ORCID Profile
0000-0001-7315-7613
Current Organisation
E O Lawrence Berkeley National Laboratory
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Publisher: Springer Science and Business Media LLC
Date: 15-02-2001
DOI: 10.1038/35057062
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
Publisher: Springer Science and Business Media LLC
Date: 15-02-2001
DOI: 10.1038/35057157
Abstract: The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.
Publisher: Proceedings of the National Academy of Sciences
Date: 03-03-2009
Abstract: Forward genetic screens with ENU ( N -ethyl- N -nitrosourea) mutagenesis can facilitate gene discovery, but mutation identification is often difficult. We present the first study in which an ENU- induced mutation was identified by massively parallel DNA sequencing. This mutation causes heterotaxy and complex congenital heart defects and was mapped to a 2.2-Mb interval on mouse chromosome 7. Massively parallel sequencing of the entire 2.2-Mb interval identified 2 single-base substitutions, one in an intergenic region and a second causing replacement of a highly conserved cysteine with arginine (C193R) in the gene Megf8. Megf8 is evolutionarily conserved from human to fruit fly, and is observed to be ubiquitously expressed. Morpholino knockdown of Megf8 in zebrafish embryos resulted in a high incidence of heterotaxy, indicating a conserved role in laterality specification. Megf8 C193R mouse mutants show normal breaking of symmetry at the node, but Nodal signaling failed to be propagated to the left lateral plate mesoderm. Videomicroscopy showed nodal cilia motility, which is required for left–right patterning, is unaffected. Although this protein is predicted to have receptor function based on its amino acid sequence, surprisingly confocal imaging showed it is translocated into the nucleus, where it is colocalized with Gfi1b and Baf60C, two proteins involved in chromatin remodeling. Overall, through the recovery of an ENU-induced mutation, we uncovered Megf8 as an essential regulator of left–right patterning.
Publisher: American Chemical Society (ACS)
Date: 17-07-2014
DOI: 10.1021/CB500244V
Publisher: Springer Science and Business Media LLC
Date: 29-04-2011
DOI: 10.4056/SIGS.1553865
Publisher: Cold Spring Harbor Laboratory
Date: 15-02-2019
DOI: 10.1101/548222
Abstract: Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis . Here we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly erse group of inoviruses. Using a new machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like genomes from microbial genomes and metagenomes. Collectively, these represent six distinct proposed inovirus families infecting nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that these viruses may have occasionally transferred from bacterial to archaeal hosts. Finally, we identified an expansive ersity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere sparks new avenues for microbial manipulation approaches and innovative biotechnological applications.
Publisher: Public Library of Science (PLoS)
Date: 20-10-2011
Publisher: Springer Science and Business Media LLC
Date: 14-07-2013
DOI: 10.1038/NATURE12352
Abstract: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional ersity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine erse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
Publisher: Proceedings of the National Academy of Sciences
Date: 28-07-2010
Abstract: Metagenomic and bioinformatic approaches were used to characterize plant biomass conversion within the foregut microbiome of Australia's “model” marsupial, the Tammar wallaby ( Macropus eugenii ). Like the termite hindgut and bovine rumen, key enzymes and modular structures characteristic of the “free enzyme” and “cellulosome” paradigms of cellulose solubilization remain either poorly represented or elusive to capture by shotgun sequencing methods. Instead, multigene polysaccharide utilization loci-like systems coupled with genes encoding β-1,4-endoglucanases and β-1,4-endoxylanases—which have not been previously encountered in metagenomic datasets—were identified, as were a erse set of glycoside hydrolases targeting noncellulosic polysaccharides. Furthermore, both rrs gene and other phylogenetic analyses confirmed that unique clades of the Lachnospiraceae, Bacteroidales, and Gammaproteobacteria are predominant in the Tammar foregut microbiome. Nucleotide composition-based sequence binning facilitated the assemblage of more than two megabase pairs of genomic sequence for one of the novel Lachnospiraceae clades (WG-2). These analyses show that WG-2 possesses numerous glycoside hydrolases targeting noncellulosic polysaccharides. These collective data demonstrate that Australian macropods not only harbor unique bacterial lineages underpinning plant biomass conversion, but their repertoire of glycoside hydrolases is distinct from those of the microbiomes of higher termites and the bovine rumen.
Publisher: Elsevier BV
Date: 06-2016
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1GC15193B
Publisher: Springer Science and Business Media LLC
Date: 09-02-2016
Publisher: Springer Science and Business Media LLC
Date: 07-2011
DOI: 10.4056/SIGS.2004648
Publisher: S. Karger AG
Date: 2006
DOI: 10.1159/000094802
Abstract: We report the first isolation and sequencing of genomic BAC clones containing the marsupial milk protein genes Whey Acidic Protein i (WAP) /i and Early Lactation Protein i (ELP) /i . The stripe-faced dunnart i WAP /i gene sequence contained five exons, the middle three of which code for the i WAP /i motifs and four disulphide core domains which characterize WAP. The dunnart i ELP /i gene sequence contained three exons encoding a protein with a Kunitz motif common to serine protease inhibitors. Fluorescence in situ hybridization located the i WAP /i gene to chromosome 1p in the stripe-faced dunnart, and the i ELP /i gene to 2q. Northern blot analysis of lactating mammary tissue of the closely related fat-tailed dunnart has shown asynchronous expression of these milk protein genes. i ELP /i was expressed at only the earlier phase of lactation and i WAP /i only at the later phase of lactation, in contrast to β-lactoglobulin i (BLG) /i and α-lactalbumin i (ALA) /i genes, which were expressed in both phases of lactation. This asynchronous expression during the lactation cycle in the fat-tailed dunnart is similar to other marsupials and it probably represents a pattern that is ancestral to Australian marsupials.
Location: United States of America
No related grants have been discovered for Jan-Fang Cheng.