Project description:As part of collaboration between the X. William Yang Lab at UCLA and CHDI, a transcriptomic study of normal murine cortex was carried out. Cortex was dissected from 6-month-old wildtype (WT) control mice. Transcriptomic analysis (RNASeq) was performed.
Project description:Investigation of whole genome gene expression level changes in S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, S. oralis KCTC 13048T, and S. pseudopneumoniae CCUG 49455T. This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains. A one chip study using total RNA recovered from S. pseudopneumoniae CCUG 49455T with three strain. For the the transcriptome of S. pseudopneumoniae CCUG 49455T was analyzed using the S. pneumoniae R6 microarray platform and compared with those of S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, and S. oralis KCTC 13048T strains.
Project description:Investigation of whole genome gene expression level changes in E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774 compared to when E. coli is cultured individually.
Project description:As part of collaboration between the X. William Yang Lab at UCLA and CHDI, a list of 52 genes that were implicated in Huntington’s disease (HD) through various computational modeling efforts was compiled, and murine lines with heterozygous knockout of these genes were obtained from public repositories or newly created. Striatum was dissected from 6-month-old mice that were either heterozygous KO for one of 52 genes or the corresponding wildtype (WT) controls. Transcriptomic analysis (RNASeq) was performed.
Project description:The Type VI Secretion System (T6SS) in bacteria is a versatile mechanism that facilitates protein transport into neighboring cells and can act as an antibacterial weapon by eliminating competing organisms in the vicinity. The objective of this study was to characterize the T6SS in Aggregatibacter aphrophilus and assess its antimicrobial capabilities through competition with Aggregatibacter actinomycetemcomitans in a multispecies biofilm. The proteomic analysis consisted of two parts, referred to as monospecies biofilm and multispecies biofilms, respectively. Initially, we examined the protein profiles of monospecies biofilms formed by two strains of Aggregatibacter aphrophilus, namely HK83 and CCUG 11575, along with their Hcp mutant derivatives (Hcp being a core protein for T6SS). Each strain was analyzed with six replicates (n=4 for HK83, HK83 hcp, CCUG 11575, and CCUG 11575 hcp). Subsequently, the HK83 and CCUG 11575 strains, as well as their Hcp mutant derivatives, were individually introduced into a multispecies biofilm. This multispecies biofilm consisted of seven species, namely A. actinomycetemcomitans JP2 strain (OMZ 295), Actinomyces oris (OMZ 745), Candida albicans (OMZ 110), Fusobacterium nucleatum subsp. nucleatum KP-F2 (OMZ 598), Streptococcus oralis SK248 (OMZ 607), Streptococcus mutans UA159 (OMZ 918), and Veillonella dispar ATCC 17748T (OMZ 493). These species were selected to mimic the natural co-habitat of A. aphrophilus and A. actinomycetemcomitans. Furthermore, control 7-species biofilms with A. aphrophilus strains HK83, HK83 hcp, CCUG 11575, and CCUG 11575 hcp (n=4 each) underwent proteomic analysis to gain insights into the protein expression and potential interactions within the biofilm community.
Project description:Investigation of whole genome gene expression level changes in S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, S. oralis KCTC 13048T, and S. pseudopneumoniae CCUG 49455T. This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.
Project description:Dr. Lebrilla's lab is working on another set of transcriptomics experiments which will measure whether HMO (human milk oligosacharides) elicit a differential response on Caco2 in the presence of B.infantis. They wish to supplement the data obtained with the Illumina platform with glycan-related expression data obtained with the Gene-chips to achieve a more complete understanding on how Caco2 cells respond to the presence of HMOs and B.infantis. The transcriptomics data is being complemented by qPCR based bacterial-epithelial cells binding assays, and glycan arrays assays for which they have initiated a collaboration with the CFG Core H (David Smith).
Project description:Set of 85 plant extracts of the Zingiberales. Includes Families: Cannacea, Costaceae, Heliconiaceae, Marantaceae, Musaceae, Zingiberacea. Collection was done by Miguel Chavez at La Selva Biological Station in Costa Rica,
The samples were measured in Geneva Switzerland, within a collaboration with Jean-Luc Wolfender's Lab. User: Luis Quiros-Guerrero
Project description:Set of 85 plant extracts of the Zingiberales. Includes Families. Cannacea, Costaceae, Heliconiaceae, Marantaceae, Musaceae, Zingiberacea. Collection was done by Miguel Chavez at La Selva Biological Station in Costa Rica.
The samples were measured in Geneva Switzerland, within a collaboration with Jean-Luc Wolfender's Lab. User Luis Quiros-Guerrero
