A5011844208- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- RNA modifications and cancer
- RNA regulation and disease
- Influenza Virus Research Studies
- Respiratory viral infections research
- Immune Cell Function and Interaction
- CAR-T cell therapy research
- Animal Disease Management and Epidemiology
- Viral Infections and Immunology Research
- Microbial infections and disease research
- Ferroptosis and cancer prognosis
- Trace Elements in Health
- Chromosomal and Genetic Variations
- Microbial Metabolic Engineering and Bioproduction
- Bacteriophages and microbial interactions
- Aquaculture disease management and microbiota
- Viral gastroenteritis research and epidemiology
- Selenium in Biological Systems
- Infectious Diseases and Mycology
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- Advanced biosensing and bioanalysis techniques
University of California, Berkeley
2019-2025
QB3
2024
Mississippi State University
2015-2020
South China Agricultural University
2018
United States Department of Agriculture
2018
St. Jude Children's Research Hospital
2018
ABSTRACT Cattle have been proposed as the natural reservoir of a novel member virus family Orthomyxoviridae , which has tentatively classified influenza D (IDV). Although isolated from sick animals, it is unclear whether IDV causes any clinical disease in cattle. To address this aspect Koch's postulates, three dairy calves (treatment animals) held individual pens were inoculated intranasally with strain D/bovine/Mississippi/C00046N/2014. At 1 day postinoculation, seronegative calf (contact...
Selfish, non-long terminal repeat (non-LTR) retroelements and mobile group II introns encode reverse transcriptases (RTs) that can initiate DNA synthesis without substantial base pairing of primer template. Biochemical characterization these enzymes has been limited by recombinant expression challenges, hampering understanding their properties the possible exploitation for research biotechnology. We investigated activities representative RTs using a modified non-LTR RT from Bombyx mori...
Abstract Influenza D virus (IDV) has been identified in domestic cattle, swine, camelid, and small ruminant populations across North America, Europe, Asia, South Africa. Our study investigated seroprevalence transmissibility of IDV feral swine. During 2012–2013, we evaluated swine 4 US states; 256 tested, 57 (19.1%) were seropositive. Among 96 archived influenza A virus–seropositive samples collected from 16 states during 2010–2013, 41 (42.7%) Infection studies demonstrated that...
Inhibitors of protein synthesis, including anisomycin, homoharringtonine, and other natural products bind in the peptidyl-transferase center (PTC) eukaryotic ribosome to inhibit translation. Recent work has demonstrated that some PTC-binding antibiotics act a sequence-selective manner, inhibiting translation elongation at specific amino acids while polypeptide is engaged PTC. However, this phenomenon yet be documented for compounds by human ribosome. Here we use structure-based design guide...
Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized types. However, molecular mechanisms underlying this translational burst and involvement initiation factors remains largely unknown. Here, we investigate role eukaryotic factor 3 (eIF3) early human pluripotent stem (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP alternative polyadenylation (APA) Seq, show eIF3 crosslinks predominantly with 3’ untranslated region...
CiBER-seq dissects genetic networks Cells integrate environmental signals and internal states to dynamically control gene expression. Muller et al. developed a technique dissect this cellular logic by linking targeted, genome-wide perturbations with deep-sequencing readout that quantitatively measured the expression phenotype induced each perturbation. The method, dubbed CiBER-seq, was able recapitulate known regulatory pathways protein synthesis nutrient availability in budding yeast cells....
Activation of T cells requires a rapid surge in cellular protein synthesis. However, the role translation initiation early induction specific genes remains unclear. Here, we show human factor eIF3 interacts with select immune system related mRNAs including those encoding cell receptor (TCR) subunits TCRA and TCRB. Binding to
ABSTRACT Among the major classes of RNAs in cell, tRNAs remain most difficult to characterize via deep sequencing approaches, as tRNA secondary structure and nucleotide modifications can both interfere with cDNA synthesis by commonly-used reverse transcriptases (RTs). Here, we benchmark a recently-developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), intact fragments budding yeast mouse tissues. We find that OTTR robustly captures full-length testis, relatively low levels...
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate developmental transcription factor CCAAT/enhancer-binding α (C/EBPα) produced different exert opposing effects during myeloid cell development. This choice between depends on sequence features CEBPA transcript, including regulatory uORF, but molecular basis is not fully understood. Here, we identify factors that affect...
Influenza D viruses (IDVs) are panzootic in multiple animal hosts, but the underlying mechanism is unclear. Through years of surveillance same order-buyer cattle facility, 32 IDV isolates were recovered from both healthy and sick animals, including those with evident antibodies against IDV. Active reassortment occurred within this facility across other areas, reassortants cocirculated animals. These shown a large extent phenotypic diversity replication efficiency pathogenesis little...
CHRONIC respiratory disease of poultry (CRD) was first reported in the United States by Delaplane and Stuart 1943. Its importance is evidenced Department Agriculture report that annual loss due to CRD 25 million dollars. (United Agriculture, 1956). The high incidence chickens infectious sinusitis turkeys (IS) has directed increased attention past few years toward an effort control or perhaps eradicate these diseases. Many investigators have concluded PPLO play important role IS turkeys. It...
Abstract Ribosome profiling has unveiled diverse regulations and perturbations of translation through a transcriptome-wide survey ribosome occupancy, read out by sequencing ribosome-protected mRNA fragments. Generation footprints their conversion into libraries is technically demanding sensitive to biases that distort the representation physiological occupancy. We address these challenges producing with P1 nuclease rather than RNase I replacing RNA ligation Ordered Two-Template Relay,...
Sequencing RNAs that are biologically processed or degraded to less than ~100 nucleotides typically involves multi-step, low-yield protocols with bias and information loss inherent ligation and/or polynucleotide tailing. We recently introduced Ordered Two-Template Relay (OTTR), a method captures obligatorily end-to-end sequences of input molecules and, in the same reverse transcription step, also appends 5′ 3′ sequencing adapters choice. OTTR has been thoroughly benchmarked for optimal...
Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized types. However, molecular mechanisms underlying this translational burst and involvement initiation factors remains largely unknown. Here, we investigate role eukaryotic factor 3 (eIF3) early human pluripotent stem (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP alternative polyadenylation (APA) Seq, show eIF3 crosslinks predominantly with 3' untranslated region...
To realize the promise of CRISPR/Cas9-based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries genetic perturbations. We address this challenge by profiling transcriptional, translational, and post-translational reporters using CRISPR interference with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach connects an entire library guides their individual phenotypic consequences pooled sequencing. show that CiBER-seq...
Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized types. However, molecular mechanisms underlying this translational burst and involvement initiation factors remains largely unknown. Here, we investigate role eukaryotic factor 3 (eIF3) early human pluripotent stem (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP alternative polyadenylation (APA) Seq, show eIF3 crosslinks predominantly with 3’ untranslated region...
Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized types. However, molecular mechanisms underlying this translational burst and involvement initiation factors remains largely unknown. Here, we investigate role eukaryotic factor 3 (eIF3) early human pluripotent stem (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP alternative polyadenylation (APA) Seq, show eIF3 crosslinks predominantly with 3’ untranslated region...
Sequencing RNAs that are biologically processed or degraded to less than ~100 nucleotides typically involves multi-step, low-yield protocols with bias and information loss inherent ligation and/or polynucleotide tailing. We recently introduced Ordered Two-Template Relay (OTTR), a method captures obligatorily end-to-end sequences of input molecules and, in the same reverse transcription step, also appends 5' 3' sequencing adapters choice. OTTR has been thoroughly benchmarked for optimal...