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46
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Introduction
Current institution
Additional affiliations
January 2015 - January 2016
Publications
Publications (46)
Microalgae remain an important feedstock in the circular bioeconomy. The discovery of new species combined with advanced biotechnology drives optimization of performance predicated on deep knowledge of algal genomics and phenotype. Understanding the contribution of epigenetic processes to algal function provides insight and better approaches for ac...
Epigenetic processes play key roles in regulating gene expression, genome stability, and metabolic output in organisms across the tree of life. Yet, the role epigenetics plays in regulating genomes and behaviors remains underdeveloped for microalgae, particularly as new species are identified and characterized. This is likely due to the cumbersome...
Environmental toxins and pathogens can influence epigenetic modifications on chromosomes, thereby leaving trace evidence of exposures. However, the avalanche of epigenomic data is difficult to parse for biological interpretation given non-linear complex patterns and relationships. This attractive challenge in epigenomic data lends itself to machine...
Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-...
Microalgae remain an important feedstock for the production of biofuels and bioproducts. Discovery of new species drives innovation for biotransformation, where bioengineering and other technological advances can significantly optimize performance. Production is predicated on deep knowledge of algal behavior predicted from genomic and phenotypic st...
The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structu...
Chromatin conformation capture followed by next-generation sequencing in combination with large-scale polymer simulations (4DHiC) produces detailed information on genomic loci interactions, allowing for the interrogation of 3D spatial genomic structures. Here, Hi-C data was acquired from the infection of fetal lung fibroblast (MRC5) cells with α-co...
Background
Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessi...
Genomic DNA folds into complex configurations that produce particular local and global structures thought to profoundly impact genome function. To understand the dynamic nature of this relationship, we investigated the extent of host chromatin structural and functional changes in response to a viral agent. We performed comprehensive assessments of...
Background and Aims
Beneficial plant–microbe interactions can improve plant performance under drought; however, we know less about how drought-induced shifts in microbial communities affect plant traits.
Methods
We cultivated Zea mays in fritted clay with soil microbiomes originating from contrasting environments (agriculture or forest) under two...
Background
Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessi...
The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physi...
Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism’s molecular adaptation to the environment, resulting in distinctive phenotypes. Epigeneti...
Roadside proximity and exposure to mixed vehicular emissions (MVE) have been linked to adverse pulmonary and vascular outcomes. However, because of the complex nature of the contribution of particulate matter (PM) versus gases, it is difficult to decipher the precise causative factors regarding PM and the copollutant gaseous fraction. To this end,...
A high-quality draft genome sequence of the microalgal species Tetraselmis striata was generated using PacBio sequencing. The assembled genome is 228 Mb, derived from 3,613 polished contigs at 84× coverage depth. This genome contains an average GC content of 57.9% and 48,906 predicted genes.
Ambient particulate matter (PM) is associated with increased mortality and morbidity, an effect influenced by the metal components of the PM. We characterized five sediment samples obtained near a tungsten-molybdenum ore-processing complex in Zakamensk, Russia for elemental composition and PM toxicity with regard to pulmonary, vascular, and neurolo...
Selection of highly productive algal strains is crucial for establishing economically viable biomass and biopro-duct cultivation systems. Characterization of algal genomes, including understanding strain-specific differences in genome content and architecture is a critical step in this process. Using genomic analyses, we demonstrate significant dif...
Several studies have demonstrated that exposure to arsenic in drinking water adversely affects brain development and cognitive function in adulthood. While the mechanism by which arsenic induces adverse neurological outcomes remains elusive, studies suggest a link between reduced levels of histone acetylation and impaired performance on a variety o...
Representative western blots for HDAC assessment in male and female frontal cortex with and without valproate treatment.
Representative western blot probed for GAPDH in 1 μg of loaded protein from nuclear (NUC) and post nuclear lysate (PNL) fractions of mouse frontal cortex.
Background:
Exposure to windblown particulate matter (PM) arising from legacy uranium (U) mine sites in the Navajo Nation may pose a human health hazard due to their potentially high metal content, including U and vanadium (V).
Objective:
To assess the toxic impact of PM derived from Claim 28 (a priority U mine) compared to background PM, and co...
The role of environmental stressors, particularly exposure to air pollution, in the development of neurodegenerative disease remains underappreciated. We examined the neurological effects of acute ozone (O3) exposure in aged mice, where increased blood brain barrier (BBB) permeability may confer vulnerability to neuroinflammatory outcomes. C57BL/6...
Significance
Inhaled particulates, such as multiwalled carbon nanotubes, can induce neuroinflammatory outcomes. The present study shows that acute neuroinflammation is dependent on the impairment of blood-brain barrier function. Pharmacologic restoration of blood-brain barrier integrity prevented the neuroinflammatory responses to pulmonary multiwa...
Background
Deleterious consequences of exposure to traffic emissions may derive from interactions between carbonaceous particulate matter (PM) and gaseous components in a manner that is dependent on the surface area or complexity of the particles. To determine the validity of this hypothesis, we examined pulmonary and neurological inflammatory outc...
In this Perspective, we expand the notion of temporal regulation of RNA in the brain and propose that the qualitative nature of RNA and its metabolism, together with RNA abundance, are essential for the molecular mechanisms underlying experience-dependent plasticity. We discuss emerging concepts in the newly burgeoning field of epitranscriptomics,...
Exposure to the common environmental contaminant arsenic impacts the epigenetic landscape, including DNA methylation and histone modifications, of several cell types. Developmental arsenic exposure (DAE) increases acetylation and methylation of histone proteins and the protein expression of several chromatin-modifying enzymes in the dentate gyrus (...
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Prenatal alcohol exposure can lead to long-lasting changes in functional and genetic programs of the brain, which may underlie behavioral alterations seen in Fetal Alcohol Spectrum Disorder (FASD). Aberrant fetal programming during gestational alcohol exposure is a possible mechanism by which alcohol imparts teratogenic effects on the brain; howeve...
Arsenic toxicity is a worldwide health concern as several millions of people are exposed to this toxicant via drinking water, and exposure affects almost every organ system in the body including the brain. Recent studies have shown that even low concentrations of arsenic impair neurological function, particularly in children. This review will focus...
Arsenic is a common and pervasive environmental contaminant found in drinking water in varying concentrations depending on region. Exposure to arsenic induces behavioral and cognitive deficits in both human populations and in rodent models. The Environmental Protection Agency (EPA) standard for the allotment of arsenic in drinking water is in the p...
Background:
Accumulating evidence indicates that several of the long-term consequences of prenatal alcohol exposure (PAE) are the result of changes in the development and function of cortico-limbic structures, including the hippocampal formation. The glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) are key regulators of hippocampal...
