Amelioration of hepatic steatosis is associated with modulation of gut microbiota and suppression of hepatic miR-34a in Gynostemma pentaphylla (Thunb.) Makino treated mice.
AuthorsJia N, Lin X, Ma S, Ge S, Mu S, Yang C, Shi S, Gao L, Xu J, Bo T, Zhao J,
JournalNutr Metab (Lond)
PubMed ID30555521
'Non-alcoholic fatty liver disease (NAFLD) is a chronic and progressive liver disease with an increased risk of morbidity and mortality. However, so far no specific pharmacotherapy has been approved. Gynostemma pentaphylla (Thunb.) Makino (GP) is a traditional Chinese medicine that is widely used against hyperlipemia as well as hyperglycemia. This study ... More
Genome Analysis of Hypomyces perniciosus, the Causal Agent of Wet Bubble Disease of Button Mushroom (Agaricus bisporus).
AuthorsLi D, Sossah FL, Sun L, Fu Y, Li Y,
JournalGenes (Basel)
PubMed ID31146507
'The mycoparasitic fungus Hypomyces perniciosus causes wet bubble disease of mushrooms, particularly Agaricus bisporus. The genome of a highly virulent strain of H. perniciosus HP10 was sequenced and compared to three other fungi from the order Hypocreales that cause disease on A. bisporus. H. perniciosus genome is ~44 Mb, encodes ... More
Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom.
AuthorsSossah FL, Liu Z, Yang C, Okorley BA, Sun L, Fu Y, Li Y,
JournalGenes (Basel)
PubMed ID30744046
'Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and ... More
Anti-Inflammatory Effects of 5a,8a-Epidioxycholest-6-en-3ß-ol, a Steroidal Endoperoxide Isolated from Aplysia depilans, Based on Bioguided Fractionation and NMR Analysis.
'Sea hares of Aplysia genus are recognized as a source of a diverse range of metabolites. 5a,8a-Endoperoxides belong to a group of oxidized sterols commonly found in marine organisms and display several bioactivities, including antimicrobial, anti-tumor, and immunomodulatory properties. Herein we report the isolation of 5a,8a-epidioxycholest-6-en-3ß-ol (EnP(5,8)) from Aplysia depilans ... More
TF-ChIP Method for Tissue-Specific Gene Targets.
AuthorsPerna A, Alberi LA,
JournalFront Cell Neurosci
PubMed ID30941015
'Chromatin immunoprecipitation (ChIP) is an assay developed in order to define the dynamic nature of transcription processes. This method has been widely employed to identify methylated and acetylated DNA sequences in a variety of organs both in animals and humans. Nevertheless, this technique is significantly less employed to study transcriptional ... More
Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.
AuthorsSteranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH,
JournalMob DNA
PubMed ID30899333
'Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic ... More
Staphylococcal superantigen-like protein 13 activates neutrophils via Formyl Peptide Receptor 2.
AuthorsZhao Y, van Kessel KPM, de Haas CJC, Rogers MRC, van Strijp JAG, Haas PA,
JournalCell Microbiol
PubMed ID30098280
'Staphylococcal Superantigen-Like (SSL) proteins, one of the major virulence factor families produced by Staphylococcus aureus, were previously demonstrated to be immune evasion molecules that interfere with a variety of innate immune defenses. However, in contrast to characterized SSLs, that inhibit immune functions, we show that SSL13 is a strong activator ... More
An Immune-Responsive Cytoskeletal-Plasma Membrane Feedback Loop in Plants.
'Cell wall appositions (CWAs) are produced reactively by the plant immune system to arrest microbial invasion through the local inversion of plant cell growth. This process requires the controlled invagination of the plasma membrane (PM) in coordination with the export of barrier material to the volume between the plant PM ... More
A Rapid LAMP-Based Method for Screening Poultry Samples for Campylobacter Without Enrichment.
AuthorsRomero MR, Cook N,
JournalFront Microbiol
PubMed ID30374336
Campylobacter is the most prominent bacterium associated with foodborne disease and the majority of human infection cases are attributed to chicken. Rapid methods capable of determining the Campylobacter status of poultry products in a short time are needed in today's fast-paced food supply chain. In this study, we developed and ... More
Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.
AuthorsPornsukarom S, van Vliet AHM, Thakur S,
JournalBMC Genomics
PubMed ID30400810
Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology ... More
Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient Derived Tumors Clinical Application of Whole-Genome Sequencing for Reporting Targetable Variants in Cancer.
AuthorsWrzeszczynski KO, Felice V, Abhyankar A, Kozon L, Geiger H, Manaa D, London F, Robinson D, Fang X, Lin D, Lamendola-Essel MF, Khaira D, Dikoglu E, Emde AK, Robine N, Shah M, Arora K, Basturk O, Bhanot U, Kentsis A, Mansukhani MM, Bhagat G, Jobanputra V,
JournalJ Mol Diagn
PubMed ID30138725
We have developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay which provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, Indels, copy number variants, structural variants, and ... More
Genotyping and quantifying Lyme pathogen strains by deep sequencing of the outer surface protein C (ospC) locus.
AuthorsDi L, Wan Z, Akther S, Ying C, Larracuente A, Li L, Di C, Nunez R, Cucura DM, Goddard NL, Krampis K, Qiu WG,
JournalJ Clin Microbiol
PubMed ID30158192
Mixed infection of a single tick or host by Lyme disease spirochetes is common and a unique challenge for diagnosis, treatment, and surveillance of Lyme disease. Here we describe a novel protocol for differentiating Lyme strains based on deep sequencing of the hypervariable outer-surface protein C locus (ospC). Improving upon ... More
Comparing DNA quantity and quality using saliva collection following food and beverage consumption.
AuthorsHughes SR, Chapleau RR,
JournalBMC Res Notes
PubMed ID30904022
With the democratization of genetic testing, researchers, clinicians, and educators must consider the varying degree of field conditions when collecting samples for genetic analyses. For genotyping or sequencing studies, study designers have multiple options from which to choose, including cheek swabs and saliva sampling. One significant benefit of saliva collection ... More
Draft Genome Sequences of Shiga Toxin-Producing Escherichia coli O157:H7 Strains Recovered from a Major Production Region for Leafy Greens in California.
AuthorsQuiñones B, Yambao JC, Silva CJ, Lee BG,
JournalMicrobiol Resour Announc
PubMed ID31270203
Shiga toxin-producing Escherichia coli O157:H7 is a foodborne pathogen and is responsible for outbreaks of human gastroenteritis. This report documents the draft genome sequences of nine O157:H7 cattle strains, which were identified to be PCR positive for a Shiga toxin gene but displayed different levels of functional toxin activity. ... More
Porcine Circovirus Type 2 Induces Single Immunoglobulin Interleukin-1 Related Receptor (SIGIRR) Downregulation to Promote Interleukin-1ß Upregulation in Porcine Alveolar Macrophage.
AuthorsYang S, Liu B, Yin S, Shang Y, Zhang X, Khan MUZ, Liu X, Cai J
JournalViruses
PubMed ID31684202
Multisystemic inflammation in pigs affected by porcine circovirus type 2 (PCV2) indicates the disordered expression of inflammatory cytokines. However, the PCV2-induced expression profile of inflammation cytokines and its regulating mechanism remain poorly understood. In this study, inflammatory cytokines and receptors in porcine alveolar macrophages (PAMs) after PCV2 infection were profiled ... More
Improved Method for DNA Extraction and Purification from Tetrahymena pyriformis.
AuthorsEl Maaiden E, El Kharrassi Y, Essamadi AK, Moustaid K, Nasser B,
JournalMethods Protoc
PubMed ID31164619
Tetrahymena pyriformis (protozoa) is intensely investigated as a model organism, offering numerous advantages in comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is a vital step of any molecular experiment, here a new mixed surfactant (Sodium dodecyl sulfate (SDS) 20%/Triton X-100) was adopted for effective DNA ... More
The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells.
AuthorsHeurtier V, Owens N, Gonzalez I, Mueller F, Proux C, Mornico D, Clerc P, Dubois A, Navarro P,
JournalNat Commun
PubMed ID30846691
Transcription factor networks, together with histone modifications and signalling pathways, underlie the establishment and maintenance of gene regulatory architectures associated with the molecular identity of each cell type. However, how master transcription factors individually impact the epigenomic landscape and orchestrate the behaviour of regulatory networks under different environmental constraints is ... More