A5055473294- Bioinformatics and Genomic Networks
- Alzheimer's disease research and treatments
- Animal Behavior and Reproduction
- Genetic Associations and Epidemiology
- Genetic diversity and population structure
- Neuroinflammation and Neurodegeneration Mechanisms
- Marine animal studies overview
- Neuroendocrine regulation and behavior
- Fish Ecology and Management Studies
- Metabolomics and Mass Spectrometry Studies
- Aquaculture disease management and microbiota
- Gene expression and cancer classification
- RNA Research and Splicing
- Retinal Development and Disorders
- Physiological and biochemical adaptations
- Reproductive biology and impacts on aquatic species
- Animal Genetics and Reproduction
- Cancer-related molecular mechanisms research
- Health, Environment, Cognitive Aging
- Dementia and Cognitive Impairment Research
- Genetic and phenotypic traits in livestock
- Marine and fisheries research
- Hypothalamic control of reproductive hormones
- Photochromic and Fluorescence Chemistry
- Bat Biology and Ecology Studies
Sage Bionetworks
2019-2024
Stanford University
2003-2016
Fred Hutch Cancer Center
2010-2016
Seattle University
2013-2014
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2012
Marine Biological Laboratory
2010
University College Cork
2001
Abstract The availability of high-quality RNA-sequencing and genotyping data post-mortem brain collections from consortia such as CommonMind Consortium (CMC) the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) enable generation a large-scale cis- eQTL meta-analysis. Here we generate cerebral cortical 1433 samples available four cohorts (identifying >4.1 million significant >18,000 genes), well cerebellar 261 874,836 >10,000 genes). We find substantially improved...
Corticosteroid hormones, including the mineralocorticoids and glucocorticoids, regulate diverse physiological functions in vertebrates. These hormones act through two classes of corticosteroid receptors (CR) that are ligand-dependent transcription factors: type I or mineralocorticoid receptor (MR) II glucocorticoid (GR). There is substantial overlap binding these types to DNA. In fish, processes controlled by CRs may be different from other vertebrates, as fish thought synthesize only...
Neuropeptides have widespread modulatory effects on behaviour and physiology are associated with phenotypic transitions in a variety of animals. Arginine vasotocin (AVT) is implicated mediating alternative male phenotypes teleost fish, but the direction association differs among species, either higher or lower AVT related to more territorial different fishes. To clarify complex relationship between phenotype, we evaluated expression an African cichlid which social status divergent...
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on has focused those that are “intrinsic,” meaning they affect viability and sterility in laboratory. Theory predicts ecological selection can also underlie hybrid incompatibilities, but tests this hypothesis using sequence data scarce. In article, we compiled genetic for F 2 crosses divergent populations threespine stickleback fish ( Gasterosteus...
Abstract The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares and other resources generated by multiple collaborative research programs focused on aging, dementia, Alzheimer's disease (AD). In this article, we highlight how to use the discover download genomic variant transcriptomic from same individuals. First, show web interface browse search for of interest using relevant file annotations. We demonstrate learn more about context surrounding data,...
Abstract INTRODUCTION Multi-omics studies in Alzheimer’s disease (AD) revealed many potential pathways and therapeutic targets. Despite their promise of precision medicine, these lacked African Americans (AA) Latin (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTS We generated data curated harmonized phenotypic from AA (n=306), LA (n=326), or (n=4)...
Identifying the proximate and ultimate mechanisms of social behavior remains a major goal behavioral biology. In particular, complex interactions mediating schooling have long fascinated biologists, leading to theoretical empirical investigations that focused on as group-level phenomenon. However, methods examine individual fish within school are needed in order investigate underlie both performance evolution behavior. We developed technique quantify an standardized but easily manipulated...
Abstract The temporal molecular changes that lead to disease onset and progression in Alzheimer’s (AD) are still unknown. Here we develop a model for these unobserved with manifold learning method applied RNA-Seq data collected from human postmortem brain samples within the ROS/MAP Mayo Clinic studies. We define an ordering across based on their similarity gene expression use this estimate stage–or pseudotime-for each sample. Disease pseudotime is strongly concordant burden of tau (Braak...
Abstract Background Alzheimer’s disease (AD) is an incurable neurodegenerative currently affecting 1.75% of the US population, with projected growth to 3.46% by 2050. Identifying common genetic variants driving differences in transcript expression that confer AD risk necessary elucidate mechanism and develop therapeutic interventions. We modify FUSION transcriptome-wide association study (TWAS) pipeline ingest gene values from multiple neocortical regions. Methods A combined dataset 2003...
Abstract INTRODUCTION Multi‐omics studies in Alzheimer's disease (AD) revealed many potential pathways and therapeutic targets. Despite their promise of precision medicine, these lacked Black Americans (BA) Latin (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership Disease (AMP‐AD) expanded brain multi‐omics profiling to multi‐ethnic donors. RESULTS We generated data curated harmonized phenotypic from BA ( n = 306), LA 326), or 4)...
Adaptation to a new environment can be facilitated by co-inheritance of suite phenotypes that are all advantageous in the habitat. Although experimental evidence demonstrates multiple often map same genomic regions, it is challenging determine whether associated due pleiotropic effects single gene or tightly linked genes. In threespine stickleback fish (Gasterosteus aculeatus), with region around Ectodysplasin (Eda), but only presence bony lateral plates has been conclusively shown caused...
Despite longstanding interest in the genetic mechanisms that underlie behavioral evolution, very few genes naturally occurring variation behavior between individuals or species are known, particularly vertebrates. Here, we build on our previous forward mapping experiments and use transgenic approaches to identify Ectodysplasin as a gene causes differences schooling wild populations of threespine stickleback (Gasterosteus aculeatus) fish. This work provides rare insight into proximate have...
Pigment pattern variation across species or populations offers a tractable framework in which to investigate the evolution of development. Juvenile threespine sticklebacks (Gasterosteus aculeatus) from marine and freshwater environments exhibit divergent pigment patterns that are associated with ecological differences. have silvery appearance, whereas vertical bars. We investigated both developmental molecular basis this population-level pattern. Time course imaging during transition larval...
Abstract Although there is a heritable basis for many animal behaviors, the genetic architecture of behavioral variation in natural populations remains mostly unknown, particularly vertebrates. We sought to identify social affiliation two threespine sticklebacks (Gasterosteus aculeatus) that differ their propensity school. Marine from Japan school strongly whereas benthic lake Canada are more solitary. Here, we expanded on our previous efforts quantitative trait loci (QTL) differences...
Identifying genes that are differentially expressed in response to social interactions is informative for understanding the molecular basis of behavior. To address this question, we described changes gene expression as a result differences extent interactions. We housed threespine stickleback (Gasterosteus aculeatus) females either group conditions or individually one week, then measured levels three brain regions using RNA-sequencing. found numerous hindbrain/cerebellum had altered...
Variation in reproductive capacity is common across the lives of all animals. In vertebrates, hypothalamic neurons that secrete GnRH are a primary mediator such plasticity. Since social interactions suppress gonadal maturity African cichlid fish, Astatotilapia (Haplochromis) burtoni, we investigated whether electrical properties were also socially regulated. Adult A. burtoni males either territorial (T) and reproductively active or nonterritorial (NT) regressed, depending upon their...
In fish the terminal nerve is comprised of a group cells with somata adjacent to olfactory bulb and processes that extend both anteriorly mucosa posteriorly telencephalon. teleost an additional axons extends along optic tract delivers putative neuromodulators retina. One peptide – gonadotropin-releasing hormone (GnRH) has been implicated as prime candidate neuromodulator based on electrophysiological evidence exogenous application influences neural activity. Here we describe expression...
Dopamine regulates reproduction in part by modulating neuronal activity within the hypothalamic-pituitary-gonadal (HPG) axis. Previous studies suggested numerous mechanisms which dopamine exerts inhibitory control over HPG axis, ultimately changing levels of sex steroids that regulate reproductive behaviors. However, it is not known whether these are conserved across vertebrate species. In particular, unknown underlying dopaminergic shared between mammals and teleost fish. mammals, directly...
Abstract The availability of high-quality RNA-sequencing and genotyping data post-mortem brain collections from consortia such as CommonMind Consortium (CMC) the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) enable generation a large-scale cis -eQTL meta-analysis. Here we generate cerebral cortical eQTL 1433 samples available four cohorts (identifying >4.1 million significant >18,000 genes), well cerebellar 261 874,836 >10,000 provide results community...
Despite the key function of Mauthner cells (M-cells) in initiating escape responses and thereby promoting survival, there are multiple examples M-cell loss across teleost phylogeny. Only a few studies have directly considered behavioral consequences naturally occurring variation species. We chose to examine this issue pufferfishes, as previous research suggested that might be variability anatomy group fish. characterized fast-start two pufferfish species, Tetraodon nigroviridis Diodon...
ABSTRACT INTRODUCTION Embedding single-omics disease associations into the wider context of multi-level molecular changes in Alzheimer’s (AD) remains one central challenge AD research. METHODS Results from numerous AD-specific omics studies AMP-AD, NIAGADS, and other initiatives were integrated a comprehensive network resource complemented with large-scale population-based to provide global view on AD. RESULTS We present Atlas, an online ( www.adatlas.org ) integrating over 20 large...
Zooplankton was collected by a diver-towed net close to the substratum at four depths (0, 6, 12 and 18 m) over 17 month period in three locations Lough Hyne, Co. Cork, Ireland. identified phylum or class levels mean numbers were calculated for each taxon, site depth. Seasonality observed several meroplanktonic groups (Echinodermata, Nemertea, Mollusca fish postlarvae), gelatinous zooplankton. Depth preference found be statistically significant polychaetes (larvae pelagic species), molluscan...