Project description:Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this study we finely map the genome-wide targets of the CREB protein across all known and predicted human promoters, and characterize the functional consequences of a subset of these binding events using high-throughput reporter assays. To measure CREB binding, we used HaloCHIP, an antibody-free alternative to the ChIP method that utilizes the HaloTag fusion protein, and also high-throughput promoter-luciferase reporter assays, which provide rapid and quantitative screening of promoters for transcriptional activation or repression in living cells.
Project description:In this manuscript we describe our work on the development of a label-free chemoproteomics screening platform for cysteine reactive covalent fragments on a 96 well plate format. This platform profiles cysteine reactive fragments by competition with the hyper-reactive iodoacetamide desthiobiotin (IA-DTB) in cell lysates and live cells. We employ label free quantification and data independent acquisition (DIA) on an Evosep One – Bruker timsTOF Pro. In this submission we report this use of global proteomics to explore protein expression in HEK293T.
Project description:To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.
Project description:Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this study we finely map the genome-wide targets of the CREB protein across all known and predicted human promoters, and characterize the functional consequences of a subset of these binding events using high-throughput reporter assays. To measure CREB binding, we used HaloCHIP, an antibody-free alternative to the ChIP method that utilizes the HaloTag fusion protein, and also high-throughput promoter-luciferase reporter assays, which provide rapid and quantitative screening of promoters for transcriptional activation or repression in living cells. CREB ChIP-chip two biologcal replicates. HaloCHIP-chip three biological replicates with and without Forskolin
Project description:Dental pulp cells of cryopreserved teeth (slow and rapid speed) were examined with microarray for screening which gene is involve in the inflammation process during the cryopreservation process. Intact caries-free, freshly extracted premolars (n=6) were collected from 3 patients for microarray assay analysis. They were classified as control and cryopreserved groups. Cryopreserved groups were divided into rapid freezing and slow freezing group.
Project description:To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the molecular level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physico-chemical properties of impurity-free single-wall carbon nanotubes (SWCNTs).
Project description:Spheroids have found broad applications across biomedical engineering, including tissue modeling and drug screening; however, current culturing methods remain limited in terms of structural stability, uniformity, and scalability. To address these challenges, we developed the Dual‑axis Rotating Capillary Containers (DRCC) platform, a contact‑free system for rapid and uniform spheroid formation. The DRCC platform consists of an array of capillary‑based containers paired with a dual‑axis rotational unit. The capillary containers efficiently capture and release cell suspensions, while the dual‑axis rotation counteracts gravitational settling and promotes homogeneous self‑assembly into compact spheroids. Using this system, spheroids with tunable diameters ranging from 100 to 1300 µm were formed within 24 h while maintaining cell viability exceeding 95 %. Compared with spheroids produced using commercial systems, DRCC‑cultured spheroids showed markedly enhanced mechanical stability and a higher compressive modulus with 4 times increase, indicative of stronger intercellular cohesion. Notably, they also exhibited enhanced drug‑penetration barriers that more closely mimic in vivo solid tumors, as evidenced by significantly reduced doxorubicin uptake. This behavior correlates with the upregulated secretion of connexins and collagen in DRCC spheroids, as revealed by transcriptomic and immunofluorescence analyses. Furthermore, the platform enabled the construction of complex co‑culture spheroids that recapitulate the spatial architecture of the tumor microenvironment. Together, the DRCC platform offers a robust, efficient, and controllable tool for generating high‑fidelity spheroids, advancing their use in disease modeling, drug screening, and tissue engineering.