Project description:<p>Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin. In acne patients, the microbiome composition at the species level and at P. acnes strain level was more diverse than in healthy individuals, with enriched virulence-associated factors and reduced abundance of metabolic synthesis genes. Based on the abundance profiles of the metagenomic elements, we constructed a quantitative prediction model, which classified the clinical states of the host skin with high accuracy in both our study cohort (85%) and an independent sample set (86%). Our results suggest that the balance between metagenomic elements, not the mere presence of disease-associated strains, shapes the overall virulence property of the skin microbiota. This study provides new insights into the microbial mechanism of acne pathogenesis and suggests probiotic and phage therapies as potential acne treatments to modulate the skin microbiota and to maintain skin health.</p>
Project description:We analyzed gene and microRNA expression profiles of purified CD14 monocytes isolated from blood of 5 healthy donors after 24 h of in vitro co-culture with exosomes exosomes isolated from the INT12 melanoma cell line generated in our laboratory from a human melanoma specimen. Differentially expressed genes and miRNAs were identified between treated and untreated monocytes.
Project description:Single-cell TCR/transcriptome analysis for a peripheral blood lymphocytes (PBL) specimen was perform on a 10X Chromium instrument using a single-cell VDJ kit
Project description:Analysis of 80 glioblastoma specimen of patients treated within clinical trials and 4 samples of "normal" brain tissue (non-tumoral). The data was used to identify factors of resistance to a chemoradiation therapy protocol of radiotherapy and concomitant and adjuvant temozolomide (alkylating agent). Experiment Overall Design: 80 glioblastoma specimen and 4 non-tumoral brain samples
Project description:The Malaria Host-Pathogen Interaction Center (MaHPIC) is an inter-disciplinary NIH systems biology contract that utilizes multiple omics types (omics, clinical, and mathematical models), to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria infections in non-human primates with the goal of better understanding human disease. These data and metadata were produced by MaHPIC in collaborations between Emory University, Georgia Institute of Technology, and The University of Georgia as part of the MaHPIC contract (NIAID Contract: # HHSN272201200031C). Curation and maintenance of these data and metadata are the responsibility of the MaHPIC. Mary Galinski mgalins@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), Esmeralda Meyer evargas@emory.edu - MaHPIC Project Manager The experimental design of this pyrimethamine administration experiment with Macaca mulatta was approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and is as follows. Five naive males (RCs13, RWr13, RUn13, RZe13 and RTi13) approximately 2 years of age were injected intravenously with a preparation of Anopheles dirus salivary gland material and then profiled for clinical and omic measurements over the course of a 100-day experiment. Samples were generated and analyzed as part of a multi-omic approach to understanding the effects that the anti-malarial drug pyrimethamine has on immune physiology in rhesus macaques (M. mulatta). There was no infection with Plasmodium parasites during this study. Whole blood and bone marrow RNA-Seq and plasma have been obtained for seven time-points before, during and after three rounds of drug administration. Samples are from either whole blood or bone marrow specimen types. 5 individuals were sampled for each specimen type, 7 times each over the 100 day experiment. 5 individuals * 2 specimen types * 7 time points = 70 samples. Biological samples (Whole Blood or Bone Marrow) were collected at 7 time points during the 100 days. These correspond to: Time Point 1 = Day 0 (Baseline Sampling Point) Time Point 2 = Day 21 Time Point 3 = Day 27 Time Point 4 = Day 52 Time Point 5 = Day 59 Time Point 6 = Day 90 Time Point 7 = Day 98 Pyrimethamine was administered on Days 21, 52, 53, 54, 90, 91, and 92.
