Surface metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA444388 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Solar panel surface microbial communities from Lawrence Berkeley National Laboratory, California, USA - L
| PRJNA444390 | ENA
Project description:Solar panel surface microbial communities from Lawrence Berkeley National Laboratory, California, USA - R
| PRJNA444389 | ENA
Project description:A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR. However, an unbiased diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for unbiased random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array developed at the Lawrence Livermore National Laboratory, California, USA, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for unbiased diagnostic analysis of all viruses in clinical samples.
2011-04-14 | GSE28597 | GEO
Project description:Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages: proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.
2013-12-25 | GSE53635 | GEO
Project description:Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages: proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells. Erythroid differentiation stage-specific transcriptome analysis was performed by RNA-seq analysis of highly purified erythroblast populations
2013-12-25 | E-GEOD-53635 | biostudies-arrayexpress
Project description:1Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. 2Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. 3Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. 4CCTS Bioinformatic Program, The Rockefeller University, New York, NY 10065, USA. 5State Key Laboratory of Genetic Engineering & Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
2021-06-30 | GSE84157 | GEO
Project description:A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR. However, an unbiased diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for unbiased random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array developed at the Lawrence Livermore National Laboratory, California, USA, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for unbiased diagnostic analysis of all viruses in clinical samples. 19 clinical samples were analyzed for presence of virus using the MDA microarray. One of the samples is a negative control (water). One HCV-positive serum sample is included twice (HCV+1 and HCV+2).
2011-04-14 | E-GEOD-28597 | biostudies-arrayexpress
Project description:Root tissues, shoot tissues and root exudates were collected from hydroponically grown B. distachyon, M. truncatula and A. thaliana. Metabolites were extracted and analyzed by LCMS. Metabolites were separated on an Agilent 1290 stack using an Agilent InfinityLab Poroshell 120 HILIC-Z column (2.1 x 150 mm, 2.7 um). Detection was performed using a Thermo QExactive hybrid quadrupole-orbitrap mass spectrometer.
This data is has been incorporated into a manuscript (in preparation as of Dec 14, 2022):
The core metabolome and root exudation dynamics of
three phylogenetically distinct plant species
Sarah McLaughlin 1,2,3 , Kateryna Zhalnina 1,2 , Suzanne Kosina 1 , Trent R. Northen 1,2 *,
Joelle Sasse 1,2, 3 *
*corresponding authors: trnorthen@lbl.gov, jsasse@botinst.uzh.ch
1 Lawrence Berkeley National Laboratory, Environmental Genomics and Systems
Biology, 1 Cyclotron Road, Berkeley, CA, 94720, USA
2 Joint Genome Institute, National Laboratory, Environmental Genomics and Systems
Biology, 1 Cyclotron Road, Berkeley, CA, 94720, USA
3 current address: Institute for Plant and Microbial Biology, University of Zurich,
8008 Zurich, Switzerland
2022-12-08 | MSV000090869 | GNPS
Project description:Mathematical modeling of mutant transferrin-CRM107 molecular conjugates for cancer therapy.
Yoon DJ1, Chen KY1, Lopes AM1, Pan AA1, Shiloach J2, Mason AB3, Kamei DT4.
Author information
1
Department of Bioengineering, University of California, Los Angeles, 420 Westwood Plaza, 5121 Engineering V, Los Angeles, CA 90095, USA.
2
Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA.
3
Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT 05405, USA.
4
Department of Bioengineering, University of California, Los Angeles, 420 Westwood Plaza, 5121 Engineering V, Los Angeles, CA 90095, USA. Electronic address: kamei@seas.ucla.edu.
Abstract
The transferrin (Tf) trafficking pathway is a promising mechanism for use in targeted cancer therapy due to the overexpression of transferrin receptors (TfRs) on cancerous cells. We have previously developed a mathematical model of the Tf/TfR trafficking pathway to improve the efficiency of Tf as a drug carrier. By using diphtheria toxin (DT) as a model toxin, we found that mutating the Tf protein to change its iron release rate improves cellular association and efficacy of the drug. Though this is an improvement upon using wild-type Tf as the targeting ligand, conjugated toxins like DT are unfortunately still highly cytotoxic at off-target sites. In this work, we address this hurdle in cancer research by developing a mathematical model to predict the efficacy and selectivity of Tf conjugates that use an alternative toxin. For this purpose, we have chosen to study a mutant of DT, cross-reacting material 107 (CRM107). First, we developed a mathematical model of the Tf-DT trafficking pathway by extending our Tf/TfR model to include intracellular trafficking via DT and DT receptors. Using this mathematical model, we subsequently investigated the efficacy of several conjugates in cancer cells: DT and CRM107 conjugated to wild-type Tf, as well as to our engineered mutant Tf proteins (K206E/R632A Tf and K206E/R534A Tf). We also investigated the selectivity of mutant Tf-CRM107 against non-neoplastic cells. Through the use of our mathematical model, we predicted that (i) mutant Tf-CRM107 exhibits a greater cytotoxicity than wild-type Tf-CRM107 against cancerous cells, (ii) this improvement was more drastic with CRM107 conjugates than with DT conjugates, and (iii) mutant Tf-CRM107 conjugates were selective against non-neoplastic cells. These predictions were validated with in vitro cytotoxicity experiments, demonstrating that mutant Tf-CRM107 conjugates is indeed a more suitable therapeutic agent. Validation from in vitro experiments also confirmed that such whole-cell kinetic models can be useful in cancer therapeutic design.
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2020-01-09 | MODEL1912160006 | BioModels
Project description:Microbial communities from bioreactor (seeded with sewage sludge) at Lawrence Berkeley National Lab, California, USA - Biofuel Metagenome 9
| PRJNA384661 | ENA