A5015793566- Cancer Genomics and Diagnostics
- Genetics, Aging, and Longevity in Model Organisms
- Evolution and Genetic Dynamics
- Genomics and Rare Diseases
- Physiological and biochemical adaptations
- Plant and animal studies
- RNA modifications and cancer
- Livestock and Poultry Management
- Invertebrate Taxonomy and Ecology
- Genetic diversity and population structure
- Genomic variations and chromosomal abnormalities
- Insect and Arachnid Ecology and Behavior
- Agricultural pest management studies
- Sarcoma Diagnosis and Treatment
- Genetic factors in colorectal cancer
- Genomics and Phylogenetic Studies
- Animal Behavior and Reproduction
- Chromosomal and Genetic Variations
- Lepidoptera: Biology and Taxonomy
- Molecular Biology Techniques and Applications
- Lymphoma Diagnosis and Treatment
- Acute Myeloid Leukemia Research
- Insect-Plant Interactions and Control
- Invertebrate Immune Response Mechanisms
- Ferroptosis and cancer prognosis
Arima Genomics (United States)
2022-2025
University of Oregon
2014-2021
University of Minnesota
2015-2020
University of Mississippi
2019-2020
University of Arizona
2006
Adaptive phenotypic plasticity provides a mechanism of developmental rescue in novel and rapidly changing environments. Understanding the underlying is important for predicting both likelihood that response adaptive associated life-history trade-offs could influence patterns subsequent evolutionary rescue. Although evolved switches may move organisms toward new peak environment, such mechanisms often result maladaptive responses. The induction generalized physiological environments...
Unprecedented reorganization in a butterfly genome sheds light on the enigma of holocentric chromosome evolution.
Many organisms can acclimate to new environments through phenotypic plasticity, a complex trait that be heritable, subject selection, and evolve. However, the rate genetic basis of plasticity evolution remain largely unknown. We experimentally evolved outbred populations nematode Caenorhabditis remanei under an acute heat shock during early larval development. When raised in nonstressful environment, ancestral were highly sensitive 36.8° exhibited high mortality. initial exposure nonlethal...
Abstract High expression of MYC and its target genes identify germinal center B-cell diffuse large lymphomas (GCB-DLBCL) associated with poor outcomes. We used CRISPR-interference profiling human lymphoma cell lines to define essential enhancers in the locus non-immunoglobulin rearrangement partner loci, including a recurrent between BCL6 control region. GCB-DLBCL without are dependent on an evolutionarily-conserved enhancer we name “germinal 1” (GME-1), which is activated by transcription...
Standard techniques for detecting genomic rearrangements in formalin-fixed paraffin-embedded (FFPE) biopsies have important limitations and may miss with clinical significance. We performed FFPE-compatible Hi-C on 44 comprising large B-cell lymphomas (n=18), plasma cell neoplasms (n=14), other diverse lymphoid cancers. detected topological differences between malignant B states identified expected oncogene high concordance FISH. revealed enhancer-hijacking recurrent of BCL2, CCND1, MYC, as...
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups ependymoma are supratentorial ZFTA-fusion associated posterior fossa group A. In both groups, tumors occur mainly in young children frequently recur after treatment. Although mechanisms underlying these diseases have recently been uncovered, they remain difficult to target innovative therapeutic approaches urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C),...
Selection in novel environments can lead to a coordinated evolutionary response across suite of characters. Environmental conditions also potentially induce changes the genetic architecture complex traits, which turn could alter pattern multivariate selection. We describe factorial selection experiment using nematode Caenorhabditis remanei two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three environmental conditions. The covariation between...
Anthropogenic increases in nutrient availability offer opportunities to study evolutionary shifts sexual selection dynamics real time. A rapid increase may reduce the utility of condition-dependent ornaments as signals quality and lessen any nutritional benefits females from re-mating. We explored these ideas using cabbage white butterflies, focusing on nitrogen a nutrient, it is important this species not only ornamentation, but also key macronutrient transferred spermatophores. compared...
Abstract Organisms can cope with stressful environments via a combination of phenotypic plasticity at the individual level and adaptation population level. Changes in gene expression play an important role both. Significant advances our understanding regulatory evolution have come from comparative studies field laboratory. Experimental provides another powerful path by which to learn about how differential regulation genes pathways contributes both acclimation adaptation. Here we present...
Abstract The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, first to be explicitly consented for public dissemination genomic data cell lines. Here, we describe comprehensive dataset from individual, HG008, including DNA an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor line (HG008-T) normal cells duodenal tissue (HG008-N-D) (HG008-N-P). come thirteen whole...
Polymorphic loci exist throughout the genomes of a population and provide raw genetic material needed for species to adapt changes in environment. The minor allele frequencies rare Single Nucleotide Polymorphisms (SNPs) within have been difficult track with Next-Generation Sequencing (NGS), due high error rate standard methods such as Illumina sequencing.We developed wet-lab protocol variant-calling method that identifies both sequencing PCR errors, called Paired-End Low Error (PELE-Seq). To...
Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation crops, pesticides, fertilizers. Here, we begin develop the cabbage white butterfly (Pieris rapae) as a system test questions novel, agricultural environments. We focus on population north central United States unique case study: here, canola, host plant, has been grown during entire flight period of over last three...
HiC sequencing is a DNA-based next-generation method that preserves the 3D conformation of genome and has shown promise in detecting genomic rearrangements translational research studies. To evaluate as potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia sarcoma specimens previously positive for clinically significant rearrangements. Archived specimen types tested included viable nonviable frozen...
Organisms encounter a wide range of toxic compounds in their environments, from chemicals that serve anticonsumption or anticompetition functions to pollutants and pesticides. Although we understand many detoxification mechanisms allow organisms consume toxins typical diet, know little about why vary ability tolerate entirely novel toxins. We tested whether variation generalized stress responses, such as antioxidant pathways, may underlie reactions and, if so, associated costs. used an...
Abstract Among the parasites of insects, endoparasitoids impose a costly challenge to host defenses because they use their host’s body for development and maturation eggs or larvae, ultimately kill host. Tachinid flies are highly specialized acoustically orienting parasitoids, with first instar mobile larvae that burrow into feed. We investigated possibility Teleogryllus oceanicus field crickets employ postinfestation strategies maximize survival when infested parasitoid fly Ormia ochracea ....
Hi-C sequencing is a DNA-based next-generation method that preserves the 3D genome conformation and has shown promise in detecting genomic rearrangements translational research studies. To evaluate as potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia sarcoma specimens. Archived viable non-viable frozen leukemic cells formalin-fixed paraffin-embedded (FFPE) tumor specimens were analyzed. Pediatric acute...
Abstract The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. structure the genotype–phenotype maps is critical because pleiotropic effects can generate widespread correlated responses selection and potentially restrict extent change. In this study, we use experimental evolution dissect genetic architecture natural variation for acute heat stress oxidative response nematode Caenorhabiditis remanei....
Abstract Chromosome evolution, an important component of mico- and macroevolutionary dynamics 1–5 , presents enigma in the mega-diverse Lepidoptera 6 . While most species exhibit constrained chromosome with nearly identical haploid counts chromosome-level shared gene content collinearity among despite more than 140 Million years divergence 7 a small fraction independently dramatic changes chromosomal count due to extensive fission fusion events that are facilitated by their holocentric...