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Characterization of Glis2, a novel gene encoding a Gli-related, Krüppel-like transcription factor with transactivation and repressor functions. Roles in kidney development and neurogenesis.

In this study, we describe the characterization of a gene encoding a novel Krüppel-like protein, named Glis2. Glis2 encodes a relatively proline-rich, basic 55.8-kDa protein. Its five tandem Cys(2)-His(2) zinc finger motifs exhibit the highest homology to those of members of the Gli and Zic subfamilies of Krüppel-like proteins. Confocal microscopic analysis demonstrated that Glis2 localizes to the nucleus. Analysis of the genomic structure of the Glis2 gene showed that it is composed of 6 exons separated by 5 introns spanning a genomic region of more than 7.5 kb. Fluorescence in situ hybridization mapped the mouse Glis2 gene to chromosome 16A3-B1. Northern blot analysis showed that the Glis2 gene encodes a 3.8-kb transcript that is most abundant in adult mouse kidney. By in situ hybridization, expression was localized to somites and neural tube, and during metanephric development predominantly to the ureteric bud, precursor of the collecting duct, and inductor of nephronic tubule formation. One-hybrid analysis using Glis2 deletion mutants identified a novel activation function (AF) at the N terminus. The activation of transcription through this AF domain was totally suppressed by two repressor functions just downstream from the AF. One of the repressor functions is contained within the first zinc finger motif. The level of transcriptional activation and repression varied with the cell line tested, which might be due to differences in cell type-specific expression of co-activators and co-repressors. Our results suggest that Glis2 behaves as a bifunctional transcriptional regulator. Both the activation and repressor functions may play an important role in the regulation of gene expression during embryonic development.

Amino Acid Motifs↗

Sulfadoxine-pyrimethamine plus artesunate versus sulfadoxine-pyrimethamine plus amodiaquine for treating uncomplicated malaria.

BACKGROUND: Artemisinin-based combination treatments are strongly advocated, but supplies are limited. Sulfadoxine combined with amodiaquine is an alternative non-artemisinin combination. OBJECTIVES: To compare sulfadoxine-pyrimethamine plus amodiaquine (SP plus AQ) with sulfadoxine-pyrimethamine plus artesunate (SP plus AS) for treating uncomplicated Plasmodium falciparum malaria. SEARCH STRATEGY: We searched the Cochrane Infectious Diseases Group Specialized Register (October 2005), CENTRAL (The Cochrane Library 2005, Issue 4), MEDLINE (1966 to October 2005), EMBASE (1988 to October 2005), LILACS (October 2005), and reference lists. We also contacted researchers and organizations working in this field. SELECTION CRITERIA: Randomized controlled trials comparing SP plus AS with SP plus AQ for treating uncomplicated P. falciparum malaria. DATA COLLECTION AND ANALYSIS: Two authors independently applied the inclusion criteria, extracted data, and assessed methodological quality. The primary outcome measure was treatment failure (parasitological or clinical evidence of treatment failure between start of treatment and day 28). We calculated the relative risk (RR) with 95% confidence intervals (CI) for dichotomous data. MAIN RESULTS: Four trials (775 participants) met the inclusion criteria. All were from areas of high and seasonal malaria transmission in Africa. Fewer participants using SP plus AQ failed treatment by day 28 (RR 0.59, 95% CI 0.42 to 0.83; 652 participants, 3 trials). Even excluding new infections, SP plus AQ performed better (RR 0.62, 95% CI 0.40 to 0.96; 649 participants, 3 trials). There was no statistically significant difference between the two treatments for treatment failure at day 14 (RR 1.14, 95% CI 0.47 to 2.78; 775 participants, 4 trials). SP plus AS was more effective at reducing gametocyte carriage at day seven (RR 2.31, 95% CI 1.36 to 3.92; 220 participants, 1 trial). One trial reported that one person - in the SP plus AQ group - developed severe malaria. Adverse events were poorly reported, but did not seem to differ in type and number between the two treatment combinations. AUTHORS' CONCLUSIONS: SP plus AQ performed better at controlling treatment failure at day 28, but was not as good as SP plus AS at reducing gametocyte carriage at day seven. Careful consideration of local resistance patterns is required because resistance to sulfadoxine-pyrimethamine and amodiaquine are high in many areas. In order to delay development of resistance to artesunate, the combination with sulfadoxine-pyrimethamine should only be considered where both drugs are known to be effective. Data on adverse events are still lacking.

Amodiaquine↗

A high-resolution comparative map of canine Chromosome 5q14.3-q33 constructed utilizing the 1.5x canine genome sequence.

A high-density map of the region of canine Chromosome 5 (CFA5) surrounding the evolutionary breakpoint between human Chromosomes 1p32 and 17pll was constructed by integrating a radiation hybrid map including 41 microsatellites, 10 BACs, and 59 genes and a linkage map including 18 markers. A collection of canine genomic survey sequences providing 1.5x coverage was used to identify dog orthologs of human genes, proving instrumental in the development of this map. Of particular interest is the canine BHD gene, within which we have previously described a single nucleotide polymorphism associated with Hereditary Multifocal Renal Cystadenocarcinoma and Nodular Dermatofibrosis (RCND) in German Shepherd dogs. The corresponding region of the human genome is particularly gene rich, containing genes involved in development, metabolism, and cancer that are likely to be of interest in future mapping studies. This current mapping effort on CFA5 expands the degree to which initial findings of linkage in canine families can be followed by successful positional cloning efforts and increases the value of the human genome sequence for defining candidate genes. Moreover, this study demonstrates the utility of genomic survey sequences when combined with accurate genome maps for rapid mapping of disease susceptibility loci.

Animals↗

Outcome measures and needs assessment tools for schizophrenia and related disorders.

BACKGROUND: There has been a recent trend to encourage routine outcome measurement and needs assessment as an aid to decision making in clinical practice and patient care. Standardised instruments have been developed which measure clinical symptoms of disorders such as schizophrenia, wider health related quality of life and patients' needs. Such measures might usefully be applied to aid the recognition of psychosocial problems and to monitor the course of patients' progress over time in terms of disease severity and associated deficits in health related quality of life. They might also be used to help clinicians to make decisions about treatment and to assess subsequent therapeutic impact. Such an approach is not, however, without cost and the actual benefit of the adoption of routine outcome and needs assessment in the day-to-day care of those with schizophrenia remains unclear. OBJECTIVES: To establish the value of the routine administration of outcome measures and needs assessment tools and the feedback they provide in improving the management and outcome of patients with schizophrenia and related disorders. SEARCH STRATEGY: The reviewers undertook electronic searches of the British Nursing Index (1994 to Sept 1999), the Cochrane Library (Issue 2, 2002), the Cochrane Schizophrenia Group Trials Register (2002), EMBASE (1980-2002), MEDLINE (1966-2002), and PsycLIT (1887-2002), together with hand searches of key journals. References of all identified studies were searched for further trials, and the reviewers contacted authors of trials. SELECTION CRITERIA: Randomised controlled trials comparing the feedback of routine standardised outcome measurement and needs assessment, to routine care for those with schizophrenia. DATA COLLECTION AND ANALYSIS: Reviewers evaluated data independently. Studies which randomised clinicians or clinical teams (rather than individual patients) were considered to be the most robust. However only those which took account of potential clustering effects were considered further. Where possible and appropriate, risk ratios (RR) and their 95% confidence intervals (CI) were calculated. For continuous data Weighted Mean Differences (WMD) were calculated. Data were inspected for heterogeneity. MAIN RESULTS: No randomised data were found which addressed the specified objectives. One unpublished and one ongoing trial was identified. REVIEWER'S CONCLUSIONS: The routine use of outcomes measures and needs assessment tools is, as yet, unsupported by high quality evidence of clinical and cost effectiveness. Clinicians, patients and policy makers alike may wish to see randomised evidence before this strategy is routinely adopted.

Humans↗

Recurrent reversible mutations at gaf1 driving metastable TORC1 inhibitor resistance in fission yeast.

Metastable phenotypic inheritance is often attributed to epigenetic mechanisms, but reversible genetic alterations can produce similar instability. Here, we investigated the basis of unstable resistance to TORC1 inhibitor (rapamycin plus caffeine) in Schizosaccharomyces pombe. Six independent, metastable resistant mutants were isolated. Genetic mapping positioned the causal lesion to a single Mendelian locus, which sequencing identified as gaf1, encoding a GATA transcription factor and a key negative regulator of growth downstream of TORC1. In each mutant, distinct loss-of-function mutations (insertions, deletions, or point mutations) were found in gaf1 in the resistant state, and these mutations precisely reverted to the wild-type sequence upon loss of resistance. Restoring the wild-type gaf1 allele abolished resistance, indicating that reversible genetic disruption of gaf1 is both necessary and sufficient for the metastable phenotype. Furthermore, strong resistance in several strains from a genome-wide deletion library was due to secondary, inactivating mutations in gaf1, underscoring its role as a recurrent adaptive target under rapamycin plus caffeine treatment. Mechanistically, gaf1 inactivation established a distinct basal transcriptome and pronounced derepression of translation and metabolic programs upon drug treatment. While rapamycin plus caffeine triggered extensive chromatin remodeling and H3K9 methylation contributed partially to resistance, these epigenetic changes were most consistent with a downstream modifying layer. Our study shows that metastable drug resistance in fission yeast is predominantly associated with recurrent, reversible genetic inactivation of the central transcriptional regulator gaf1, demonstrating how rapidly reversible genetic switches can drive adaptive evolution.IMPORTANCEDistinguishing between genetic and epigenetic inheritance is fundamental to understanding how cells adapt to environmental stress. In the fission yeast Schizosaccharomyces pombe, rapid and reversible drug resistance is often assumed to be driven by epigenetic switches that change gene activity without altering DNA. However, our study reveals that this instability can be caused by physical mutations in a single gene, gaf1, which acts as a genetic toggle. These mutations appear under drug pressure and precisely revert to the original sequence when the drug is removed. We also demonstrate that these spontaneous mutations can contaminate standard laboratory yeast collections, leading to potential misinterpretation of experimental data. These findings broaden our understanding of unstable inheritance and show that DNA sequences can be far more dynamic than previously recognized during rapid evolution and the development of drug resistance.

TORC1 signaling↗

Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus.

BACKGROUND: Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. RESULTS: An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested. CONCLUSION: Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses.

Biomarkers↗

Progesterone or progestogen-releasing intrauterine systems for heavy menstrual bleeding.

BACKGROUND: Heavy menstrual bleeding (HMB) is an important cause of ill health in women and it accounts for 12% of all gynaecology referrals in the UK. Heavy menstrual bleeding is clinically defined as greater than or equal to 80 ml of blood loss per menstrual cycle. However, women may complain of excessive bleeding when their blood loss is less than 80 ml. Hysterectomy is often used to treat women with this complaint but medical therapy may be a successful alternative. The intrauterine coil device was originally developed as a contraceptive but the addition of uterine relaxing hormones, progestogens, to these devices resulted in a large reduction in menstrual blood loss. Case studies of two types of progesterone or progestogen-releasing systems, Progestasert and Mirena, reported reductions of up to 90% and that dysmenorrhoea may be improved. Insertion, however, may be regarded as invasive by some women, which affects its acceptability as a treatment. Frequent intermenstrual bleeding and spotting is also likely during the first few months. OBJECTIVES: To determine the effectiveness and acceptability of progesterone or progestogen-releasing intrauterine devices in achieving a reduction in heavy menstrual bleeding. SEARCH STRATEGY: All studies which might describe randomised controlled trials of progesterone or progestagen-releasing intrauterine devices for the treatment of heavy menstrual bleeding were obtained by electronic searches of The Cochrane Library, MEDLINE (1966 to 2005) and EMBASE (1980 to 2005). Companies producing progestogen-releasing intrauterine devices and experts in the field were contacted for information on published and unpublished trials. SELECTION CRITERIA: Randomised controlled trials in women of reproductive age treated with progesterone or progestogen-releasing intrauterine devices versus no treatment, placebo, or other medical or surgical therapy for heavy menstrual bleeding within primary care, family planning or specialist clinic settings were eligible for inclusion. Women with postmenopausal bleeding, intermenstrual or irregular bleeding, or pathological causes of heavy menstrual bleeding were excluded. DATA COLLECTION AND ANALYSIS: Potential trials were independently assessed by three review authors and nine trials met the criteria for inclusion in the review. The reviewers extracted the data independently and data were pooled where appropriate. Odds ratios (OR) were estimated from the data for dichotomous outcomes and weighted mean differences (WMD) for continuous outcomes. The primary outcome was reduction in menstrual blood loss but incidence of side effects, changes in quality of life, satisfaction and acceptability measures were also assessed. MAIN RESULTS: Progesterone or progestogen-releasing intrauterine systems have not been compared to placebo or no treatment. Progestasert has been compared to a number of different medical therapies in one small study but no conclusions can be made about its effectiveness. The levonorgestrel-releasing intrauterine device (LNG IUS) has been compared to oral cyclical norethisterone (NET) administered on days 5 to 26 of the menstrual cycle in one trial and was significantly more effective although there was a large reduction in loss from baseline in both groups. Some short term side effects were more common in the LNG IUS group but a significantly greater proportion of women in this group were satisfied and willing to continue with their treatment. In one trial of women awaiting hysterectomy, where the LNG IUS was compared with a control group taking their existing medical therapy, a higher proportion of the women in the intrauterine device group cancelled their planned surgery after six months of treatment. The LNG IUS has been compared to an endometrial ablation: either transcervical resection of the endometrium (TCRE) (two trials) or balloon ablation (three trials). There was a significantly greater mean reduction in menstrual bleeding in one trial in those undergoing balloon ablation (WMD -45.2 units, 95% CI -56.9 to -33.5), a lower score on the pictorial blood loss chart (PBAC) (WMD 33.2 units, 95% CI 27.2 to 39.2) and higher rates of successful treatment in 3 trials including both balloon and TCRE (OR 0.28, 95% CI 0.14 to 0.58) but the rates of satisfaction with treatment was were similar. There was no conclusive evidence of changes in quality of life between groups but women with the LNG IUS had a greater incidence of progestogenic side effects within one year. The LNG IUS has been compared to hysterectomy in one trial. There was no evidence of a change in quality of life scores but the LNG IUS treatment had lower costs than with hysterectomy, both at one and five-years follow up. AUTHORS' CONCLUSIONS: The levonorgestrel-releasing intrauterine device (LNG IUS) is more effective than cyclical norethisterone (for 21 days) as a treatment for heavy menstrual bleeding. Women with an LNG IUS are more satisfied and willing to continue with treatment but experience more side effects, such as intermenstrual bleeding and breast tenderness. The LNG IUS results in a smaller mean reduction in menstrual blood loss (as assessed by the PBAC chart) than endometrial ablation but there is no evidence of a difference in the rate of satisfaction with treatment. Women with an LNG IUS experience more progestogenic side effects compared to women having TCRE for treatment of their heavy menstrual bleeding but there is no evidence of a difference in their perceived quality of life. The LNG IUS treatment costs less than hysterectomy but there is no evidence of a difference in quality of life measures between these groups. There are no data available from randomised controlled trials comparing progesterone-releasing intrauterine systems to either placebo or other commonly used medical therapies for heavy menstrual bleeding.

Female↗

A new concept of sequence data distribution on wide area networks.

Accepted concepts in distributed applications design have been applied in the development of a network-based system for the synchronization of remote sequence database access sites by an incremental update mechanism. Computer hardware requirements, network bandwidth, and stability considerations make centralized access to essential computerized resources undesirable. A network model has been developed to distribute access over a collection of remotely situated computer centers. The formally independent database-access nodes join to form a heterogeneous, long distance, co-operating network that can compensate for the deficiencies of unstable network links thereby ensuring uninterrupted access to the resource. In order to guarantee consistency among these nodes, several distributed transaction protocols have been investigated; based on these results, a prototype system has been implemented. A layered software architecture makes the distributed transaction protocol transparent to the individual database system and the underlying network. Individual components of this network communicate by means of Remote Procedure Calls (RPCs). A prototype software system operates to synchronize up to data copies of the PIR-International Protein Sequence Database (Barker et al., 1993) at a number of different sites using the public Internet as the transport vehicle.

Computer Communication Networks↗

Interlibrary loan in primary access libraries: challenging the traditional view.

INTRODUCTION: Primary access libraries serve as the foundation of the National Network of Libraries of Medicine (NN/LM) interlibrary loan (ILL) hierarchy, yet few published reports directly address the important role these libraries play in the ILL system. This may reflect the traditional view that small, primary access libraries are largely users of ILL, rather than important contributors to the effectiveness and efficiency of the national ILL system. OBJECTIVE: This study was undertaken to test several commonly held beliefs regarding ILL system use by primary access libraries. HYPOTHESES: Three hypotheses were developed. HI: Colorado and Wyoming primary access libraries comply with the recommended ILL guideline of adhering to a hierarchical structure, emphasizing local borrowing. H2: The closures of two Colorado Council of Medical Librarians (CCML) primary access libraries in 1996 resulted in twenty-three Colorado primary access libraries' borrowing more from their state resource library in 1997. H3: The number of subscriptions held by Colorado and Wyoming primary access libraries is positively correlated with the number of items they loan and negatively correlated with the number of items they borrow. METHODS: The hypotheses were tested using the 1992 and 1997 DOCLINE and OCLC data of fifty-four health sciences libraries, including fifty primary access libraries, two state resource libraries, and two general academic libraries in Colorado and Wyoming. The ILL data were obtained electronically and analyzed using Microsoft Word 98, Microsoft Excel 98, and JMP 3.2.2. RESULTS: CCML primary access libraries comply with the recommended guideline to emphasize local borrowing by supplying each other with the majority of their ILLs, instead of overburdening libraries located at higher levels in the ILL hierarchy (H1). The closures of two CCML primary access libraries appear to have affected the entire ILL system, resulting in a greater volume of ILL activity for the state resource library and other DOCLINE libraries higher up in the ILL hierarchy and highlighting the contribution made by CCML primary access libraries (H2). CCML primary access libraries borrow and lend in amounts that are proportional to their collection size, rather than overtaxing libraries at higher levels in the ILL hierarchy with large numbers of requests (H3). LIMITATIONS: The main limitations of this study were the small sample size and the use of data collected for another purpose, the CCML ILL survey. CONCLUSIONS: The findings suggest that there is little evidence to support several commonly held beliefs regarding ILL system use by primary access libraries. In addition to validating the important contributions made by primary access libraries to the national ILL system, baseline data that can be used to benchmark current practice performance are provided.

Benchmarking↗

Leo Doyle, master surgeon.

On 3 March 1953 Leo Doyle died at the Mercy Hospital, Melbourne. The day before he died Leo Doyle had been operating at the Mercy Hospital when he took ill. Doyle's final illness was almost certainly the result of the severe aortic stenosis that had been developing over some years. His death at the relatively young age of 61 ended the career of a man described by Sir Gordon Gordon Taylor as the greatest technical surgeon that he had ever seen. In all likelihood Australian surgery will never see the likes of Doyle, a virtuoso surgeon, again. And yet to many of the surgeons who were Doyle's contemporaries and to those who followed him he remained somewhat of an enigma. Perhaps in some way the description of the great French surgeon Baron Dupuytren may also be applicable to Leo Doyle: known to all, loved by many, understood by few. By all accounts Leo Doyle's surgical repertoire knew no bounds. He operated with equal facility on the central nervous system, the head and neck, in the thorax, abdomen and pelvis and he was more than competent in gynaecology, urology and orthopaedics. In the latter part of his career he became, par excellence, a cancer surgeon. He was, arguably, Australia's first surgical oncologist. No procedure was deemed too complicated or demanding. Like some other superb technicians his judgement at times did not match his technical ability. Doyle was one of the first surgeons in Australia to perform hindquarter amputation and he helped to pioneer the operations of total gastrectomy and oesophagogastrectomy. An avid reader of the surgical literature, he possessed an enormous library which was matched by an equally large collection of surgical instruments. Unlike Devine he published relatively little. He was not a good clinical teacher, preferring to teach by example in the operating theatre. Although interested in music and the visual arts, surgery was his life.

Australia↗

Community animal health services for improving household wealth and health status of low income farmers.

BACKGROUND: Community animal health services in low income countries aim to improve the health of animals. They are thought to directly improve the wealth and health or livelihood of their owners. These services have been promoted since the 1970s by aid organizations. OBJECTIVES: To summarize reliable research of community animal health services on indicators for household wealth and health. SEARCH STRATEGY: We searched the Cochrane Infectious Diseases Group specialized trials register (up to May 2002); the AGRIS database (January 1975 to April 2002); STN SIGLE database (January 1976 to 2002); CAB database (January 1973 to January 2002); AGRICultural OnLine Access (US National Agricultural Library; accessed 30 April 2002); MEDLINE (PubMed; 1966 to April 2002); the Science Citation Index (2000 to April 2002); and checked the reference lists of articles. We searched 24 relevant web sites and contacted 22 organizations between July and September 2000. SELECTION CRITERIA: Individual, cluster and quasi-randomized controlled trials, and controlled before and after studies: comparing community animal health services with no community animal health services, or with an alternative animal health service. DATA COLLECTION AND ANALYSIS: We independently assessed studies for inclusion in the review. We contacted study authors for additional information. MAIN RESULTS: No studies met the inclusion criteria. Subsidiary analysis of excluded studies indicate a need for methodological rigor in evaluating programmes. REVIEWER'S CONCLUSIONS: No studies met the inclusion criteria. Reports that draw on observational data show insufficient rigor to conclude benefit. Given the amount of money and time invested in this area, these observations need to be confirmed by well-designed trials using pragmatic outcomes.

Animal Husbandry↗

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Animals↗

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.

BACKGROUND: Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. RESULTS: We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. CONCLUSION: MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

Computational Biology↗

Antibiotics for whooping cough (pertussis).

BACKGROUND: Whooping cough is a highly contagious disease. Infants are the population at highest risk of severe disease and death. Erythromycin for 14 days is recommended for treatment and contact prophylaxis but this regime is considered inconvenient and prolonged. The value of contact prophylaxis is uncertain. OBJECTIVES: To study the benefits and risks of antibiotic treatment of and contact prophylaxis against whooping cough. SEARCH STRATEGY: The Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library Issue 1, 2004); MEDLINE (January 1966 to February 2004); EMBASE (January 1974 to August 2003); conference abstracts and reference lists of articles were searched. Study investigators and pharmaceutical companies were approached for additional information (published or unpublished studies). There were no constraints based on language or publication status. SELECTION CRITERIA: All randomised and quasi-randomised controlled trials of antibiotics for treatment of and contact prophylaxis against whooping cough were included in the systematic review. DATA COLLECTION AND ANALYSIS: At least three reviewers independently extracted data and assessed the quality of each trial. MAIN RESULTS: Twelve trials with 1,720 participants met the inclusion criteria. Ten trials investigated treatment regimens and two investigated prophylaxis regimens. The quality of the trials was variable. Results showed that short-term antibiotics (azithromycin for three days, clarithromycin for seven days, or erythromycin estolate for seven days) were equally effective with long-term antibiotic treatment (erythromycin estolate or erythromycin for 14 days) in the microbiological eradication of Bordetella pertussis (B. pertussis) from the nasopharynx. The relative risk (RR) was 1.02 (95% confidence interval (CI) 0.98 to 1.05). Side effects were fewer with short-term treatment (RR 0.66; 95% CI 0.52 to 0.83). There were no differences in clinical improvement or microbiological relapse between short and long-term treatment regimens. Contact prophylaxis (of contacts older than six months of age) with antibiotics did not significantly improve clinical symptoms or the number of cases that developed culture positive B. pertussis. AUTHORS' CONCLUSIONS: Antibiotics are effective in eliminating B. pertussis from patients with the disease, rendering them non-infectious, but do not alter the subsequent clinical course of the illness. Effective regimens include: three days of azithromycin, seven days of clarithromycin, seven or 14 days of erythromycin estolate, and 14 days of erythromycin ethylsuccinate. Considering microbiological clearance and side effects, three days of azithromycin or seven days of clarithromycin are the best regimens. Seven days of trimethoprim/sulfamethoxazole also appeared to be effective for the eradication of B. pertussis from the nasopharynx and may serve as an alternative antibiotic treatment for patients who cannot tolerate a macrolide. There is insufficient evidence to determine the benefit of prophylactic treatment of pertussis contacts.

Anti-Bacterial Agents↗

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.

BACKGROUND: The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). RESULTS: We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. CONCLUSION: This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.

Arabidopsis↗

Identification of up-regulated Ras-like GTPase, Rap1b, by suppression subtractive hybridization.

BACKGROUND: Diabetic nephropathy accounts for over 30% of the end-stage renal disease (ESRD). A number of defined mechanisms and molecules that are involved in its pathogenesis are known, while others remain to be identified. METHODS: Suppression subtraction hybridization (SSH)-polymerase chain reaction (PCR) was employed to search for new genes that may be relevant to the pathogenesis of diabetic nephropathy during embryonic development, the time when the kidney is most susceptible to various forms of stress. A diabetic state was induced in pregnant mice at day-13 of gestation by administration of streptozotocin. The kidneys of newborn mice with blood glucose level> 200 mg/dL were harvested, mRNA isolated and subjected to SSH-PCR. Several differentially expressed cDNA fragments with up-regulated expression were isolated. One of the cDNA fragments had homology with human Ras-like guanine 5'-triphosphate (GTPase), Rap1b gene. By utilizing the lambdaZAP II mouse cDNA library and SMART RACE amplification, a full-length Rap1b cDNA was isolated. A recombinant protein was generated in pET15b bacterial expression system. An anti-Rap1b antibody was raised in rabbits by immunizing them with the fusion protein, and its specificity was confirmed by Western blot analysis. RESULTS: Rap1b cDNA had an open reading frame of 552 bp with a predicted putative protein size of approximately 21 kD. In vitro translation verified the authentication of the Rap1b cDNA clone. Northern blot analyses revealed a single approximately 2.3 kb Rap1b mRNA transcript. Its expression was up-regulated in several tissues, including the kidney of newborn diabetic mice. The degree of up-regulation of Rap1b mRNA expression was proportional to the blood glucose levels. Western blot analyses confirmed the hyperglycemia-induced up-regulation of the Rap1b expression. In situ hybridization and immunofluorescence studies revealed that Rap1b was expressed in the inner medullary collecting tubules. During hyperglycemia, its expression was accentuated and extended into the outer medullary and cortical collecting tubules. Similar up-regulation of Rap1b was observed when embryonic kidneys, harvested at day-13 of gestation, were exposed to high glucose ambience. CONCLUSION: The data suggest that Rap1b, a GTP-binding protein that plays a critical role in various signaling intracellular events, is another molecule that may be relevant to the pathobiology of diabetic nephropathy.

Amino Acid Sequence↗

Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development.

Little is known about gene action in the preimplantation events that initiate mammalian development. Based on cDNA collections made from each stage from egg to blastocyst, 25438 3'-ESTs were derived, and represent 9718 genes, half of them novel. Thus, a considerable fraction of mammalian genes is dedicated to embryonic expression. This study reveals profound changes in gene expression that include the transient induction of transcripts at each stage. These results raise the possibility that development is driven by the action of a series of stage-specific expressed genes. The new genes, 798 of them placed on the mouse genetic map, provide entry points for analyses of human and mouse developmental disorders.

Animals↗

Polysaccharide vaccines for preventing serogroup A meningococcal meningitis.

BACKGROUND: Randomised trials carried out over two decades ago showed that the polysaccharide vaccine prevented serogroup A meningococcal meningitis. Subsequent non-randomised studies, however, suggested significant variations in the age-specific duration of protection among young children. OBJECTIVES: The aim of the review was to determine the effect of polysaccharide serogroup A vaccine for preventing serogroup A meningococcal meningitis. The specific objectives were to assess the age-specific effects of the vaccine, the effect of booster doses in children under five years of age, and the duration of protection in children and adults. SEARCH STRATEGY: In 2004, the review was updated. The following databases were searched for records of new trials: the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library Issue 4, 2004); MEDLINE (January 1966 to November Week 1 2004); and EMBASE (January 1990 to September 2004). SELECTION CRITERIA: The first stage of the review included randomised trials. The second stage included non- randomised studies that addressed specific outcomes not answered by the randomised trials. DATA COLLECTION AND ANALYSIS: One reviewer assessed the methodological quality of the randomised trials and two reviewers independently identified and assessed the non-randomised studies. Of the twelve eligible Randomized trials, four were excluded because of the high risk of bias in assessing vaccine efficacy. Data from the trials were pooled using the Exact method to assess vaccine efficacy at one, two and three years post vaccination. Of the 15 non-randomised studies, only two addressed the specific objectives not answered by the randomised trials but were assessed to be at high risk of bias. MAIN RESULTS: The protective effect within the first year of vaccination was consistent across the randomised trials, and the summary vaccine efficacy was 95% (95% confidence interval (CI) 87% to 99%). Protection extended into the second and third year after vaccination but the results did not attain statistical significance. The vaccine was protective in Finnish children aged 3 months to five years. The latter was also the only trial that assessed the effect of a booster dose in children under two years of age but lacked power to yield statistically significant results. The vaccine was protective in one- to five-year old children in developing countries (Nigeria and Sudan) but the age-specific efficacy in strata between one and five years of age could not be determined. AUTHORS' CONCLUSIONS: For the first year after vaccination, the polysaccharide serogroup A vaccine was strongly protective against serogroup A meningococcal meningitis in participants over five years of age. It was also protective beyond the first year after vaccination in this age group but the level of vaccine efficacy could not be determined with precision. Children aged one to five years in developing countries were also protected but the level of efficacy in this age group could not be determined. While the vaccine was strongly protective among children aged three months to five years in developed countries the level of efficacy across age strata within this age group could not be determined. The number of children aged under two years was too small to draw conclusions on the protective effect of a booster dose of vaccine.

Humans↗