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PubMed2006

[Valorization of biological resources in tumour libraries].

The transfer and commercialization of biological materials, whether in the form of tumour samples, tissue samples or chemicals, and of the data base pertaining to such material have become a subject of considerable importance for both the private and public sectors involved in medical research. In order to fully appreciate and apprehend the process for the protection and the valuation of the transferred material, intellectual property law must be taken into account. As a result, a distinction is made between the tangible and intangible elements of the biological material and of the attached data base, thus providing the transferring entity the possibility to claim property rights to future intellectual property arising from the research regarding the transferred material. The transfer of biological material and attached data base without such contractual provisions can lead to the loss of this potential value as well as of physical and legal control over the material transferred by the providing entity. The intentions and the assumptions of the parties must be negotiated and written into terms of contract, at the risk of losing future value due to unexpressed assumptions concerning intangible property rights.

Databases, Factual↗
PubMed2000

Construction of an equalized cDNA library from Colletotrichum lagenarium and its application to the isolation of differentially expressed genes.

To establish an efficient screening system for differentially expressed genes of a phytopathogenic fungus Colletotrichum lagenarium, we constructed an equalized (normalized) cDNA library from C. lagenarium and used this library for differential screening. For the isolation of genes involved in infection-related developments of conidia, conidia undergoing appressorium differentiation were selected as the source of materials for construction of the cDNA library. The equalization of cDNA was performed twice using a kinetic method, and the products were cloned into a plasmid vector. Colony hybridization with nine probes of different abundance showed a reduction in abundance variation from at least 276-fold in the original library to 10-fold in the equalized cDNA library, which demonstrated that the cDNA was successfully equalized. By differential hybridization of 1900 cDNA clones in the equalized cDNA library and RNA blot analysis of candidate clones, we identified 11 independent cDNA clones, designated CAD1 through CAD11, that were expressed in appressorium-differentiating conidia, but not in vegetative mycelia. The transcripts of CAD1 and CAD2 hardly accumulated in preincubated conidia, whereas those of CAD3 and CAD4 accumulated highly and slightly, respectively. The amount of the four CAD transcripts increased at the early stage of the appressorium formation process. Sequence analysis of CAD1 revealed that CAD1 would encode for 101 amino acid polypeptides, which showed homology to metallothioneins. Deduced amino acid sequence of CAD2 would encode 278 amino acid polypeptides, and showed high homology to genes in aflatoxin, and sterigmatocystin gene clusters of Aspergillus parasiticus and A. nidulans, respectively.

Amino Acid Sequence↗
PubMed1988

Comparative usefulness of MEDLINE searches performed by a drug information pharmacist and by medical librarians.

The usefulness of MEDLINE searches conducted by a drug information pharmacist who had received online training was compared with the usefulness of searches conducted by medical librarians. Searches for literature pertinent to select drug information requests received at a university drug consultation service during a three-month period were conducted independently by the pharmacist and one of three reference librarians. The three librarians had received extensive online search training and were experienced in conducting MEDLINE searches; the pharmacist was trained by a fourth experienced librarian-searcher using National Library of Medicine (NLM) training materials. For each drug information request, the pharmacist and the librarian searched two MEDLINE files on the NLM service. The printouts generated by the two searchers were evaluated by two drug information pharmacists in terms of how useful each list of citations would be in enabling the drug information pharmacists to answer the related question. The majority of printouts in 48 sets of searches were judged to be useful. Of the 96 possible "best search" votes (two votes for each of the 48 sets of printouts), the pharmacist's searches received 34 votes, the librarians' searches received 28 votes, and there were 34 tie votes. The numbers of useful primary and alternate citations were found to be the best predictors of whether a given printout would receive the "best search" rating. MEDLINE searches performed by a drug information pharmacist with online training, in response to drug information requests, were judged by drug information pharmacists to be as useful as searches performed by librarians.

Drug Information Services↗
PubMedDate not supplied

Measurement of volume changes after sinus floor augmentation with a phycogenic hydroxyapatite.

PURPOSE: The purpose of this study was the determination of time-dependent volumetric changes of particulate sinus inlay grafts. A mixture of phycogenic hydroxyapatite (Algipore/C-Graft) and autologous bone collected from the surgical access area was used as the grafting material. MATERIALS AND METHODS: Thirty-three sinus floor augmentations using phycogenic hydroxyapatite combined with autologous bone collected at the augmentation site and venous blood were performed on 18 patients aged 57.4 +/- 12.5 years (mean +/- SD) with severe atrophy of the posterior maxilla. Graft volume was measured 1 to 14 days postoperatively and before the placement of dental implants 6.1 +/- 2.1 months later (mean +/- SD; range, 4 to 11 months) to evaluate the amount of time-dependent resorption of the implanted material on computerized tomographic (CT) images of the augmented region. The images were put into Digital Imaging and Communications in Medicine (DICOM) format and evaluated using the software library Analyze. The implanted bone replacement material was plotted manually on each CT slice, and the volume of the implanted material was calculated. RESULTS: The average volume loss of the bone replacement material during the observation period was 13.9% +/- 1.9% (mean +/- SEM). All sinus floor augmentations healed without complications except for delayed membrane exposure in 2 cases. DISCUSSION: The results indicate that the graft material, a mixture of Algipore, bone chips from the access area, and venous blood, exhibited a small volume loss over a period of approximately 6 months, thus providing predictable height for second-stage implant surgery. CONCLUSION: Further investigations are needed to evaluate long-term stability and implant success.

Adult↗
PubMed2005

Collaborating to enhance patient education and recovery.

OBJECTIVE: The paper describes a collaborative project between librarians and health care staff to enhance patient recovery by distributing educational videos and evaluating the acceptability of this "information intervention." BACKGROUND: On inpatient units, nurses experience decreased time to teach patients. Text handouts do not include multimedia information, and reading levels may limit comprehension. Because the postoperative period is not the optimal time for patient instruction, another format and opportunity for postsurgical instruction was needed. METHODS: Nurses, therapists, educators, and librarians partnered to select a video designed for home viewing by discharged patients. It was added to the existing text-based educational program for coronary patients. An evaluation component was incorporated into this collaboration. RESULTS: The library's role extended to all aspects of the program's implementation and management. The library's circulation system was used to coordinate borrowing with minimal loss. Ongoing preparation of the video materials for distribution and return remained a library function, and the evaluation component showed patients' positive reception of the video. DISCUSSION: Patients received a greater amount of information to enhance self-care during the recovery period without consuming more nursing time. Video circulation and reuse enhanced cost effectiveness of the program, and patients benefited from the library's resources.

Cooperative Behavior↗
PubMed1967

PIL: a control procedure for technical services management.

An acquisitions control procedure at the University of New Mexico Library of the Medical Sciences is described. Using an IBM 360/40, a program has been written to keep the acquisitions section and the administration apprised of the status of materials ordered or donated to the library. Future modifications of the program are also described.

Computers↗
PubMed2000

Neurologist or psychiatrist? The public and private domains of Jean-Martin Charcot.

The emergence of neurology as an autonomous, prestigious field in late-nineteenth-century Paris is well known. Less appreciated is the role that neurologists played vis-à-vis the cognate older field of psychiatry. Taking Jean-Martin Charcot, the most influential neurologist of his time, as a test case, this paper contrasts his attitudes and practice in the public setting of teaching and hospital work with his private practice. A staunch defender of a clear distinction between his field and psychiatry, Charcot's private practice displayed more flexibility. Treating hysteria and neurasthenia created a middle ground of nervous diseases for him to cultivate. Unpublished case histories and other materials, especially from the Charcot library, support the conception of neurologists as active agents in constituting a new psychological medicine.

Famous Persons↗
PubMed2002

The chemistry of the antibody molecule.

Immunochemistry has traditionally focused on understanding the molecular basis of antibody binding affinity and specificity. In the last 20 years a major shift has occurred in the field. We are now asking how we can exploit the remarkable properties of the antibody molecule and the immune response in chemistry-from testing basic theories of enzymatic catalysis to the synthesis of new catalysts. Moreover, the concept of molecular diversity, which underlies these experiments, is now being applied to a large number of other problems-from libraries of biopolymers to libraries of solid-state materials. Importantly, theses studies are providing fundamental molecular insights into many biological, chemical, and physical phenomena, as well as changing the way we approach the synthesis of new molecular function.

Antibodies↗
PubMed2001

A Penicillium chrysogenum gene ( aox) identified by specific induction upon shifting pH encodes for a protein which shows high homology to fungal alcohol oxidases.

Parallel cultures of Penicillium chrysogenum were grown in controlled bioreactors under conditions of penicillin production and one was shifted from the initial pH 6.0 to pH 8.0. RNA was isolated from both cultures and used for a differential hybridization experiment to identify genes specifically induced upon this pH shift. About 2,000 plaques of a cDNA library constructed from pH 8.0 material were screened with a pH 8.0 to pH 6.0 subtracted probe. Two independent clones of which the RNA was highly abundant in pH 8-shifted material and essentially not present in pH 6 material were isolated. Both clones were found to belong to one specific gene, which could be identified by sequence homology as an alcohol oxidase. The identified aox gene encoded for a peptide of 666 amino acids, interrupted by nine introns; and it showed high homology (>65% identity) to alcohol oxidases from Cladosporium fulvum and the methanol-utilizing yeasts Candida boidinii, Hansenula polymorpha (now Pichia angusta) and P. pastoris. The transcription start was identified by primer extension analysis. Southern analysis revealed that related genes are widely distributed among fungal species.

Alcohol Oxidoreductases↗
PubMed1997

Comparative genomic hybridization reveals a partial de novo trisomy 6q23-qter in an infant with congenital malformations: delineation of the phenotype.

We report the use of comparative genomic hybridization (CGH) to define the origin of a small extra segment (unidentifiable by classical cytogenetics) present in a de novo add(13)q34 chromosome that we found in the karyotype of a newly born boy with congenital heart defects, brain anomalies and dysmorphic signs. Initial investigation with fluorescence in situ hybridization (FISH) and a chromosome-13-specific library revealed that the excess material was not derived from chromosome 13. To uncover the origin of the unknown chromosome material, CGH was carried out on DNA isolated from blood lymphocytes of the patient. By using a conventional fluorescence microscope with no digital imaging devices, a single distinct region with gain of fluorescent intensity was observed on distal chromosome 6q. Confirmation of this finding by FISH with a chromosome-6-specific paint and a subtelomeric yeast artificial chromosome clone from 6q26-q27, in combination with the band morphology of the small extra chromosomal segment, allowed us to diagnose the additional material as being derived from chromosome 6q23-qter. FISH with a telomere 13q probe detected a terminal deletion of 13q34-qter on the derivative chromosome 13, indicating that the der(13) was a result of a translocation event. Genotyping of the hypervariable apolipoprotein (a) gene, which lies within 6q26-q27, showed that the additional chromosome 6 material was inherited from the mother. The karyotype of the proposita is therefore: 46,XY,-13,+der(13)t(6;13)(q23;q34) de novo (mat). Our results confirm the usefulness of CGH as an attractive alternative method for the characterization of constitutional small genetic imbalances and contribute to the delineation of the trisomy 6q23-qter phenotype.

Abnormalities, Multiple↗
PubMed2005

Computer-aided tissue engineering of a human vertebral body.

Tissue engineering is developing into a less speculative science involving the careful interplay of numerous design parameters and multidisciplinary professionals. Problem solving abilities and state of the art research tools are required to develop solutions for a wide variety of clinical issues. One area of particular interest is orthopedic biomechanics, a field that is responsible for the treatment of over 700,000 vertebral fractures in the United States alone last year. Engineers are currently lacking the technology and knowledge required to govern the subsistence of cells in vivo, let alone the knowledge to create a functional tissue replacement for a whole organ. Despite this, advances in computer-aided tissue engineering are continually growing. Using a combinatory approach to scaffold design, patient-specific implants may be constructed. Computer-aided design, optimization of geometry using voxel finite element models or other optimization routines, creation of a library of architectures with specific material properties, rapid prototyping, and determination of a defect site using imaging modalities highlight the current availability of design resources. This study proposes a novel methodology from start to finish which could, in the future, be used to design a tissue-engineered construct for the replacement of an entire vertebral body.

Biocompatible Materials↗
PubMed1994

Saturation mutagenesis at dihydrofolate reductase codons 22 and 31. A variety of amino acid substitutions conferring methotrexate resistance.

Naturally occurring amino acid substitutions conferring resistance to methotrexate (MTX) have been reported previously at codon positions 22 (leu-->arg, phe) and 31 (phe-->ser, trp) of mammalian dihydrofolate reductases (DHFR). To explore the character of other substitutions, a polymerase chain reaction (PCR)-assisted saturation mutagenesis protocol was devised to introduce all possible codon sequences at positions 22 and 31 of the murine DHFR coding sequence in an expressible simian virus 40 (SV40)-regulated transcription unit. Nucleotide sequencing confirmed the presence of all four nucleotides at each of the three codon positions in the mutagenized material. Transfection of these "codon libraries" into DHFR-deficient Chinese hamster ovary cells resulted in an increased frequency of MTX-resistant colony formation in comparison with wild-type DHFR transfected cells. DHFR variants contained in different clones were characterized by PCR amplification and DNA sequencing, identifying six different amino acid substitutions at position 22 and seven substitutions at position 31. DHFR variants were extracted for determination of MTX inhibition character and catalytic activity, normalizing for the amount of DHFR protein by western blot analysis. A wide range of MTX sensitivities and catalytic activities were observed which is consistent with the role of these side chains in DHFR catalytic function. We observed that codon 22 variants were generally more resistant to MTX, but codon 31 variants retained substantially more catalytic activity (about 2.5-fold) at a given level of MTX resistance. This heterogeneity in catalytic and inhibition character has important implications for the function of different DHFR variants as mediators of drug resistance.

Animals↗
PubMed2006

Components of the peptidome and transcriptome persist in lin wa pi: the dried skin of the Heilongjiang brown frog (Rana amurensis) as used in traditional Chinese medicine.

Although the ancient practice of traditional Chinese medicine (TCM) utilizes predominantly herbal ingredients, many of which are now the subject of intense scientific scrutiny, significant quantities of animal tissue-derived materials are also employed. Here we have used contemporary molecular techniques to study the material known as lin wa pi, the dried skin of the Heilongjiang brown frog, Rana amurensis, that is used commonly as an ingredient of many medicines, as a general tonic and as a topical antimicrobial/wound dressing. Using a simple technology that has been developed and validated over several years, we have demonstrated that components of both the skin granular gland peptidome and transcriptome persist in this material. Interrogation of the cDNA library constructed from the dried skin by entrapment and amplification of polyadenylated mRNA, using a "shotgun" primer approach and 3'-RACE, resulted in the cloning of cDNAs encoding the precursors of five putative antimicrobial peptides. Two (ranatuerin-2AMa and ranatuerin-2AMb) were obvious homologs of a previously described frog skin peptide family, whereas the remaining three were of sufficient structural novelty to be named amurins 1-3. Mature peptides were each identified in reverse phase HPLC fractions of boiling water extracts of skin and their structures confirmed by MS/MS fragmentation sequencing. Components of traditional Chinese medicines of animal tissue origin may thus contain biologically active peptides that survive the preparation procedures and that may contribute to therapeutic efficacy.

Air↗
PubMed2006

Structural characterization of self-assembled multifunctional binary nanoparticle superlattices.

Nanocrystals of different size and functionality (e.g., noble metals, semiconductors, oxides, magnetic alloys) can be induced to self-assemble into ordered binary superlattices (also known as opals or colloidal crystals), retaining the size tunable properties of their constituents. We have built a variety of binary superlattices from monodisperse PbS, PbSe, CoPt3, Fe2O3, Au, Ag, and Pd nanocrystals, mixing and matching these nanoscale building blocks to yield multifunctional nanocomposites (metamaterials). Superlattices with AB, AB2, AB3, AB4, AB5, AB6, and AB13 stoichiometry with cubic, hexagonal, tetragonal, and orthorhombic symmetries have been identified. Assemblies with the same stoichiometry can be produced in several polymorphous forms by tailoring the particle size and deposition conditions. We have identified arrays isostructural with NaCl, CuAu, AlB2, MgZn2, MgNi2, Cu3Au, Fe4C, CaCu5, CaB6, NaZn13, and cub-AB13 compounds emphasizing the parallels between nanoparticle assembly and atomic scale crystal growth and providing confidence that many more structures will follow. Recently, we have demonstrated that electrical charges on sterically stabilized nanoparticles in addition to such parameters as particle size ratio and their concentrations can provide the formation of a much broader pallet of binary nanoparticle superlattices as compared with the limited number of possible superlattices formed by hard noninteracting spheres. In this contribution, we demonstrate a large variety of different binary superlattices, provide their detailed structural characterization, and discuss the role of energetic and kinetic factors in the cocrystallization process. We found that Coulomb, van der Waals, charge-dipole, dipole-dipole, and other interactions can contribute equally to cocrystallization, allowing superlattice formation to be dependent on a number of tunable parameters. We present binary superlattices as a new class of materials with a potentially unlimited library of constituents over a wide range of tunable structures.

Calcium↗
PubMed2004

Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry.

The ability of Serial Analysis of Gene Expression (SAGE) to provide a quantitative picture of global gene expression relies not only on the depth and accuracy of sequencing into the SAGE library, but also on the efficiency of each step required to generate the SAGE library from the starting mRNA material. The first critical step is the ligation of adaptors containing a Type IIS recognition sequence to the anchored 3' end cDNA population that permits the release of short sequence tags (SSTs) from defined sites within the 3' end of each transcript. Using an in vitro transcript as a template, we observed that only a small fraction of anchored 3' end cDNA are successfully ligated with added SAGE adaptors under typical reaction conditions currently used in the SAGE protocol. Although the introduction of approximately 500-fold molar excess of adaptor or the inclusion of 15% (w/v) PEG-8000 increased the yield of the adaptor-modified product, complete conversion to the desired adaptor:cDNA hetero-ligation product is not achieved. An alternative method of ligation, termed as directed ligation, is described which exploits a favourable mass-action condition created by the presence of NlaIII during ligation in combination with a novel SAGE adaptor containing a methylated base within the ligation site. Using this strategy, we were able to achieve near complete conversion of the anchored 3' end cDNA into the desired adaptor-modified product. This new protocol therefore greatly increases the probability that a SST will be generated from every transcript, greatly enhancing the fidelity of SAGE. Directed ligation also provides a powerful means to achieve near-complete ligation of any appropriately designed adaptor to its respective target.

Combinatorial Chemistry Techniques↗
PubMed2000

Why we need to write openly about our clinical cases.

To learn more about what is and is not effective in the psychoanalytic situation, analysts need to develop a library of detailed analytic case material. Open case writing, by not overconstraining readers, allows them enough access to the analytic couple's affective experience to persuade them of the authenticity and validity of the analyst-author's views. They are then free to rethink the material creatively on their own, to use it as they need to, and to learn from others, in order to enhance their analytic skills. Closed case writing hinders readers' creative freedom to understand and interpret, and hence to learn. To encourage analyst-authors to share their affective experiences in the analytic situation more openly, analysts need to establish a constructively collaborative attitude toward playing with clinical material. They need to take for granted that new readers, even authors themselves newly rereading their work, will discover something new. A dialectical process can then be established in which clinical authors and readers contribute to each other in an ongoing imaginative interchange.

Humans↗
PubMed2006

Mitochondria-associated satellite I RNA binds to hnRNP K protein.

hnRNP K protein, which localizes to the nucleus, cytoplasm and mitochondria, is involved in the various cellular processes that compose gene expression. We used a SAGE-based assay to profile RNAs associated with hnRNP K protein in rat mitochondria. RNA was isolated from mitoplasts obtained from highly purified and RNase-treated mitochondria. Total RNA and RNA associated with hnRNP K protein were then used as input material for generating two SAGE libraries. Mitochondrion-derived tags isolated from the total mitoplast RNA library represented 86.3%, while those isolated from the library constructed from RNA associated with hnRNP K protein represented only 28.2% of selected tags. Thus, an unexpected number of nuclear-encoded RNAs were purified from mitochondria. Many of these transcripts were co-purified with hnRNP K protein, and high levels of nuclear-encoded RNAs co-immunoprecipitating with K protein corresponded to elevated hnRNP K protein levels of the organelle. The most abundant RNAs that were co-purified with hnRNP K protein represented transcripts originating from satellite I DNA. While satellite I RNA levels were higher in the nucleus and cytoplasm than in mitochondria, the most abundant binding of satellite I transcripts to hnRNP K protein was found in mitochondria. The role of satellite I RNA in mitochondria remains to be elucidated.

Animals↗
PubMed1984

Meeting the educational and psychosocial needs produced by a diagnosis of pediatric/adolescent cancer.

Childhood cancer affects not only children with the illness, but their families and their communities as well. Both children with cancer and their parents have need of complete, honest, and regularly updated medical information at their own level of understanding. Children with cancer and their parents also need psychosocial support to help them cope with the impact of childhood cancer on their daily lives, family dynamics, and interactions in their communities. Candlelighters, treatment centers, community organizations such as the American Cancer and Leukemia Societies, and the Office of Cancer Communications of the National Cancer Institute are among those groups meeting these needs with mutual-support groups, educational programs, special libraries, and written and audiovisual materials.

Adolescent↗