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Developmental care for promoting development and preventing morbidity in preterm infants.

BACKGROUND: Preterm infants experience a range of morbidity related to the immaturity of their organ systems and to concurrent disease states. An unfavourable environment in the neonatal intensive care unit (NICU) may compound this morbidity. Modification of the environment could minimize the iatrogenic effects. Developmental care is a broad category of interventions designed to minimize the stress of the NICU environment. These interventions may include one or more elements such as control of external stimuli (vestibular, auditory, visual, tactile), clustering of nursery care activities, and positioning or swaddling of the preterm infant. Individual strategies have also been combined to form programs, such as the 'Neonatal Individualized Developmental Care and Assessment Program' (NIDCAP) (Als 1986). OBJECTIVES: In preterm infants, do developmental care interventions reduce neurodevelopmental delay, poor weight gain, length of hospital stay, length of mechanical ventilation, physiological stress and other clinically relevant adverse outcomes? SEARCH STRATEGY: The Neonatal Review Group search strategy was utilized. Searches were made of Medline from 1966 to July, 2000, and of CINAHL, The Cochrane Library, and conference and symposia proceedings in the English language from 1990 to July, 2000. A list of all relevant articles was sent to two experts in the field to identify any omissions or additional unpublished studies. SELECTION CRITERIA: Randomized trials in which elements of developmental care are compared to routine nursery care for infants < 37 weeks gestation and that measured clinically relevant outcomes. Reports were in English or a language for which a translator was available. Computerized searches were conducted and all potentially relevant titles and abstracts were extracted. Retrieved articles were assessed for relevance independently by two reviewers, based on predetermined criteria. Articles that met all criteria for relevance were assessed for methodological quality based on predetermined criteria. Articles judged to have the appropriate quality by both reviewers were included in the analysis. DATA COLLECTION AND ANALYSIS: Data were extracted independently by the two authors. Meta-analyses were conducted for each intervention where the same outcome measures and/or instruments were used within comparable time points. MAIN RESULTS: This review detected 31 eligible randomized controlled trials involving four major groups of developmental care interventions, 19 sub-groups and multiple clinical outcomes. The results of the review indicate that developmental care interventions demonstrate some benefit to preterm infants with respect to: improved short-term growth outcomes, decreased respiratory support, decreased length and cost of hospital stay, and improved neurodevelopmental outcomes to 24 months corrected age. These findings were based on two or three small trials for each outcome, and did not involve meta-analyses of more than two trials for any one outcome. Although a number of other benefits were demonstrated, those results were from single studies with small sample sizes. The lack of blinding of the assessors was a significant methodological flaw in half of the studies. The cost of the interventions and personnel was not considered in any of the studies. REVIEWER'S CONCLUSIONS: Because of the inclusion of multiple interventions in most studies, the determination of the effect of any single intervention is difficult. Although there is evidence of some benefit of developmental care interventions overall, and no major harmful effects reported, there were a large number of outcomes for which no or conflicting effects were demonstrated. The single trials that did show a significant effect of an intervention on a major clinical outcome were based on small sample sizes, and the findings were often not supported in other small trials. Before a clear direction for practice can be supported, evidence demonstrating more consistent effects of developmental care interventions on important short- and long-term clinical outcomes is needed. The economic impact of the implementation and maintenance of developmental care practices should be considered by individual institutions.

Developmental Disabilities↗

Genetic and physical mapping of the progressive epilepsy with mental retardation (EPMR) locus on chromosome 8p.

Progressive epilepsy with mental retardation (EPMR) is an autosomal recessive disorder discovered recently from an isolated region in Finland. The disorder is characterized by normal early development, generalized tonic-clonic seizures with onset at 5-10 years of age, and progressive mental retardation beginning 2-5 years after the onset of seizures. We recently mapped the EPMR locus to a 7-cM region on chromosome 8p between markers AFM185xb2 and D8S262. A recombination detected with a new microsatellite marker AFMa054td9 narrows the region to 4 cM. A yeast artificial chromosome (YAC) contig containing 22 YACs was constructed across the disease gene region. The YAC contig is characterized by a collection of 19 YAC-end sequence-tag sites together with seven microsatellite markers. The entire YAC contig spans a minimum of 3 Mb. Moreover, the distal end of the contig contains a subtelomeric YAC yRM2205 that anchors the contig to the telomere. Construction of a YAC contig across the disease gene region is an essential step toward the isolation of the EPMR gene.

Chromosome Mapping↗

Identification of an extracellular matrix protein adhesin, EmaA, which mediates the adhesion of Actinobacillus actinomycetemcomitans to collagen.

Actinobacillus actinomycetemcomitans is an aetiologic agent in the development of periodontal and some systemic diseases in humans. This pathogen localizes to the underlying connective tissue of the oral cavity in individuals with periodontal disease. The adhesion of A. actinomycetemcomitans to extracellular matrix components of the connective tissue prompted this study to identify gene products mediating the interaction of A. actinomycetemcomitans to these molecules. A transposon mutagenesis system was optimized for use in A. actinomycetemcomitans and used to generate an insertional mutant library. A total of 2300 individual insertion transposon mutants were screened for changes in the adhesion to collagen and fibronectin. Mutants were identified which exhibited the following phenotypes: a decrease in collagen binding; a decrease in fibronectin binding; a decrease in binding to both proteins; and an increase in binding to both collagen and fibronectin. The identification of mutants defective in adhesion to the individual proteins indicates that distinct adhesins are expressed by this organism. Molecular analysis of these mutants implicated 11 independent loci in protein adhesion. One gene, emaA, is likely to encode a direct mediator of collagen adhesion, based on predicted protein features homologous to the collagen-binding protein YadA of Yersinia enterocolitica. EmaA was localized to the outer membrane, as expected for an adhesin. Reduction in fibronectin adhesion appeared to be influenced by abrogation of proteins involved in molybdenum-cofactor biosynthesis. Several other loci identified as reducing or increasing adhesion to both collagen and fibronectin are suggested to be involved in regulatory cascades that promote or repress expression of collagen and fibronectin adhesins. Collectively, the results support the hypothesis that A. actinomycetemcomitans host colonization involves afimbrial adhesins for extracellular matrix proteins, and that the expression of adhesion is modulated by global regulatory mechanisms.

Adhesins, Bacterial↗

Vitamin E supplementation in pregnancy.

BACKGROUND: Vitamin E supplementation may help reduce the risk of pregnancy complications involving oxidative stress, such as pre-eclampsia. There is a need to evaluate the efficacy and safety of vitamin E supplementation in pregnancy. OBJECTIVES: To assess the effects of vitamin E supplementation, alone or in combination with other separate supplements, on pregnancy outcomes, adverse events, side-effects and use of health services. SEARCH STRATEGY: We searched the Cochrane Pregnancy and Childbirth Group Trials Register (23 June 2004), the Cochrane Central Register of Controlled Trials (The Cochrane Library, Issue 2, 2004), MEDLINE (1966 to May 2004), Current Contents (1998 to May 2004) and EMBASE (1980 to May 2004). SELECTION CRITERIA: All randomised or quasi-randomised controlled trials evaluating vitamin E supplementation in pregnant women. We excluded interventions using a multivitamin supplement that contained vitamin E. DATA COLLECTION AND ANALYSIS: Two authors independently assessed trials for inclusion, extracted data and assessed trial quality. MAIN RESULTS: Four trials, involving 566 women either at high risk of pre-eclampsia or with established pre-eclampsia, were eligible for this review. All trials assessed vitamin E in combination with other supplements and two trials were published in abstract form only. No difference was found between women supplemented with vitamin E in combination with other supplements during pregnancy compared with placebo for the risk of stillbirth (relative risk (RR) was 0.77, 95% confidence intervals (CI) 0.35 to 1.71, two trials, 339 women), neonatal death (RR 5.00, 95% CI 0.64 to 39.06, one trial, 40 women), perinatal death (RR 1.29, 95% CI 0.67 to 2.48, one trial, 56 women), preterm birth (RR 1.29, 95% CI 0.78 to 2.15, two trials, 383 women), intrauterine growth restriction (RR 0.72, 95% CI 0.49 to 1.04, two trials, 383 women) or birthweight (weighted mean difference -139.00 g, 95% CI -517.68 to 239.68, one trial, 100 women), using fixed-effect models. Substantial heterogeneity was found for pre-eclampsia. Women supplemented with vitamin E in combination with other supplements compared with placebo were at decreased risk of developing clinical pre-eclampsia (RR 0.44, 95% CI 0.27 to 0.71, three trials, 510 women) using fixed-effect models; however, this difference could not be demonstrated when using random-effects models (RR 0.44, 95% CI 0.16 to 1.22, three trials, 510 women). There were no differences between women supplemented with vitamin E compared with placebo for any of the secondary outcomes. AUTHORS' CONCLUSIONS: The data are too few to say if vitamin E supplementation either alone or in combination with other supplements is beneficial during pregnancy.

Antioxidants↗

Ralstonia solanacearum genes induced during growth in tomato: an inside view of bacterial wilt.

The phytopathogen Ralstonia solanacearum has over 5000 genes, many of which probably facilitate bacterial wilt disease development. Using in vivo expression technology (IVET), we screened a library of 133 200 R. solanacearum strain K60 promoter fusions and isolated approximately 900 fusions expressed during bacterial growth in tomato plants. Sequence analysis of 307 fusions revealed 153 unique in planta-expressed (ipx) genes. These genes included seven previously identified virulence genes (pehR, vsrB, vsrD, rpoS, hrcC, pme and gspK) as well as seven additional putative virulence factors. A significant number of ipx genes may reflect adaptation to the host xylem environment; 19.6%ipx genes are predicted to encode proteins with metabolic and/or transport functions, and 9.8%ipx genes encode proteins possibly involved in stress responses. Many ipx genes (18%) encode putative transmembrane proteins. A majority of ipx genes isolated encode proteins of unknown function, and 13% were unique to R. solanacearum. The ipx genes were variably induced in planta; beta-glucuronidase reporter gene expression analysis of a subset of 44 ipx fusions revealed that in planta expression levels were between two- and 37-fold higher than in culture. The expression of many ipx genes was subject to known R. solanacearum virulence regulators. Of 32 fusions tested, 28 were affected by at least one virulence regulator; several fusions were controlled by multiple regulators. Two ipx fusion strains isolated in this screen were reduced in virulence on tomato, indicating that gene(s) important for bacterial wilt pathogenesis were interrupted by the IVET insertion; mutations in other ipx genes are necessary to determine their roles in virulence and in planta growth. Collectively, this profile of ipx genes suggests that in its host, R. solanacearum confronts and overcomes a stressful and nutrient-poor environment.

Chromosomes, Bacterial↗

Management of urinary tract infections: historical perspective and current strategies: Part 1--Before antibiotics.

PURPOSE: Urinary tract infections (UTIs) have plagued mankind long before bacteria were recognized as the causative agents of disease and before urology became an established medical specialty. To our knowledge a comprehensive review of the recorded medical history of UTI from its first description in ancient Egyptian papyri through today has not been attempted until now. MATERIALS AND METHODS: Numerous resources were used to collect the information described in this review. Older textbooks from the school of medicine library at our institution were used to collect information on UTI in ancient times. Medical texts from the 19th century contains information regarding the treatment of UTI during that era. Early volumes of the Journal of Urology from the beginning of the 20th century are rich with information on the first attempts at chemotherapy for UTI. MEDLINE searches were used to collect appropriate information after 1969. RESULTS: The Ebers papyrus from ancient Egypt recommended herbal treatments to ameliorate urinary symptoms without providing insight into pathological mechanisms. Hippocrates believed that disease was caused by disharmony of the 4 humors and accordingly diagnosed urinary disorders. Roman medicine further expanded the conservative approach (bed rest, diet, narcotics and herbs) advocated by Greek physicians, while also improving invasive techniques (surgical lithotomy for stones and catheterization for retention). The Arabian physician Aetius refined uroscopy and created a detailed classification and interpretation of urinary disease based on this technique. During the Middle Ages no major advances occurred, although existing therapies were refined and treatments for gonococcal urethritis were well described. The early 19th century provided vivid and detailed descriptions of UTIs without the knowledge that they were caused by microorganisms. Management included hospitalization, bed rest, attention to diet, plasters, narcotics, herbal enemas and douches, judicious bleeding (direct bleeding, cupping and leeches), and surgery for stones, abscess and retention. The discovery of microorganisms as the etiological agents of infectious diseases in general and inflammation associated with urinary diseases in particular provided an impetus for physicians critically to examine management approaches and develop evidence based strategies for UTI treatment. Various antibacterial agents, such as hexamine, mercurochrome and others (hexylresorcinol, methylene blue, pyridium, acriflavin and mandelic acid), showed promise in laboratory studies but their efficacy in clinical investigations was disappointing. CONCLUSIONS: Treatments for UTI until the discovery of antibiotics were largely palliative because the bacterial origin of UTI was not recognized and no specific antimicrobial therapies were available.

China↗

Carbon source utilization profiles as a method to identify sources of faecal pollution in water.

AIMS: Carbon source utilization profiles as a phenotypic fingerprinting methodology for determining sources of faecal pollution in water were evaluated. METHODS AND RESULTS: Three hundred and sixty-five Enterococcus isolates were collected from known faecal sources in four different geographical regions and were identified to species with the commercial Biolog system. Discriminant analysis (DA) was used to identify the substrate-containing wells that best classified the 365 isolates by source. By using 30 of the 95 wells for the analysis, the average rate of correct classification (ARCC) by source was 92.7% for a human vs non-human two-way classification when isolates from all regions were combined into one library. Corresponding ARCCs for other classification schemes were 81.9% for a four-way classification of human vs livestock vs wildlife vs domestic pets, and 85.7% for a three-way classification without human isolates. When three individual libraries were made based on classification of sources within Enterococcus species, the ARCC was 95.3% for the Ent. faecalis library, 95.8% for the Ent. gallinarum library and 94.7% for the Ent. mundtii library. Thirty Enterococcus isolates (unknown sources) were obtained from each of three stream sites where a specific source of pollution was apparent; 90.0% of the isolates from a human-suspected source were classified as human, 86.6% were classified as livestock from a livestock-suspected site, and 93.3% were classified as wildlife from a wildlife-suspected site. CONCLUSIONS: Phenotypic fingerprinting with carbon source utilization profiles provided levels of correct classification by sources from an Enterococcus library that were in the upper range of those reported in the literature. ARCCs for three Enterococcus species-specific libraries were very high and may be the best approach for further developing this concept and methodology. SIGNIFICANCE ANC IMPACT OF THE STUDY: The results, based on a modest Enterococcus library and a preliminary field validation test, demonstrated the potential for carbon source utilization profiles to be employed as a phenotypic method for determining sources of faecal pollution in water.

Animals↗

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↗

Regulation of carbonic anhydrase gene expression in cotyledons of cotton (Gossypium hirsutum L.) seedlings during post-germinative growth.

Recently, plastidial carbonic anhydrase (CA) cDNA clones encoding functional carbonic anhydrase enzymes were isolated from a 48 h dark-grown cotton seedling (cotyledons) cDNA library (Hoang et al., Plant Cell Physiol. 40: 1999). Here we examined the levels of relative transcript abundance and enzyme activities in cotyledons at different developmental stages and under different environmental conditions (i.e. altering CO2 and light conditions), during post-germinative seedling growth. Relative CA transcript levels and total CA enzyme activity in cotyledons of cotton seedlings increased from 18 h to 72 h of post-germinative growth in the dark, although somewhat later than the glyoxylate cycle enzyme, MS. When 24 h old seedlings were exposed to light for an additional 24 h, CA activity in greening cotyledons increased about 2-fold (compared with controls kept in the dark), whereas relative CA transcript levels were essentially the same. Removal of seed coats from cotyledons of 24 h old seedlings dramatically increased relative CA transcript abundance (measured 24 h later) in the dark, but did not influence CA enzyme activity. Manipulation of external CO2 environments (zero, ambient, or high) modulated coordinately the relative transcript abundance of CA (and rbcS) in cotyledons, but did not affect enzyme activity. On the other hand, regardless of the external CO2 conditions, cotyledons of seedlings exposed to light exhibited increased CA activity, concomitant with increased Rubisco activity and increased chlorophyll content. Collectively, our data suggest that steady-state levels of CA and rbcS transcripts are increased in response to environmental CO2 conditions, while CA (and Rubisco) enzyme activities are likely modulated at the post-transcriptional level following exposure of seedlings to light, and in parallel with development of functional chloroplasts.

Blotting, Northern↗

Antibiotics for community acquired pneumonia in adult outpatients.

BACKGROUND: Community-acquired pneumonia (CAP) is a common condition representing a significant disease burden for the community, particularly for the elderly. Because antibiotics are helpful in treating CAP, they are the standard treatment and CAP thus contributes significantly to antibiotic use, which is associated with the development of bacterial resistance and side-effects. Although several studies have been published concerning CAP and its treatment, the available data arises mainly from studies conducted in hospitalized patients and outpatients. There is no concise summary of the available evidence that can help clinicians in choosing the most appropriate antibiotic. OBJECTIVES: Our goal was to summarize the evidence currently available from randomized controlled trials (RCTs) concerning the efficacy of alternative antibiotic treatments for CAP in ambulatory patients above 12 years of age. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library, Issue 2, 2003) which contains the Cochrane Acute Respiratory Infections Group's trial register; MEDLINE (January 1966 to September week 3, 2003), and EMBASE (January 1974 to March 2003). Studies were also identified by checking the bibliographies of studies and review articles retrieved as well as by perusing medical journals. To identify any additional published or unpublished studies, we contacted the following antibiotics manufacturers: Abbott, AstraZeneca, Aventis, Boehringer-Ingelheim, Bristol-Myers-Squibb, GlaxoSmithKline, Hoffmann-LaRoche, Lilly, Merck, Merck Sharp & Dohme, Novartis, Pfizer, Pharmacia, Sanofi, and Yamanouchi. No language restrictions were applied in any of the search strategies. SELECTION CRITERIA: We included all randomized controlled trials (RCTs) in which one or more antibiotics were tested for the treatment of CAP in ambulatory adolescent or adult patients. Studies testing one or more antibiotic and reporting the diagnostic criteria used in selecting patients as well as the clinical outcomes achieved were included. No language restrictions were applied. DATA COLLECTION AND ANALYSIS: Data were extracted and study reports assessed by two independent reviewers (LMB and TJMV). Authors of studies were contacted as needed to resolve any ambiguities in the study reports. The data were analyzed using the Cochrane Collaboration's RevMan 4.2.2 Software. Differences between reviewers were resolved by discussion and consensus. MAIN RESULTS: Three randomized controlled trials involving a total of 622 patients aged 12 years and older diagnosed with community acquired pneumonia were included. The quality of the studies and of the reporting was variable. A variety of clinical, radiological and bacteriological diagnostic criteria and outcomes were reported. Overall there was no significant difference in the efficacy of the various antibiotics under study. REVIEWERS' CONCLUSIONS: Currently available evidence from RCTs is insufficient to make evidence-based recommendations for the choice of antibiotic to be used for the treatment of community acquired pneumonia in ambulatory patients. Pooling of study data was limited by the very low number of studies. Individual study results do not reveal significant differences in efficacy between various antibiotics and antibiotic groups. Multi-drug comparisons using similar administration schedules are needed to provide the evidence necessary for practice recommendations.

Adult↗

Recombinant versus urinary human chorionic gonadotrophin for ovulation induction in assisted conception.

BACKGROUND: For the last few decades urinary human chorionic gonadotrophin has been used to induce final follicular maturation and for triggering ovulation in assisted conception. Recombinant technology has allowed the production of two drugs that can be used for the same purpose: to mimic the endogenous luteinizing hormone (LH) surge. This would allow commercial production to be adjusted according to market requirements. In addition all urinary contaminants would also be removed. Hence, this would allow the safe subcutaneous administration of a compound with less batch-to-batch variation. However, prior to a change in practice, the effectiveness of the recombinant drugs should be known, compared to the currently used urinary human chorionic gonadotrophins. OBJECTIVES: To assess the safety and efficacy of subcutaneous rhCG and high dose rLH compared with intramuscular uhCG for inducing final oocyte maturation and triggering ovulation. SEARCH STRATEGY: We searched the Cochrane Menstrual Disorders and Subfertility Group trials register (27 August 2003), the Cochrane Central Register of Controlled Trials (CENTRAL on The Cochrane Library, issue 4, 2003), MEDLINE (1966 to Feb 2004) and EMBASE (1980 to Feb 2004). Searches were not limited by language. The bibliographies of included, excluded trials and abstracts of major meetings were searched for additional trials. Authors and pharmaceutical companies were contacted for missing and unpublished data. SELECTION CRITERIA: Two reviewers independently scanned titles and abstracts, and selected those that appeared relevant for collection of the full paper. Only truly randomised controlled trials comparing rhCG or high dose r-LH with urinary hCG for triggering ovulation in assisted conception for treatment of infertility in normogonadotrophic women were included. DATA COLLECTION AND ANALYSIS: Assessment of inclusion/exclusion, quality assessment and data extraction were performed independently by at least two reviewers. Discrepancies were discussed in the presence of a third reviewer and a consensus reached. Quality assessment included method of randomisation, allocation concealment, blinding of participants and assessors, reporting of a power calculation, intention to treat analysis, and handling of dropouts. Data extraction included characteristics of participants, the intervention and control procedures, and outcomes. MAIN RESULTS: Seven RCTs were identified, four comparing rhCG and uhCG and three comparing rhLH and uhCG. There was no statistically significant difference between rhCG vs uhCG regarding the ongoing pregnancy/ live birth rate (OR 0.98, 95% CI 0.69 to 1.39), pregnancy rate, miscarriage or incidence of OHSS. There was no statistically significant difference between rhLH vs uhCG regarding the ongoing pregnancy/ live birth rate (OR 0.94, 95% CI 0.50 to 1.76), pregnancy rate, miscarriage or incidence of OHSS. The manufacturer of rhLH has decided not to further develop this product. rhCG was associated with a reduction in the incidence of local site reactions and other minor adverse effects (OR 0.47, 95% CI 0.32 to 0.70). AUTHORS' CONCLUSIONS: There is no evidence of difference in clinical outcomes between urinary and recombinant gonadotrophins for induction of final follicular maturation. Additional factors should be considered when choosing gonadotrophin type, including safety, cost and drug availability.

Chorionic Gonadotropin↗

What do clinicians want from us? An evaluation of Brighton and Sussex University Hospitals NHS Trust clinical librarian service and its implications for developing future working patterns.

BACKGROUND: The Clinical Librarian (CL) Service at Brighton was established in 2003 with the aim of providing high-quality evidence to designated teams and fostering an evidence-based culture. OBJECTIVE: To evaluate the CL service at Brighton and discuss the implication of the findings. METHODS: A combination of internally collected data (n = 167), and an external evaluation of the service by questionnaires (n = 86) of users and non-users and interviews (n = 9) of users. RESULTS: Internal data suggest that the service is valued by its users and that patient care and continuing professional development are the most common uses for searches (confirmed by the external study); that searches generally result in some change in knowledge; and that this knowledge is disseminated. The external study found that visibility of the CL was crucial to the effectiveness of the role and that clinicians used the service mostly to get access to a wider range of resources and/or to save time. Users wanted the CL to include evaluative annotation with the results, and for the CL role to become more embedded in the team. Interview results expanded on the issues of integration of the CL and the need for annotation of results. CONCLUSIONS: To be most effective, CLs would be dedicated to one team, but financial constraints make this unlikely. Alternative working patterns are suggested as a possible compromise.

Access to Information↗

Development of a core RFLP map in maize using an immortalized F2 population.

A map derived from restriction fragment length polymorphisms (RFLPs) in maize (Zea mays L.) is presented. The map was constructed in an immortalized Tx303 x CO159 F2 mapping population that allowed for an unlimited number of markers to be mapped and pooled F3 seed to be distributed to other laboratories. A total of 215 markers consisting of 159 genomic clones, 16 isozymes and 35 cloned genes of defined function have been placed on 10 chromosomes. An examination of segregation data has revealed several genomic regions with aberrant segregation ratios favoring either parent or the heterozygote. Mapping of cloned genes and isozymes that have been previously mapped by functional criteria has provided 29 points of alignment with the classical maize genetic map. Screening of all mapped RFLP probes against a collection of U.S. Corn Belt germplasm using EcoRI, HindIII and EcoRV has resulted in a set of 97 core markers being defined. The designation of a set of core markers allows the maize genome to be subdivided into a series of bins which serve as the backbone for maize genetic information and database boundaries. The merits and applications of core markers and bins are discussed.

Crosses, Genetic↗

Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics.

Brachypodium is well suited as a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed 2 bacterial artificial chromosome (BAC) libraries from an inbred diploid Brachypodium distachyon line, Bd21, using restriction enzymes HindIII and BamHI. A total of 73,728 clones (36,864 per BAC library) were picked and arrayed in 192,384-well plates. The average insert size for the BamHI and HindIII libraries is estimated to be 100 and 105 kb, respectively, and inserts of chloroplast origin account for 4.4% and 2.4%, respectively. The libraries individually represent 9.4- and 9.9-fold haploid genome equivalents with combined 19.3-fold genome coverage, based on a genome size of 355 Mb reported for the diploid Brachypodium, implying a 99.99% probability that any given specific sequence will be present in each library. Hybridization of the libraries with 8 starch biosynthesis genes was used to empirically evaluate this theoretical genome coverage; the frequency at which these genes were present in the library clones gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, 2185 BAC end sequences (BES) representing 1.3 Mb of random genomic sequence were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation value of E<10-10, only 3.3% of the BESs showed similarity to repetitive sequences in the existing database, whereas 40.0% had matches to the sequences in the EST database, suggesting that a considerable portion of the Brachypodium genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize, although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Moreover, 122 BESs have significant matches to wheat ESTs mapped to individual chromosome bin positions. These BACs represent colinear regions containing the mapped wheat ESTs and would be useful in identifying additional markers for specific wheat chromosome regions.

Chromosomes, Artificial, Bacterial↗

Molecular portraits of B cell lineage commitment.

In an attempt to characterize early B cell development including the commitment of progenitor cells to the B cell lineage, we generated and compared genomewide gene expression profiles of human hematopoietic stem cells (HSCs) and pre-B cells (PBCs) by using serial analysis of gene expression. From more than 100,000 serial analysis of gene expression tags collected from human CD34(+) HSCs and CD10(+) CD19(+) PBCs, 42,399 unique transcripts were identified in HSCs but only 16,786 in PBCs, suggesting that more than 60% of transcripts expressed in HSCs were silenced during or after commitment to the B cell lineage. On the other hand, mRNAs of pre-B cell receptor (pre-BCR)-associated genes are virtually missing in HSCs but account for more than 10% of the transcriptome of PBCs, which also show increased expression of apoptosis-related genes. Both concentration of the transcriptional repertoire on pre-BCR-related genes together with marked up-regulation of apoptosis mediators in PBC might reflect selection for the expression of a functional pre-BCR within the bone marrow. Besides known regulator genes of early B cell development such as PAX5, E2A, and EBF, the most abundantly expressed genes in PBCs include ATM, PDGFRA, SIAH1, PIM2, C/EBPB, WNT16, and TCL1, the role of which has not been established yet in early B cell development.

Antigens, CD↗

Selective conservation of an E-protein gene promoter during vertebrate evolution.

The murine E-protein gene ME1 encodes a non-tissue-specific, helix-loop-helix transcription factor that is associated with morphological development. ME1 gene expression is regulated by a TATA-less promoter that contains multiple Sp1 consensus elements, E-boxes, and a novel transcription initiation site. In this study, we compared DNA homologous to the ME1 promoter from vertebrate species ranging from frog to human. A region of striking sequence similarity was identified in a region corresponding to the ME1 transcription initiation site (ME1 Inr). Within this region, a poly d(A) tract and a 9-bp inverted repeat (5'-GTCCGCCTG) were highly conserved in all species that were examined. Protein complexes that recognized these DNA elements were present among distant vertebrates (frog, chick, monkey and human), and were able to bend the ME1 Inr to a similar extent (approximately 60 degrees) as the previously described murine MBP alpha and MBP beta proteins. Collectively, these results suggest that an ME1 Inr-like element and its associated proteins functioned in an ancestral vertebrate more than 350 million years ago.

Animals↗

Molecular cloning of a novel T cell-directed CC chemokine expressed in thymus by signal sequence trap using Epstein-Barr virus vector.

Precursors of most secreted and cell surface molecules carry signal sequences at their amino termini. Here we describe an efficient signal sequence trap method and isolation of a novel CC chemokine. An expression library was constructed by inserting 5' portion-enriched cDNAs from phytohemagglutinin-stimulated peripheral blood mononuclear cells into upstream of signal sequence-deleted CD4 cDNA in an Epstein-Barr virus shuttle vector. After electroporation into Raji cells, CD4 antigen-positive cells were enriched by repeated cell sorting and plasmids were recovered in Escherichia coli. Out of 100 plasmid clones examined, 42 clones directed expression of CD4 antigen on the cell surface. Among them were signal sequences of CD6, beta2-microglobulin, MGC-24, and T cell receptor epsilon-chain, and at least four novel potential signal sequences. A cDNA clone encoding a novel CC chemokine was isolated by using one of the trapped fragments. The gene designated as TARC from Thymus and Activation-Regulated Chemokine was expressed transiently in phytohemagglutinin-stimulated peripheral blood mononuclear cells and constitutively in thymus. Radiolabeled recombinant TARC specifically bound to T cell lines and peripheral T cells but not to monocytes or granulocytes. The binding of radiolabeled TARC to the high-affinity receptor (Kd, 2.1 nM) on Jurkat was displaced by TARC but not by interleukin-8, MIP-1alpha, RANTES, or MCP-1. TARC also bound to the promiscuous chemokine receptor on erythrocytes (Kd, 17 nM). TARC induced chemotaxis in T cell lines Hut78 and Hut102. Pretreatment of Hut78 with pertussis toxin abolished the TARC-induced cell migration. Collectively, T cells express a highly selective receptor for TARC that is coupled to pertussis toxin-sensitive G-protein. TARC may a factor playing important roles in T cell development in thymus as well as in trafficking and activation of mature T cells.

Amino Acid Sequence↗

Beta lactam antibiotic monotherapy versus beta lactam-aminoglycoside antibiotic combination therapy for sepsis.

BACKGROUND: Optimal antibiotic treatment for sepsis is imperative. Combining a beta-lactam antibiotic with an aminoglycoside antibiotic may have certain advantages over beta-lactam monotherapy. OBJECTIVES: We compared clinical outcomes for beta lactam-aminoglycoside combination therapy versus beta lactam monotherapy for sepsis. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), (The Cochrane Library, Issue 3, 2004); MEDLINE (1966 to July 2004); EMBASE (1980 to March 2003); LILACS (1982 to July 2004); and conference proceedings of the Interscience Conference of Antimicrobial Agents and Chemotherapy (1995 to 2003). We scanned citations of all identified studies and contacted all corresponding authors. SELECTION CRITERIA: We included randomized and quasi-randomized trials comparing any beta-lactam monotherapy to any combination of one beta-lactam and one aminoglycoside for sepsis. DATA COLLECTION AND ANALYSIS: The primary outcome was all-cause fatality. Secondary outcomes included treatment failure, superinfections, colonization, and adverse events. Two authors independently collected data. We pooled relative risks (RR) with their 95% confidence intervals (CI) using the fixed effect model. We extracted outcomes by intention-to-treat analysis whenever possible. MAIN RESULTS: We included 64 trials, randomizing 7586 patients. Twenty trials compared the same beta-lactam in both study arms, while the remaining compared different beta-lactams using a broader spectrum beta-lactam in the monotherapy arm. In studies comparing the same beta-lactam, we observed no difference between study groups with regard to all-cause fatality, RR 1.01 (95% CI 0.75-1.35) and clinical failure, RR 1.11 (95% CI 0.95-1.29). In studies comparing different beta-lactams, we observed an advantage to monotherapy: all cause fatality RR 0.85 (95% CI 0.71-1.01), clinical failure RR 0.77 (95% CI 0.69-0.86). No significant disparities emerged from subgroup and sensitivity analyses, including the assessment of patients with Gram-negative and Pseudomonas aeruginosa infections. We detected no differences in the rate of resistance development. Adverse events rates did not differ significantly between the study groups overall, although nephrotoxicity was significantly more frequent with combination therapy, RR 0.30 (95% CI 0.23-0.39). We found no heterogeneity for all comparisons. We included a small subset of studies addressing patients with Gram-positive infections, mainly endocarditis. We identified no difference between monotherapy and combination therapy in these studies. AUTHORS' CONCLUSIONS: The addition of an aminoglycoside to beta-lactams for sepsis should be discouraged. All-cause fatality rates are unchanged. Combination treatment carries a significant risk of nephrotoxicity.

Aminoglycosides↗