Biomedical subjects

Hua Shi

Publications and source records attributed to Hua Shi.

8 recordsLinked to original sources

PubMed2006

An RNA aptamer that interferes with the DNA binding of the HSF transcription activator.

Heat shock factor (HSF) is a conserved and highly potent transcription activator. It is involved in a wide variety of important biological processes including the stress response and specific steps in normal development. Reagents that interfere with HSF function would be useful for both basic studies and practical applications. We selected an RNA aptamer that binds to HSF with high specificity. Deletion analysis defined the minimal binding motif of this aptamer to be two stems and one stem-loop joined by a three-way junction. This RNA aptamer interferes with normal interaction of HSF with its DNA element, which is a key regulatory step for HSF function. The DNA-binding domain plus a flanking linker region on the HSF (DL) is essential for the RNA binding. Additionally, this aptamer inhibits HSF-induced transcription in vitro in the complex milieu of a whole cell extract. In contrast to the previously characterized NF-kappaB aptamer, the HSF aptamer does not simply mimic DNA binding, but rather binds to HSF in a manner distinct from DNA binding to HSF.

Animals↗

PubMed2005

Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP.

The TATA-binding protein (TBP) is a general factor that is involved in transcription by all three types of nuclear RNA polymerase. To delineate the roles played by the DNA-binding surface of TBP in these transcription reactions, we used a set of RNA aptamers directed against TBP and examined their ability to perturb transcription in vitro by the different RNA polymerases. Distinct responses to the TBP aptamers were observed for transcription by different types of polymerase at either the initiation, reinitiation or both stages of the transcription cycle. We further probed the TBP interactions in the TFIIIB*DNA complex to elucidate the mechanism for the different sensitivity of Pol III dependent transcription before and after preinitiation complex (PIC) formation. Lastly, the aptamers were employed to measure the time required for Pol III PIC formation in vitro. This approach can be generalized to define the involvement of a particular region on the surface of a protein at particular stages in a biological process.

Cytochromes c↗

PubMed2005

Interconversion studies of betamethasone acetate polymorphs.

The polymorph interconversions of Betamethasone Acetate (BA) were studied under various pharmaceutical conditions, such as grinding, heating and suspending in water, based on differential scanning calorimetry, thermogravimetric analysis, and X-ray powder diffraction. There existed enantiotropic relationships between the three polymorphs of BA, which were named form II, Ialpha, and Ibeta work, respectively. It was concluded that form II was the most stable form when suspended in water.

Betamethasone↗

PubMed2004

Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes.

The TATA-binding protein (TBP) is a critical general transcription factor that associates with the core promoter and acts as a nexus for gene regulation through its interactions with other factors. A large number of proteins recognize the relatively small yet highly conserved C-terminal domain of TBP. One subset of these proteins (general transcription factors) interacts with the TBP.TATA complex and RNA polymerase II to create the preinitiation complex. To study TBP functions in preinitiation complex and other complexes, we generated a set of RNA aptamers with high affinity to yeast TBP. These aptamers act on TBP in different ways: all of them bind TBP competitively with DNA bearing the TATA element, and some can actively disrupt the TBP.TATA interaction in preformed, higher-order complexes containing the additional general transcription factors TFIIB and TFIIA. In crude cell extracts, the aptamers inhibit transcription in ways that reveal the dynamic nature of TBP interactions during initiation and reinitiation.

Base Sequence↗

PubMed2003

Specific SR protein-dependent splicing substrates identified through genomic SELEX.

The Drosophila pre-mRNA splicing factor B52 (SRp55) is essential for fly development, but splicing of RNAs of specific genes tested previously is normal in B52-null animals, presumably due to partial functional redundancy with other SR proteins. To identify B52-dependent splicing substrates in vivo, we selected genomic sequence fragments whose transcripts bind B52. Almost all of the corresponding genes having a known function encode either transcription factors or components of signal transduction pathways, with the B52- binding fragments located to not only exonic but also intronic regions. Some pre-mRNAs from these genes showed splicing defects in the B52-null mutant. These results indicate that B52 has unique functions in the removal of some introns during development, and plays a critical role in cellular regulatory networks.

Animals↗

PubMed2003

Status and interconnections of selected environmental issues in the global coastal zones.

This study focuses on assessing the state of population distribution, land cover distribution, biodiversity hotspots, and protected areas in global coastal zones. The coastal zone is defined as land within 100 km of the coastline. This study attempts to answer such questions as: how crowded are the coastal zones, what is the pattern of land cover distribution in these areas, how much of these areas are designated as protected areas, what is the state of the biodiversity hotspots, and what are the interconnections between people and coastal environment. This study uses globally consistent and comprehensive geospatial datasets based on remote sensing and other sources. The application of Geographic Information System (GIS) layering methods and consistent datasets has made it possible to identify and quantify selected coastal zones environmental issues and their interconnections. It is expected that such information provide a scientific basis for global coastal zones management and assist in policy formulations at the national and international levels.

Conservation of Natural Resources↗

PubMed2002

Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets.

Iterative cycles of in vitro selection and amplification allow rare functional nucleic acid molecules, aptamers, to be isolated from large sequence pools. Here we present an analysis of the progression of a selection experiment that simultaneously yielded two families of RNA aptamers against two disparate targets: the intended target protein (B52/SRp55) and the partitioning matrix. We tracked the sequence abundance and binding activity to reveal the enrichment of the aptamers through successive generations of selected pools. The two aptamer families showed distinct trajectories of evolution, as did members within a single family. We also developed a method to control the relative abundance of an aptamer family in selected pools. This method, involving specific ribonuclease digestion, can be used to reduce the background selection for aptamers that bind the matrix. Additionally, it can be used to isolate a full spectrum of aptamers in a sequential and exhaustive manner for all the different targets in a mixture.

Base Sequence↗

PubMed2002

[Enhancement of antigen presenting function of dendritic cells by IL-2 gene modification and its mechanism].

OBJECTIVE: To investigate the effects of IL-2 gene modification enhancement of the antigen-presenting function of the mouse bone marrow derived dendritic cells and on the activation of CTL induced by MHC class I molecule restricted antigen peptides as well as the related immunological mechanisms. METHODS: DCs were prepared from mouse bone marrow and modified by recombinant IL-2 adenovirus (DC-IL-2). The IL-12 and IFN-gamma levels in culture supernatant of DC and CTL were examined by ELISA, the expression of costimulatory molecules and fluorescent intensity of endocytosis of OVA-FITC in DC by FACS, the capacity of presenting 3LL cell tumor antigen by (3)H-TdR incorporation method, the MHC class I-restricted tumor-antigen-peptide Mut1 of 3LL cells pulsed DC-IL-2 to induce CTL cytotoxicity by (51)Cr 4-hr releasing assay. RESULTS: After IL-2 gene modification, DC-IL-2 could produce high level of IL-12 [(78.4 +/- 6.6) pg.(1 x 10(6) cells)(-1).ml(-1)]. The expression of costimulatory molecules on DC-IL-2 was increased, the fluorescent intensity of DC captured OVA-FITC was enhanced, and the proliferation of allo-T cells from 3LL bearing mouse pulsed with Mut1 was also enhanced. Mut1 antigen peptide pulsed DC-IL-2 could induce more potent antigen-specific CTL cytotoxicity and excrete high concentration of IFN-gamma [(1 168 +/- 58.4) pg/ml] in vivo. CONCLUSION: IL-2 gene modification of DC can activate second signal for DC presenting antigen, and enhance the function for capturing and presenting tumor antigen. DC-IL-2 pulsed with MHC class I restricted tumor-antigen-peptide can induce specific anti-tumor immune response more effectively. Owing to IL-2 gene modification, the functions of IL-12 excretion and T cell activation of DC were promoted, so that the capacity of CTL excreting IFN-gamma was enhanced, which are relevant to the immune mechanism.

Adenoviridae↗