Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Library Materials”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 937 records · Page 52Linked to original sources
PubMedDate not supplied

Combining ethnopharmacology and virtual screening for lead structure discovery: COX-inhibitors as application example.

Virtual screening of large libraries of organic compounds combined with pharmacological high throughput screening is widely used for drug discovery in the pharmaceutical industry. Our aim was to explore the efficiency of using a biased 3D database comprising secondary metabolites from antiinflammatory medicinal plants as a source for the virtual screening. For this study pharmacophore models of cyclooxygenase I and II (COX-1, COX-2), key enzymes in the inflammation process, were generated with structure-based as well as common feature based modeling, resulting in three COX hypotheses. Four different multiconfomational 3D databases limited in molecular weight between 300 and 700 Da were applied to the screening in order to compare and analyze the obtained hit rates. Two of them were created in-house (DIOS, NPD). The database DIOS consists of 2752 compounds from phytochemical reports of antiinflammatory medicinal plants described by the ethnopharmacological source 'De material medica' of Pedanius Dioscorides, whereas NPD contains almost 80,000 compounds gathered arbitrarily from natural sources. In addition, two available multiconformational 3D libraries comprising marketed and development drug substances (DWI and NCI), mainly originating from synthesis, were used for comparison. As a test of the pharmacophore models' capability in natural sources, the models were used to search for known COX inhibitory natural products. This was achieved with some exceptions, which are discussed in the paper. Depending on the hypothesis used, DWI and NCI library searches produced hit rates in the range of 6.6% to 13.7%. A slight increase of the number of molecules assessed for binding was achieved with the database of natural products (NPD). Using the biased 3D database DIOS, however, the average increase of efficiency reached 77% to 133% compared to the hit rates resulting from WDI and NCI. The statistical benefit of a combination of an ethnopharmacological approach with the potential of computer aided drug discovery by in silico screening was demonstrated exemplified on the applied targets COX-1 and COX-2.

Computer Simulation↗
PubMedDate not supplied

Solid-phase combinatorial library of norstatine-type isosters by the nitroaldol reaction.

A combinatorial library of norstatine-type peptide isosters as putative inhibitors of aspartic proteases is presented. The library was synthesized using a split-and-mix strategy designed to afford a one-bead-two-compounds library with the isosteric elements positioned centrally in peptide chains. Application of ladder synthesis during library generation enabled structure identification by MALDI-TOF mass spectroscopy. The library was screened against aspartic protease renin, and two types of inhibitors were identified, that is, XXX-psi[CHRCHOH)-XXX and an aldehyde arising from unreacted starting material. Selected hits were resynthesized and assayed in solution, revealing inhibitors of nanomolar potency.

Amino Acids↗
PubMedDate not supplied

Application of capillary-scale NMR for the structure determination of phytochemicals.

Employing a capillary-scale NMR probe enables the miniaturisation of structure determination and de-replication of purified natural products from plants using only 5-100 microg of material. Approximately 5 microg are required to perform one-dimensional proton and two-dimensional homonuclear (COSY and NOESY) NMR experiments; some 30 microg are needed to acquire HMQC- or HSQC-NMR spectra; ca. 75-100 microg are necessary to measure HMBC-NMR spectra; and around 200 microg of a compound are needed to perform 13C- and DEPT-NMR experiments. In order to illustrate the integration of the outputs from high-throughput natural product chemistry methods with the capabilities of the state-of-the-art CapNMR technology, the preparation of a natural product library from the extract of Penstemon centranthifolius, and the subsequent isolation, purification and structure determination of six known iridoid glycosides with 25-300 microg of material are presented.

Glycosides↗
PubMedDate not supplied

Mass spectrometry in combinatorial chemistry.

In the fast expanding field of combinatorial chemistry, profiling libraries has always been a matter of concern--as illustrated by the buoyant literature over the past seven years. Spectroscopic methods, including especially mass spectrometry and to a lesser extent IR and NMR, have been applied at different levels of combinatorial library synthesis: in the rehearsal phase to optimize the chemistry prior to library generation, to confirm library composition, and to characterize after screening each structure that exhibits positive response. Most of the efforts have been concentrated on library composition assessment. The difficulties of such analyses have evolved from the infancy of the combinatorial concept, where large mixtures were prepared, to the recent parallel syntheses of collections of discrete compounds. Whereas the complexity of the analyses has diminished, an increased degree of automation was simultaneously required to achieve efficient library component identification and quantification. In this respect, mass spectrometry has been found to be the method of choice, providing rapid, sensitive, and informative analyses, especially when coupled to chromatographic separation. Fully automated workstations able to cope with several hundreds of compounds per day have been designed. After a brief introduction to describe the combinatorial approach, library characterization will be discussed in detail, considering first the solution-based methodologies and secondly the support-bound material analyses.

Chemistry, Organic↗
PubMed2006

A new approach for the removal of protein impurities from purified biologicals using combinatorial solid-phase ligand libraries.

The removal of last impurity traces from a purified protein is generally called polishing. It is an important step in downstream processing since protein impurities may generate undesirable side effects when the preparation is intended for research, diagnostic and more importantly therapeutic applications. Polishing is generally achieved by using orthogonal separation methods to previous steps, the most common being gel permeation chromatography. In spite of its polishing effectiveness, this technique suffers from a poor separation capacity and modest productivity as a result of low speed. Other approaches, for instance, based on anion exchange or on hydrophobic chromatography, that may be optimized for a given process cannot be used as generic methods. This document reports for the first time the use of a combinatorial solid-phase peptide library as a general method for the removal of impurity traces. Several examples of impurity trace removal are reported; starting material is either a pure protein spiked with serum proteins or with Escherichia coli extracts or current purified proteins still containing a small percentage of impurities. Among polished proteins are recombinant human albumin expressed in Pichia pastoris and human transferrin purified from whole plasma. This new method is used in neutral or even physiological pH and ionic strength conditions, with a remarkable capability to remove impurities. The process is as rapid as current adsorption chromatography procedures usable for the removal of a large number of protein impurities, with each one present in small amounts, such as host cell proteins.

Biological Products↗
PubMed2007

2B or not 2B, that is the question: further investigations into the use of pencil as a matrix for matrix-assisted laser desorption/ionisation.

The effective use of pencil as a matrix for matrix-assisted laser desorption/ionisation (MALDI) for the study of actinides has previously been demonstrated (Black et al., Rapid Commun. Mass Spectrom. 2006; 20: 1053). Here, the scope of the types of molecules amenable to analysis by this method has been extended, establishing that approximately 90% of a library containing 50 diverse small molecules can be successfully analysed by this technique. Further, the role played by the bulk materials present in the different pencil leads has been investigated and a simple one-step deposition of matrix and calibration materials has been achieved through the fabrication of different calibration pencils (Cali-Pens).

Journal Article↗
PubMed1998

The mouse Y chromosome: enrichment, sizing, and cloning by bivariate flow cytometry.

In this report, we demonstrate the utility of interleukin-2 (IL-2) stimulation of spleen cell cultures and bivariate flow cytometry in the analysis and purification of the C57BL/6J mouse Y Chromosome. We determined that the DNA content of the C57BL/6J Y Chromosome is approximately 94.7 Mb, making it similar in size to human Chromosome 16 and significantly larger than previous estimates. In addition, we describe the bulk isolation of mouse Y Chromosomes and demonstrate enrichment of the isolated material using a fluorescence in situ hybridization strategy. We detail the construction of two small insert Y Chromosome-specific libraries, ideal for sampling Y Chromosome sequences. From these libraries 1566 clones were analyzed. We provide a detailed characterization of 103 clones, generating nearly 50 kb of sequence. For 30 of these clones, we identify regions of homology to known Y chromosomal sequences, confirming the enrichment of the sorted DNA. From the remaining characterized clones, we describe the development of 15 male-specific PCR assays and 19 male-female PCR assays potentially originating from the pseudoautosomal region or other areas of X-Y or autosome-Y homology.

Animals↗
PubMed1993

Prospects of applying a combination of DNA transposition and site-specific recombination in plants: a strategy for gene identification and cloning.

The concept of gene identification and cloning using insertional mutagenesis is well established. Many genes have been isolated using T-DNA transformation or transposable elements. Maize transposable elements have been introduced into heterologous plant species for tagging experiments. The behaviour of these elements in heterologous hosts shows many similarities with transposon behaviour in Zea mays. Site-specific recombination systems from lower organisms have also been shown to function efficiently in plant cells. Combining transposon and site-specific recombination systems in plants would create the possibility to induce chromosomal deletions. This 'transposition-deletion' system could allow the screening of large segments of the genome for interesting genes and may also permit the cloning of the DNA corresponding to the deleted material by the same site-specific recombination reaction in vitro. This methodology may provide a unique means to construct libraries of large DNA clones derived from defined parts of the genome, the phenotypic contribution of which is displayed by the mutant carrying the deletion.

Chromosome Deletion↗
PubMed2005

Identification of peptides that bind to irradiated pancreatic tumor cells.

PURPOSE: Peptides targeting tumor vascular cells or tumor cells themselves have the potential to be used as vectors for delivering either DNA in gene therapy or antitumor agents in chemotherapy. We wished to determine if peptides identified by phage display could be used to target irradiated pancreatic cancer cells. METHODS AND MATERIALS: Irradiated Capan-2 cells were incubated with 5 x 10(12) plaque-forming units of a phage display library. Internalized phage were recovered and absorbed against unirradiated cells. After five such cycles of enrichment, the recovered phage were subjected to DNA sequencing analysis and synthetic peptides made. The binding of both phage and synthetic peptides was evaluated by fluorescence staining and flow cytometry in vitro and in vivo. RESULTS: We identified one 12-mer peptide (PA1) that binds to irradiated Capan-2 pancreatic adenocarcinoma cells but not to unirradiated cells. The binding of peptide was significant after 48 h incubation with cells. In vivo experiments with Capan-2 xenografts in nude mice demonstrated that these small peptides are able to penetrate tumor tissue after intravenous injections and bind specifically to irradiated tumor cells. CONCLUSION: These data suggest that peptides can be identified that target tumors with radiation-induced cell markers and may be clinically useful.

Animals↗
PubMedDate not supplied

A solid-phase labeling strategy for the preparation of technetium and rhenium bifunctional chelate complexes and associated peptide conjugates.

A new solid-phase labeling strategy for the preparation of (99m)Tc and Re chelate complexes and associated peptide derivatives, was developed. Resin-bound monoamide monoamine (MAMA) chelates were prepared in such a manner that upon the addition of a suitable Re(V) and Tc(V) precursor the target metal complexes were selectively released from the resin. The desired products were isolated from unreacted ligand by a simple filtration/solid-phase extraction procedure. In addition to the preparation of a series of functionalized ligands, a peptide conjugate was constructed from one of the resin-bound chelates using a conventional automated peptide synthesizer. The yields of the Re chelate complexes were typically greater than 70%, while the maximum yield for reactions run at the tracer level using (99m)Tc was 50%. The reported approach has a number of attractive features, including the opportunity to prepare libraries of novel agents, the ability to isolate macroscopic amounts of Re complexes for use in in vitro screening studies and as well-characterized standards for tracer level work, and the ability to produce (99m)Tc complexes that are free of any unreacted starting material without having to employ preparative HPLC.

Amines↗
PubMedDate not supplied

Solid-supported synthesis of putative peptide beta-turn mimetics via Ugi reaction for diketopiperazine formation.

The scope and limitations of the solid-supported synthesis of a bicyclic diketopiperazine, an internal, putative peptide beta-turn mimetic, are presented. The 4CC multicomponent Ugi reaction of alpha-N-Boc-diaminopropionic acid resin ester (an amine input), optically active alpha-bromoacid, aldehyde, and isocyanide is the key step in the proposed synthetic protocol. Application of cyclitive cleavage as the final step led to desired products in high purity.

Biomimetic Materials↗
PubMed2004

Localization of aquaporin-7 in human testis and ejaculated sperm: possible involvement in maintenance of sperm quality.

PURPOSE: We have previously reported the expression of aquaporin-7 (AQP7) in the rat testis and cloned human AQP7 from the testicular cDNA library. However, to our knowledge the spatial expression pattern and biological roles of AQP7 remain to be elucidated in humans. MATERIALS AND METHODS: We investigated AQP7 expression in the human testis and ejaculated sperm from fertile men and from infertile patients. RESULTS: AQP7 was expressed at the tail of spermatids and spermatozoa in the human testis. AQP7 protein was also detected at the middle piece and the anterior tale portion of ejaculated sperm. However, some infertile patients lacked AQP7 expression in ejaculated sperm, although all fertile men expressed AQP7 protein. The motility rate of AQP7 negative sperm was significantly lower than that of AQP7 positive sperm, while the sperm concentration was not different between AQP7 positive and negative subjects. CONCLUSIONS: AQP7 shows a spatial expression pattern in the human testis. AQP7 may be involved in the maintenance of sperm motility. Furthermore, a lack of AQP7 expression in sperm may be an underlying mechanism of male infertility.

Aquaporins↗
PubMed2006

Preparing digitized cervigrams for colposcopy research and education: determination of optimal resolution and compression parameters.

OBJECTIVE: Visual assessment of digitized cervigrams through the Internet needs to be optimized. The National Cancer Institute and National Library of Medicine are involved in a large effort to improve colposcopic assessment and, in preparation, are conducting methodologic research. MATERIALS AND METHODS: We selected 50 cervigrams with diagnoses ranging from normal to cervical intraepithelial neoplasia 3 or invasive cancer. Those pictures were scanned at 5 resolution levels from 1,550 to 4,000 dots per inch (dpi) and were presented to 4 expert colposcopists to assess image quality. After the ideal resolution level was determined, pictures were compressed at 7 compression ratios from 20:1 to 80:1 to determine the optimal level of compression that permitted full assessment of key visual details. RESULTS: There were no statistically significant differences between the 3,000 and 4,000 dpi pictures. At 2,000 dpi resolution, only one colposcopist found a slightly statistically significant difference (p = 0.02) compared with the gold standard. There was a clear loss of quality of the pictures at 1,660 dpi. At compression ratio 60:1, 3 of 4 evaluators found statistically significant differences when comparing against the gold standard. CONCLUSIONS: Our results suggest that 2,000 dpi is the optimal level for digitizing cervigrams, and the optimal compression ratio is 50:1 using a novel wavelet-based technology. At these parameters, pictures have no significant differences with the gold standard.

Biomedical Research↗
PubMedDate not supplied

Phage display antibody-based proteomic device using resonance-enhanced detection.

The combination of phage display antibody arrays with a novel nanotransducer technique based on resonant nanoparticles in a nanosandwiched film enables the sensitive parallel screening of proteins. Using the resonance of nanoparticles with their induced mirror dipoles in a thin-film structure, limitations of fluorophores, such as unspecific background and nonvisibility to the eye, can be overcome, thereby leading to an optical signal significantly more sensitive than that of standard colloid techniques. The signal can be both directly observed as a color change of a microdot at the sensor surface and tuned throughout the visible range of the spectrum. Here we report the application of an optical chip using scFv-antibody-antigen interactions. Artificial scFv-antibodies against a variety of proteins, including yeast enzymes and bovine serum albumin (as a standard), were constructed via Phage Display. These scFv-antibodies were then coated onto metal nanoclusters and bound to their antigens that were arrayed as nanodroplets at the resonance layer of the chip. ScFv-Antibody-antigen interaction resulted in a visible array of microdots. Using resonance-enhanced absorption, the absorption signal of the spots was amplified by one to two orders of magnitude (compared to colloid-based techniques). For quantitative analysis, either an 8-micron scanner or a CCD camera (resolution 4 microns) was employed to gain direct-reflection spectra rather than unspecific scatter data (prone to dust and unspecific interaction). Our results demonstrate that this device enables high-throughput proteomics to overcome some limitations of fluorescence, enzyme labels, and colloid techniques.

Antibodies↗
PubMed2002

Global amplification of cDNA from limiting amounts of tissue. An improved method for gene cloning and analysis.

In this study we present an improved polymerase chain reaction (PCR)-based methodology to generate large amounts of high-quality complementary DNA (cDNA) from small amounts of initial total RNA. Global amplification of cDNA makes it possible to simultaneously clone many cDNAs and to construct directional cDNA libraries from a sequence-abundance-normalized cDNA population, and also permits rapid amplification of cDNA ends (RACE), from a limited amount of starting material. The priming of cDNAs with an adapter oligo-deoxythymidine (oligo-dT) primer and the ligation of a modified oligonucleotide to the 3' end of single-stranded cDNAs, through the use of T4 RNA ligase, generates known sequences on either end of the cDNA population. This helps in the global amplification of cDNAs and in the sequence-abundance normalization of the cDNA population through the use of PCR. Utilization of a long-range PCR enzyme mix to amplify the cDNA population helps to reduce bias toward the preferential amplification of shorter molecules. Incorporation of restriction sites in the PCR primers allows the amplified cDNAs to be directionally cloned into appropriate cloning vectors to generate cDNA libraries. RACE-PCR done with biotinylated primers and streptavidin-coated para-magnetic particles are used for the efficient isolation of either full-length coding or noncoding strands.

Base Sequence↗
PubMedDate not supplied

Incisional hernia: a review.

BACKGROUND: Otherwise known as post operative ventral hernia, incisional hernia is a common complication following abdominal surgery and is a significant cause of morbidity. This review examines incisional hernia from its historical perspective to the present. METHOD: A Literature review of the topic was carried out using manual library search of journal articles on the topic published both locally and internationally. The search also made use of intemet material from Pubmed and Medline on relevant parts of the topic. All relevant articles from the reference lists of these papers were also studied. RESULT: Incisional hernia is a common complication of abdominal surgery. Its incidence is about 1% following primary healing and increasing to about 11% with postoperative wound infection. The most consistent causative factor is wound infection and the incidence may rise to 30% after abdominal wound dehiscenece and resuture. It may be difficult to repair and a wide range of surgical procedures have been developed for such repair. The repair may be direct suture or prosthetic mesh using the open or laparoscopic technique. Prosthetic mesh has revolutionized the repair of incisional hernias. Laparoscopic repair, which was introduced in the 1990's, has been adjudged feasible, safe and as effective as the open methods of repair. Recurrence rates of up to 49% with direct suture repair have been reported. Open and laparoscopic mesh repair have recurrent rates of 0-10% and 0-9% respectively. CONCLUSION: Despite improved surgical techniques and the use of prosthetic mesh incisional herniation remains a major problem for the general surgeon.

Hernia, Abdominal↗
PubMed1999

Characterization of a small supernumerary ring marker derived from chromosome 2 by forward and reverse chromosome painting.

A small ring-shaped supernumerary marker chromosome (SMC) was detected in 50% of metaphase cells in an 18-month-old boy with mental retardation and multiple congenital anomalies. Conventional cytogenetic methods had failed to identify the origin of the marker. When the patient was age 11.5 years, we defined the origin of the SMC by fluorescence in situ hybridization using a battery of centromere-specific DNA probes. The marker was positive with the probe for locus D2Z. More detailed characterization was achieved by using chromosome 2 arm-specific and marker-specific DNA libraries, which were constructed by microdissection of the two arms chromosome 2 and SMC with subsequent amplification of the chromosomal material by a degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). The marker was identified as r(2)(p11.2-->q14.1). The propositus had dolichocephaly, coarse hair, low-set ears, exophthalmos, epicanthal folds, strabismus, depressed nasal bridge, high-arched palate, excess of skin on the neck, tapered fingers with mild clinodactyly, talipes varus on the right, inguinal hernia, hypogenitalism, muscular hypotonia, and mental retardation. This is the first case of SMC derived from chromosome 2 that was characterized by forward and reverse chromosome painting.

Abnormalities, Multiple↗