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  • 1
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    Online Resource
    Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 46 ( 2022-11-15)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 46 ( 2022-11-15)
    Abstract: Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] 〈 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance ( P 〈 3.64e–7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense ( n = 41) or truncating ( n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden ( DDX3X , MECP2 , WDR45 , and HDAC8) . This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2203491119
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 2
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    De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Abstract: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains 〈 1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1902766117
    RVK:
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    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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    detail.hit.zdb_id: 1461794-8
    SSG: 11
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  • 3
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    History of Previous Midlife Estradiol Treatment Permanently Alters Interactions of Brain Insulin-like Growth Factor-1 Signaling and Hippocampal Estrogen Synthesis to Enhance Cognitive Aging in a Rat Model of Menopause
    Society for Neuroscience ; 2022
    In:  The Journal of Neuroscience Vol. 42, No. 42 ( 2022-10-19), p. 7969-7983
    Details
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 42, No. 42 ( 2022-10-19), p. 7969-7983
    Abstract: Across species, including humans, elevated levels of brain estrogen receptor (ER) α are associated with enhanced cognitive aging, even in the absence of circulating estrogens. In rodents, short-term estrogen treatment, such as that commonly used in the menopausal transition, results in long-term increases in ERα levels in the hippocampus, leading to enhanced memory long after termination of estrogen treatment. However, mechanisms by which increased levels of brain ERα enhances cognitive aging remain unclear. Here we demonstrate in aging female rats that insulin-like growth factor-1 (IGF-1), which can activate ER via ligand-independent mechanisms, requires concomitant synthesis of brain-derived neuroestrogens to phosphorylate ERα via MAPK signaling, ultimately resulting in enhanced memory. In a rat model of menopause involving long-term ovarian hormone deprivation, hippocampal neuroestrogen activity decreases, altering IGF-1 activity and resulting in impaired memory. However, this process is reversed by short-term estradiol treatment. Forty days of estradiol exposure following ovariectomy results in maintenance of neuroestrogen levels that persist beyond the period of hormone treatment, allowing for continued interactions between IGF-1 and neuroestrogen signaling, elevated levels of hippocampal ERα, and ultimately enhanced memory. Collectively, results demonstrate that short-term estradiol use following loss of ovarian function has long-lasting effects on hippocampal function and memory by dynamically regulating cellular mechanisms that promote activity of ERα in the absence of circulating estrogens. Translational impacts of these findings suggest lasting cognitive benefits of short-term estrogen use near menopause and highlight the importance of hippocampal ERα, independent from the role of circulating estrogens, in regulating memory in aging females. SIGNIFICANCE STATEMENT Declines in ovarian hormones following menopause coincide with increased risk of cognitive decline. Because of potential health risks, current recommendations are that menopausal estrogen therapy be limited to a few years. Long-term consequences for the brain and memory of this short-term midlife estrogen therapy are unclear. Here, in a rodent model of menopause, we determined mechanisms by which short-term midlife estrogen exposure can enhance hippocampal function and memory with cognitive benefits and molecular changes enduring long after termination of estrogen exposure. Our model indicates long-lasting benefits of maintaining hippocampal estrogen receptor function in the absence of ongoing estrogen exposure and suggests potential strategies for combating age-related cognitive decline.
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    URL: Article
    DOI: 10.1523/JNEUROSCI.0588-22.2022
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2022
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  • 4
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    Apparent-time study of interdental-stopping among English-monolingual Finnish- and Italian-heritage Michiganders
    Acoustical Society of America (ASA) ; 2017
    In:  The Journal of the Acoustical Society of America Vol. 141, No. 5_Supplement ( 2017-05-01), p. 3983-3983
    Details
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 141, No. 5_Supplement ( 2017-05-01), p. 3983-3983
    Abstract: The production of coronal oral stops in place of interdental fricatives, referred to as interdental-stopping, has been documented in Michigan’s Upper Peninsula (UP) [3, 2], as well as, in other ethnic-heritage influenced English varieties. However, there is a lack of quantitative inquiry into the degree to which this salient feature is present among Michigan UP's now predominantly monolingual English-speaking communities; recent studies have focused primarily on the last remaining older-aged bilinguals [1] . Michigan’s UP is in an ideal position to examine to what extent this feature is present among a rural and predominantly monolingual English-speaking community. The present study examines 40 Finnish-Americans and 44 Italian-Americans, whom are all monolingual speakers from Michigan’s Marquette County. Both samples are stratified by age, sex, and socioeconomic status. All data are obtained from a passage task. To what degree, if any, does stopping occur among the Finnish- and Italian-heritage monolingual-English speaking communities? This study reveals interdental-stopping occurring most often among working-class males but least among Italian middle- and younger-aged groups. The study's apparent-time construct highlights a potential change in the covert prestige that has been typically associated with this feature among the older generation [1]. The decrease of interdental-stopping among the younger generation indicates a shift in the feature's prestige within the community.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    URL: Article
    DOI: 10.1121/1.4989102
    RVK:
    EQ 1000
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2017
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  • 5
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    The Geological Record of Ocean Acidification
    American Association for the Advancement of Science (AAAS) ; 2012
    In:  Science Vol. 335, No. 6072 ( 2012-03-02), p. 1058-1063
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 335, No. 6072 ( 2012-03-02), p. 1058-1063
    Abstract: Ocean acidification may have severe consequences for marine ecosystems; however, assessing its future impact is difficult because laboratory experiments and field observations are limited by their reduced ecologic complexity and sample period, respectively. In contrast, the geological record contains long-term evidence for a variety of global environmental perturbations, including ocean acidification plus their associated biotic responses. We review events exhibiting evidence for elevated atmospheric CO 2 , global warming, and ocean acidification over the past ~300 million years of Earth’s history, some with contemporaneous extinction or evolutionary turnover among marine calcifiers. Although similarities exist, no past event perfectly parallels future projections in terms of disrupting the balance of ocean carbonate chemistry—a consequence of the unprecedented rapidity of CO 2 release currently taking place.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1208277
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2012
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  • 6
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    Interdental-stopping among older-aged bilingual and monolingual Finnish- and Italian-heritage Upper Peninsula Michiganders
    Acoustical Society of America (ASA) ; 2017
    In:  The Journal of the Acoustical Society of America Vol. 141, No. 5_Supplement ( 2017-05-01), p. 3519-3519
    Details
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 141, No. 5_Supplement ( 2017-05-01), p. 3519-3519
    Abstract: The realization of interdental fricatives as coronal oral stops, referred to as interdental-stopping, is often attributed to substrate effects of ethnicity and immigrant-heritage. Michigan’s Upper Peninsula (UP) is an excellent case to examine this feature’s complex variation within bilingual and monolingual older-aged cross-sections of a rural immigrant speech community. To what degree, if any, is interdental-stopping occurring among Michigan’s UP Finnish and Italian-heritage speech communities? Interdental-stopping has been documented in UP English [3, 2], but only a more recent report has provided any quantitative account that tracks this salient feature and its sociophonetic trends within the community [1] . The present study examines this feature among 41 Finnish-Americans and 30 Italian-Americans, whom are all older-aged residents from Michigan’s Marquette County. Both samples are stratified by gender, socioeconomic status and lingua-dominance. All data is obtained from a reading passage task. This study reveals interdental-stopping occurring most often among Italian working-class males and least among English-dominant bilinguals. Such findings goes beyond the claim that this feature of UP English indexes working-class [2]. Interdental-stopping indexes working-class masculinity—held with prestige and used by older-aged, working-class males, primarily among Italians, as a linguistic marker of local identity in the UP English speech community.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    URL: Article
    DOI: 10.1121/1.4987400
    RVK:
    EQ 1000
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2017
    detail.hit.zdb_id: 1461063-2
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  • 7
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    Germline selection shapes human mitochondrial DNA diversity
    American Association for the Advancement of Science (AAAS) ; 2019
    In:  Science Vol. 364, No. 6442 ( 2019-05-24)
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 364, No. 6442 ( 2019-05-24)
    Abstract: Approximately 2.4% of the human mitochondrial DNA (mtDNA) genome exhibits common homoplasmic genetic variation. We analyzed 12,975 whole-genome sequences to show that 45.1% of individuals from 1526 mother–offspring pairs harbor a mixed population of mtDNA (heteroplasmy), but the propensity for maternal transmission differs across the mitochondrial genome. Over one generation, we observed selection both for and against variants in specific genomic regions; known variants were more likely to be transmitted than previously unknown variants. However, new heteroplasmies were more likely to match the nuclear genetic ancestry as opposed to the ancestry of the mitochondrial genome on which the mutations occurred, validating our findings in 40,325 individuals. Thus, human mtDNA at the population level is shaped by selective forces within the female germ line under nuclear genetic control, which ensures consistency between the two independent genetic lineages.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aau6520
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2019
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  • 8
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    Response to Comment on "Phytoplankton Calcification in a High-CO 2 World"
    American Association for the Advancement of Science (AAAS) ; 2008
    In:  Science Vol. 322, No. 5907 ( 2008-12-05), p. 1466-1466
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 322, No. 5907 ( 2008-12-05), p. 1466-1466
    Abstract: Recently reported increasing calcification rates and primary productivity in the coccolithophore Emiliania huxleyi were obtained by equilibrating seawater with mixtures of carbon dioxide in air. The noted discrepancy with previously reported decreasing calcification is likely due to the previously less realistic simulation of bicarbonate due to addition of acid or base to obtain simulated future CO 2 partial pressure conditions.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1161501
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2008
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 9
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    Comment on “Calcareous Nannoplankton Response to Surface-Water Acidification Around Oceanic Anoxic Event 1a”
    American Association for the Advancement of Science (AAAS) ; 2011
    In:  Science Vol. 332, No. 6026 ( 2011-04-08), p. 175-175
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 332, No. 6026 ( 2011-04-08), p. 175-175
    Abstract: Erba et al . (Reports, 23 July 2010, p. 428) attributed calcareous nannofossil morphology and assemblage changes across Cretaceous Oceanic Anoxic Event 1a to the effects of surface ocean acidification. We argue that the quality of carbonate preservation in these sequences, the unsupported assumptions of the biotic response to acidity, and the absence of independent proxy estimates for ocean pH or atmospheric p CO 2 render this conclusion questionable.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1199459
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2011
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 10
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    Phytoplankton Calcification in a High-CO 2 World
    American Association for the Advancement of Science (AAAS) ; 2008
    In:  Science Vol. 320, No. 5874 ( 2008-04-18), p. 336-340
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 320, No. 5874 ( 2008-04-18), p. 336-340
    Abstract: Ocean acidification in response to rising atmospheric CO 2 partial pressures is widely expected to reduce calcification by marine organisms. From the mid-Mesozoic, coccolithophores have been major calcium carbonate producers in the world's oceans, today accounting for about a third of the total marine CaCO 3 production. Here, we present laboratory evidence that calcification and net primary production in the coccolithophore species Emiliania huxleyi are significantly increased by high CO 2 partial pressures. Field evidence from the deep ocean is consistent with these laboratory conclusions, indicating that over the past 220 years there has been a 40% increase in average coccolith mass. Our findings show that coccolithophores are already responding and will probably continue to respond to rising atmospheric CO 2 partial pressures, which has important implications for biogeochemical modeling of future oceans and climate.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1154122
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2008
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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