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Insulin regulation of a novel WD-40 repeat protein in adipocytes.

A 400 bp PCR product generated with degenerate primers derived from the glucagon-like peptide-1 receptor was used to screen a rat skeletal muscle cDNA library. The predicted amino acid sequence of the 978 bp open reading frame has a predicted M(r) of 35 804, an estimated isoelectric point (pI) of 5.31 and contains seven WD-40 repeats, which are common to G-protein beta subunits (Gbeta). Although chemically and structurally similar to Gbeta subunits, the predicted amino acid sequence, when compared with the previously cloned Gbeta isoforms, was found to be only 31-41% similar and thus was named Gbeta-like (GbetaL, 'Gable'). Western blotting of whole-cell lysates and immunoprecipitates of membrane and cytosolic fractions of HEK 293 cells stably overexpressing a carboxy-terminal His-tagged GbetaL indicates that the protein is cytosolic and that it migrates at 42 kDa. A 4 kb transcript was detected in all tissues surveyed by northern blotting; however, an additional 2 kb transcript was detected in testis. Expression of GbetaL mRNA was highest in the brain and testis, followed by lung, heart, kidney, skeletal muscle, spleen and liver. In addition, reverse transcriptase/PCR showed that several other tissues and cell lines express GbetaL. The ubiquitous nature of the tissue expression pattern of GbetaL is similar to that of the insulin receptor, which suggests that insulin may influence GbetaL expression. Indeed, GbetaL protein and mRNA levels, in fully differentiated 3T3-L1 adipocytes, were upregulated by insulin in a concentration-dependent fashion. These changes were highly sensitive to insulin stimulation, being minimally affected by doses as low as 0.1 nM and maximally elevated by 1 nM doses. These data suggest that insulin regulates GbetaL production and imply that some of the actions of insulin may be mediated, in part, by this novel intracellular protein.

Adipocytes↗

Monoclonal antibodies as tools for studying the osteoblast lineage.

Knowledge of the number and kinds of differentiation steps characterizing cells of the osteoblast lineage is inadequate. To analyze further osteoblast differentiation, a number of labs have generated monoclonal antibodies to osteogenic cells, derived from both normal bone and osteosarcomas. A variety of immunolabelling patterns on primary cell cultures, cell lines, and tissue sections has been reported, including cell surface, cytoplasmic, and extracellular matrix-associated patterns. Most of the antibodies selected recognize predominantly the mature osteoblast and osteocyte; in addition, however, antibodies have been generated that recognize pre-osteoblasts. Some recognize cells of both the osteoblast and chondroblast lineages and may contribute to a better understanding of the lineage and phenotypic relationships between these two cell types. In addition to recognition in vivo of cell subpopulations of discrete maturational stages, changes in the immunolabelling patterns in vitro have also documented a differentiation sequence in cells undergoing osteogenesis in cell and tissue cultures. In at least two cases, the antibodies have been used to isolate subpopulations of cells from bone, including relatively pure populations of osteocytes. With the exception of several antibodies that are against alkaline phosphatase or known matrix proteins including osteocalcin, the nature of the macromolecular species recognized by most of the antibodies generated to date are unknown. Recently, however, one antibody was used to clone the cDNA for the beta-galactoside-binding lectin, galectin 3 or epsilon binding protein (epsilon BP; IgE-binding protein; Mac-2), from a lambda gt11 osteoblast expression library; another was used to clone from an ROS 17/2.8-COS cell expression library the cDNA for OTS-8, a putative target gene of early response genes stimulated in response to phorbol esters in MC3T3-E1 cells. Neither of these macromolecules had previously been identified in bone cells, but the recent molecular and cellular analyses have shown them to be developmentally and/or hormonally regulated in osteoblastic cells. These antibodies extend the available markers and support earlier observations that a variety of molecules are differentially expressed by cells at different stages of the osteoblast lineage. This chapter will not be an exhaustive survey of all immunocytochemical and immunohistochemical analyses of osteogenic cells and tissues but will focus on the approach of eliciting novel monoclonal antibodies by the injection of osteogenic cells or crude bone extracts and its potential for establishing new markers of the osteoblast lineage. We have not included a large number of studies documenting the use of antibodies raised against several known bone matrix proteins; while these have been crucial in developing our current understanding of osteogenic differentiation, we sought rather to highlight the potential of the "random" injection approach.

Animals↗

Organization and evolution of resistance gene analogs in peanut.

The scarcity of genetic polymorphism in Arachis hypogaea (peanut), as in other monophyletic polyploid species, makes it especially vulnerable to nematode, bacterial, fungal, and viral pathogens. Although no disease resistance genes have been cloned from peanut itself, the conserved motifs in cloned resistance genes from other plant species provide a means to isolate and analyze similar genes from peanut. To survey the number, diversity, evolutionary history, and genomic organization of resistance gene-like sequences in peanut, we isolated 234 resistance gene analogs (RGAs) by using primers designed from conserved regions of different classes of resistance genes including NBS-LRR, and LRR-TM classes. Phylogenetic and sequence analyses were performed to explore evolutionary relationships both among peanut RGAs and with orthologous genes from other plant taxa. Fifty-six overgos designed from the RGA sequences on the basis of their phyletic association were applied to a peanut BAC library; 736 hybridizing BAC clones were fingerprinted and contigs were formed in order to gain insights into the genomic organization of these genes. All the fingerprinting gels were blotted and screened with the respective overgos in order to verify the authenticity of the hits from initial screens, and to explore the physical organization of these genes in terms of both copy number and distribution in the genome. As a result, we identified 250 putative resistance gene loci. A correlation was found between the phyletic positions of the sequences and their physical locations. The BACs isolated here will serve as a valuable resource for future applications, such as map-based cloning, and will help improve our understanding of the evolution and organization of these genes in the peanut genome.

Amino Acid Sequence↗

Direct sequencing of terminal regions of genomic P1 clones. A general strategy for the design of sequence-tagged site markers.

A method for the preparation of P1 DNA is presented, which allows the direct sequencing of ends of inserts in genomic P1 clones using the Applied Biosystems 373A DNA Sequencer and the Dye Terminator sequencing methodology. We surveyed several common methods of DNA preparation including alkaline lysis, Triton-lysozyme lysis, CsCl density-gradient purification, and a commercial column matrix DNA purification kit manufactured by Qiagen. We found that a modified alkaline lysis preparation of P1 DNA was most successful for generating P1 DNA that could be sequenced directly. We also noted that the host bacterial strain from which the P1 DNA was purified dramatically affected the quality of sequencing templates. The bacterial strains NS3145 and NS3529, in which the Drosophila melanogaster and human P1 genomic libraries are harbored, routinely yielded poor-quality sequencing templates. However, the bacterial strain DH10B routinely yielded P1 DNA that was sequenced successfully. A bacterial mating scheme is presented that exploits gamma delta transposition events to allow the transfer of P1 clones from the library host strain to DH10B. Using either an SP6 or a T7 primer, an average of 350 base pairs of DNA sequence was obtained with an uncalled base frequency of approximately 2%. About 4% of P1 end sequences generated corresponded to unique Drosophila loci present in the Genbank database. These single-pass DNA sequences were used to design sequence-tagged site markers for physical mapping studies in both humans and Drosophila.

Animals↗

Using Petri Net tools to study properties and dynamics of biological systems.

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats.

Algorithms↗

Quality of life after acute respiratory distress syndrome: a meta-analysis.

OBJECTIVE: To summarize long-term quality of life (QOL) and the degree of variation in QOL estimates across studies of acute respiratory distress (ARDS) survivors. DESIGN: A systematic review of studies evaluating QOL in ARDS survivors was conducted. Medline, EMBASE, CINAHL, pre-CINAHL, and the Cochrane Library were searched, and reference lists from relevant articles were evaluated. Two authors independently selected studies reporting QOL in adult survivors of ARDS or acute lung injury at least 30 days after intensive care unit discharge and extracted data on study design, patient characteristics, methods, and results. MEASUREMENTS AND RESULTS: Thirteen independent observational studies (557 patients) met inclusion criteria. Eight of these studies used eight different QOL instruments, allowing only qualitative synthesis of results. The five remaining studies (330 patients) measured QOL using the Medical Outcomes Study 36-Item Short Form survey (SF-36). Mean QOL scores were similar across these studies, falling within a range of 20 points for all domains. Pooled domain-specific QOL scores in ARDS survivors 6 months or later after discharge ranged from 45 (role physical) to 66 (social functioning), or 15-26 points lower than population norms, in all domains except mental health (11 points) and role physical (39 points). Corresponding confidence intervals were no wider than +/-9 points. Six studies all found stable or improved QOL over time, but only one found significant improvement beyond 6 months after discharge. CONCLUSIONS: ARDS survivors in different clinical settings experience similar decrements in QOL. The precise magnitude of these decrements helps clarify the long-term prognosis for ARDS survivors.

Humans↗

S.C.A.L.E.--spiritual care at life's end: a multi-disciplinary approach to end-of-life issues in a hospital setting.

End-of-life care is a hot topic in many hospitals of late, in part due to an aging society, which is forcing health care professionals to address the issue. A culture that places enormous value on youth and avoids the topic of death also contributes to the discomfort many health care professionals feel discussing this topic with their patients and family members. Inpatient satisfaction survey scores at Thunderbird Samaritan Medical Center (TSMC) were very inconsistent on the question of how the institution was meeting the emotional and/or spiritual needs of patients. A staff survey and needs assessment was also conducted regarding end-of-life care, which pointed out communication issues among staff members. All of these factors led to the development of an inter-disciplinary team to examine the issue of end-of-life care at TSMC.

Arizona↗

The measurement of health-related quality of life (QOL) in paediatric clinical trials: a systematic review.

BACKGROUND: The goal of much care in chronic childhood illness is to improve quality of life (QOL). However, surveys suggest QOL measures are not routinely included. In addition, there is little consensus about the quality of many QOL measures. OBJECTIVES: To determine the extent to which quality of life (QOL) measures are used in paediatric clinical trials and evaluate the quality of measures used. DESIGN: Systematic literature review. REVIEW METHODS: Included paediatric trials published in English between 1994 and 2003 involving children and adolescents up to the age of 20 years, and use of a standardised QOL measure. Data Sources included MEDLINE, CINAHL, EMB Reviews, AMED, BNI, PSYCHINFO, the Cochrane library, Internet, and reference lists from review articles. RESULTS: We identified 18 trials including assessment of QOL (4 Asthma, 4 Rhinitis, 2 Dermatitis, and single studies of Eczema, Cystic fibrosis, Otis media, Amblyopia, Diabetes, Obesity associated with a brain tumour, Idiopathic short stature, and Congenital agranulocytosis). In three trials, parents rated their own QOL but not their child's. Fourteen different QOL measures were used but only two fulfilled our minimal defined criteria for quality. CONCLUSIONS: This review confirms previous reports of limited use of QOL measures in paediatric clinical trials. Our review provides information about availability and quality of measures which will be of especial value to trial developers.

Adolescent↗

cDNA cloning of androgen-stimulated mRNAs in rat seminal vesicles: partial characterization of newly isolated cDNA clones, pSv-1 and pSv-2.

As the first step in surveying the molecular mechanism of androgen-responsive gene expression in rat seminal vesicles, the effect of androgen on the mRNAs was examined by in vitro translation assay. When the in vitro translation products of mRNAs from castrated animals (48 h) were compared with those from castrated and testosterone-treated animals (48 h) by SDS-PAGE, several discrete bands which were stimulated or repressed in response to androgen were observed in addition to major peptide bands of SVS IV and SVS V. From these findings, we constructed a partial cDNA library from the seminal vesicle poly(A +)RNAs of androgen-treated rats and screened by differential colony hybridization. Two distinct cDNA clones, pSv-1 and pSv-2, whose mRNAs were differentially stimulated in response to androgen and seemed to be expressed specifically in the seminal vesicles, were isolated. pSv-1 and pSv-2 hybridized to mRNAs of 1,600 and 3,500 nucleotides in length, respectively. These cDNA sequences, newly isolated in the present study, may provide useful probes for the study of molecular mechanism of androgen-responsive gene expression.

Androgens↗

Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field.

Lost City is a unique off-axis hydrothermal vent field characterized by highly alkaline and relatively low-temperature fluids that harbours huge carbonate chimneys. We have carried out a molecular survey based on 18S rDNA sequences of the eukaryotic communities associated with fluid-seawater interfaces and with carbonates from venting areas and the chimney wall. Our study reveals a variety of lineages belonging to eight major taxa: Metazoa, Fungi, Heterokonta (Stramenopiles), Alveolata, Radiolaria, Cercozoa, Heterolobosea and Euglenozoa. We detected one fungal lineage that appears to be widespread in hydrothermal systems both submarine and continental. Alveolates were the most abundant and diverse group in Lost City samples, although their distribution was very different in carbonate, where ciliates dominated, and in fluid-seawater libraries, where dinoflagellates, Group I and Group II (Syndiniales) marine alveolates were profuse. Similarly, Euglenozoa also displayed a differential distribution, kinetoplastids being present on carbonates and a novel group of diplonemids so far exclusively observed in the deep sea being dominant in fluid-seawater libraries. Protist lineages identified in this ecosystem likely correspond to grazers, decomposers and parasites, playing key roles in the food web of the Lost City ecosystem.

Biodiversity↗

First insight into the genome of an uncultivated crenarchaeote from soil.

Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large-insert genomic libraries. Using archaea-specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.

Crenarchaeota↗

Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation.

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- or Archaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.

Bacteria↗

A survey of trinucleotide/tandem repeat-containing transcripts (TNRTs) isolated from human spinal cord to identify genes containing unstable DNA regions as candidates for disorders of motor function.

Expansion of unstable DNA regions containing trinucleotide/tandem repeats (TNRs) represents a common genetic mutation in hereditary forms of neurological disorders. The spectrum of neurological diseases linked to TNR expansions has recently broadened to include conditions with both dominant and recessive inheritance and those with or without clinical anticipation. In view of the frequent involvement of the spinal cord in neurodegenerative disorders, we have analysed this key tissue to identify pathological TNRs. We have used two approaches to isolate a wide range of trinucleotide/tandem repeat-containing transcripts (TNRTs) from human spinal cord, firstly a polymerase chain reaction (PCR)-based method and secondly by screening a spinal cord cDNA library immobilised on a membrane. Overall, 97 TNRTs belonging to a number of key protein families, the most highly represented being transcription factors, intracellular signalling molecules and cytoskeletal proteins, have been isolated most of which have not previously been considered as potential disease-causing genes. The commonest repeat motifs found in our study were CAG (37%) and CCG (24%). Known genes involved in DNA repeat expansion-related neurological disorders (e.g., AAD10, Ataxin-3, Huntingtin) were detected which validated our methods. We have characterised homogeneous TNRs among the detected gene candidates in a search for potential pathological repeat expansions. The potential role of the gene candidates identified is discussed in terms of their contribution to neurodegenerative processes.

Gene Library↗

Fluorescence in situ hybridization mapping of human chromosome 19: mapping and verification of cosmid contigs formed by random restriction enzyme fingerprinting.

Automated restriction enzyme fingerprinting of 7900 cosmids from chromosome 19 and calculation of the likelihood of their overlap based on shared fragments have resulted in the assembly of 743 sets of overlapping cosmids (contigs). We have mapped 22% of the formed contigs (n = 165) and all of the contigs with minimal tiling paths exceeding 6 members (n = 50) to chromosomal bands by fluorescence in situ hybridization using DNA from at least one member cosmid. The estimated average size of the formed contigs is 60-70 kb. Thus, members of a correctly formed contig are expected to lie close to each other in metaphase and interphase chromatin. Therefore, we tested the contig assembly process by comparing the band assignment of two or more members selected from each of 97 contigs. Forty-two of these contigs were further characterized for valid assembly by determining the proximity of members in interphase chromatin. Using these tests, we surveyed a total of 431 joins counted along the minimal tiling path (280 in interphase as well as metaphase) and found 6 erroneous joins, one in each of 6 contigs (6% of tested).

Chromosomes, Human, Pair 19↗

Study provides admission, payment data for academic vs. non-academic providers.

Data Library: Admissions and cost data. This month's column looks at a Medstat study on the use of academic facilities and costs per admission compared to non-academic providers--under both managed care and fee-for-service scenarios and comparing national figures with those of highly penetrated managed care areas of the country.

Benchmarking↗

Dental considerations in upper airway sleep disorders: A review of the literature.

STATEMENT OF PROBLEM: Upper airway sleep disorders are becoming recognized as common medical concerns. Multiple treatment options have been advocated, including the use of dental devices. Dental practitioners are being asked by the medical profession to become a part of the treatment team. This may be a challenging task because of the large number of dental devices available, rapid advancement in the understanding of this disease, and numerous publications. PURPOSE: This article reviews the anatomic features and etiologic factors of upper airway sleep disorders and medical and dental treatment options. METHODS: The literature review was conducted with an accepted literature research tool, PubMed, developed by the National Library of Medicine. Key words searched included "obstructive sleep apnea," "sleep apnea," "sleep disorders," and "snoring". CONCLUSION: Dental devices are indicated in snoring and mild-to-moderate obstructive sleep apnea patients after medical evaluation and referral.

Humans↗

Characterization of late response genes sequentially expressed during renewed growth of fibroblastic cells.

Many proto-oncogenes are rapidly and transiently activated during the early stages of the cellular transition from a resting G0 state to the DNA synthesis (S) phase. To get better understanding of the gene complexity involved at later stages, we isolated, by cDNA cloning, and identified 17 genes that are activated sequentially during the period of time from proto-oncogene expression to the onset of DNA synthesis in the hamster CCL39 fibroblastic cell line. When protein synthesis is inhibited, induced expression of these genes is unaffected for 10 of them, enhanced for four, in a fashion similar to the immediate-early response genes, and inhibited for three, as observed for delayed early-response genes. In addition to rhoG, a new member of the ras homolog gene family (Vincent et al., 1992), cDNA sequencing indicated that six of them correspond to cytoskeletal proteins (alpha-tubulin, vascular alpha-actin and skeletal gamma-actin), extracellular matrix protein (thrombospondin), secreted protease (plasminogen activator inhibitor-1) and energy-linked transporter (mitochondrial proton/phosphate symporter). This overall survey shows that numerous differentially regulated gene activations are associated with the cell cycle progression, and suggests that proteins involved in cellular reshaping participate actively in the control of cellular growth.

Actins↗

A survey of the content of BSc courses in pharmacology in UK universities--is it time for a core curriculum?

The 18 UK universities offering three--of four--year BSc pharmacology courses were surveyed by questionnaire to determine course content, laboratory-practical content and project or dissertation requirements. In this article David Dewhurst and Clive Page provide an overview of the study, which highlighted the fact that there is no core curriculum. There was considerable variation in course content [only a limited number of common topics were taught in depth (> 15 h timetabled time)] and the time spent doing 'wet' laboratory practicals varied considerably (range 0-145 h). A research project in the final year was the norm (although the time allocation varied considerably), but some universities used a library-based dissertation as an alternative.

Curriculum↗