A5000290640- Microbial infections and disease research
- Bacteriophages and microbial interactions
- Mycobacterium research and diagnosis
- Aquaculture disease management and microbiota
- CRISPR and Genetic Engineering
- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- Respiratory viral infections research
- Genomics and Phylogenetic Studies
- Fungal and yeast genetics research
- Genomics and Chromatin Dynamics
- Myxozoan Parasites in Aquatic Species
- Herpesvirus Infections and Treatments
- COVID-19 Clinical Research Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Gut microbiota and health
- Tuberculosis Research and Epidemiology
- Cytomegalovirus and herpesvirus research
- Virus-based gene therapy research
- Microbial Metabolic Engineering and Bioproduction
- Ferroptosis and cancer prognosis
- Epigenetics and DNA Methylation
- Animal Disease Management and Epidemiology
J. Craig Venter Institute
2016-2025
Brigham Young University
2024
Google (United States)
2012
Johns Hopkins Medicine
2001
Johns Hopkins University
2001
The University of Texas at Austin
1993-1998
We report the design, synthesis, and assembly of 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized sequence information its transplantation into a M. capricolum recipient cell to create new cells that are controlled only by synthetic chromosome. The DNA in is designed sequence, including "watermark" sequences other gene deletions polymorphisms, mutations acquired during building process. have expected phenotypic properties capable continuous self-replication.
We recently reported the chemical synthesis, assembly, and cloning of a bacterial genome in yeast. To produce synthetic cell, must be transferred from yeast to receptive cytoplasm. Here we describe methods accomplish this. cloned Mycoplasma mycoides as centromeric plasmid then transplanted it into capricolum viable M. cell. While yeast, was altered by using genetic systems new strain mycoides. These allow construction strains that could not produced with tools available for this bacterium.
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that have mutations associated with increased transmission and antibody escape arisen over the course of current pandemic. Although vaccines largely been effective against past variants, number found on Omicron (B.1.1.529) spike protein appear to diminish protection conferred by preexisting immunity. Using vesicular stomatitis virus (VSV) pseudoparticles expressing several SARS-CoV-2 we evaluated magnitude breadth...
We report that a highly purified human origin recognition complex (HsORC) has intrinsic DNA-binding activity, and this activity is modestly stimulated by ATP. HsORC binds preferentially to synthetic AT-rich polydeoxynucleotides, but does not effectively discriminate between natural DNA fragments contain known origins control fragments. The fully restores replication ORC-depleted Xenopus egg extracts, providing strong evidence for its initiator function. Strikingly, stimulates initiation from...
Most microbes have not been cultured, and many of those that are cultivatable difficult, dangerous or expensive to propagate genetically intractable. Routine cloning large genome fractions whole genomes from these organisms would significantly enhance their discovery genetic functional characterization. Here we report the bacterial in yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) mycoides subspecies capri (1.1...
Abstract In mice, the maternal microbiome influences fetal immune development and postnatal allergic outcomes. Westernized populations have high rates of disease low gastrointestinal carriage Prevotella , a commensal bacterial genus that produces short chain fatty acids endotoxins, each which may promote tolerance. this study, we use prebirth cohort ( n = 1064 mothers) to conduct nested case-cohort study comparing 58 mothers babies with clinically proven food IgE mediated allergy 258...
The ongoing COVID-19 pandemic is a major public health crisis. Despite the development and deployment of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), persists. continued spread virus largely driven by emergence viral variants, which can evade current through mutations in spike protein. Although these differences are important terms transmission vaccine responses, variants possess other parts their genome that may also affect pathogenesis. Of particular...
The six-subunit origin recognition complex (ORC) was originally identified in the yeast<i>Saccharomyces cerevisiae</i>. Yeast ORC binds specifically to origins of replication and serves as a platform for assembly additional initiation factors, such Cdc6 Mcm proteins. Human homologues all six subunits have been by sequence similarity their yeast counterparts, but little is known about biochemical characteristics human (HsORC). We extracted HsORC from HeLa cell chromatin probed its subunit...
Mycoplasmas are "minimal" bacteria able to infect humans, wildlife, and a large number of economically important livestock species. Mycoplasma infections include spectrum clinical manifestations ranging from simple fever fulminant inflammatory diseases with high mortality rates. These mostly chronic, suggesting that mycoplasmas have developed means evade the host immune response. Here we present functionally characterize two-protein system mycoides subspecies capri is involved in capture...
Significance Viruses with large DNA genomes, such as herpesviruses, are difficult to manipulate existing genetic tools. We describe an application of synthetic genomics assembly tools that enables rapid and efficient generation combinatorial mutations in herpesvirus genomes. The method provides the capacity design, generate, test numerous multiloci mutants parallel, which can help us understand basic virus biology, facilitate vaccine development, aid development next-generation virus-based...
Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing resulting organisms to adopt genotype and phenotype conferred by donor cells. This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies intractable economically important microbial species. So far, this has only been reported using two closely related bacteria, Mycoplasma mycoides subsp. capri (Mmc) capricolum (Mcap), main factors driving...
One remarkable achievement in synthetic biology was the reconstruction of mycoplasma genomes and their cloning yeast where they can be modified using available genetic tools. Recently, CRISPR/Cas9 editing tools were developed for mutagenesis. Here, we report adaptation engineering bacterial cloned yeast. A seamless deletion glycerol-3-phosphate oxidase-encoding gene (glpO) achieved without selection one step, 90 nt paired oligonucleotides as templates to drive recombination. Screening...
Previously, we had developed synthetic genomics methods to assemble an infectious clone of herpes simplex virus type-1 (HSV-1) strain KOS. To do this, the genome was assembled from 11 separate cloned fragments in yeast using transformation-associated recombination. Using this method, generated null mutations five tegument protein-coding genes as well different combinations these mutants. The single-locus mutants were all able plaque on Vero cells. However, one multi-locus combination,...
African swine fever (ASF) is a deadly viral disease in domestic pigs that has large global economic impact for the industry. It present Africa, Europe, Asia, and Caribbean island of Hispaniola. There are no effective treatments or broadly licensed vaccines to prevent disease. Efforts counteract ASF have been hampered because lack convenient tools engineer its etiological agent, virus (ASFV), largely due noninfectious genome. Here, we report use synthetic genomics methodology develop reverse...
The GAL4 protein of Saccharomyces cerevisiae is the prototype a family transcription factors that contain Zn2Cys6 coordination complex in DNA-binding domain. activates genes involved galactose and melibiose metabolism by binding to sites one or more copies sequence 5'-CGGN5TN5CCG-3'. Other proteins S. also recognize sequences containing two CGG triplets, but with different spacings between them. In this report we investigate mechanism which distinguishes its bona fide site from similar as...
Genetic engineering of cytomegalovirus (CMV) currently relies on generating a bacterial artificial chromosome (BAC) by introducing origin replication into the viral genome using in vivo recombination virally infected tissue culture cells. However, this process is inefficient, results adaptive mutations, and involves deletion genes to avoid oversized genomes when inserting BAC cassette. Moreover, technology does not permit simultaneous manipulation multiple loci cannot be used construct...
Development of a new generation vaccines is key challenge for the control infectious diseases affecting both humans and animals. Synthetic biology methods offer ways to engineer bacterial chassis that can be used as vectors present heterologous antigens train immune system against pathogens. Here, we describe construction based on fast-growing Mycoplasma feriruminatoris, first steps toward its application live vaccine contagious caprine pleuropneumonia (CCPP). To do so, M. feriruminatoris...
The virus severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, is the causative agent of current COVID-19 pandemic. It possesses a large 30 kilobase (kb) genome that encodes structural, non-structural, and accessory proteins. Although not necessary to cause disease, these proteins are known influence viral replication pathogenesis. Through synthesis novel infectious clones SARS-CoV-2 lack one or more virus, we have found proteins, ORF8, critical for modulation host inflammatory...
The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding basic biological processes. Mycoplasma bacteria, smallest known among free-living cellular organisms, are ideal models this purpose, but natural versions these cells have genome complexities still too great to offer a comprehensive view fundamental life form. Here we describe an efficient method reducing from by identifying individually deletable regions using...
Mycoplasmas are the smallest free-living organisms and cause a number of economically important diseases affecting humans, animals, insects plants. Here, we demonstrate that highly virulent Mycoplasma mycoides subspecies capri (Mmc) can be fully attenuated via targeted deletion non-essential genes encoding, among others, potential virulence traits. Five genomic regions, representing approximately ten percent original Mmc genome, were successively deleted using Saccharomyces cerevisiae as an...
African swine fever virus (ASFV) is the causative agent of (ASF), resulting in up to 100% mortality pigs. Although endemic most sub-Saharan countries, where all known ASFV genotypes have been reported, disease has caused pandemics significant economic impact Eurasia, and no vaccines or therapeutics are available date. In endeavors develop live-attenuated against ASF, deletions several ~170 genes shown contrasting results depending on genotype investigated ASFV. Here, we report vivo outcome a...