A5091060795- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Fungal and yeast genetics research
- Entomopathogenic Microorganisms in Pest Control
- RNA Research and Splicing
- Tracheal and airway disorders
- Plant Virus Research Studies
- Chromosomal and Genetic Variations
- Congenital Diaphragmatic Hernia Studies
- Plant and Fungal Interactions Research
- Neonatal Respiratory Health Research
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Insect Resistance and Genetics
- Insect symbiosis and bacterial influences
- Probiotics and Fermented Foods
- Microbial Natural Products and Biosynthesis
- Insect Pest Control Strategies
- Evolution and Genetic Dynamics
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
- Plant Stress Responses and Tolerance
- Plant nutrient uptake and metabolism
- DNA Repair Mechanisms
Institute for Systems Biology
2018-2025
Jilin Academy of Agricultural Sciences
2022-2025
Institute of Plant Protection
2023-2025
Shanghai East Hospital
2020-2025
Tongji University
2025
Beijing Chao-Yang Hospital
2024
Capital Medical University
2024
Jilin Agricultural University
2024
Ministry of Agriculture and Rural Affairs
2024
The University of Texas Southwestern Medical Center
2023
Abstract A novel coronavirus SARS-CoV-2 was identified in Wuhan, Hubei Province, China December of 2019. According to WHO report, this new has resulted 76,392 confirmed infections and 2,348 deaths by 22 February, 2020, with additional patients being a rapidly growing number internationally. reported share the same receptor, Angiotensin-converting enzyme 2 (ACE2), SARS-CoV. Here based on public database state-of-the-art single-cell RNA-Seq technique, we analyzed ACE2 RNA expression profile...
We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; reduced Pre4 protein accumulation by half. Completing specifies consolidation 16 chromosomes into a single strain. investigated phenotypic, transcriptional, proteomewide consequences poly-synthetic strains. Another "bug" was discovered through...
The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual chromosomes assembled. Here, we describe the consolidation of multiple using advanced endoreduplication intercrossing tRNA expression cassettes to generate strain 6.5 chromosomes. 3D chromosome organization and transcript isoform profiles were evaluated Hi-C long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or...
Abstract The loss of the tail is among most notable anatomical changes to have occurred along evolutionary lineage leading humans and ‘anthropomorphous apes’ 1–3 , with a proposed role in contributing human bipedalism 4–6 . Yet, genetic mechanism that facilitated tail-loss evolution hominoids remains unknown. Here we present evidence an individual insertion Alu element genome hominoid ancestor may contributed evolution. We demonstrate this element—inserted into intron TBXT gene 7–9 —pairs...
Here, we report the design, construction, and characterization of a tRNA neochromosome, designer chromosome that functions as an additional, de novo counterpart to native complement Saccharomyces cerevisiae. Intending address one central design principles Sc2.0 project, ∼190-kb neochromosome houses all 275 relocated nuclear genes. To maximize stability, incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, presence 283 rox recombination sites enables...
Objective. To describe coronavirus disease 2019 (COVID-19) patient presentations requiring otolaryngology consultation and provide recommendations for protective measures based on the experience of ear, nose, throat (ENT) departments in 4 Chinese hospitals during COVID-19 pandemic. Study Design. Retrospective case series. Setting. Multicenter. Subjects Methods. Twenty hospitalized patients ENT from 3 designated Wuhan, Shanghai, Shenzhen were identified. Data demographics, comorbidities,...
ABSTRACT Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Chromosome Rearrangement Modification by LoxP-mediated Evolution (SCRaMbLE) is an system intrinsic to the synthetic yeast that can rapidly drive structural variations. Here, we detect over 260 000 rearrangement events after SCRaMbLEing of strain harboring 5.5 chromosomes (synII, synIII, synV, circular synVI, synIXR synX). Remarkably, find exhibit specific...
We describe construction of the synthetic yeast chromosome XI (synXI) and reveal effects redesign at non-coding DNA elements. The 660-kb genome project (Sc2.0) was assembled from synthesized fragments before CRISPR-based methods were used in a process bug discovery, redesign, repair, including precise compaction 200 kb repeat sequence. Repaired defects related to poor centromere function mitochondrial health associated with modifications regions. As part Sc2.0 design, loxPsym sequences for...
is known as a pathogenic fungus that infects humans and plants but has never been reported an entomophagous (EPF) can provide other functions endotype.
Irreversible damage of the lung epithelium in idiopathic pulmonary fibrosis (IPF) patients causes high mortality worldwide, with no repair approaches available currently. Here we show that murine and monkey models, KRT5+ P63+ progenitor cells airway basal layer can enter alveolar area post fibrotic injury. Aided an automated culture system, clone characterize from 44 donors various conditions. Transplantation human into mouse efficiently re-epithelializes injured area, forms new respiratory...
Whether synthetic genomes can power life has attracted broad interest in the biology field. Here, we report de novo synthesis of largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with hierarchical integration strategy, which significantly increased accuracy flexibility construction. Besides drastic sequence changes, further manipulated 3D structure synIV to explore...
Pioneering advances in genome engineering, and specifically writing, have revolutionized the field of synthetic biology, propelling us toward creation genomes. The Sc2.0 project aims to build first fully eukaryotic organism by assembling Saccharomyces cerevisiae. With completion chromosome VIII (synVIII) described here, this goal is within reach. In addition writing yeast genome, we sought manipulate an essential functional element: point centromere. By relocating native centromere sequence...
Abstract Fungal polyketides display remarkable structural diversity and bioactivity, therefore the biosynthesis engineering of this large class molecules is therapeutically significant. Here, we successfully recode, construct characterize biosynthetic pathway bikaverin, a tetracyclic polyketide with antibiotic, antifungal anticancer properties, in S. cerevisiae . We use green fluorescent protein (GFP) mapping strategy to identify low expression Bik1 (polyketide synthase) as major bottleneck...
With the completion of Sc2.0 chromosomes, synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) becomes more critical for in-depth investigation fundamental biological questions screening industrially valuable characteristics. Further applications, however, are hindered due to lack facile tight regulation SCRaMbLE process, limited understanding key factors that may affect outcomes. Here we propose an approach precisely regulate recombination in a...
We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was for attachment to another synthetic due concerns surrounding potential instability karyotype imbalance now attached synIII, yielding first yeast fusion chromosome. Additional chromosomes were constructed study nuclear function. ChrIII-I chrIX-III-I have twisted structures, depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special...
Abstract The CRISPR–Cas12a is a class II, type V clustered regularly interspaced short palindromic repeat (CRISPR) system with both RNase and DNase activity. Compared to the CRISPR–Cas9 system, it recognizes T-rich PAM sequences has advantage of multiplex genomic editing. Here, in fission yeast Schizosaccharomyces pombe, we successfully implemented for versatile editing manipulation. In addition rrk1 promoter, used new pol II promoters from endogenous coding genes express crRNA Cas12a...
Use of synthetic genomics to design and build 'big' DNA has revolutionized our ability answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, become the major platform assemble large constructs thanks its powerful homologous recombination machinery availability well-established molecular biology techniques. However, introducing designer variations episomal assemblies with high efficiency fidelity remains challenging. Here we...
Abstract The Sc2.0 global consortium to design and construct a synthetic genome based on the Saccharomyces cerevisiae commenced in 2006, comprising 16 chromosomes new-to-nature tRNA neochromosome. In this paper we describe assembly debugging of 902,994-bp chromosome synXVI project. Application CRISPR D-BUGS protocol identified defective loci, which were modified improve sporulation recover wild-type like growth when grown glycerol as sole carbon source at 37˚C. LoxPsym sites inserted...
Abstract BACKGROUND Aphids are important agricultural and forestry pests that not only directly harm plants, but also transmit various plant viruses. Biological control, including the use of entomopathogenic fungi (EPFs) predatory natural enemies, can effectively control aphids. However, there few reports on combined enemies carrying EPF to enhance efficiency aphid control. RESULTS In present study, we evaluated compatibility five strains with adults Harlequin ladybird ( Harmonia axyridis )....
Abstract Background Beauveria bassiana ( B. ) is a famous entomopathogenic fungus that could parasitize on hundreds of insect species, which are being used as an environmentally friendly mycoinsecticide. Nevertheless, the possible effect genetic diversity these isolates from different hosts virulence has not been explored before. In order to explore issue, we compared genome sequences among seventeen 17 insects using whole re-sequencing, with strain ARSEF 2860 reference genome. Results There...
Clubroot caused by Plasmodiophora brassicae is a devastating disease of cabbage (Brassica oleracea). To identify quantitative trait loci (QTLs) for clubroot resistance (CR) in B. oleracea, genomic resequencing was carried out two sets extreme pools, group I and II, which were constructed separately from 110 74 F2 cloned lines derived the cross between clubroot-resistant (R) "GZ87" (against race 4) susceptible (S) "263." Based on QTL-sequencing (QTL-Seq) analysis three QTLs (i.e., qCRc7-2,...
Abstract Here we describe the engineering of a distant homolog Tet repressor, CamR, isolated from Pseudomonas putida, that is regulated by camphor, very inexpensive small molecule (at micromolar concentrations) for use in Saccharomyces cerevisiae. The repressor was engineered expression constitutive yeast promoter, fusion to viral activator protein cassette, and codon optimization. A suitable promoter responsive CamR embedding P. putida operator binding sequence within an upstream activating...
Abstract Objectives The high mortality of severe 2019 novel coronavirus disease (COVID‐19) cases is mainly caused by acute respiratory distress syndrome (ARDS), which characterized increased permeability the alveolar epithelial barriers, pulmonary oedema and consequently inflammatory tissue damage. Some but not all patients showed full functional recovery after devastating lung damage, so far there little knowledge about repair process. We focused on crucial roles progenitor cells in cell...