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PubMed2004

Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE.

In order to study the effect of different chloroethenes (electron acceptors) on the bacterial composition of dechlorinating communities, two reductive dechlorinating enrichment cultures were developed that were able to reduce trichloroethene (TCE) and cis-1,2-dichloroethene (cis-DCE) to ethene using hydrogen as electron donor, respectively. The inoculum for the cultures was material from a methanogenic fluidized bed reactor (FBR), which was originally seeded with digester sludge and showed a stable capacity for tetrachloroethene (PCE) reduction to ethene for over six years. Molecular methods were used to determine and compare the microbial communities of these two enrichment cultures. A clone library of bacterial 16S rRNA genes was generated for each enrichment. The clones were screened into different groups by restriction fragment length polymorphism (RFLP) analysis using two different four base pair recognition restriction enzymes. A total of 12 sequence types were identified by phylogenetic analysis of nearly complete 16S rDNA sequences ( approximately 1450 bp). The sequences were affiliated with six recognized phyla of the domain Bacteria: Firmicutes (low G+C Gram-positives), Chloroflexi (green non-sulphur bacteria), Actinobacteria (high G+C Gram-positives), Bacteroidetes (Cytophaga-Flexibacter-Bacteroides), Nitrospira and Spirochaetes. The results led to the identification of an organism closely related to Dehalococcoides ethenogenes to be the presumptive dechlorinator in both enrichments. Different electron acceptors affected the bacterial diversity and the community profiles of the two enrichments. Most of the sequences identified in our dechlorinating enrichments shared high similarities with sequences previously obtained from other enriched dechlorinating cultures and chlorinated-compound-contaminated sediments or aquifers, suggesting these bacteria may have direct or indirect roles in reductive dechlorination.

Anaerobiosis↗
PubMed1998

Purification, cloning, and expression of an apyrase from the bed bug Cimex lectularius. A new type of nucleotide-binding enzyme.

An enzyme that hydrolyzes the phosphodiester bonds of nucleoside tri- and diphosphates, but not monophosphates, thus displaying apyrase (EC 3.6.1.5) activity, was purified from salivary glands of the bed bug, Cimex lectularius. The purified C. lectularius apyrase was an acidic protein with a pI of 5.1 and molecular mass of approximately 40 kDa that inhibited ADP-induced platelet aggregation and hydrolyzed platelet agonist ADP with specific activity of 379 units/mg protein. Amplification of C. lectularius cDNA corresponding to the N-terminal sequence of purified apyrase produced a probe that allowed identification of a 1.3 kilobase pair cDNA clone coding for a protein of 364 amino acid residues, the first 35 of which constituted the signal peptide. The processed form of the protein was predicted to have a molecular mass of 37.5 kDa and pI of 4.95. The identity of the product of the cDNA clone with native C. lectularius apyrase was proved by immunological testing and by expressing the gene in a heterologous host. Immune serum made against a synthetic peptide with sequence corresponding to the C-terminal region of the predicted cDNA clone recognized both C. lectularius apyrase fractions eluted from a molecular sieving high pressure liquid chromatography and the apyrase active band from chromatofocusing gels. Furthermore, transfected COS-7 cells secreted a Ca2+-dependent apyrase with a pI of 5.1 and immunoreactive material detected by the anti-apyrase serum. C. lectularius apyrase has no significant sequence similarity to any other known apyrases, but homologous sequences have been found in the genome of the nematode C. elegans and in mouse and human expressed sequence tags from fetal and tumor EST libraries.

Amino Acid Sequence↗
PubMed2003

Pathophysiology of priapism: dysregulatory erection physiology thesis.

PURPOSE: While a modest amount of medical literature has been written on the topic of priapism, reports heretofore have focused predominantly on diagnostic and management related aspects of the disorder, providing meager information in regard to its pathophysiology. Accordingly the intent of this review was to explore the etiological and pathogenic factors involved in priapism. MATERIALS AND METHODS: The review entailed an overview of traditional and modern concepts that have been applied to the pathophysiology of priapism and an evaluation of assorted observational and experimental data relating to this field of study. The basic exercise consisted of a literature search using the National Library of Medicine PubMed Services, index referencing provided through the Historical Collection of the Institute of Medicine of The Johns Hopkins University and a survey of abstract proceedings from national meetings relevant to priapism. RESULTS: Insight into the pathophysiology of priapism was derived from a synthesis of evolutionary clinical experiences, mythical beliefs, clinical variants and scientific advances associated with the field of priapism. The results can be summarized. 1) Clinicopathological manifestations of priapism support its basic classification into low flow (ischemic) and high flow (nonischemic) hemodynamic categories, commonly attributed to venous outflow occlusion and unregulated arterial overflow of the penis, respectively. 2) Factual information is insufficient to substantiate etiological roles for urethral infection, bladder distention, failed ejaculation, satyriasis and sleep apnea in priapism. 3) Features of the variant forms of priapism invoke changes in nervous system control of erection and penile vascular homeostasis as having pathogenic roles in the disorder. 4) Clinical therapeutic and basic science investigative studies have revealed various effector mechanisms of the erectile tissue response that may act in dysregulated fashion to subserve priapism. CONCLUSIONS: This exercise suggested that, while priapism is commonly defined in terms of adverse mechanical contexts affecting penile circulation, it may also be viewed at least in some situations as an unbalanced erectile response involving derangements in possibly diverse systems of regulatory control. An integrative scientific approach that encompasses tissular, cellular and molecular levels of investigation may allow further understanding of the pathophysiology of the disorder. Ongoing elucidation of this pathophysiology can be expected to promote the development of new priapism therapies.

Greece, Ancient↗
PubMed1998

Solution phase combinatorial chemistry.

Combinatorial chemistry and parallel array synthesis techniques are now used extensively in the drug discovery process. Although published literature has been dominated by solid phase chemistry approaches, the use of solution phase techniques has also been widely explored. This review considers the advantages and disadvantages of choosing solution phase approaches in the various stages of drug discovery and optimisation, and assesses the practical issues related to these approaches. The uses of standard solution chemistry, the related liquid phase approach, and of supported materials to enhance solution phase chemistry are all illustrated by a comprehensive review of the published literature over the past three years.

Chemistry, Pharmaceutical↗
PubMed2001

Abuse: a risk factor for low birth weight? A systematic review and meta-analysis.

BACKGROUND: Abuse during pregnancy is considered to be a potentially modifiable risk factor for low birth weight (LBW). We conducted a systematic review and meta-analysis to determine the strength of association between physical, sexual or emotional abuse during pregnancy and LBW. METHODS: We selected papers for review from an electronic search of MEDLINE (1966-1999), CINAHL (1982-1997) and the Cochrane Library. We retrieved articles using the following MeSH headings and keywords: "infant low birth weight," "fetus," "perinatal care," "pregnancy," "prenatal care," "infant mortality," "violence," "battered women," "spouse abuse," "infant morbidity," "antenatal" and "neonatal." When necessary, we contacted authors to obtain data that were not included in the published material. We analyzed the methodological quality of each eligible study and selected those of the highest quality for meta-analysis. RESULTS: We reviewed 14 studies, of which 8 were selected for meta-analysis. Using a fixed-effects model, we found that women who reported physical, sexual or emotional abuse during pregnancy were more likely than nonabused women to give birth to a baby with LBW (odds ratio 1.4, 95% confidence interval 1.1-1.8). INTERPRETATION: Abuse may be part of a complex interaction of factors that contribute to LBW.

Domestic Violence↗
PubMed1994

Evaluation of the Omniflow collagen-polymer vascular prosthesis.

The Omniflow Vascular Prosthesis (OVP) is a truly integrated bio-synthetic composite of polyester mesh and ovine connective tissue components. In animal and human studies, the prosthesis has demonstrated long-term patency rates comparable and often better than alternate surgical replacements, with minimal aneurysmal or thrombotic problems. Immunohistological and TEM analysis of explants of OVP I provide good evidence for the excellent in vivo performance and are reviewed below. In addition, new data from explants of the OVP II, a later version of the Omniflow, are also described. These explant analyses have been enhanced by use of a library of highly specific monoclonal antibodies which can discriminate between collagens from different species.

Animals↗
PubMed2001

Getting a library of activities from a single compound: tunability and very large shifts in acidity constants induced by sol--gel entrapped micelles.

Acidity constants (in terms of K(i) values) can be fine-tuned, their values can be pushed to extremes, and their location can be placed either at the basic or acidic range of the pH scale, by tailoring intra-cage properties of SiO(2) sol--gel materials with surfactants. With the entrapped "solid-state pseudomicelles", an 8-orders magnitude K(i) shift--from the high-basic pH region to the acidic one--was obtained for acid fuchsin (AF); and tunability of the pK(i) values of the solvatochromic dye E(T)(30) and of crystal violet over much of the pH scale was achieved. This tailoring of various activities from the same dopant was achieved either by utilizing surfactants of different nature or by utilizing mixtures of anionic/cationic surfactants. The extraction of a wide range of reactivities from a single compound and the ability to fine-tune it is a powerful concept with potential extensions beyond acid/base reactions.

Journal Article↗
PubMed2003

Xylose metabolism in the anaerobic fungus Piromyces sp. strain E2 follows the bacterial pathway.

The anaerobic fungus Piromyces sp. strain E2 metabolizes xylose via xylose isomerase and d-xylulokinase as was shown by enzymatic and molecular analyses. This resembles the situation in bacteria. The clones encoding the two enzymes were obtained from a cDNA library. The xylose isomerase gene sequence is the first gene of this type reported for a fungus. Northern blot analysis revealed a correlation between mRNA and enzyme activity levels on different growth substrates. Furthermore, the molecular mass calculated from the gene sequence was confirmed by gel permeation chromatography of crude extracts followed by activity measurements. Deduced amino acid sequences of both genes were used for phylogenetic analysis. The xylose isomerases can be divided into two distinct clusters. The Piromyces sp. strain E2 enzyme falls into the cluster comprising plant enzymes and enzymes from bacteria with a low G+C content in their DNA. The d-xylulokinase of Piromyces sp. strain E2 clusters with the bacterial d-xylulokinases. The xylose isomerase gene was expressed in the yeast Saccharomyces cerevisiae, resulting in a low activity (25+/-13 nmol min(-1)mg protein(-1)). These two fungal genes may be applicable to metabolic engineering of Saccharomyces cerevisiae for the alcoholic fermentation of hemicellulosic materials.

Aldose-Ketose Isomerases↗
PubMed2004

The development of SSR markers by a new method in plants and their application to gene flow studies in azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi].

To gain a better understanding of wild and weedy azuki population structures in relation to the cultigens we have developed simple sequence repeat (SSR) markers based on a new methodology for plant material. In the azuki bean genome, the number of (AG)(n) and (AC)(n) motif loci per haploid genome has been estimated to be 3,500 and 2,100, respectively, indicating that (AG)(n) motifs are a rich source of markers. We constructed a (AG)(n)-SSR-enriched library in azuki bean in order to obtain a comprehensive range of SSR markers efficiently. The method applied in this study resulted in a 116-fold enrichment over the non-enriched genomic library, with a high percentage (98%) of successful single-locus amplification by the primer pairs designed. Consequently, this method can be applied to construct SSR-enriched libraries suitable for large-scale sequencing. We obtained 255 unique sequences from an (AG)(n)-enriched library for azuki bean. Fifty primer pairs were designed and screened against five populations of wild azuki bean. Among these five populations, one population from Bato town, Tochigi prefecture, Japan, showed greater polymorphism using these primers than the others and was therefore chosen for the in-depth study. The genotypes of 20 individuals were investigated using eight of the SSR primers developed. The genetic relationships among individuals revealed a complex spatial pattern of population structure. Although azuki bean is considered to be a predominantly self-pollinating species, 3 of the 20 individuals tested in the population showed heterozygous genotypes, indicating outcrossing. Allele size and DNA sequence in each of the 20 individuals were compared with those of landraces and released cultivars of azuki bean. Plants in part of the population had many alleles of the same size and with the same sequence as those in cultivated azuki bean, suggesting that gene flow from the cultigen to wild plants has occurred in this population. Unintentional transgene escape from azuki could therefore occur when transgenic azuki is grown in areas where its wild and weedy relatives occur. The approach used here could be applied to biosafety monitoring of transgenic azuki bean.

Alleles↗
PubMed2003

Expression of G-protein alpha subunit genes in the vestibular periphery of Rattus norvegicus and their chromosomal mapping.

OBJECTIVE: Heterotrimeric G-proteins play an important role in mediating signals transduced across the cell membrane by membrane-bound receptors. The precise role of G-proteins and their coupled receptors in the physiology of the vestibular neuroepithelium is not well understood. The purpose of this study was to better define the role of these proteins by examining their expression in the rat vestibular periphery and characterizing their chromosomal location. MATERIAL AND METHODS: To characterize G-protein alpha subunit gene expression in the target tissue of interest, we performed polymerase chain reaction (PCR) using degenerate G-protein primers corresponding to conserved regions in the G-protein alpha subunit coding sequence on a normalized rat vestibular cDNA library. PCR amplicons were cloned and 50 clones were randomly selected and sequenced. Radiation hybrid (RH) mapping was used to determine the chromosomal location of G alpha(olf) and two previously identified G-protein alpha subunits--G alpha(i2) and G alpha(i2(vest))--in the rat genome. RESULTS: The following G-protein alpha subunits were identified in the normalized cDNA library: G alpha(olf), G alpha(s), G alpha(o) and G alpha(s2). G alpha(olf) maps to chromosome 18 between markers D18Mit17b and D18Mgh2. G alpha(i2) maps to chromosome 8 between markers D8Rat65 and D8Mgh2. G alpha(i2(vest)) maps to chromosome 1 between markers D1Rat132 and D1Rat202. These chromosomal locations in the rat genome are syntenic to chromosomal regions in which the homologous G-protein alpha subunit genes have been localized in the human and mouse genomes, further validating RH mapping as an effective and accurate tool. We were unable to RH map the location of G alpha(o) due to its extensive homology with the hamster gene. CONCLUSION: The characterization of G-protein alpha subunit gene expression in the vestibular periphery and the chromosomal localization of these genes in the rat revealed that a diverse group of these second messengers are expressed.

Amino Acid Sequence↗
PubMed2004

Identification of some polymeric materials by low-temperature pyrolysis mass spectrometry.

The application of low-temperature pyrolysis mass spectrometry to the identification of some commercial and synthetic polymers using a direct insertion probe and electron ionization has been studied. The polymers were analyzed directly in the solid probe of a mass spectrometer within the ion source at 70 eV electron impact. The quadrupole mass spectrometer, equipped with a gas chromatogram software and library of low molecular weight compounds, was used to characterize the polymers by measuring the chemical structure of the repeat units and the end groups, and to examine the thermal degradation pathways. The polymers investigated show different degradation pathways. Investigation of sequences and determination of composition of copolymers were studied. Total ion pyrogram and spectrum subtractions were used to separate and measure spectra of pyrolysis steps at distinctly different temperatures.

Acrylic Resins↗
PubMed1999

IAIMS and JCAHO: implications for hospital librarians. Integrated Academic Information Management Systems. Joint Commission on Accreditation of Healthcare Organizations.

The roles of hospital librarians have evolved from keeping print materials to serving as a focal point for information services and structures within the hospital. Concepts that emerged from the Integrated Academic Information Management Systems (IAIMS) as described in the Matheson Report and the 1994 Joint Commission on Accreditation of Healthcare Organizations (JCAHO) standards have combined to propel hospital libraries into many new roles and functions. This paper will review the relationship of the two frameworks, provide a view of their commonalities, and establish the advantages of both for hospital librarianship as a profession.

Humans↗
PubMedDate not supplied

[The intimate Charcot].

Charcot's first inner circle of relationships was at work at the Salpêtrière, face to face with his intern who Charcot then invited to his home. At the Clinic, Charcot gave his official lectures that attracted crowds, but the small circle of "his" students--interns, residents and other rare and privileges students saw some of the "best" moments, as long as they aquiesced totally and did not question the "maître". They all got together for dinner on Tuesday night at his sumptuous "hôtel" on Boulevard Saint-Germain, followed by a reception where they could meet writers, artists and politicians. When the outsiders had left, Charcot tightened together his inner circle, those he would invite to his summer home in Neuilly. Léon Daudet was one of these. He saw the art-lover, the enlightened connaisseur of classical literature. He saw Charcot let down his severe mask of a professor and become a pleasant joking man, yet his fascination with Charcot did not stop him from criticizing Charcot's materialism and anticlericalism. He also repudiated Charcot's autoritarism and depotism over his family (whom he adored) and recognized in Charcot a certain timidity and "proud malaise". These evenings, rare occasions in a life filled with work, went on long into the night in the solitary silence of his library. Only his long trips which he used as a "cure" broke the intimacy of his inner circle. His letters to his wife, who never accompanied him, offer a glimpse into the personality of this secret man. They let us perceive the effect of overwhelming scientific success and flattering applause, but also the shadow of susceptibility as seen by his daughter Jeanne who accompanied him on his last trips. He never gave up, never confided in others, yet he was a charmer, one whose silence was often a prelude to an explosion of rage.

France↗
PubMed1996

[Centrosomal proteins].

The review summarizes recent data on structure and function of nearly two dozen centrosomal proteins of the animal cells; centrosome is an organelle that organizes cellular microtubules. Most of these data were obtained by molecular biology techniques including screening of phage expression cDNA libraries with centrosome-specific antibodies, bacterial expression of recombinant proteins recognized by these antibodies, analysis of multiple non-allelic gene of cytoskeletal proteins, etc. new classification of centrosomal proteins is suggested based on their possible centrosomal function comprising proteins of microtubule polymerization templates, structural proteins of pericentriolar material, microtubule severing proteins, microtubule-dependent transport-catalyzing motor proteins, regulatory proteins (specific protein kinases, phosphatases, etc), and centriolar proteins.

Animals↗
PubMed1998

Frequencies and types of exchange aberrations induced by X-rays and neutrons in Chinese hamster splenocytes detected by FISH using chromosome-specific DNA libraries.

PURPOSE: To estimate the frequencies of radiation- (low and high LET) induced chromosome aberrations in Chinese hamster splenocytes by two-colour fluorescence in situ hybridization using DNA painting probes specific for chromosomes 2, 3, 8, X and Y and to determine (1) the ratio of radiation-induced translocations and dicentrics; (2) the spectrum of exchange aberrations induced by X-rays and neutrons; and (3) the relative involvement of the different chromosomes in the formation of aberrations. MATERIALS AND METHODS: Isolated splenocytes from the Chinese hamster were irradiated in vitro with different doses of 200 kV X-rays (0.75, 1.5, 3.0 Gy) and 1 MeV fast neutrons (0.25, 0.5, 1.0 Gy). Conventional analysis of chromosome aberrations was carried out in Giemsa-stained preparations. Chromosome aberrations involving chromosomes 2, 3, 8, X and Y were analysed in first division metaphases using two-colour FISH. RESULTS: The results indicate that when all types of translocations are taken into account both X-rays and neutrons induce more translocations than dicentrics, the ratio between the two types of exchanges being 1.4 and 1.8 respectively. The ratio of 'apparently simple' reciprocal translocations and reciprocal complete dicentrics was close to 1 for both types of radiation. The RBE of neutrons for induction of exchanges was found to be between 5 and 8. Neutron irradiation was more efficient at inducing insertions. Among the chromosomes studied, an increased involvement was observed for chromosome 8 in dicentrics and translocations than that expected on the basis of its chromosome length. The high content of interstitial telomeric sequences in chromosome 8 may be responsible for the observed sensitivity of this chromosome. CONCLUSIONS: The results obtained in this study indicate that: (1) more translocations are found than dicentrics; (2) heterogeneity exists among Chinese hamster chromosomes for involvement in radiation-induced exchanges; (3) the spectrum and distribution of exchange aberrations are different between X-rays and neutrons; and (4) the relative frequencies of insertions could be used as a 'fingerprint' for exposure to high LET radiation.

Animals↗
PubMed2002

Why collect medical books?

The study of the original sources in the medical literature is an essential part and condition for doing good medical research. The love of books is conducive to a proper use of the source material. To support this statement, a short description of some famous book collectors in medical history is presented in this article.

Book Collecting↗
PubMed2005

From mapping to sequencing, post-sequencing and beyond.

The Rice Genome Research Program (RGP) in Japan has been collaborating with the international community in elucidating a complete high-quality sequence of the rice genome. As the pioneer in large-scale analysis of the rice genome, the RGP has successfully established the fundamental tools for genome research such as a genetic map, a yeast artificial chromosome (YAC)-based physical map, a transcript map and a phage P1 artificial chromosome (PAC)/bacterial artificial chromosome (BAC) sequence-ready physical map, which serve as common resources for genome sequencing. Among the 12 rice chromosomes, the RGP is in charge of sequencing six chromosomes covering 52% of the 390 Mb total length of the genome. The contribution of the RGP to the realization of decoding the rice genome sequence with high accuracy and deciphering the genetic information in the genome will have a great impact in understanding the biology of the rice plant that provides a major food source for almost half of the world's population. A high-quality draft sequence (phase 2) was completed in December 2002. Since then, much of the finished quality sequence (phase 3) has become available in public databases. With the completion of sequencing in December 2004, it is expected that the genome sequence would facilitate innovative research in functional and applied genomics. A map-based genome sequence is indispensable for further improvement of current rice varieties and for development of novel varieties carrying agronomically important traits such as high yield potential and tolerance to both biotic and abiotic stresses. In addition to genome sequencing, various related projects have been initiated to generate valuable resources, which could serve as indispensable tools in clarifying the structure and function of the rice genome. These resources have been made available to the scientific community through the Rice Genome Resource Center (RGRC) of the National Institute of Agrobiological Sciences (NIAS) to enable rapid progress in research that will lead to thorough understanding of the rice plant. As the next trend in rice genome research will focus on determining the function of about 40,000-50,000 genes predicted in the genome as well as applying various genomics tools in rice breeding, an unlimited access to rice DNA and seed stocks will provide a broad community of scientists with the necessary materials for formulating new concepts, developing innovative research and making new scientific discoveries in rice genomics.

Centromere↗
PubMedDate not supplied

[Features of the structure and evolution of complex tandemly organized Bsp-repeats in the fox genome. II. Tissue-specific and recombinant BamHI-dimer sites].

The complex structure of the clustered Bsp-repeats in fox genome seems to have evolved throughout a long period of time as a result of multiplication, recombination and divergence events. The sequence of the subrepeat (SR) approximately 245 b.p long is the basic substructure for the hierarchically arranged Bam HI-repeat 1468 b.p. long. The monomer consists of 3 SRs with a 43-59% homology. A dimer is composed of 2 monomers with a 93% homology. Amplification of the Bsp-repeats during evolution seems to have occurred at least twice: first--on the SR ancestral form level, second--on the monomer level. Despite profound divergence, there are still conservative regions in SRs with sequences homologous to known functional sites in eukaryotes. However qualitative and quantitative composition of most functional motifs is stringently individual in every SR. The performed analysis revealed that throughout evolution SRs acquired significant amount of motifs homologous to promoter and enhancer regions in tissue-specific genes and virus regulatory regions. Functional motifs in separate SRs are being differently grouped. Most inducible motifs are located in the III and II subrepeats, putative promoters--in the II one; elements participating both in transcriptional and replicational processes--mainly in the I subrepeat. A few ensembles of functional motifs remotely resemble extended regulatory regions of some tissue-specific genes. The monomers are potentially capable of ensuring diverse aspects of transcriptional regulation. As a whole, motifs of the 3 SRs are potentially capable of regulating the RNA synthesis periodicity with respect to the cellular cycle, activation and repression of genetical material in response to signals from the environment (AP-1, AP-2, AP-4, T-antigen, etc) and temporal ("octamers") etc. Apart from the BamHI-dimer, a few homologues fragments were isolated from fox genome and sequenced. Some of them were rearranged with respect to the BamHI-dimer. Inversion locally alters the composition of motifs and the sequence acquires new functional potential. Thus, the analysis of the emergence and development of Bsp-repeat structural variations allows us to consider repetitive DNA sequences as an ideal material in constructing multiprofile regulatory sequences.

Animals↗