PubMed Health⌕ Search

Biomedical subjects

Weimin Zhu

Publications and source records attributed to Weimin Zhu.

At least 19 recordsLinked to original sources
PubMed2007

Proteomic data exchange and storage: the need for common standards and public repositories.

The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiatives has highlighted issues when collaborators cannot import data generated within the same project but generated by different hardware types and processed by laboratory-specific work flows and analyses packages. There is an increasing need for common data standards that will allow the interchange of data between different instrumentation, search engines, and between laboratory databases. This could then lead to the establishment of data repositories from where benchmark datasets could be accessed and reanalyzed. The Human Proteome Organization is currently supporting efforts to establish such standards. The work of the Proteomics Standards Initiative has lead to the development of the mzData XML interchange standard and is now broadening its scope to produce a spectral analysis output format, mzIdent. Accompanying controlled vocabularies allow the accurate, while systematic, representation of metadata throughout both schema.

Benchmarking↗
PubMed2006

EMBL Nucleotide Sequence Database in 2006.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying annotation. The database is maintained in collaboration with DDBJ and GenBank. Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation, alignments and bulk data. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. In 2006, the volume of data has continued to grow exponentially. Access to the data is provided via SRS, ftp and variety of other methods. Extensive external and internal cross-references enable users to search for related information across other databases and within the database. All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk/. Changes over the past year include changes to the file format, further development of the EMBLCDS dataset and developments to the XML format.

Base Sequence↗
PubMed2006

UniSave: the UniProtKB sequence/annotation version database.

SUMMARY: The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries are loaded into the UniSave as part of the public bi-weekly UniProtKB releases. Unlike the UniProtKB, which contains only the latest Swiss-Prot and TrEMBL entry versions, the UniSave provides access to previous versions of these entries. AVAILABILITY: http://www.ebi.ac.uk/uniprot/unisave

Database Management Systems↗
PubMed2006

EMBL Nucleotide Sequence Database: developments in 2005.

The EMBL Nucleotide Sequence Database (www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to all. Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly submitted sequence, sequence recorded in support of patent applications and much more. The database continues to offer submission tools, data retrieval facilities and user support. In 2005, the volume of data offered has continued to grow exponentially. In addition to the newly presented data, the database encompasses a range of new data types generated by novel technologies, offers enhanced presentation and searchability of the data and has greater integration with other data resources offered at the EBI and elsewhere. In stride with these developing data types, the database has continued to develop submission and retrieval tools to maximise the information content of submitted data and to offer the simplest possible submission routes for data producers. New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information.

Animals↗
PubMed2006

Development of new rabbit monoclonal antibody to progesterone receptor (Clone SP2): no heat pretreatment but effective for paraffin section immunohistochemistry.

Evaluation of estrogen and progesterone receptor (ER, PgR) status in breast cancer is widely used for the prediction of the response to endocrine therapy and as a biologic parameter closely related to disease prognosis. The IHC method is considered to be a specific, sensitive, and economical method for determining ER and PgR status. The authors developed the first rabbit anti-PgR mAb (clone SP2) used in IHC on formalin-fixed, paraffin-embedded tissue sections from breast carcinomas. This new antibody, compared with currently available anti-PgR antibodies, has important advantages, including its reactivity even without heat-based antigen retrieval of fixed-embedded tissue sections in IHC and the predominance of nuclear immunostaining with only very low cytoplasmic signal. A comparative study of IHC on 107 histologic specimens from breast cancer cases showed that SP2 yields the same results as the wellknown mouse mAb to PgR (clone 1A6). The antibody affinity of SP2 is 12 times higher than that of 1A6. Thus, SP2 may prove of great value in the assessment of PgR status in human breast cancer.

Animals↗
PubMed2005

Bispecific and human disease-related anti-keratin rabbit monoclonal antibodies.

Rabbit antibodies may have favorable properties compared to mouse antibodies, including high affinities and better antigen recognition. We used a biochemical and reverse immunologic approach to generate and characterize rabbit anti-phospho-keratin and anti-keratin monoclonal antibodies (MAb). Human keratins 8 and 18 (K8/K18) were used as immunogens after isolation from cells pretreated with okadaic acid or pervanadate to promote Ser/Thr or Tyr hyperphosphorylation, respectively. Selected rabbit MAb were tested by immunofluorescence staining, immunoprecipitation, and 2-dimensional gels. Keratin phospho and non-phospho-mutants were used for detailed characterization of two unique antibodies. One antibody recognizes a K8 G61-containing epitope, an important epitope given that K8 G61C is a frequent mutation in human liver diseases. This antibody binds K8 that is not phosphorylated on S73, but its binding is ablated by G61 but not S73 mutation. The second antibody is bispecific in that it simultaneously recognizes two epitopes: one phospho (K8 pS431) conformation-independent and one non-phospho conformation-dependent, with both epitopes residing in the K8 tail domain. Therefore, a reverse immunologic and biochemical approach is a viable tool for generating versatile rabbit MAb for a variety of cell biologic applications including the potential identification of physiologic phosphorylation sites.

Animals↗
PubMed2005

Chemical library screen for novel inhibitors of Kaposi's sarcoma-associated herpesvirus processive DNA synthesis.

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma and certain lymphoproliferative disorders. The role of KSHV lytic replication has been implicated in the tumor pathogenesis. A highly specific molecular complex formed by the KSHV DNA polymerase (POL8) and processivity factor (PF8) is indispensable for lytic viral DNA synthesis and may serve as an excellent molecular anti-KSHV target. The majority of conventional nucleoside-based anti-herpetic DNA synthesis inhibitors require intracellular phosphorylation/activation before they can exert inhibitory activity as competitive substrates for viral DNA polymerases. Novel and more potent inhibitors of KSHV DNA synthesis may be discovered through POL8/PF8-targeted high throughput screening (HTS) of small molecule chemical libraries. We developed a microplate-based KSHV POL8/PF8-mediated DNA synthesis inhibition assay suitable for HTS and screened the NCI Diversity Set that comprised 1992 synthetic compounds. Twenty-eight compounds exhibited greater than 50% inhibition. The inhibitory activity was confirmed for 25 of the 26 hit compounds available for further testing, with the 50% inhibitory concentrations ranging from 0.12+/-0.07 microM (mean+/-S.D.) to 10.83+/-4.19 microM. Eighteen of the confirmed active compounds efficiently blocked KSHV processive DNA synthesis in vitro. One of the hit compounds, NSC 373989, a pyrimidoquinoline analog, was shown to dose-dependently reduce the levels of KSHV virion production and KSHV DNA in lytically induced KSHV-infected BCBL-1 cells, suggesting that the compound blocked lytic KSHV DNA synthesis. HTS for KSHV POL8/PF8 inhibitors is feasible and may lead to discovery of novel non-nucleoside KSHV DNA synthesis inhibitors.

Animals↗
PubMed2005

Mfge8 is critical for mammary gland remodeling during involution.

Apoptosis is a critical process in normal mammary gland development and the rapid clearance of apoptotic cells prevents tissue injury associated with the release of intracellular antigens from dying cells. Milk fat globule-EGF-factor 8 (Mfge8) is a milk glycoprotein that is abundantly expressed in the mammary gland epithelium and has been shown to facilitate the clearance of apoptotic lymphocytes by splenic macrophages. We report that mice with disruption of Mfge8 had normal mammary gland development until involution. However, abnormal mammary gland remodeling was observed postlactation in Mfge8 mutant mice. During early involution, Mfge8 mutant mice had increased numbers of apoptotic cells within the mammary gland associated with a delay in alveolar collapse and fat cell repopulation. As involution progressed, Mfge8 mutants developed inflammation as assessed by CD45 and CD11b staining of mammary gland tissue sections. With additional pregnancies, Mfge8 mutant mice developed progressive dilatation of the mammary gland ductal network. These data demonstrate that Mfge8 regulates the clearance of apoptotic epithelial cells during mammary gland involution and that the absence of Mfge8 leads to inflammation and abnormal mammary gland remodeling.

Animals↗
PubMed2005

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.

Base Sequence↗
PubMed2005

Rapid determination of methyl salicylate, a plant-signaling compound, in tomato leaves by direct sample introduction and thermal desorption followed by GC-MS.

Many plants infested by herbivores or viruses can rapidly produce and accumulate a plant-signaling compound, methyl salicylate (MeSA), in their leaves to activate disease resistance. In the present work, a simple, rapid, and sensitive method was developed for the determination of MeSA in tomato leaves by direct sample introduction and thermal desorption followed by GC-MS. Results show that the proposed method has a low detection limit (0.08 ng mg(-1)) and good precision (RSD = 8.9%). The present method was applied to the investigation of tomato plant defense response to tobacco mosaic virus (TMV) by rapid analysis of volatile compounds in plant leaves. It was found that tomato plants can produce large amounts of MeSA as a defense response to TMV. This indicates that MeSA may be a plant-signaling compound in tomato plant defense response to TMV.

Gas Chromatography-Mass Spectrometry↗
PubMed2005

Rapid determination of C6-aldehydes in tomato plant emission by gas chromatography-mass spectrometry and solid-phase microextraction with on-fiber derivatization.

A simple, rapid, sensitive, and solvent-free method was developed for determination of plant-signalling compounds, the three C6-aldehydes hexanal, (Z)-3-hexenal, and (E)-2-hexenal, in tomato plant emission by gas chromatography-mass spectrometry (GC-MS) and solid-phase microextraction (SPME) with on-fiber derivatization. In this method, O-2,3,4,5,6-(pentafluorobenzyl)hydroxylamine (PFBHA) in aqueous solution was first headspace adsorbed onto a 65 microm poly(dimethylsiloxane)/divinylbenzene (PDMS/DVB) fiber at 25 degrees C for 5 min, and then the fiber with adsorbed PFBHA was used for headspace extraction of tomato plant emission at 25 degrees C for 6 min. Finally, the resulting oximes adsorbed on the fiber were desorbed and analyzed by GC-MS. Extraction conditions and method validation were studied. The proposed method had low detection limit values for the three aldehydes from 0.1 to 0.5 ng/L and good precision (RSD less than 10%). In this work, the method was applied to investigation of tomato plant defense response to Helicoverpa armigera.

Adsorption↗
PubMed2005

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.

The increasing volume of proteomics data currently being generated by increasingly high-throughput methodologies has led to an increasing need for methods by which such data can be accurately described, stored and exchanged between experimental researchers and data repositories. Work by the Proteomics Standards Initiative of the Human Proteome Organisation has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. The progress of these efforts, and the direct benefits already accruing from them, were described at a plenary session of the 3(rd) Annual HUPO congress. Parallel sessions allowed the three work groups to present their progress to interested parties and to collect feedback from groups already implementing the available formats.

China↗
PubMed2005

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).

The spring workshop of the HUPO-PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI-MI, MIF) and Mass Spectrometry data (PSI-MS, mzData) whilst significant progress was made on PSI-MS' mzIdent, which will allow the capture of data from analytical tools such as peak list search engines. A new focus for PSI (GPS, gel electrophoresis) was explored; as was the need for a common representation of protein modifications by all workers in the field of proteomics and beyond. All these efforts are contextualised by the work of the General Proteomics Standards workgroup; which in addition to the MIAPE reporting guidelines, is continually evolving an object model (PSI-OM) from which will be derived the general standard XML format for exchanging data between researchers, and for submission to repositories or journals.

Mass Spectrometry↗
PubMed2005

Development of new rabbit monoclonal antibody to estrogen receptor: immunohistochemical assessment on formalin-fixed, paraffin-embedded tissue sections.

Evaluation of estrogen and progesterone receptors in breast cancer is widely used for the prediction of the response to endocrine therapy and as a biologic parameter closely related to disease prognosis. Immunohistochemistry is considered a specific, sensitive, and economic method for the determination of estrogen receptor/progesterone receptor status. The authors developed the first rabbit antiestrogen receptor monoclonal antibody (clone SP1) used in immunohistochemistry on formalin-fixed, paraffin-embedded tissue sections especially from breast carcinomas. This new antibody, compared with currently available antiestrogen receptor antibodies, has important advantages, including its reactivity even without heat-based antigen retrieval of fixed, embedded tissue sections in immunohistochemistry, and the predominance of nuclear immunostaining with only a very low cytoplasmic signal. A comparative study of immunohistochemistry on 61 histologic specimens from breast cancer cases showed that SP1 yields the same results as the well-known, standardized mouse monoclonal antibody to estrogen receptor (clone 1D5). Antibody affinity of SP1 is 8 times higher than that of 1D5. Thus, SP1 may prove of great value in the assessment of estrogen receptor status in human breast cancer.

Animals↗
PubMed2005

Potent antiviral activity of north-methanocarbathymidine against Kaposi's sarcoma-associated herpesvirus.

Kaposi's sarcoma-associated herpesvirus (KSHV) infection is a prerequisite for the development of Kaposi's sarcoma (KS). Blocking lytic KSHV replication may hinder KS tumorigenesis. Here, we report potent in vitro anti-KSHV activity of 2'-exo-methanocarbathymidine [North-methanocarbathymidine (N-MCT)], a thymidine analog with a pseudosugar ring locked in the northern conformation, which has previously been shown to block the replication of herpes simplex virus types 1 and 2. N-MCT inhibited KSHV virion production in lytically induced KSHV-infected BCBL-1 cells with a substantially lower 50% inhibitory concentration (IC50) than those of cidofovir (CDV) and ganciclovir (GCV) (IC50, mean +/- standard deviation: 0.08 +/- 0.03, 0.42 +/- 0.07, and 0.96 +/- 0.49 microM for N-MCT, CDV, and GCV, respectively). The reduction in KSHV virion production was accompanied by a corresponding decrease in KSHV DNA levels in the N-MCT-treated BCBL-1 cells, indicating that the compound blocked lytic KSHV DNA replication. A time- and dose-dependent accumulation of N-MCT-triphosphate (TP) was demonstrated in lytically induced BCBL-1 cells, while uninfected cells showed virtually no accumulation. The levels of N-MCT-TP were significantly decreased in the presence of 5'-ethynylthymidine, a potent inhibitor of herpesvirus thymidine kinase, resulting in the abrogation of anti-KSHV activity of N-MCT. N-MCT-TP more effectively blocked in vitro DNA synthesis by KSHV DNA polymerase with an IC50 of 6.24 +/- 0.08 microM (mean +/- standard deviation) compared to CDV-diphosphate (14.70 +/-2.47 microM) or GCV-TP (24.59 +/- 5.60 microM). Taken together, N-MCT is a highly potent and target-specific anti-KSHV agent which inhibits lytic KSHV DNA synthesis through its triphosphate metabolite produced in KSHV-infected cells expressing a virally encoded thymidine kinase.

Antiviral Agents↗
PubMed2005

Discovery of small-molecule human immunodeficiency virus type 1 entry inhibitors that target the gp120-binding domain of CD4.

The interaction between human immunodeficiency virus type 1 (HIV-1) gp120 and the CD4 receptor is highly specific and involves relatively small contact surfaces on both proteins according to crystal structure analysis. This molecularly conserved interaction presents an excellent opportunity for antiviral targeting. Here we report a group of pentavalent antimony-containing small molecule compounds, NSC 13778 (molecular weight, 319) and its analogs, which exert a potent anti-HIV activity. These compounds block the entry of X4-, R5-, and X4/R5-tropic HIV-1 strains into CD4(+) cells but show little or no activity in CD4-negative cells or against vesicular stomatitis virus-G pseudotyped virions. The compounds compete with gp120 for binding to CD4: either immobilized on a solid phase (soluble CD4) or on the T-cell surface (native CD4 receptor) as determined by a competitive gp120 capture enzyme-linked immunosorbent assay or flow cytometry. NSC 13778 binds to an N-terminal two-domain CD4 protein, D1/D2 CD4, immobilized on a surface plasmon resonance sensor chip, and dose dependently reduces the emission intensity of intrinsic tryptophan fluorescence of D1/D2 CD4, which contains two of the three tryptophan residues in the gp120-binding domain. Furthermore, T cells incubated with the compounds alone show decreased reactivity to anti-CD4 monoclonal antibodies known to recognize the gp120-binding site. In contrast to gp120-binders that inhibit gp120-CD4 interaction by binding to gp120, these compounds appear to disrupt gp120-CD4 contact by targeting the specific gp120-binding domain of CD4. NSC 13778 may represent a prototype of a new class of HIV-1 entry inhibitors that can break into the gp120-CD4 interface and mask the gp120-binding site on the CD4 molecules, effectively repelling incoming virions.

Animals↗
PubMed2004

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), maintained at the European Bioinformatics Institute (EBI), incorporates, organizes and distributes nucleotide sequences from public sources. The database is a part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. The web-based tool, Webin, is the preferred system for individual submission of nucleotide sequences, including Third Party Annotation (TPA) and alignment data. Automatic submission procedures are used for submission of data from large-scale genome sequencing centres and from the European Patent Office. Database releases are produced quarterly. The latest data collection can be accessed via FTP, email and WWW interfaces. The EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases as well as many other specialist molecular biology databases. For sequence similarity searching, a variety of tools (e.g. FASTA and BLAST) are available that allow external users to compare their own sequences against the data in the EMBL Nucleotide Sequence Database, the complete genomic component subsection of the database, the WGS data sets and other databases. All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk.

Animals↗