A5046098892- Chromosomal and Genetic Variations
- Plant Disease Resistance and Genetics
- Fungal and yeast genetics research
- Silicon Effects in Agriculture
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Microbial Natural Products and Biosynthesis
- Protist diversity and phylogeny
- Plant-Microbe Interactions and Immunity
- Plant Pathogens and Fungal Diseases
- Mycotoxins in Agriculture and Food
- Light effects on plants
- Genomics and Chromatin Dynamics
- Probiotics and Fermented Foods
- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- Plant Reproductive Biology
- Circadian rhythm and melatonin
- Cancer-related gene regulation
- Plant Gene Expression Analysis
- Mitochondrial Function and Pathology
- RNA modifications and cancer
- Bacterial biofilms and quorum sensing
- Legume Nitrogen Fixing Symbiosis
- Biofuel production and bioconversion
Regional Medical Center
2025
Oregon State University Cascades
2014-2025
Oregon State University
2009-2019
Biocom
2008-2018
Raigmore Hospital
2017
Northwest College
2014
University of Oregon
2004-2010
University at Buffalo, State University of New York
2002-2003
Weatherford College
1996
The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity whole arsenal natural compounds and their role in fungus' interaction with remained unknown. Here, we present a high-quality genome sequence F. that was assembled into 12 scaffolds corresponding chromosomes described fungus. We used along ChIP-seq, transcriptome, proteome, HPLC-FTMS-based metabolome...
The cereal pathogen Fusarium graminearum produces secondary metabolites toxic to humans and animals, yet coordinated transcriptional regulation of gene clusters remains largely a mystery. By chromatin immunoprecipitation high-throughput DNA sequencing (ChIP-seq) we found that regions with metabolite are enriched for trimethylated histone H3 lysine 27 (H3K27me3), modification associated silencing. H3K27me3 was predominantly in lack synteny other species, generally subtelomeric regions. Di- or...
Trichoderma reesei is an industrial producer of enzymes that degrade lignocellulosic polysaccharides to soluble monomers, which can be fermented biofuels. Here we show the expression genes for lignocellulose degradation are controlled by orthologous T. protein methyltransferase LAE1. In a lae1 deletion mutant observed complete loss all seven cellulases, auxiliary factors cellulose degradation, β-glucosidases and xylanases were no longer expressed. Conversely, enhanced resulted in...
ABSTRACT Light signaling pathways and circadian clocks are inextricably linked have profound effects on behavior in most organisms. Here, we used chromatin immunoprecipitation (ChIP) sequencing to uncover direct targets of the Neurospora crassa regulator White Collar Complex (WCC). The WCC is a blue-light receptor key transcription factor oscillator. It controls transcriptional network that regulates ∼20% all genes, generating daily rhythms responses light. We found response light, binds...
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous have been sequenced, most them by Sanger sequencing. While next-generation sequencing techniques revolutionized genome resequencing, e.g. strain comparisons, genetic mapping, or transcriptome ChIP analyses, de novo assembly eukaryotic still presents significant hurdles, because their large size stretches repetitive sequences....
The functional significance of mono-, di-, and tri-methylation lysine residues within histone proteins is under investigation. Evidence from several model organisms suggests that different methylated states H3 Lys(9) (H3K9) are generated by specific methyltransferases (MTases) to mark distinct types silent chromatin. Sequence alignment all MTases with known product specificity suggested a key residue in the active site determines how many methyl groups they add. We examined this possibility...
Since the preindustrial era, average surface ocean pH has declined by 0.1 units and is predicted to decline an additional 0.3 year 2100. Although subtle, this decreasing profound effects on seawater saturation state of carbonate minerals thus impact calcifying organisms. Among these are scleractinian corals, which main builders tropical coral reefs. Several recent studies have evaluated physiological low pH, particularly in relation growth calcification. However, very few focused at global...
Supernumerary chromosomes have been found in many organisms. In fungi, these "accessory" or "dispensable" are present at different frequencies populations and usually characterized by higher repetitive DNA content lower gene density when compared to the core chromosomes. reference strain of wheat pathogen, Zymoseptoria tritici, eight discrete accessory found. So far, no functional role has assigned chromosomes; however, they existed as separate entities karyotypes species over evolutionary...
Neurospora crassa has been for decades a principal model filamentous fungal genetics and physiology as well understanding the mechanism of circadian clocks. Eukaryotic animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription substantial fraction these transcriptomes, yielding changes in protein abundance mediate regulation metabolism: Understanding gene expression is key to eukaryotic, including fungal, physiology. Indeed, isolation...
Centromeres serve as platforms for the assembly of kinetochores and are essential nuclear division. Here we identified Neurospora crassa centromeric DNA by chromatin immunoprecipitation followed high-throughput sequencing (ChIP-seq) associated with tagged versions centromere foundation proteins CenH3 (CENP-A) CEN-C (CENP-C) kinetochore protein CEN-T (CENP-T). On each chromosome found an ∼150- to 300-kbp region enrichment all three proteins. These regions correspond intervals predicted be...
Abstract The putative methyltransferase LaeA is a global regulator that affects the expression of multiple secondary metabolite gene clusters in several fungi, and it can modify heterochromatin structure Aspergillus nidulans. We have recently shown ortholog Trichoderma reesei (LAE1), fungus an industrial producer cellulase hemicellulase enzymes, regulates cellulases polysaccharide hydrolases. To learn more about function LAE1 T. reesei, we assessed effect deletion overexpression lae1 on...
Chromosome and genome stability are important for normal cell function as instability often correlates with disease dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has many eight chromosomes, which highly unstable during meiosis mitosis, transcriptionally repressed, show enrichment repetitive elements, heterochromatic histone methylation marks, e.g.,...
The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism light, RNA-seq was used analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 hr dark then exposed 0 (control) 15, 60, 120, 240 min. More than three-quarters all defined protein coding genes (79%) were expressed these cells. increased sensitivity compared with previous microarray studies revealed that RNA levels 31% affected...
Global change and its associated temperature increase has directly or indirectly changed the distributions of hosts pathogens, affected host immunity, pathogen virulence growth rates. This resulted in increased disease natural plant animal populations worldwide, including scleractinian corals. While effects on immunity have been clearly identified, their interaction, synergy relative weight during pathogenesis remain poorly documented. We investigated these phenomena interaction between...
Silencing of genes inserted near telomeres provides a model to investigate the function heterochromatin. We initiated study telomeric silencing in Neurospora crassa, fungus that sports DNA methylation, unlike most other organisms which has been characterized.The selectable marker, hph, was at subtelomere Linkage Group VR an nst-1 (neurospora sir two-1) mutant and silenced when restored. show NST-1 is H4-specific histone deacetylase. A second bar, tested two subtelomeres, similarly sensitive...
ABSTRACT With the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined sequencing with bulk segregant analysis expedite mutation mapping. The general map location a can be identified by single backcross strain enriched in SNPs compared standard wild-type strain. Bulk simultaneously increases likelihood determining precise nature mutation. We present here SNP between Neurospora...
Inflammatory bowel disease (IBD) is increasing among mammals around the world, and domestic dogs are no exception. There approved cure for canine IBD with limited treatment options. Novel probiotic bacteria discovery from free-ranging animals of in pets can likely yield promising candidates. Consequently, overall aim was to isolate that could potentially be utilized as novel probiotics. Two identified unique Paenibacillus spp. strains by small ribosomal RNA (16S) gene sequencing were...
Introduction: It is unclear why differences in patient location change organisms causing ventilator-associated pneumonia (VAP). We investigated VAP three geographically separate trauma intensive care units (TICUs).
Abstract Fusarium oxysporum is an economically important pathogen causing wilting or rotting disease symptoms in a large number of crops. It proposed to have structured, “two-speed” genome: i.e. regions containing genes involved pathogenicity cluster with transposons on separate accessory chromosomes. This hypothesized enhance evolvability. Given the continuum adaptation all encoded genome, however, one would expect more complex genome structure. By comparing reference strain Fol4287 those...
Abstract Telomeres and subtelomere regions have vital roles in cellular homeostasis can facilitate niche adaptation. However, information on telomere/subtelomere structure is still limited to a small number of organisms. Prior initiation this project, the Neurospora crassa genome assembly contained only 3 14 telomeres. The missing telomeres were identified through bioinformatic mining raw sequence data from project clones new cosmid plasmid libraries. Their chromosomal locations assigned...