Apollo: a sequence annotation editor.

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects.

The practices and attitudes of primary care nurse practitioners and physician assistants with respect to colorectal cancer screening.

OBJECTIVES: Although nurse practitioners and physician assistants form a large and growing portion of the primary care workforce, little is known about their colorectal cancer screening practices. The aim of this study was to assess the colorectal cancer screening practices, training, and attitudes of nurse practitioners and physician assistants practicing primary care medicine. METHODS: All nurse practitioners (827) and physician assistants (1178) licensed by the Medical Board of the State of North Carolina were surveyed by mail. Both groups were further divided into primary care versus non-primary care by self-described roles. Self-reported practices, training, and attitudes with respect to colorectal cancer screening were elicited. RESULTS: Response rates were 71.4% and 61.2%, for nurse practitioners and physician assistants respectively. A total of 51.3% of nurse practitioners and 50.3% of physician assistants described themselves as adult primary care providers. No primary care nurse practitioners and only 3.8% of primary care physician assistants performed screening flexible sigmoidoscopy. However, 76% of primary care physician assistants and 69% of primary care nurse practitioners reported recommending screening flexible sigmoidoscopy. A total of 95% primary care physician assistants and 92% of primary care nurse practitioners reported performing fecal occult blood testing. Only 9.4% of physician assistants and 2.8% of nurse practitioners received any formal instruction in flexible sigmoidoscopy while in their training. Additionally, 41.4% of primary care physician assistants and 27.7% of primary care nurse practitioners reported that they would be interested in obtaining formal training in flexible sigmoidoscopy. CONCLUSIONS: Physician assistants and nurse practitioners are motivated, willing and underutilized groups with respect to CRC screening. Efforts to increase education and training of these professionals may improve the availability of CRC screening modalities.

Is there publication bias in the reporting of cancer risk in Barrett's esophagus?

BACKGROUND & AIMS: The published risk of adenocarcinoma in the setting of Barrett's esophagus (BE) varies. Publication bias, the selective reporting of studies featuring positive or extreme results, may result in overestimation of this cancer risk in the literature. The aim of this study was to assess those publications reporting a cancer risk in BE for evidence of publication bias. METHODS: A MEDLINE search for all published estimates between 1966 and 1998 of cancer risk in BE was performed. All studies reporting a cancer risk expressible in cancers per patient-year of follow-up were retrieved. Bibliographies of these studies were surveyed for additional estimates. All publications that required an initial endoscopy with histologic confirmation of BE and any cancer were included. The relationship of reported cancer risk to size of the study was assessed. Multivariable regression controlling for differences in definition of BE, as well as other study characteristics, was performed. The data were also analyzed by means of a funnel diagram, an epidemiologic method to assess publication bias. RESULTS: Five hundred fifty-four abstracts were reviewed. Twenty-seven publications met the stated criteria for inclusion. There was a strong correlation between cancer risk and the size of the study, with small studies reporting much higher risks of cancer than larger studies. This association persisted when differences in the definition of BE, retrospective vs. prospective nature of the study, surveillance interval, and the effect of cancer detected in the first year were considered. The funnel diagram analysis suggested publication bias. CONCLUSIONS: The cancer risk in BE may be overestimated in the literature due to publication bias.

Hyoscyamine as a pharmacological adjunct in colonoscopy: a randomized, double blinded, placebo-controlled trial.

OBJECTIVE: Investigators have assessed the utility of antispasmodic agents in colonoscopy, with conflicting results. The aim of this study is to determine the effects of premedication with hyoscyamine, an anticholinergic antispasmodic, on outcomes in colonoscopy. METHODS: A total of 165 patients undergoing elective colonoscopy were randomized in a double blinded fashion to one of three arms: intravenous hyoscyamine (0.25 mg), oral hyoscyamine (0.25 mg), or placebo, administered 20-40 min before colonoscopy. Primary outcome measures included insertion time to cecum, patient's assessment of pain, and physician assessment of spasm. Secondary outcome measures included amount of analgesic medications used, total procedure time, amount and type of pathology visualized, and physician assessment of patient's pain. RESULTS: Bivariate analysis showed no difference between the three groups in insertion time (13.8 min, 14.8 min, and 13.8 min for placebo, intravenous hyoscyamine, and oral hyocyamine, respectively), analgesic medication necessary, or any other primary or secondary outcome variable. Multivariate analysis controlling for potential confounders also failed to demonstrate any differences between the groups. Women had higher procedure duration and analgesic requirement, and reported more pain than did men. CONCLUSIONS: This randomized, double blinded, placebo-controlled trial did not demonstrate efficacy of either intravenous or oral hyoscyamine as a premedication for colonoscopy.

The trithorax group gene moira encodes a brahma-associated putative chromatin-remodeling factor in Drosophila melanogaster.

The genes of the trithorax group (trxG) in Drosophila melanogaster are required to maintain the pattern of homeotic gene expression that is established early in embryogenesis by the transient expression of the segmentation genes. The precise role of each of the diverse trxG members and the functional relationships among them are not well understood. Here, we report on the isolation of the trxG gene moira (mor) and its molecular characterization. mor encodes a fruit fly homolog of the human and yeast chromatin-remodeling factors BAF170, BAF155, and SWI3. mor is widely expressed throughout development, and its 170-kDa protein product is present in many embryonic tissues. In vitro, MOR can bind to itself and it interacts with Brahma (BRM), an SWI2-SNF2 homolog, with which it is associated in embryonic nuclear extracts. The leucine zipper motif of MOR is likely to participate in self-oligomerization; the equally conserved SANT domain, for which no function is known, may be required for optimal binding to BRM. MOR thus joins BRM and Snf5-related 1 (SNR1), two known Drosophila SWI-SNF subunits that act as positive regulators of the homeotic genes. These observations provide a molecular explanation for the phenotypic and genetic relationships among several of the trxG genes by suggesting that they encode evolutionarily conserved components of a chromatin-remodeling complex.

The 3' regulatory region of the Abdominal-B gene: genetic analysis supports a model of reiterated and interchangeable regulatory elements.

The Abdominal-B (Abd-B) gene is one of three genes in the bithorax complex, a cluster of homeotic genes in Drosophila. During embryogenesis Abd-B is expressed in a complex pattern, producing four different transcript classes, each of which exhibits a unique spatial pattern of expression. Proper regulation of the class A transcripts is required for appropriate development of the fifth through eighth abdominal segments and is mediated, in part, by a 60-kb regulatory region located 3' of the gene. We have isolated a new mutation, designated Abd-BCorset, which is caused by a deletion that leaves 15 kb of the 3' regulatory sequences immediately adjacent to the gene, but removes 45 kb of the more distant 3' regulatory elements. This mutation produces an unexpected homeotic segmental transformation of the fourth through seventh abdominal segments, and has been analyzed by genetic and molecular techniques. In situ hybridization to Abd-BCorset embryos shows a uniform and moderate level of the Abd-B class A transcript in the posterior abdomen, rather than the normal graded pattern of expression. Our analysis of the Abd-BCorset mutation has prompted a model of the 3' regulatory region of Abd-B based on reiterated cell type-specific elements controlled by adjacent position-sensitive activating elements. The gradient of Abd-B expression normally observed in the posterior abdomen appears to be achieved by varying the number of reiterated elements that are active in each segment.

The Abdominal-B gene of Drosophila melanogaster: overlapping transcripts exhibit two different spatial distributions.

The Abdominal-B (Abd-B) gene of Drosophila controls the specification of segment identities in the posterior abdomen. We describe here the spatial and temporal distribution of Abd-B transcripts. At least five RNA species are detected on Northern blots with probes within the region of the Abd-B homeobox. We have identified probes specific for subsets of these transcripts and have used these probes to study the distribution of each subset by in situ hybridization to embryonic tissue sections. The transcripts can be divided into two groups: one group is expressed maximally in parasegment (PS)13 and extends anteriorly to PS10; the other is expressed only in PS14 and 15. These two different patterns of expression correspond to the anatomical domains defined by two classes of mutations in Abd-B. These results help explain the complex genetic interactions and phenotypes of mutations within this gene.

Drosophila glue gene Sgs-3: sequences required for puffing and transcriptional regulation.

The 68C intermolt puff of Drosophila melanogaster contains a cluster of three glue protein genes, Sgs-3, Sgs-7, and Sgs-8. By analysis of chromosomal rearrangements which break near the glue gene cluster, we have established that a region of no more than 20 kb is required for normal expression of the glue genes and for formation of the 68C puff. Using P element-mediated transformation, we have introduced defined segments of the 68C region into the fly genome and assayed the expression of the Sgs-3 gene. Based on the criteria of correct tissue- and stage-specific expression, transcription of an RNA of appropriate size and abundance, and production of an sgs-3 protein, the correctly regulated expression of the Sgs-3 gene requires less than 3.4 kb of total flanking sequences, approximately 2.3 kb 5' and 1.1 kb 3'. Formation of a new intermolt puff at the site of insertion is not observed for all transformants which produce high levels of Sgs-3 RNA. Only transformants in which the introduced DNA from 68C also contains the Sgs-7 and Sgs-8 genes cause a new intermolt puff at the chromosomal location of the insert.

Sequences sufficient for correct regulation of Sgs-3 lie close to or within the gene.

The Drosophila melanogaster 68C chromosomal locus is the site of a prominent polytene chromosome puff that harbors the genes Sgs-3, Sgs-7 and Sgs-8. These genes code for proteins that are part of the salivary glue that Drosophila larvae secrete as a means of fixing themselves to an external substrate for the duration of the pre-pupal and pupal period. The 68C glue genes are regulated by the steroid hormone ecdysterone, with the hormone required for both initiation and cessation of gene expression during the third larval instar. Previous work has defined sequences sufficient for expression of abundant levels of Sgs-3 mRNA at the correct time and in the correct tissue. We show here that sequences sufficient for normal tissue- and stage-specific accumulation of Sgs-3 RNA, but adequate only for low levels of expression, lie within 130 bp of the 5' end of the gene, or within the gene.

Lethal mutations flanking the 68C glue gene cluster on chromosome 3 of Drosophila melanogaster.

We have conducted a genetic analysis of the region flanking the 68C glue gene cluster in Drosophila melanogaster by isolating lethal and semilethal mutations uncovered by deficiencies which span this region. Three different mutagens were used: ethyl methanesulfonate (EMS), ethyl nitrosourea (ENU) and diepoxybutane (DEB). In the region from 68A3 to 68C11, 64 lethal, semilethal, and visible mutations were recovered. These include alleles of 13 new lethal complementation groups, as well as new alleles of rotated, low xanthine dehydrogenase, lethal(3)517 and lethal(3)B76. Six new visible mutations from within this region were recovered on the basis of their reduced viability; all proved to be semiviable alleles of lethal complementation groups. No significant differences were observed in the distributions of lethals recovered using the three different mutagens. Each lethal was mapped on the basis of complementation with overlapping deficiencies; mutations that mapped within the same interval were tested for complementation, and the relative order of the lethal groups within each interval was determined by recombination. The cytological distribution of genes within the 68A3-68C11 region is not uniform: the region from 68A2,3 to 68B1,3 (seven to ten polytene chromosome bands) contains at least 13 lethal complementation groups and the mutation low xanthine dehydrogenase; the adjoining region from 68B1,3 to 68C5,6 (six to nine bands) includes the 68C glue gene cluster, but no known lethal or visible complementation groups; and the interval from 68C5,6 to 68C10,11 (three to five bands) contains at least three lethal complementation groups and the visible mutation rotated. The developmental stage at which lethality is observed was determined for a representative allele from each lethal complementation group.

Activity of cefoperazone and two beta-lactamase inhibitors, sulbactam and clavulanic acid, against Bacteroides spp. correlated with beta-lactamase production.

A total of 102 isolates of Bacteroides spp. were studied for beta-lactamase production and susceptibility to cefoperazone alone or in combination with either of the beta-lactamase inhibitors sulbactam and clavulanic acid. The geometric mean minimal inhibitory concentration of cefoperazone alone was 31.5 micrograms/ml and when combined with 10 micrograms of sulbactam per ml or 2 micrograms of clavulanic acid per ml was reduced to 5.4 and 9.2 micrograms/ml, respectively. When bacterial suspensions were tested for beta-lactamase production with nitrocefin, 91 (89.2%) of these isolates produced the enzyme. The geometric mean minimal inhibitory concentrations of cefoperazone rose only slightly for isolates with low or intermediate enzyme activity but rose significantly for those with high activity. The addition of EDTA to cefoperazone significantly more frequently enhanced the activity of cefoperazone against beta-lactamase-negative as opposed to beta-lactamase-positive isolates. Furthermore, EDTA resulted in synergistic activity of the cefoperazone-sulbactam combination on beta-lactamase-positive isolates for which the combination had previously not shown a synergistic effect. This study demonstrates the relationship between beta-lactamase production and the resistance of Bacteroides spp. to cefoperazone and shows that inhibition of these enzymes can reverse this resistance.