A5018956397- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- CRISPR and Genetic Engineering
- Photosynthetic Processes and Mechanisms
- Plant Reproductive Biology
- Algal biology and biofuel production
- Plant tissue culture and regeneration
- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Plant Stress Responses and Tolerance
- RNA Research and Splicing
- Plant nutrient uptake and metabolism
- Protist diversity and phylogeny
- RNA and protein synthesis mechanisms
- Marine and coastal plant biology
- MicroRNA in disease regulation
- Photoreceptor and optogenetics research
- ATP Synthase and ATPases Research
- Genome Rearrangement Algorithms
- Diatoms and Algae Research
- RNA modifications and cancer
- Mitochondrial Function and Pathology
- Polar Research and Ecology
Bayer (United States)
2019-2024
Biotechnology Institute
2006-2014
University of Delaware
2006-2014
Monsanto (United States)
2013
Delaware Technical Community College
2012
Joint Genome Institute
2007
Institut de Biologie Physico-Chimique
2007
Sorbonne Université
2007
Centre National de la Recherche Scientifique
2007
Duke University
2007
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It model system for studying chloroplast-based photosynthesis, as well the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited common ancestor animals, but lost in plants. We sequenced ∼120-megabase nuclear genome performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated...
Regulation of gene expression by small RNAs (∼20–30 nucleotides in length) plays an essential role developmental pathways and defense responses against genomic parasites eukaryotes. MicroRNAs (miRNAs) interfering (siRNAs) commonly direct the inactivation cognate sequences through a variety mechanisms, including RNA degradation, translation inhibition, transcriptional repression. Recent studies have provided considerable insight into biogenesis mode action miRNAs siRNAs. However, relatively...
In metazoans, cleavage by the endoribonuclease SMG6 is often first degradative event in non-sense-mediated mRNA decay (NMD). However, exact sites of have yet to be determined for any endogenous targets, and most evidence as identity substrates indirect. Here, we use Parallel Analysis RNA Ends specifically identify 5′ termini intermediates whose production dependent on universal NMD factor UPF1. this manner, hundreds targets human cells been mapped at high resolution. addition, a preferred...
The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key eukaryotic gene regulation, been limited in B. studies examining few samples or that rely on computational predictions. Similarly an in-depth miRNA-mediated target cleavage using parallel RNA ends (PARE) data is lacking distachyon. small RNAs were cloned deeply sequenced from 17 libraries represent different tissues...
One of the major players controlling RNA decay is cytoplasmic 5′-to-3′ exoribonuclease, which conserved among eukaryotic organisms. In Arabidopsis , exoribonuclease XRN4 involved in disease resistance, response to ethylene, RNAi, and miRNA-mediated decay. Curiously, appears display selectivity its substrates because certain 3′ cleavage products formed by decay, such as from ARF10 mRNA, accumulate xrn4 mutant, whereas others, AGO1 do not. To examine nature this selectivity, transcripts that...
MicroRNAs (miRNAs) are a class of small RNAs that typically function by guiding the cleavage target messenger RNAs. They have been shown to play major roles in variety plant processes, including development, and responses pathogens environmental stresses. To identify new miRNAs regulation Arabidopsis (Arabidopsis thaliana), 27 RNA libraries were constructed sequenced from various tissues, stresses, biogenesis mutants, resulting 95 million genome-matched sequences. The use rdr2 enrich miRNA...
Novel disease resistance gene paralogues are generated by targeted chromosome cleavage of tandem duplicated NBS-LRR complexes and subsequent DNA repair in soybean. This study demonstrates accelerated diversification innate immunity plants using CRISPR. Nucleotide-binding-site-leucine-rich-repeat (NBS-LRR) families key components effector-triggered immunity. They often arranged arrays the genome, a configuration that is conducive to recombinations will lead new, chimeric genes. These...
Abstract Background Genome rearrangements influence gene order and configuration of clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved content with notable exceptions, largely co-linear order. Conserved orders may reflect slow intrinsic rate neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes are random adaptive. We investigate the natural selection on association increased rearrangement. use...
Abstract Chlamydomonas reinhardtii is an excellent model system for plant biologists because of its ease manipulation, facile genetics, and the ability to transform nuclear, chloroplast, mitochondrial genomes. Numerous forward genetics studies have been performed in Chlamydomonas, many cases elucidate regulation photosynthesis. One resultant challenges moving from mutant phenotype gene mutation causing that phenotype. To date, complementation has primary method cloning, but this impractical...
Little is known about the genetic and biochemical mechanisms that underlie red algal development, for example, why group failed to evolve complex parenchyma tissue differentiation. Here we examined expressed sequence tag (EST) data from two closely related species, Porphyra umbilicalis (L.) J. Agardh P. purpurea (Roth) C. Agardh, conserved developmental regulators model eukaryotes, their expression levels in several stages. Genes most major families were present, including MADS-box...
Summary Chloroplast RNA processing and degradation are orchestrated by nucleus‐encoded factors. Although several transcript‐specific factors have been identified, those involved in global metabolism mostly remained elusive. Using Chlamydomonas reinhardtii , we identified three pleiotropic nuclear mutations, mcd3 mcd4 mcd5 which cause quantitative variation between polycistronic transcripts accumulation of with novel 3′ ends. The mutants were initially isolated as photoautotrophic suppressors...
Maize plants with mutations at brachytic 2 (br2) reduce plant height through internode shortening while maintaining the rest of plant's relative size. The gene product Br2 encodes an ATP binding cassette type B (ABCB) auxin transporter. Several br2 have been previously reported, notably independent characterizations 8 bp and 241 deletions (br2-23 br2-qpa1, respectively), a single missense mutation (br2-qph1), MITE transposon insertion (br2-NC238). Two new (designated br2-7081 br2-7861) now...
High efficiency site-directed chromosomal integration of exogenous DNA in plants remains a challenge despite recent advances genome editing technologies. One approach to mitigate this problem is increase the effective concentration donor at target site interest. HUH endonucleases (ENs) coordinate rolling circle replication. In vitro, they can form stable covalent bonds with that carries their recognition motifs. When fused CRISPR-associated endonuclease, ENs may improve rates by increasing...
Clustered regularly interspaced short palindromic repeats (CRISPR) technology has revolutionized creating targeted genetic variation in crops. Although CRISPR enzymes have been reported to high sequence-specificity, careful design of the editing reagents can also reduce unintended edits at highly homologous sites. This work details first large-scale study heritability on-target and rate off-target sites soybean (