A5014335552- Viral Infectious Diseases and Gene Expression in Insects
- CRISPR and Genetic Engineering
- Environmental and Agricultural Sciences
- Crop Yield and Soil Fertility
- Microbial Metabolic Engineering and Bioproduction
- Soil Carbon and Nitrogen Dynamics
- RNA and protein synthesis mechanisms
- Virus-based gene therapy research
- Rice Cultivation and Yield Improvement
- Molecular Biology Techniques and Applications
- Irrigation Practices and Water Management
- Transgenic Plants and Applications
- Bioinformatics and Genomic Networks
- Monoclonal and Polyclonal Antibodies Research
- Viral Infections and Immunology Research
- Metabolomics and Mass Spectrometry Studies
- Plant Virus Research Studies
- Biofuel production and bioconversion
- Malaria Research and Control
- Soil Mechanics and Vehicle Dynamics
- Soil erosion and sediment transport
- Microplastics and Plastic Pollution
- Genomic variations and chromosomal abnormalities
- Agricultural Productivity and Crop Improvement
- Mosquito-borne diseases and control
Ministry of Agriculture and Rural Affairs
2024
Gansu Academy of Agricultural Sciences
2005-2024
University of California, San Diego
2014-2021
Foundation Center
2016-2021
Novo Nordisk (United States)
2016-2021
Novo Nordisk Foundation
2020-2021
Pfizer (United States)
2021
The human genome-scale metabolic reconstruction details all known reactions occurring in humans, and thereby holds substantial promise for studying complex diseases phenotypes. Capturing the whole is an on-going task since last community effort generated a consensus reconstruction, several updates have been developed. We report new version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing further key objectives...
Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current assemblies for Cricetulus griseus, the Chinese hamster, fragmented replete with gap misassemblies, consistent most short-read-based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing merged this Illumina-based This generated a more contiguous assembly than either technology alone, reducing number of scaffolds by...
Abstract In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on secretion different proteins. Unraveling diverse is particularly important for biopharmaceutical production. Here we delineate core functions and integrate them with genome-scale metabolic reconstructions human, mouse, Chinese hamster ovary cells. resulting enable computation energetic costs machinery demands each secreted protein....
Recombinant protein production coopts the host cell machinery to provide high yields of industrial enzymes or biotherapeutics. However, since translation is energetically expensive and tightly controlled, it unclear if highly expressed recombinant genes are translated as efficiently genes. Furthermore, how expression impacts global translation. Here, we present first genome-wide view in an IgG-producing CHO line, measured with ribosome profiling. Through this found that our mRNAs were...
Abstract The exoerythrocytic stage of Plasmodium infection is a critical window for prophylactic intervention. Using genome-wide dual RNA sequencing flow-sorted infected and uninfected hepatoma cells we show that the human mucosal immunity gene, mucin-13 (MUC13), strongly upregulated during hepatic-stage infection. We confirm MUC13 transcript increases in cell lines primary hepatocytes. In immunofluorescence assays, host protein expression distinguishes from adjacent shows similar...
Abstract Chinese hamster ovary (CHO) cells are widely used for biopharmaceutical protein production. One challenge limiting CHO cell productivity is apoptosis stemming from cellular stress during Here we applied CRISPR interference (CRISPRi) to downregulate the endogenous expression of apoptotic genes Bak , Bax and Casp3 in cells. In addition reduced apoptosis, mitochondrial membrane integrity was improved caspase activity reduced. Moreover, optimized CRISPRi system enhance gene repression...
Omics experiments are ubiquitous in biological studies, leading to a deluge of data. However, it is still challenging connect changes these data cell functions because complex interdependencies between genes, proteins, and metabolites. Here, we present framework allowing researchers infer how metabolic change on the basis omics To enable this, curated standardized lists tasks that mammalian cells can accomplish. Genome-scale networks were used define gene sets associated with each task. We...
Chinese hamster ovary (CHO) cells are the preferred workhorse for biopharmaceutical industry, and CRISPR/Cas9 has proven powerful generating targeted gene perturbations in CHO cells. Here, we expand CRISPR engineering toolbox with activation (CRISPRa) to increase transcription of endogenous genes. We successfully increased Mgat3 St6gal1, verified their activity on a functional level by subsequently detecting that appropriate glycan structures were produced. This study demonstrates CRISPRa...
Pooled CRISPR screens have been widely applied to mammalian and other organisms elucidate the interplay between genes phenotypes of interest. The most popular method for delivering components into cells is lentivirus based. However, because not always an option, virus-free protocols are starting emerge. Here, we demonstrate improved virus-free, genome-wide screening platform Chinese hamster ovary with 75,488 gRNAs targeting 15,028 genes. Each gRNA expression cassette in library precisely...
Drought stress is one of the premier limitations to global agricultural production. Increasing water and nitrogen (N) use efficiencies in dryland agroecosystems maintain high output are key responsibilities assure food security, especially on semiarid Loess Plateau region China, as it important grain production areas China. The impact controlled-release urea (CRU) soil content, enzyme activities, N biomass accumulation, yield, efficiency (WUE), agronomic fertilizer (AEN) were examined maize...
ABSTRACT To understand the role of glycosaminoglycans in bacterial cellular invasion, xylosyltransferase-deficient mutants Chinese hamster ovary (CHO) cells were created using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR- cas9 ) targeting. When these compared to pgsA745 cell line, a CHO xylosyltransferase mutant generated previously chemical mutagenesis, an unexpected result was obtained. Bacterial invasion by group B Streptococcus...
Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of on downstream analyses is limited. The lack common quality metrics that sufficiently sensitive to RNA degradation, e.g. Integrity Score, makes such assessments challenging.Here we quantify repeated cycles reliability by examining poly(A)-enriched ribosomal depleted RNA-seq from frozen leukocytes drawn a toddler Autism cohort. To do so, estimate relative noise, or percentage random counts, separating...
Abstract Viral contamination in biopharmaceutical manufacturing can lead to shortages the supply of critical therapeutics. To facilitate protection bioprocesses, we explored basis for susceptibility CHO cells RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, fail generate a significant interferon (IFN) response. Nonetheless, downstream machinery generating IFN responses its antiviral activity is intact these cells: treatment exogenously-added type I or poly I:C prior...
A high-quality genome annotation greatly facilitates successful cell line engineering. Standard draft pipelines are based largely on de novo gene prediction, homology, and RNA-Seq data. However, annotations can suffer from incorrect predictions of translated sequence, inaccurate splice isoforms, missing genes. Here, we generated a for the newly assembled Chinese hamster used RNA-Seq, proteomics, Ribo-Seq to experimentally annotate genome. We identified 3529 new proteins compared RefSeq...
Abstract Chinese hamster ovary (CHO) cells are the primary host for manufacturing of therapeutic proteins. However, productivity loss is a major problem and associated with genome instability, as chromosomal aberrations reduce transgene copy number decrease protein expression. We analyzed whole‐genome sequencing data from 11 CHO cell lines found deleterious single‐nucleotide variants in DNA repair genes. Comparison confirmed to be compromised CHO. Correction key genes by variant reversal or...
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality affordability. However, or activating silent genes requires accurate annotation of the underlying regulatory elements transcription start sites (TSSs). Unfortunately, most TSSs published genome sequence were computationally predicted frequently inaccurate. Here, we use nascent site sequencing methods revise TSS annotations 15 308 3034...