patient sample. Overall, these data support the efficacy of GMT in the rehabilitation of executive functioning deficits.
Journal Article
SIMPSON'S IMAGE WAS MORE PERFECT THAN TRUE `THE JUICE' OVERCAME IMPOSSIBLE ODDS BUT REMAINED `ON THE EDGE OF TROUBLE'
Several dozen of Simpson's friends, teammates and business associates interviewed over the last week, as well as reams of court documents, provide small hints that the image of Simpson was more perfect than true. There were allegations of cocaine use in Buffalo, widespread womanizing throughout his careers and, most recently, hints that his finances, while strong, were the source of some worry. Still, from the potholed streets of the San Francisco ghetto where he grew up to the gold-lined boulevards of West Los Angeles where he lived, those who knew Simpson are amazed at what has befallen. Marguerite Whitley was Simpson's high school sweetheart; he stole her from his best friend, Al Cowlings, married her and later divorced her in 1980, only months after their 23-month-old daughter, Aaren, drowned in their swimming pool. Whitley described Simpson's early life in a 1968 Look magazine interview.
Newspaper Article
Rare variant associations with late‐life cognitive performance
2025
Background Despite evidence that Alzheimer's Disease (AD) is a highly heritable disease, there remains substantial “missing” heritability, likely due to the clinical and neuropathologic heterogeneity inherent in the disease. Here, we leverage sensitive longitudinal cognitive measures as endophenotypes in a rare variant analysis to identify novel genetic drivers of cognitive decline in aging and disease. Method We leveraged 8 cohorts of cognitive aging with whole genome sequencing data from the AD Sequencing Project to conduct rare variant analyses of multiple domains of cognition (N = 8,481; mean age=73; 56% female; 52% cognitively unimpaired). Harmonized scores for memory, executive function, and language were derived using confirmatory factor analysis models. Longitudinal scores were generated for each domain using linear mixed model regressions. Participants of European ancestry inferred using SNPweights and 1000G reference panel were included. Variants included had a minor allele frequency < 0.01 and were annotated as a high or moderate impact SNP using VEP. We performed SKAT‐O testing for genes with at least two variants contributing and with a minimum aggregate minor allele count >10. All tests were adjusted for sex, baseline age at cognitive assessment, sequencing center and platform, and the first 5 principal components of genetic ancestry. Correction for multiple comparisons was completed using the false discovery rate (FDR) procedure. Result We identified 9 genes associated with our cognitive domains. Two genes (APOE, PSEN1) were associated with baseline memory (both pFDR=0.07), one (PEDS1‐UBE2V1) with baseline language (pFDR=0.01), and six (HPN, HPN‐AS1, GAB1, CXCL3, SIGIRR, PLA2G4A) with executive function decline (pFDR range=0.01‐0.08). SIGIRR, PLA2G4A, and HPN all had high impact variants contributing to the gene score that were significantly associated with executive function decline. Conclusion These results highlight novel rare variants associated with cognition. GAB1 is an AGORA nominated gene target for potential AD treatment. Decreased expression was found in cholinergic neurons in AD patients and decreased learning and memory in a mouse model of AD. PLA2G4A has increased expression in AD patients that is evident in early stages but is decreased in healthy aging brains. Future work will incorporate other ancestries.
Journal Article
Basic Science and Pathogenesis
2025
Despite evidence that Alzheimer's Disease (AD) is a highly heritable disease, there remains substantial \"missing\" heritability, likely due to the clinical and neuropathologic heterogeneity inherent in the disease. Here, we leverage sensitive longitudinal cognitive measures as endophenotypes in a rare variant analysis to identify novel genetic drivers of cognitive decline in aging and disease.
We leveraged 8 cohorts of cognitive aging with whole genome sequencing data from the AD Sequencing Project to conduct rare variant analyses of multiple domains of cognition (N = 8,481; mean age=73; 56% female; 52% cognitively unimpaired). Harmonized scores for memory, executive function, and language were derived using confirmatory factor analysis models. Longitudinal scores were generated for each domain using linear mixed model regressions. Participants of European ancestry inferred using SNPweights and 1000G reference panel were included. Variants included had a minor allele frequency < 0.01 and were annotated as a high or moderate impact SNP using VEP. We performed SKAT-O testing for genes with at least two variants contributing and with a minimum aggregate minor allele count >10. All tests were adjusted for sex, baseline age at cognitive assessment, sequencing center and platform, and the first 5 principal components of genetic ancestry. Correction for multiple comparisons was completed using the false discovery rate (FDR) procedure.
We identified 9 genes associated with our cognitive domains. Two genes (APOE, PSEN1) were associated with baseline memory (both p
=0.07), one (PEDS1-UBE2V1) with baseline language (p
=0.01), and six (HPN, HPN-AS1, GAB1, CXCL3, SIGIRR, PLA2G4A) with executive function decline (p
range=0.01-0.08). SIGIRR, PLA2G4A, and HPN all had high impact variants contributing to the gene score that were significantly associated with executive function decline.
These results highlight novel rare variants associated with cognition. GAB1 is an AGORA nominated gene target for potential AD treatment. Decreased expression was found in cholinergic neurons in AD patients and decreased learning and memory in a mouse model of AD. PLA2G4A has increased expression in AD patients that is evident in early stages but is decreased in healthy aging brains. Future work will incorporate other ancestries.
Journal Article
Novel rare variant associations with late‐life cognitive performance
2025
Background Despite evidence that Alzheimer’s disease (AD) is highly heritable, there remains substantial “missing” heritability, likely due in part to the effect of rare variants and to the past reliance on case‐control analysis. Here, we leverage powerful endophenotypes of AD (cognitive performance across multiple cognitive domains) in a rare variant analysis to identify novel genetic drivers of cognition in aging and disease. Method We leveraged 8 cohorts of cognitive aging with whole genome sequencing data from the AD Sequencing Project to conduct rare variant analyses of multiple domains of cognition (N = 9,317; mean age = 73; 56% female; 52% cognitively unimpaired). Harmonized scores for memory, executive function, and language were derived using confirmatory factor analysis models. Participants genetically similar to the 1000Genomes EUR reference panel were included in analysis. Variants included in the analysis had a minor allele frequency < 0.01, a minor allele count of ≥ 10, and were annotated as a high or moderate impact SNP using VEP. Associations of baseline scores in each cognitive domain were performed using SKAT‐O, including 92,905 rare variants among 16,243 genes. All tests were adjusted for sex, baseline age, sequencing center and platform, and genetic principal components. Correction for multiple comparisons was completed using the Benjamini‐Hochberg false discovery rate (FDR) procedure. Result APOE was associated with baseline memory, language, and executive function, though only memory survived multiple‐test correction (p.FDR = 0.001). Outside of APOE, ITPKB was associated with baseline executive function (p.FDR = 0.048). AKTIP, SHCBP1L, and CCNF showed nominal associations with multiple domains of cognition that did not survive correction for multiple comparisons (p.FDRs<0.07). Conclusion These results highlight novel rare variants associated with cognition. IPTKB is an AGORA nominated gene target for potential AD treatment. It is important in the regulation of immune cells and displays higher expression in the cortex of AD patients compared to controls. CCNF and AKTIP are brain eQTLs and have differential RNA expression in AD brains. Previously, variants in AKTIP have been associated with educational attainment, intelligence, and memory, while variants in CCNF have been associated with neuritic plaques and neurofibrillary tangles. Future analyses will incorporate longitudinal cognition and expand into additional populations.
Journal Article
How carefully crafte image was shattered by killings
Marguerite Whitley was O.J.'s high school sweetheart. Simpson stole her from [Al Cowlings], married her and later divorced her in 1980, only months after their 23-month-old daughter, Aaren, drowned in their swimming pool. As a senior, Simpson's team took on mighty St. Ignatius, winners of 23 straight. As expected, Galileo trailed, 25-10, and then Simpson took over, scoring touchdowns of 90, 80 and 60 yards for the biggest upset in the city's high school history. Simpson's transformation from college golden boy to professional superstar occurred in Buffalo, a hard-scrabble city in an economic downturn. The city needed a spark, a savior of sorts, and it came in the form of Simpson, the prize draft choice of the Buffalo Bills.
Newspaper Article
O.J. - trouble under the surface Accounts emerge of violence, drug use, financial woes that belie a well-cultivated image
PHOTO; CAPTION:1. At his San Francisco high school, [O.J. Simpson] moved in two social worlds. / FILE PHOTO 2. 1975 -- Simpson, a Hall of Fame running back with the Buffalo Bills, eludes Patriots linebacker Kevin Reilly with another of his electrifying moves. / GLOBE STAFF PHOTO / GEORGE RIZER 3. 1993 -- [Nicole Brown Simpson] and son Justin join Simpson on the sideline during a Thanksgiving game in Texas. / AP PHOTO 4. 1968 -- The Heisman Trophy, awarded to college football's finest player. / UPI PHOTO 5. 1977 -- The TV drama \"Roots\" cast Simpson as an African tribesman giving a lesson in manners. / AP PHOTO 6. 1994 -- After Friday's chase, a mug shot by Los Angeles police. / AP PHOTO 7. 1973 - Simpson with [Marguerite Whitley] and their children, Jason and Arnelle. / AP PHOTO 8. 1988 -- Relaxing on the grounds of his estate, Simpson enjoys time with his daughter Sydney. / DEWEY HICKS/OUTLINE PHOTO 9. 1991 - The dashing Hollywood couple: O.J. and Nicole Simpson. / GERARDO SOMOZA / OUTLINE PHOTO 10. 1980 - At \"O.J. Simpson Day\" in Buffalo, the star's parents and son joined him for the ceremonies retiring his number. / UPI PHOTO 11. 1992 - Simpson with [Paula Barbieri], a model he began dating over a year ago. / GERARDO SOMOZA / OUTLINE PHOTO 12. 1970s - Running for Hertz in a series of ads made Simpson famous among the non-sporting public as well. / AP PHOTO
Newspaper Article