A5043470393- Plant Molecular Biology Research
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Plant nutrient uptake and metabolism
- Photosynthetic Processes and Mechanisms
- Microbial Community Ecology and Physiology
- Malaria Research and Control
- RNA regulation and disease
- Fungal and yeast genetics research
- Microbial Natural Products and Biosynthesis
- Computational Drug Discovery Methods
- Plant responses to water stress
- Microbial infections and disease research
- Bacteriophages and microbial interactions
- Mosquito-borne diseases and control
- Protist diversity and phylogeny
Howard Hughes Medical Institute
2008-2023
Indiana University Bloomington
2017-2023
Indiana University
2017-2023
University of Washington
2008-2012
Abstract Background Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be fermentatively at price competitive with that of anhydride, though, it replace as the precursor many bulk chemicals, transforming multi-billion dollar petrochemical market into one based on renewable resources. Actinobacillus succinogenes naturally converts sugars and CO 2 high concentrations succinic acid part mixed-acid fermentation. Efforts...
Abstract Background In order to establish a successful infection in the human host, malaria parasite Plasmodium falciparum must interactions with variety of proteins on surface different cell types, as well inside host cells. To better understand this aspect pathogenesis, study was conducted goal identifying between and those its host. Methods A modified yeast two-hybrid methodology that preferentially selects protein fragments can be expressed used conduct high-throughput screens P. against...
Plant multisubunit RNA polymerase V (Pol V) transcription recruits Argonaute-small interfering (siRNA) complexes that specify sites of RNA-directed DNA methylation (RdDM) for gene silencing. Pol V's largest subunit, NRPE1, evolved from the subunit II but has a distinctive C-terminal domain (CTD). We show CTD is dispensable catalytic activity in vitro yet essential vivo. One subdomain (DeCL) required function at virtually all loci. Other subdomains have locus-specific effects. In yeast...
Arabidopsis thaliana has two ribosomal RNA (rRNA) gene loci, nucleolus organizer regions NOR2 and NOR4, whose complete sequences are missing in current genome assemblies. Ultralong DNA assembled using an unconventional approach yielded ~5.5- 3.9-Mbp for NOR4 the reference strain, Col-0. The distinct rRNA subtype compositions of NORs enabled positional mapping their active inactive regions, sequencing to identify subtype-specific transcripts subtypes associated with flow-sorted nucleoli....
SUMMARY Nucleolus organizer regions (NORs) are eukaryotic chromosomal loci where ribosomal RNA (rRNA) genes clustered, typically in hundreds to thousands of copies. Transcription these rRNA by polymerase I and processing their transcripts results the formation nucleolus, sub‐nuclear domain which ribosomes assembled. Approximately 90 years ago, cytogenetic observations revealed that NORs inherited from different parents an interspecific hybrid sometimes differ morphology at metaphase. Fifty...
The assessment of transcriptional regulation requires a genome-wide survey active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels and captures nascent transcripts, with high-throughput DNA sequencing to examine activity in exponentially growing Saccharomyces cerevisiae. Sequence read data from these libraries revealed that yeast occurs not only at level polymerase recruitment promoters but also postrecruitment steps. Nascent synthesis signals are strongly enriched...
Oxidative RNA damage has been linked to loss of function and the development many human age-related diseases. Consequently, a need exists for methods identify quantify extent oxidation on genome-wide basis. We developed such method by combining affinity selection mRNA containing 8-hydroxyguanine with high throughput DNA sequencing. demonstrate that this assay is suitable detecting differences in between transcripts. applied yeast Saccharomyces cerevisiae grown under physiological conditions...
Rhodopseudomonas palustris CGA009 is a versatile model purple nonsulfur bacterium used for both fundamental and applied research. Here, we present new genome sequence the derivative strain CGA0092. We further an improved assembly that differs from original at three positions.
Nuclear multisubunit RNA polymerases IV and V (Pol Pol V) evolved in plants as specialized forms of II. Their functions are best understood the context RNA-directed DNA methylation (RdDM), a process which IV-dependent 24 nt siRNAs direct de novo cytosine regions transcribed by V. has additional functions, independent siRNA biogenesis, maintaining repression transposons genomic repeats whose silencing depends on maintenance methylation. Here we report that play unexpected roles defining 3'...
ABSTRACT In eukaryotes, hundreds of ribosomal RNA (rRNA) genes are clustered at chromosomal loci called nucleolus organizer regions (NORs). Arabidopsis thaliana has two NORs, one on chromosome 2 ( NOR2 ) and the other 4 NOR4 ). Each NOR consists ∼ 400 rRNA gene copies. We recently showed that subtypes map to silenced during development, whereas those active. several DNA methylation mutants Arabidopsis, we show disruption silencing varying degrees. Significantly, highest correlates with a...
Abstract Arabidopsis thaliana has two ribosomal RNA gene loci, nucleolus organizer regions NOR2 and NOR4 , whose complete sequences remain undefined. Ultra-long DNA assembled using an unconventional approach yielded 5.5 3.9 Mbp for (in the reference strain, Col-0), revealing their distinct subtype compositions. sequencing identification of genes associated with flow-sorted nucleoli wild-type or silencing-defective mutant plants shows that most is comprised active whereas most, but not all,...
Abstract Plant multisubunit RNA Polymerase V transcription recruits Argonaute siRNA complexes that specify sites of RNA-directed DNA methylation (RdDM) for gene silencing. Pol V's largest subunit, NRPE1, evolved from the subunit II but has a distinctive carboxyl-terminal domain (CTD). We show CTD is dispensable catalytic activity in vitro , yet essential vivo. One subdomain (DeCL), required function at virtually all loci. other subdomains have locusspecific effects. In yeast two-hybrid...
Large regions of nearly identical repeats, such as the 45S ribosomal RNA (rRNA) genes Nucleolus Organizer Regions (NORs), can account for major gaps in sequenced genomes. To assemble these regions, ultra-long sequencing reads that span multiple repeats have potential to reveal sets collectively sufficient sequence variation unambiguously define interval and recognize overlapping reads. Because individual repetitive loci typically represent a small proportion genome, methods enrich interest...
Abstract Nuclear multisubunit RNA polymerases IV and V (Pol Pol V) evolved in plants as specialized forms of II. Their functions are best understood the context RNA-directed DNA methylation (RdDM), a process which IV-dependent 24 nt siRNAs direct de novo cytosine regions transcribed by V. has additional functions, independent siRNA biogenesis, maintaining repression transposons genomic repeats whose silencing depends on maintenance methylation. Here we report that play unexpected roles...