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"Single sample concept": theoretical model for a combinatorial approach to solid-state inorganic materials.

A theoretical model for a "single sample concept" (SSC) applied to the combinatorial chemistry of solid-state inorganic compounds is presented. The SSC is performed by reacting N starting materials (randomly mixed) in a single sample of approximately 1 cm(3). Combinatorial calculations demonstrate that the number of reasonably estimated phases to be found in the space of N components grouped into compounds (e.g. oxides, sulfides, or halogenides) containing up to q < or = 6 metallic elements is smaller than combinations set up by starting conditions for local reactions within the bulk of a single ceramic sample. Recently, the SSC proved to work in the case of synthesizing libraries of 3d metal oxides, from which magnetic particulate matter was extracted by a magnetic separation technique. The SSC may be applied in a first screening cycle followed by 2D approaches of combinatorial chemistry.

Combinatorial Chemistry Techniques↗

PubMed2006

Books for free? How can this be? - A PubMed resource you may be overlooking.

The NCBI (National Center for Biotechnology Information) at the National Institutes of Health collects a wide range of molecular biological data, and develops tools and databases to analyse and disseminate this information. Many life scientists are familiar with the website maintained by the NCBI (http://www.ncbi.nlm.nih.gov), because they use it to search GenBank for homologues of their genes of interest or to search the PubMed database for scientific literature of interest. There is also a database called the Bookshelf that includes searchable popular life science textbooks, medical and research reference books and NCBI reference materials. The Bookshelf can be useful for researchers and educators to find basic biological information. This article includes a representative list of the resources currently available on the Bookshelf, as well as instructions on how to access the information in these resources.

Biological Science Disciplines↗

PubMed1997

Alternative splicing of the human serotonin transporter gene.

To explore the structural basis for regulation of human serotonin transporter (hSERT) gene expression, we used primer extension and 5' rapid amplification of cDNA ends (5'RACE) techniques to estimate levels of and identify 5'-noncoding elements of hSERT mRNAs and genomic cloning to place these elements within the overall map of the hSERT gene. Primer extension on JAR cell mRNA suggested the presence of significant hSERT mRNA sequence upstream of the 5' end of our cloned hSERT cDNA. Using 5'RACE and reverse transcription-PCR (RT-PCR) methodologies, we cloned these sequences from brain and placenta and found this material to be composed of alternatively spliced exons using a previously reported noncoding exon (1A) and a novel 97-bp noncoding exon (1B). RT-PCR of JAR cell mRNA blotted with exon-specific oligonucleotides revealed both exons 1A and 1B to be regulated in a cholera toxin-dependent manner. To clarify the structure of the hSERT gene including exon 1B, we isolated and characterized genomic hSERT clones from Lambda Fix II and P1 artificial chromosome libraries. In agreement with previous findings, a single hSERT gene was identified that accounts for hybridizing bands on genomic Southern blots and was found to utilize 13 exons to encode the transporter's coding sequences along with the two noncoding 5' exons. Exon 1B was identified approximately 14 kb downstream of exon 1A in the hSERT gene and 737 bp upstream of exon 2, where the initiation site for translation is located. Exon 1B is surrounded by several elements potentially suitable for regulating serotonin transporter gene expression in vivo, including consensus sites for transcription factors AP-1, AP-2, CREB/ATF, and NF-kappaB. These data reveal additional complexity in hSERT gene structure and expression that may be relevant to regulated and compromised transporter expression in vivo.

Alternative Splicing↗

PubMed2004

Efficient reversal of Alzheimer's disease fibril formation and elimination of neurotoxicity by a small molecule.

The Abeta1-42 peptide that is overproduced in Alzheimer's disease (AD) from a large precursor protein has a normal amino acid sequence but, when liberated, misfolds at neutral pH to form "protofibrils" and fibrils that are rich in beta-sheets. We find that these protofibrils or fibrils are toxic to certain neuronal cells that carry Ca-permeant alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Disrupting the structure of the Abeta1-42 fibrils and protofibrils might lead to the discovery of molecules that would be very useful in the treatment of AD. A high-throughput screen of a library of >3,000 small molecules with known "biological activity" was set up to find compounds that efficiently decrease the beta-sheet content of aggregating Abeta1-42. Lead compounds were characterized by using thioflavin T (ThT) as a beta-sheet assay. The most effective of six compounds found was 4,5-dianilinophthalimide (DAPH) under the following conditions: DAPH at low micromolar concentrations abolishes or greatly reduces previously existing fully formed Abeta1-42 fibrils, producing instead amorphous materials without fibrils but apparently containing some protofibrils and smaller forms. Coincubation of the Abeta1-42 peptide with DAPH produces either amorphous materials or empty fields. Coincubation of DAPH and Abeta1-42 greatly reduces the beta-sheet content, as measured with ThT fluorescence, and produces a novel fluorescent complex with ThT. When the Abeta1-42 peptide was coincubated with DAPH at very low micromolar concentrations, the neuronal toxicity mentioned above (Ca(2+) influx) was eliminated. Clearly, DAPH is a promising candidate for AD therapy.

Alzheimer Disease↗

PubMed2002

Ordering of quantum dots using genetically engineered viruses.

A liquid crystal system was used for the fabrication of a highly ordered composite material from genetically engineered M13 bacteriophage and zinc sulfide (ZnS) nanocrystals. The bacteriophage, which formed the basis of the self-ordering system, were selected to have a specific recognition moiety for ZnS crystal surfaces. The bacteriophage were coupled with ZnS solution precursors and spontaneously evolved a self-supporting hybrid film material that was ordered at the nanoscale and at the micrometer scale into approximately 72-micrometer domains, which were continuous over a centimeter length scale. In addition, suspensions were prepared in which the lyotropic liquid crystalline phase behavior of the hybrid material was controlled by solvent concentration and by the use of a magnetic field.

Bacteriophage M13↗

PubMed2005

A study of personal digital assistants to enhance undergraduate clinical nursing education.

This study reports on personal digital assistants (PDAs) as a means to prepare nurse professionals who value and seek current information. An interdisciplinary team of nursing and library faculty, information technology and bookstore staff, students, and educational consultants developed this project. A pre-post and comparative group design of second-degree students in the accelerated and traditional baccalaureate nursing degree (BSN) options was used to examine students' information-seeking behaviors, and the effectiveness and cost of innovation strategies associated with incorporation of PDAs into students' clinical practice. Results of this study support PDAs as an effective student learning resource, especially for reference materials. The student group with PDAs had increasing numbers of questions associated with clinical situations and a greater recognition of the need to use current resources. Students made substantial use of their PDAs and health team members, while decreasing reliance on textbooks and clinical faculty. Students' use of and satisfaction with this technology is linked to access speed and readability. Providing faculty with PDAs is recommended to enhance their comfort with and incorporation of PDAs into clinical teaching.

Attitude of Health Personnel↗

PubMed2001

[Homeopathic collections at the Institute of Medical History of Stuttgart's R. Bosch Foundation].

The author contains the history, review and characteristics of the homeopathic collections kept at the Institute of Medical History in Stuttgart. This is the legacy of Samuel and Melania Hahnemann and other German homeopathic physicians. It encompasses printed texts, documentation of diseases, personal manuscripts and elements of 'homeopathic material culture'. The review of the collections described in the article has been arranged in such a way as to serve as a guide for those researching this area.

Academies and Institutes↗

PubMed1997

Characterization of events during the late stages of HPV16 infection in vivo using high-affinity synthetic Fabs to E4.

HPV late gene expression is initiated as an infected basal cell migrates through the differentiating layers of the epidermis, resulting in the onset of vegetative viral DNA replication and the expression of viral late proteins. We have used a large synthetic immunoglobulin library displayed on phage (diversity 6.5 x 10(10) phage) to isolate three Fabs (TVG405, 406, and 407) which recognize distinct epitopes on the E4 late protein of HPV16. A C-terminal monoclonal (TVG404) was generated by hybridoma technology, and N-terminal polyclonal antiserum was prepared by peptide immunization (alpha N-term). The most potent antibody (TVG405) had an affinity for E4 of approximately 1.0 nM. All antibodies recognized the protein in paraffin-embedded archival material, allowing us to map events in the late stages of virus infection. Expression of E4 in vivo does not coincide with synthesis of the major virus coat protein L1, but precedes it by 1 or 2 cell layers in premalignant lesions caused by HPV16 and by up to 20 cell layers in HPV63-induced warts. In higher grade lesions associated with HPV16, E4 is produced in the absence of L1. By contrast, vegetative viral DNA replication and E4 expression correlate exactly and in some lesions begin as the infected epithelial cell leaves the basal layer. Differentiation markers such as filaggrin, loricrin, and certain keratins are not detectable in E4-positive cells, and nuclear degeneration is delayed. HPV16 E4 has a filamentous distribution in the lower epithelial layers, but associates with solitary perinuclear structures in more differentiated cells. Antibodies to the N-terminus of the protein stained these structures poorly. Our findings are compatible with a role for the HPV16 E4 protein in vegetative DNA replication or in modifying the phenotype of the infected cell to favor virus synthesis or virus release. The Fabs will be of value in the evaluation of model systems for mimicking HPV infection in vitro.

Amino Acid Sequence↗

PubMed2004

Online annotation tool for digital mammography.

RATIONALE AND OBJECTIVES: To develop a software tool for radiologists to annotate mammograms online. MATERIALS AND METHODS: The tool is web-based with a Java development environment and composed of a Digital Image and Communication in Medicine (DICOM) image viewer, a clinical information collector, and a database. The use of the tool with a sample case is demonstrated in this article. RESULTS: An online tool for the annotation of digital mammograms for teaching and research purposes has been developed. CONCLUSION: This annotation tool can be used to provide an annotated-case library on mammography education for residents and fellows.

Education, Medical, Continuing↗

PubMed1988

Use of RecA protein to enrich for homologous genes in a genomic library.

RecA protein-coated probe has been utilized to enrich genomic digests for desired genes in order to facilitate cloning from genomic libraries. Using a previously cloned HLA-B27 gene as the recA-coated enrichment probe, we obtained a mean 108x increase in the ratio of specific to nonspecific plaques in lambda libraries screened for B27 variant alleles of estimated 99% homology to the probe. Class I genes of lesser homology were less enriched: 6.7x for non-B27 genes of estimated greater than 95% homology and 3.7x for other-Class I genes of greater than 80% homology. Loss of genomic DNA during the enrichment procedure can, however, restrict application of this technique whenever starting genomic DNA is very limited. Nevertheless, the impressive reduction in cloning effort and material makes recA enrichment a useful new tool for cloning homologous genes from genomic DNA.

Alleles↗

PubMed2006

Peptide uptake in the ectomycorrhizal fungus Hebeloma cylindrosporum: characterization of two di- and tripeptide transporters (HcPTR2A and B).

Constraints on plant growth imposed by low availability of nitrogen are a characteristic feature of ecosystems dominated by ectomycorrhizal plants. Ectomycorrhizal fungi play a key role in the N nutrition of plants, allowing their host plants to access decomposition products of dead plant and animal materials. Ectomycorrhizal plants are thus able to compensate for the low availability of inorganic N in forest ecosystems. The capacity to take up peptides, as well as the transport mechanisms involved, were analysed in the ectomycorrhizal fungus Hebeloma cylindrosporum. The present study demonstrated that H. cylindrosporum mycelium was able to take up di- and tripeptides and use them as sole N source. Two peptide transporters (HcPTR2A and B) were isolated by yeast functional complementation using an H. cylindrosporum cDNA library, and were shown to mediate dipeptide uptake. Uptake capacities and expression regulation of both genes were analysed, indicating that HcPTR2A was involved in the high-efficiency peptide uptake under conditions of limited N availability, whereas HcPTR2B was expressed constitutively.

Agaricales↗

PubMed2001

Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method).

We describe a format for production of protein arrays termed 'protein in situ array' (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced by PCR using primers designed from information in DNA databases. Coupled transcription and translation is carried out on a surface to which the tagged protein adheres as soon as it is synthesised. Because proteins generated by cell-free synthesis are usually soluble and functional, this method can overcome problems of insolubility or degradation associated with bacterial expression of recombinant proteins. Moreover, the use of PCR-generated DNA enables rapid production of proteins or domains based on genome information alone and will be particularly useful where cloned material is not available. Here we show that human single-chain antibody fragments (three domain, V(H)/K form) and an enzyme (luciferase) can be functionally arrayed by the PISA method.

Animals↗

PubMed2004

Properties of a recombinant beta-glucosidase from polycentric anaerobic fungus Orpinomyces PC-2 and its application for cellulose hydrolysis.

A beta-glucosidase (BglA, EC 3.2.1.21) gene from the polycentric anaerobic fungus Orpinomyces PC-2 was cloned and sequenced. The enzyme containing 657 amino acid residues was homologous to certain animal, plant, and bacterial beta-glucosidases but lacked significant similarity to those from aerobic fungi. Neither cellulose- nor protein-binding domains were found in BglA. When expressed in Saccharomyces cerevisiae, the enzyme was secreted in two forms with masses of about 110 kDa and also found in two forms associated with the yeast cells. Km and Vmax values of the secreted BglA were 0.762 mM and 8.20 micromol/(min x mg), respectively, with p-nitrophenyl-beta-D-glucopyranoside (pNPG) as the substrate and 0.310 mM and 6.45 micromol/(min.mg), respectively, for the hydrolysis of cellobiose. Glucose competitively inhibited the hydrolysis of pNPG with a Ki of 3.6 mM. Beta-glucosidase significantly enhanced the conversion of cellulosic materials into glucose by Trichoderma reesei cellulase preparations, demonstrating its potential for use in biofuel and feedstock chemical production.

Amino Acid Sequence↗

PubMed1996

A 4.5-megabase YAC contig and physical map over the hemochromatosis gene region.

We have constructed a yeast artificial chromosome (YAC) contig over the candidate hemochromatosis gene region. This contig comprises 16 YACs from the CEPH, Washington University, and ICI YAC libraries and covers 4.5 Mb at 6p21.3-6p22. The complete contig has been restriction mapped, enabling the precise relationship between the YACs to be determined and the mapping of a total of 12 STSs. Nine of these are highly polymorphic STSs that are closely linked to hemochromatosis; this series includes D6S265 and D6S1260, which comprise the most proximal and distal markers linked to HC. This is the first YAC contig that spans the hemochromatosis candidate region, and it provides valuable resource material for the cloning of this and other genes in the region distal to the MHC class I complex.

Base Sequence↗

PubMed1999

Tracheal ligation increases mitogen-activated protein kinase activity and attenuates surfactant protein B mRNA in fetal sheep lungs.

BACKGROUND: Tracheal ligation has been shown to accelerate fetal pulmonary growth in normal and hypoplastic lungs. Our aim was to study the effects of tracheal ligation on established molecular markers of growth and differentiation [mitogen-activated protein (MAP) kinase] and maturity [surfactant protein B (SPB) and fatty acid synthase (FAS)]. MATERIALS AND METHODS: Tracheal ligation was performed on four 100-day-gestation fetal sheep, with four age-matched fetuses undergoing maternal laparotomy and hysterotomy as control. Lungs from surviving fetuses (n = 2 in each group) were harvested after 4 days and frozen in liquid nitrogen. Protein lysates were prepared, and MAP kinase enzymatic assays [extracellular signal regulated protein kinase (ERK)-1 and -2] and Western blots were performed. Total RNA was isolated, and a fetal sheep lung cDNA library was created. The sheep SPB and FAS genes were cloned and sequenced. Northern blots were performed with the new clones, normalizing to beta-actin. RESULTS: Tracheal ligation lungs contained a larger volume of fluid (40 ml) compared with age-matched controls (8 ml). MAP kinase enzymatic ERK-1 activity was increased and SPB mRNA expression was reduced in fetal lungs after tracheal ligation. Neither ERK-2 enzymatic activities and FAS mRNA nor ERK protein levels were affected by tracheal ligation, by Western blot analysis. CONCLUSION: Tracheal ligation-induced fetal lung growth may be mediated in part via the MAP kinase pathway. Expression of SPB mRNA is attenuated by tracheal ligation, whereas FAS, one of the key enzymes that synthesizes the lipid portion of surfactant, is not affected.

Animals↗

PubMed2001

Ultrasound-assisted lipoplasty.

BACKGROUND: Ultrasound-assisted lipoplasty (UAL) has been associated with particular types of complications and uncertain long-term effects arising from interactions between ultrasonic energy and living tissue. The present review seeks to address these issues. METHODS: Search strategy Three search strategies were devised to retrieve literature from Medline, Current Contents, Embase and Cochrane Library databases up until April 2000. Study selection Inclusion of papers was largely determined using a predetermined protocol. English language papers were selected. Acceptable study designs included randomized controlled trials, controlled clinical trials, case series or case reports. Data collection and analysis Thirty-six papers met the inclusion criteria. They were tabulated and critically appraised in terms of methodology and design, outcomes, and the possible influence of bias, confounding and chance. Other papers were also included to provide background material. RESULTS: There was little high-level evidence available comparing UAL and suction-assisted lipoplasty (SAL), with no conclusive evidence that UAL has a safety benefit, although low-quality evidence suggests that UAL is associated with reduced surgeon fatigue as well as increased operating times, slower aspiration rates and an increased learning curve. There is inadequate evidence to determine whether the theoretical potential for DNA damage from ultrasound is realized in the clinical setting. CONCLUSIONS: The evidence base for UAL is inadequate to determine the procedure's safety and efficacy. The potential for DNA damage must be investigated with appropriate in vivo animal models. Recommendations for the safe use of UAL are discussed.

Adipose Tissue↗

PubMed2006

In vitro evolution of proteins.

Consecutive rounds of diversification and selection of the fittest is believed to be the main driving force for the evolution of life. For the evolution of life to proceed, all living cells are surrounded by a lipid bilayer that separates their own genes from the external environment and from those of other organisms. In this way, the genetic information of an individual is replicated on the basis of their phenotype; thus the enrichment of the fittest will occur. Hence, evolution is based on linkage between genotype and phenotype owing to the surrounding of the genetic material with a barrier. The linkage between genotype and phenotype is also known to be essential for the directed evolution of proteins. Indeed, systems for molecular evolution, including phage display, ribosome display, and in vitro compartmentalization, all satisfy this requirement in different ways. These systems have been shown to be powerful tools for high-throughput screening for the functions of proteins, screening as many as <10(12) molecules in 1 d. These selection systems in combination with various gene libraries yield proteins with improved or altered biophysical properties, and may even allow the generation of proteins with novel functions.

Amino Acid Sequence↗

PubMed1986

Rapid sexing of native amniotic cells by hybridization to a cloned Y chromosome DNA probe.

A cloned DNA fragment from a Y chromosome genomic library was used for prenatal sex determination. Native cells from as little as 0.5 ml of amniotic fluid were analyzed by a dot blot hybridization technique without prior cell culture. Identification of male fetuses was possible within 3 days and confirmed by subsequent conventional karyotyping. This method of rapid sex screening is an alternative to the other methods of prenatal determination to the conventional chromosome analysis because it is a more rapid method, and to the karyotyping of chorion biopsy material because amniocentesis seems to have a lower risk and can still be performed when chorion biopsy is not more possible.

Amniotic Fluid↗