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PubMed2001

Proteomic analysis of rare molecular species of translated polypeptides from a mouse fetal thymus cDNA library.

Proteomic patterns from an ordered cDNA library of mouse fetal thymus origin of an overall complexity of 1536 clones are described. Patterns have been analyzed at 96, 12, or 8 clones in a mixture, or as individual clones. Clones yield in some instances a single spot, in other cases a complex cluster or family of spots is formed. The determination of the clonal address (a six-digit number, indicating the interception of three pooling dimensions) by inspection of pools of 8, 12 or 16 clones is a reliable approach; nevertheless a complete proof consists in retrieving the clone and then submitting to transcription, translation and proteomic analysis. The spot clusters are meaningful clone identifiers; cluster components (families of polypeptides) are characteristic of individual clones and are independent of clones coexisting (and being co-expressed) in a given pool. A 'cluster' originates from a single cloned message and might be due to post-translational modification (offered by the reticuleocyte machinery) or as a result of programmed degradation. Thirteen clones or families of clonal products are shown, and the heterogeneity of the 'appearance' of clones is documented. In about half, the assignment of a clonal polypeptide product to a storage well position has failed; this might be due to a variety of considerations elaborated herein. The arguments are presented, that analysis of abundant proteins of a cell (activated lymphocyte) comprises 'classical proteomics', but for the analysis of the rare molecular species of proteins, Poissonian approaches of replicable material have to be used.

Animals↗
PubMed2006

Retention of retrospective print journals in the digital age: trends and analysis.

PURPOSE: The issue of retaining retrospective print journals is examined in light of the shift to electronic titles, the reallocation of library budgets from print to electronic, and the changing research practices of today's library users. This article also examines the evolving role of the physical library and its impact on space allocation. METHODS: To determine current practice and opinion, a survey of health sciences librarians and academic librarians was conducted. To demonstrate the use patterns of older journal issues, citation analyses and interlibrary loan statistics were examined. RESULTS: All methods indicate that recent material is accessed more frequently than older material, with a significant drop in use of materials greater than 15 years old. Materials greater than 20 years old constituted less than 5% of interlibrary loans and less than 9% of articles noted in the citation analysis. CONCLUSIONS: It is possible to eliminate older years of a print journal collection without a large impact on the needs of researchers. Librarians' preference to maintain full runs of journal titles may be motivated by reasons outside of actual usage or patrons needs.

Humans↗
PubMed1993

Clarification of subtle reciprocal rearrangements using fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) using chromosome-specific DNA libraries as painting probes was applied in the analysis of six subtle, balanced chromosome rearrangements. Both fresh and older slides, some of which had been previously G-banded, were used to determine if FISH could identify unambiguously very small amounts of translocated material. Our results indicate that this procedure can clearly and precisely distinguish the specific components of extremely subtle translocations, in different cell types, such as leukocytes, aminocytes, and chorionic villus, and irregardless of preparation age. This ability makes FISH a valuable tool in clinical cytogenetics for the confirmation of preliminary G-banded karyotypes.

Chromosomes, Human, Pair 1↗
PubMed1989

Cloning of the gene for cell-surface protein antigen A from Streptococcus sobrinus (serotype d).

A gene library of Strep. sobrinus B13N (serotype d) chromosomal DNA was constructed in Escherichia coli, with the bacteriophage vector lambda L47.1. A recombinant phage, lambda MDSM49, containing a 15.5 kb DNA insert, directed the expression of a 210 kDa antigenic protein. The recombinant 210 kDa protein was shown by Western blot analysis to be identical with cell-surface protein antigen A (spaA) from a serotype g strain. However, the restriction patterns of a subclone plasmid, pMD51, from lambda MDSM49 differed from those of serotype g strain. The cell-surface protein antigen I/II from serotype c Streptococcus mutans is a potential immunogen for vaccination against dental caries and corresponds to the spaA from serotype d and g strains. A recombinant clone, pDM51, will be a useful tool for serological and molecular biological studies. The recombinant spaA provides useful material for assessment of its diagnostic and immunogenic potential.

Antigens, Bacterial↗
PubMed1996

A solution-phase strategy for the synthesis of chemical libraries containing small organic molecules: a universal and dipeptide mimetic template.

A general approach to the solution phase, parallel synthesis of chemical libraries, which allows the preparation of multi-milligram quantities of each individual member, is exemplified with both a universal and dipeptide mimetic template. In each step of the sequence, the reactants, unreacted starting material, reagents and their byproducts are removed by simple liquid/ liquid or liquid/solid extractions providing the desired intermediates and final compounds in high purities (> or = 90-100%) independent of the reaction yields and without deliberate reaction optimization.

Dipeptides↗
PubMed2000

Enhanced proteolysis of pre-mRNA splicing factors in myeloid cells.

OBJECTIVE: Molecular identification and characterization of the bone marrow nuclear protein detected by the B92 monoclonal antibody. MATERIALS AND METHODS: The protein was purified to homogeneity from acute myeloid leukemia cells and was subjected to peptide digestion and amino acid sequencing. Identified sequences were used to screen a bone marrow cDNA library in search of matching transcripts. The protein was further studied in different cells and tissues by examination of protease inhibitors and harsh lytic conditions and during apoptosis in HL-60 cells. RESULTS: We found that the apparent bone marrow specific protein is a 47 kD proteolytic cleavage product of PSF, an essential pre-mRNA splicing factor. PSF is completely cleaved to p47 during lysis of immature myeloid cells due to potent proteolytic activity found in these cells but is rare in other cells and tissues. Furthermore, p47 is abundant in intact normal and tumor myeloid cells while in other cell types it is undetectable. The cleavage of PSF is accompanied by digestion of the PTB splicing regulator but not other proteins tested. In contrast, during apoptosis PTB is degraded while PSF remains intact. CONCLUSIONS: The bone marrow 47 kD protein is a fragment constituting the N-terminal, protease-resistant half of the splicing factor PSF. Proteolytic degradation of PSF specifically occurs in intact myeloid cells and this process is enhanced upon myeloid cell lysis.

Amino Acid Sequence↗
PubMed2006

Protein ligand design: from phage display to synthetic protein epitope mimetics in human antibody Fc-binding peptidomimetics.

Phage display is a powerful method for selecting peptides with novel binding functions. Synthetic peptidomimetic chemistry is a powerful tool for creating structural diversity in ligands as a means to establish structure-activity relationships. Here we illustrate a method of bridging these two methodologies, by starting with a disulfide bridged phage display peptide which binds a human antibody Fc fragment (Delano et al. Science 2000, 287, 1279) and creating a backbone cyclic beta-hairpin peptidomimetic with 80-fold higher affinity for the Fc domain. The peptidomimetic is shown to adopt a well-defined beta-hairpin conformation in aqueous solution, with a bulge in one beta-strand, as seen in the crystal structure of the phage peptide bound to the Fc domain. The higher binding affinity of the peptidomimetic presumably reflects the effect of constraining the free ligand into the conformation required for binding, thus highlighting in this example the influence that ligand flexibility has on the binding energy. Since phage display peptides against a wide variety of different proteins are now accessible, this approach to synthetic ligand design might be applied to many other medicinally and biotechnologically interesting target proteins.

Biomimetic Materials↗
PubMed1997

Characterization of oleosins in the pollen coat of Brassica oleracea.

Mature Brassica oleracea pollen grains are covered with a lipophilic pollen coat containing a variety of proteins. Screening of an anther cDNA expression library for the coding sequences of such proteins resulted in the isolation of a number of cDNA clones encoding glycine-rich oleosins. The proteins were shown to be attached to the lipophilic coat material only and to be absent elsewhere in the plant. Within the coat, several forms of the pollen coat oleosin with different molecular weights were detected. The forms are encoded by different transcripts that originate from a single gene. Expression of this gene is restricted to the tapetum and is quantitatively regulated by the water content of the anther. Similar oleosins were found in the pollen coat of B. alboglobra and B. napus.

Amino Acid Sequence↗
PubMed1999

A mouse monoclonal antibody to a thyrotropin receptor ectodomain variant provides insight into the exquisite antigenic conformational requirement, epitopes and in vivo concentration of human autoantibodies.

We used the secreted TSH receptor (TSHR) ectodomain variant TSHR-289 (truncated at amino acid residue 289 with a 6-histidine tail) to investigate properties of TSHR autoantibodies in Graves' disease. Sequential concanavalin A and Ni-chelate chromatography extracted milligram quantities of TSHR-289 (approximately 20-40% purity) from the culture medium. Nanogram quantities of this material neutralized the TSH binding inhibitory activity in all 15 Graves' sera studied. We generated a mouse monoclonal antibody (mAb), 3BD10, to partially purified TSHR-289. Screening of a TSHR complementary DNA fragment expression library localized the 3BD10 epitope to 27 amino acids at the N-terminus of the TSHR, a cysteine-rich segment predicted to be highly conformational. 3BD10 preferentially recognized native, as opposed to reduced and denatured, TSHR-289, but did not interact with the TSH holoreceptor on the cell surface. Moreover, mAb 3BD10 could extract from culture medium TSHR-289 nonreactive with autoantibodies, but not the lesser amount (approximately 25%) of TSHR-289 molecules capable of neutralizing autoantibodies. Although the active form of TSHR-289 in culture medium was stable at ambient temperature, stability was reduced at 37 C, explaining the mixture of active and inactive molecules in medium harvested from cell cultures. In conclusion, studies involving a TSHR ectodomain variant indicate the exquisite conformational requirements of TSHR autoantibodies. Even under "native" conditions, only a minority of molecules in highly potent TSHR-289 preparations neutralize patients' autoantibodies. Therefore, Graves' disease is likely to be caused by even lower concentrations of autoantibodies than previously thought. Finally, reciprocally exclusive binding to TSHR-289 by human autoantibodies and a mouse mAb with a defined epitope suggests that the extreme N-terminus of the TSHR is important for autoantibody recognition.

Animals↗
PubMed2004

Cell-free protein synthesis with prokaryotic combined transcription-translation.

Cell-free biology exploits and studies complex biological processes in a controlled environment without intact cells. One model system is prokaryotic cell-free protein synthesis. This technology offers an attractive and convenient approach to produce properly folded recombinant DNA (rDNA) proteins on a laboratory scale, screen PCR fragment libraries in a high-throughput format, express pharmaceutical proteins, incorporate labeled or unnatural amino acids into proteins, and activate microbial physiology to allow for investigation of biological systems. We describe the preparation of materials necessary for the expression, quantification, and purification of rDNA proteins from active Escherichia coli extracts.

Autoradiography↗
PubMed2006

Complete shape retention in the transformation of silica to polymer micro-objects.

Controlled morphogenesis and shape replication are challenges for several rapidly developing fields of materials science. Indeed, although complex forms have been generated by the condensation of inorganic matter in organized media, the shaping of plastic matter on the micrometre scale is still limited to simple forms that are typically obtained as inverse replicas of channel-like cavities and colloidal crystals. Here we report the fabrication of individual plastic micro-objects that follow an elaborate design and are faithful copies of nanoporous inorganic morphotypes. The direct replica method produces an unprecedented library of curved geometrical solids made of plastics, such as cones, bicones, hollow cylinders, rings, test tubes, clubs and vases. The shape retention of the original structures on the microscale and the creation of a new nanostructure produced objects with homogeneous nanopores of 7 nm and cylindrical microcavities as large as 1 microm. This strategy of shape transcription from one material to another opens new perspectives in microfabrication, separation, anchorage and storage of chemical and biological species. Until now it has not been possible to realize such transformations.

Evaluation Study↗
PubMed2005

Construction of a cloning system for the mass production of a virus-binding protein specific for poliovirus type 1.

In our previous study, virus-binding proteins (VBPs) demonstrating the ability to strongly bind poliovirus type 1 (PV1) were recovered from a bacterial culture derived from activated sludge. The isolated VBPs would be useful as viral adsorbents for water and wastewater treatments. The VBP gene of activated sludge bacteria was isolated, and the cloning system of the VBP was established. The isolation of the VBP gene from DNA libraries for activated sludge bacteria was achieved with the colony hybridization technique. The sequence of the VBP gene consisted of 807 nucleotides encoding 268 amino acids. Fifteen amino acid sequences were retrieved from 2,137,877 sequences by a homology search using the BLAST server at the National Center for Biotechnology Information. The protein encoded in the isolated genome was considered to be a newly discovered protein from activated sludge culture, because any sequences in protein databases were not perfectly matched with the sequence of the VBP. It was confirmed that Escherichia coli BL21 transformed by pRSET carrying the isolated VBP gene could extensively produce the VBP clones. Enzyme-linked immunosorbent assay (ELISA) revealed that the VBP clone exhibited the binding ability with intact particles of PV1. The equilibrium binding constant between PV1 and VBP in the ELISA well was estimated to be 2.1 x 10(7) (M(-1)), which also indicated that the VBP clones have a high affinity with the PV1 particle. The VBP cloning system developed in this study would make it possible to produce a mass volume of VBPs and to utilize them as a new material of the specific adsorbent in several technologies, including virus removal, concentration, and detection.

Amino Acid Sequence↗
PubMed2005

Probing the interface between biomolecules and inorganic materials using yeast surface display and genetic engineering.

Although promising for biomimetic materials applications, polypeptides binding inorganic material surfaces and the mechanism of their function have been difficult to characterize. This paper reports sequence-activity relationships of peptides interfacing with semiconductor CdS, and presents methodologies broadly applicable to studying peptide-solid surface interactions. We first employed yeast surface display with a human repertoire antibody library and identified rarely-occurring scFv fragments as CdS-binding polypeptides. Using our semi-quantitative cell-surface binding assay, site-directed mutational analysis, and genetic engineering we defined short distal regions of the displayed polypeptides necessary and sufficient for CdS binding. Alanine scanning mutagenesis in combination with a series of engineered polyhistidine peptides elucidated a direct relationship between histidine number and binding strength, which appeared to be further modulated by arginine and basic residues. The minimum strength of interaction was established by competition studies using soluble synthetic peptide analogs, which showed half-maximal inhibition of yeast binding to CdS at approximately 2 microM peptide. We then showed the ability of cells displaying material-specific polypeptides to form self-healing biofilms and discriminate between materials of fabricated heterostructure surfaces. Furthermore, we demonstrated the synthetic potential of the selected soluble CdS peptide in mediating aqueous synthesis of fluorescent CdS nanoparticles at room temperature. This platform may be further applied to elucidate mechanisms governing interfacial interactions and to generate material-specific reagents useful in medicine, biosensors, and bioproduction of high value inorganic materials.

Amino Acid Sequence↗
PubMed1998

[Isolation of novel expression sequences of C2H2 type zinc finger protein gene from human brain tissue according to the conservation of zinc finger motif].

By low stringency PCR amplification of genomic DNA using the primers designed based on the conservation of zinc finger motif, we got 8 gradient eletrophoretic bands. After recovery of the second and third bands, the DNA fragments in them were cloned and sequenced. Compared to the GenBank database, among these 60 segments containing zinc finger motif, 23 segments were novel zinc finger genes' genomic segments. Then the human brain tissue cDNA library was screened, using these segments as probes, and 44 positive clones were obtained. Rescreening 28 of them, we got 20 rescreened clones. All of them were sequenced and sent to the GenBank DNA database for sequence analysis, the results showed that 16 were novel C2H2 type zinc finger protein cDNA segments. The cDNA segments encoding the novel C2H2 type zinc finger proteins provide the basic materials for cloning of full length cDNA of valuable novel zinc finger protein genes.

Amino Acid Sequence↗
PubMed2005

Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode).

Roots of soybean, Glycine max cv. Kent L. Merr., plants susceptible to the soybean cyst nematode (SCN), Heterodera glycines Ichinohe, were inoculated and allowed to develop feeding sites (syncytia) for 8 days. Root samples enriched in syncytial cells were collected using laser capture microdissection (LCM). RNA was extracted and used to make a cDNA library and expressed sequence tags (ESTs) were produced and used for a Gene Ontology (GO) analysis. RT-PCR results indicated enhanced expression of an aquaporin (GmPIP2,2), alpha-tubulin (GmTubA1), beta-tubulin (GmTubB4) and several other genes in syncytium-enriched samples as compared to samples extracted from whole roots. While RT-PCR data showed increased transcript levels of GmPIP2,2 from LCM tissue enriched in syncytial cells, in situ hybridization showed prominent GmPIP2,2 hybridization to RNA in the parenchymal cells tightly juxtaposed to the syncytium. Immunolocalization indicated stronger alpha-tubulin signal within the syncytium as compared to surrounding tissue. However, alpha-tubulin labeling appeared diffuse or clumped. Thus, LCM allowed for the isolation of tissue enriched for syncytial cells, providing material suitable for a variety of molecular analyses.

Amino Acid Sequence↗
PubMed1992

Information excess in medicine. Overview, relevance to dermatology, and strategies for coping.

BACKGROUND: The amount of biomedical information contained in scientific journals has grown to the point that complete coverage of this material is impossible. The number of articles and journals being published has been growing at an exponential rate since 1750. Thirty-four thousand references from 4000 journals are added each month to the National Library of Medicine MEDLINE database from among the more than 100,000 scientific journals now published. This increase in scientific literature reflects not greater productivity but simply a larger number of scientists at work. Most articles written are eventually published in the medical literature, but a large number of scientific articles are of less than optimal quality, and most scientific articles that are published are never cited. Articles of higher quality and usefulness cluster in a few journals that enjoy great use in medical libraries and high scores on bibliometric scores such as the Science Citation Index. OBSERVATIONS: To assess the reading habits of dermatologic trainees and evaluate how they cope with this information excess, a survey was distributed to 36 residents in three training programs. The average number of medical journal reading hours per month was 17; the number of hours devoted to reading issues of the Archives of Dermatology, the Journal of the American Academy of Dermatology, and the Journal of Investigative Dermatology were 3.2, 5.0, and 1.4, respectively; and the average resident read seven peer-reviewed journals, two to four dermatologic tabloids, and four peer-reviewed medical journals. CONCLUSIONS: Critically and consistently reading a limited number of high-quality peer-reviewed journals as well as taking advantage of information available through computer networks and bibliographic and full-text databases is the best approach to coping with the volume of medical literature. Translating this information into a change in attitude and modification of physician behavior is best accomplished when local role models incorporate new ideas into their practice and teaching. Modifications that would, in fact, bring about truly useful changes, such as decreasing the number of new publications, melding journals already present into smaller numbers of publications rather than instituting new journals, altering the "publish-or-perish" rules, and writing more comprehensive articles rather than multiple small contributions, all await fundamental alterations in long-accepted policies in medicine.

Dermatology↗
PubMed2004

Mammaglobin and CRxA-01 in pleural effusion cytology: potential utility of distinguishing metastatic breast carcinomas from other cytokeratin 7-positive/cytokeratin 20-negative carcinomas.

BACKGROUND: The most common causes of malignant pleural effusions in women are metastatic lung carcinomas and breast carcinomas. It is often very difficult to distinguish between breast carcinomas and other metastatic carcinomas when they share a similar morphology and a similar cytokeratin profile (CK7-positive/CK20-negative [CK7+/CK20-]). To better differentiate between metastatic mammary carcinomas and other metastatic carcinomas in pleural effusion cytology, the authors studied the potential use of a novel antibody, CRxA-01, which was identified by a cDNA subtraction library, together with a well characterized antibody against mammaglobin. METHODS: A computer search for patients with malignant pleural effusion specimens between January 1992 and November 2002 generated 228 patients, 71 of whom had cell block material and a known clinical history. Primary malignancies among these patients included 20 breast carcinomas, 32 lung carcinomas, 4 endometrial carcinomas, 9 ovarian carcinomas, 4 gastrointestinal carcinomas, and 2 genitourinary carcinomas. All specimens were immunostained with anti-CK7, CK20, CRxA-01, and mammaglobin antibodies. Only CK7-positive/CK20-negative (CK7+/CK20-) specimens were included in the current study, and only definitive membranous staining for CRxA-01 and cytoplasmic staining for mammaglobin were considered to be positive. RESULTS: For patients with metastatic breast carcinomas, mammaglobin was positive in 11 of 20 (55%) tissue specimens and CRxA-01 was positive in 12 of 20 (60%) tissue specimens. When CRxA-01 and mammaglobin were used together, 16 of 20 (80%) tissue specimens were positive for mammaglobin or/and CRxA-01 antibodies. This staining pattern was not seen for tissue specimens from patients with other metastatic carcinomas. Two of 4 (50%) uterine carcinoma specimens and 6 of 9 (67%) ovarian carcinoma specimens were positive for CRxA-01 only. CONCLUSIONS: CRxA-01 and mammaglobin were expressed in most metastatic breast carcinoma specimens. Other CK7+/CK20- carcinoma specimens did not express mammaglobin and showed weak or negative staining for CRxA-01. When used together, CRxA-01 and mammaglobin greatly improved the sensitivity and specificity for the detection of metastatic breast carcinoma in pleural effusion specimens.

Antibodies, Neoplasm↗
PubMed2001

Aspergillus nidulans alpha-1,3 glucanase (mutanase), mutA, is expressed during sexual development and mobilizes mutan.

We established a subtractive cDNA library of Aspergillus nidulans to identify differentially expressed genes during sexual development. One of the clones displayed homology to fungal alpha-1,3 glucanases (mutanase). Since alpha-1,3 glucan is considered the main reserve material accumulated during vegetative growth as a cell wall component and consumed during sexual development, we analyzed this gene in detail. The gene, mutA, is disrupted by three introns and encodes a putative protein of 48 kDa molecular mass with a signal peptide for secretion at the N terminus. The deduced protein displays amino acids 24-42% identical to mutanases of other fungi. A proposed mutan binding domain characterized in, e.g., Penicillium is not present in A. nidulans. Mutanase transcript and GFP reporter analysis in A. nidulans revealed specific induction of the gene during sexual development in Hülle cells. To study the role of mutA during sexual differentiation, we constructed a mutA deletion strain. Although degradation of mutan was affected in this strain, it was still able to form cleistothecia at a number similar to that of wildtype. These results suggest that additional carbon sources are available during sexual development.

Amino Acid Sequence↗