The influence of neonatal BCG vaccination on in vitro cytokine responses to Plasmodium falciparum

BACKGROUND

Bacillus Calmette-Guérin (BCG) vaccination has off-target protective effects against infections unrelated to tuberculosis. Among these, murine and human studies suggest that BCG vaccination may protect against malaria. We investigated whether BCG vaccination influences neonatal in vitro cytokine responses to Plasmodium falciparum. Blood samples were collected from 108 participants in the Melbourne Infant Study BCG for Allergy and Infection Reduction (MIS BAIR) randomised controlled trial (Clinical trials registration NCT01906853, registered July 2013), seven days after randomisation to neonatal BCG (n = 66) or no BCG vaccination (BCG-naïve, n = 42). In vitro cytokine responses were measured following stimulation with P. falciparum-infected erythrocytes (PfIE) or E. coli.

RESULTS

No difference in the measured cytokines were observed between BCG-vaccinated and BCG-naïve neonates following stimulation with PfIE or E. coli. However, age at which blood was sampled was independently associated with altered cytokine responses to PfIE. Being male was also independently associated with increased TNF-a responses to both PfIE and E. coli.

CONCLUSION

These findings do not support a role for BCG vaccination in influencing in vitro neonatal cytokine responses to P. falciparum. Older neonates are more likely to develop P. falciparum-induced IFN-γ and IFN-γ-inducible chemokine responses implicated in early protection against malaria and malaria pathogenesis.

Fetal fraction-based risk algorithm for non-invasive prenatal testing: screening for trisomies 13 and 18 and triploidy in women with low cell-free fetal DNA

OBJECTIVE

To identify pregnancies at increased risk for trisomy 13, trisomy 18 or triploidy attributable to low fetal fraction (FF).

METHODS

A FF-based risk (FFBR) model was built using data from more than 165 000 singleton pregnancies referred for single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT). Based on maternal weight and gestational age (GA), FF distributions for normal, trisomy 13, trisomy 18 and triploid pregnancies were constructed and used to adjust prior risks for these abnormalities. A risk cut-off of ≥ 1% was chosen to define pregnancies at high risk for trisomy 13, trisomy 18 or triploidy (high FFBR score). The model was evaluated on an independent blinded set of pregnancies for which SNP-based NIPT did not return a result, and for which pregnancy outcome information was gathered retrospectively.

RESULTS

The evaluation cohort comprised 1148 cases, of which approximately half received a high FFBR score. Compared with rates expected based on maternal age (MA) and GA, cases with a high FFBR score had a significantly increased rate of trisomy 13, trisomy 18 or triploidy combined (5.7% vs 0.7%; P < 0.001) and also of unexplained pregnancy loss (14.7% vs 10.4%; P < 0.001). For cases that did not receive a high FFBR score, the incidence of a chromosomal abnormality or pregnancy loss was not significantly different from that expected based on MA and GA. In this study cohort, the sensitivity of the FFBR model for detection of trisomy 13, trisomy 18 or triploidy was 91.4% (95% CI, 76.9-98.2%) with a positive predictive value of 5.7% (32/564; 95% CI, 3.9-7.9%).

CONCLUSIONS

For pregnancies with a FF too low to receive a result on standard NIPT, the FFBR algorithm identified a subset of cases at increased risk for trisomy 13, trisomy 18 or triploidy. For the remainder of cases, the risk of a fetal chromosomal abnormality was unchanged from that expected based on MA and GA. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Extended right hemicolectomy and left hemicolectomy for colorectal cancers between the distal transverse and proximal descending colon

INTRODUCTION

We report our experience with extended right hemicolectomy (ERH) and left hemicolectomy (LH) for the treatment of cancers located between the distal transverse and the proximal descending colon, and compare postoperative morbidity, mortality, pathological results and survival for the two techniques.

METHODS

A retrospective review was performed of a single institution series over ten years. Patients who underwent different operations, had benign disease or received palliative resections were excluded. Data collected were patient demographics, type and duration of surgery, tumour site, postoperative complications and histology results.

RESULTS

Ninety-eight patients were analysed (64 ERHs, 34 LHs). ERH was conducted using an open approach in 93.8% of cases compared with 73.5% for LH. The anastomotic leak rate was similar for both groups (ERH: 6.3%, LH: 5.9%). This was also the case for other postoperative complications, mortality (ERH: 1.6%, LH: 2.9%) and overall survival (ERH: 50.4 months, LH: 51.8 months). All but one patient in the ERH cohort had clear surgical margins. Nodal evaluation for staging was adequate in 78.1% of ERH cases and 58.8% of LH cases.

CONCLUSIONS

In our experience, both ERH and LH are adequate for tumours located between the distal transverse and the proximal descending colon.

The use of infliximab in X-linked agammaglobulinaemia associated enteropathy

Granulomatous small bowel enteropathy is an unusual presentation associated with X-linked agammaglobulinaemia. We present a rare case of this condition that was further complicated by an enterocutaneous fistula and report our experience managing this condition successfully with infliximab, which has not been documented in the literature previously.

Systematic review and meta-analysis of randomized clinical trials of self-expanding metallic stents as a bridge to surgery versus emergency surgery for malignant left-sided large bowel obstruction

Background

Use of self-expanding metallic stents (SEMS) as a bridge to surgery has been suggested as an alternative management for acute malignant left-sided colonic obstruction, as emergency surgery has a high risk of morbidity and mortality. This meta-analysis evaluated high-quality evidence comparing preoperative SEMS with emergency surgery.

Methods

Relevant randomized clinical trials (RCTs) were identified from the Cochrane Central Register of Controlled Trials, MEDLINE, Embase and PubMed (1990–2011). Primary outcomes were primary anastomosis, stoma and in-hospital mortality rates. Secondary outcomes included anastomotic leak, 30-day reoperation and surgical-site infection rates.

Results

Four RCTs with 234 patients were included. Technical and clinical success rates for stenting were 70·7 per cent (82 of 116) and 69·0 per cent (80 of 116) respectively. The clinical perforation rate was 6·9 per cent (8 of 116) and the silent perforation rate 14 per cent (11 of 77). SEMS intervention resulted in significantly higher successful primary anastomosis (risk ratio (RR) 1·58, 95 per cent confidence interval 1·22 to 2·04; P &lt; 0·001) and lower overall stoma (RR 0·71, 0·56 to 0·89; P = 0·004) rates. There was no difference in primary anastomosis, permanent stoma, in-hospital mortality, anastomotic leak, 30-day reoperation and surgical-site infection rates. Three trials were stopped prematurely, one because the emergency surgery group had a significantly increased anastomotic leak rate, and two others because of stent-related complications and increased 30-day morbidity following SEMS management.

Conclusion

Technical and clinical success rates for stenting were lower than expected. SEMS is associated with a high incidence of clinical and silent perforation. However, as a bridge to surgery, SEMS has higher successful primary anastomosis and lower overall stoma rates, with no significant difference in complications or mortality.

Surgical experience with small bowel damage secondary to pelvic radiotherapy

BACKGROUND

Patients undergoing pelvic radiotherapy are at risk of developing radiation enteritis. This study reviewed patients with radiation enteritis referred to a specialist colorectal unit.

METHODS

Patients referred with radiation enteritis secondary to pelvic radiotherapy (July 2001 to July 2005) were analysed regarding: indication, duration, dosage/fractionation of radiotherapy, nutritional/biochemical assessment, investigation, surgery, histopathology, and hospital stay.

RESULTS

Eleven patients underwent pelvic radiotherapy. The median interval between radiotherapy and referral was 17 months. The majority were nutritionally deficient at presentation (haemoglobin < 12 g/l: 91%; magnesium < 0.75 mmol/l: 64%; albumin < 35 g/l: 91%). Eight (73%) patients had either a BMI < 20 or weight loss of >10% within 3 months prior to referral. Radiation enteritis was diagnosed by preoperative radiology, laparotomy and at histopathology. All patients underwent surgery (resection/ilesotomy/bypass) and median post-operative stay was 24 days.

CONCLUSIONS

Radiation enteritis is associated with prolonged symptoms. Majority of patients are undernourished and despite nutritional support a high morbidity is noted.

Probiotics for induction of remission in ulcerative colitis

BACKGROUND

Ulcerative Colitis (UC) is an inflammatory condition affecting the colon with an incidence of approximately 10-20 per 100,000 per year. No existing intervention is effective in all patients with a proportion requiring colectomy. There are significant proportion of patients who experience adverse effects with current therapies. Consequently, new alternatives for the treatment of UC are constantly being sought. Probiotics are live microbial feed supplements that may beneficially affect the host by improving intestinal microbial balance, enhancing gut barrier function and improving local immune response.

OBJECTIVES

To assess the efficacy of probiotics compared with placebo or standard medical treatment (5-aminosalicylates, sulfasalazine or corticosteroids) for the induction of remission in active ulcerative colitis.

SEARCH STRATEGY

A comprehensive search for relevant randomised controlled trials (RCT's) was carried out using MEDLINE (1966-January 2006), EMBASE (January 1985- 2006) and CENTRAL. The Cochrane IBD/FBD Review Group Specialised Trials Registrar was also searched. The Australasian Medical Index, Chinese Biomedical Literature Database, Latin American Caribbean Health Sciences Literature (LILACS), and the Japan Information Centre of Science and Technology File on Science, Technology and Medicine (JICST-E) were also used to identify abstracts. Conference proceedings from the Falk Symposium, Digestive Disease Week (DDW) and the United European Digestive Disease week were hand-searched. Authors of relevant studies and drug companies were contacted regarding ongoing or unpublished trials that may be relevant to the review.

SELECTION CRITERIA

Randomised controlled trials investigating the effectiveness of probiotics compared to standard treatments in the induction of remission of active ulcerative colitis

DATA COLLECTION AND ANALYSIS

Two authors independently assessed trial quality and extracted data for analysis. Data were analysed using RevMan 4.2.7. A formal meta-analysis was not preformed due to differences in probiotics, outcomes and trial methodology.

MAIN RESULTS

None of the included studies reported any statistically significant differences in remission or clinical improvement rates between probiotic and placebo or active comparator groups.

AUTHORS' CONCLUSIONS

Conventional therapy combined with a probiotic does not improve overall remission rates in patients with mild to moderate ulcerative colitis. However, there is limited evidence that probiotics added to standard therapy may provide modest benefits in terms of reduction of disease activity in patients with mild to moderately severe ulcerative colitis. Whether probiotics are as effective in patients with severe and more extensive disease and whether they can be used as an alternative to existing therapies is unknown. Further well designed, larger randomised controlled trials are needed to determine whether probiotics can be used as an alternative to current treatment modalities.

Potential gene sequence isolation and regional mapping in human chromosome 21

The transcription start sites of many genes are associated with CpG-rich DNA regions (CpG islands) containing clusters of rare cutting, methylation-sensitive restriction enzyme sites [Bird, 1986]. To detect gene sequences from human chromosome 21, we have screened cloned DNA fragments from a chromosome 21-specific cosmid library for the presence of such restriction sites. Several DNA fragments containing rare cutter sites, including Sac II, were isolated and five of them partially characterized. The average insert size of the fragments was 38.4 kb. By using a panel of somatic cell hybrids, one insert was assigned to the distal part of region 21q21, three fragments to the region 21q22.1, and one sequence to the segment 21q22.2-22.3. Restriction mapping showed clusters of rare cutter sites in at least three of the cloned fragments, suggesting the presence of CpG islands. These fragments are thus good candidates for carriers of coding sequences.

Predicting pathway perturbations in Down syndrome

Comparative annotation of human chromosome 21 genomic sequence with homologous regions of mouse chromosomes 16, 17 and 10 has identified 170 orthologous gene pairs. Functional annotation of these genes, based on literature reports and computationally-derived predictions, shows that a broad range of cellular processes are represented. A goal of Down syndrome research is to determine which of these processes are perturbed by overexpression of chromosome 21 genes, and which may, therefore, contribute to the cognitive deficits that characterize Down syndrome. Eleven chromosome 21 genes are annotated to interact with or be affected by components of the MAP Kinase pathway and eight are involved in Ca2+/calcineurin signaling. Both pathways are critical for normal neurological function, and consequently their perturbations are proposed as candidates for phenotypic relevance. We present evidence suggesting that the MAP Kinase pathway is perturbed in the Ts65Dn mouse model of Down syndrome at 4-6 months of age. Analysis is complicated by the observation that overexpression of chromosome 21 genes in trisomy may be affected by method of detection, organism, tissue or brain region, and/or developmental age.

What is the problem with breast-feeding? A qualitative analysis of infant feeding perceptions

AIMS AND OBJECTIVES

Breast-feeding rates are low in Northern Ireland (NI) compared with other regions of Europe. The aim of this study has therefore been to define and explore factors determining infant feeding decisions with a view to the planning of future research and intervention needs.

METHOD

Participants were approached at convenience from the throughput of women attending a large teaching hospital antenatal clinic to take part in focus group discussion.

RESULTS

Dominant themes indicated that the main barriers to breast-feeding are restricted freedom and independence associated with family issues, return to work, societal embarrassment and perceived social isolation. The dialogue suggested that breast-feeding leads to inability to carry out everyday activities and social exclusion.

CONCLUSIONS

Incompatible social norms make it difficult for mothers to breast-feed successfully. This implies that future promotional efforts should take a societal approach.

Pneumatosis coli, a benign form of necrotising enterocolitis

Necrotising enterocolitis (NEC) is the most common acquired gastrointestinal emergency in neonates. Presence of pneumatosis intestinalis is taken as evidence of definite NEC. A distinctive but rare form of NEC called "pneumatosis coli" has been described, presenting with gross blood in stools and minimal or absent local and systemic signs. Radio-graph characteristically reveal isolated colonic pneumatosis without small bowel involvement. Pneumatosis coli has a more benign course compared with definite NEC. Total parenteral nutrition, antibiotics, an appropriate duration off feeds and close observation remain the corner stones of therapy assuring a benign course.

Omental and extraperitoneal abscesses complicating cholecystocolic fistula

BACKGROUND

Acute cholecystitis resolves with conservative treatment in most patients, but empyema or perforation of an ischaemic area may develop, resulting in a pericholecystic abscess, bile peritonitis or a cholecysto-enteric fistula.

CASE OUTLINE

A 63-year-old man presented with extraperitoneal and omental abscess formation complicating a cholecystocolic fistula secondary to gallbladder disease. Histological examination of the gallbladder and omentum showed xanthogranulomatous inflammation.

CONCLUSION

A detailed literature review failed to demonstrate a previous report of this combination of rare complications of gallbladder disease.

Phylogenetic comparison of the pre-mRNA adenosine deaminase ADAR2 genes and transcripts: conservation and diversity in editing site sequence and alternative splicing patterns

Adenosine deaminase that acts on RNA -2 (ADAR2) is a member of a family of vertebrate genes that encode adenosine (A)-to-inosine (I) RNA deaminases, enzymes that deaminate specific A residues in specific pre-mRNAs to produce I. Known substrates of ADAR2 include sites within the coding regions of pre-mRNAs of the ionotropic glutamate receptors, GluR2-6, and the serotonin receptor, 5HT2C. Mammalian ADAR2 expression is itself regulated by A-to-I editing and by several alternative splicing events. Because the biological consequences of ADAR2 function are significant, we have undertaken a phylogenetic comparison of these features. Here we report a comparison of cDNA sequences, genomic organization, editing site sequences and patterns of alternative splicing of ADAR2 genes from human, mouse, chicken, pufferfish and zebrafish. Coding sequences and intron/exon organization are highly conserved. All ADAR2 genes show evidence of transcript editing with required sequences and predicted secondary structures very highly conserved. Patterns and levels of editing and alternative splicing vary among organisms, and include novel N-terminal exons and splicing events.

Longitudinal analyses of chest radiographs from the European Carbon Black Respiratory Morbidity Study

High levels of exposure to carbon black have been linked with an increased prevalence of chest radiograph abnormalities. However, it is unclear to what extent current levels of exposure in the carbon black manufacturing industry are associated with new cases of and progression in small opacities. Longitudinal analyses were carried out on data from workers in the European carbon black manufacturing industry who provided three full-size chest radiographs sequentially between 1987-1995. All chest radiographs were independently read by three experienced readers according to the International Labour Organisation (ILO) classification. After exclusion of participants with previous lung diseases or injuries, females, unreadable chest radiographs and from factories with a low participation rate, data from 675 workers were available for the longitudinal analyses. An association was observed between cumulative carbon black exposure and new cases of chest radiograph abnormalities (ILO category > or = 1/0) and progression in small opacities. These associations were mainly related to changes in chest radiographs from workers at one factory. A large percentage of workers with chest radiograph abnormalities reversed to normal chest films; however, after adjusting for other factors, this was not associated with levels of exposure to carbon black dust. In conclusion, the results show that exposure to carbon black is associated with increased risk of chest radiographic abnormalities, which may be reversible after reduction or cessation of exposure.

[New forms of gene transcripts in human and mouse intersectin]

New human and mouse cDNAs which are homologous to human intersectin gene (ITSN) mapped on a q22.1-22.2 region of human chromosome 21 have been obtained. ITSN gene structure has been determined using nucleotide sequences of human chromosome 21 presented in nucleotide's data bases. The analysis of human and mouse ITSN gene transcripts revealed that their pre-mRNA splicing could occur in different ways. New form of ITSN gene transcripts with alternatively spliced SH3C domain (exon 25 and 26) was detected in different human and mouse tissues. The other splice form with absence of exons 6-14 that results in reading frame shift and stop-codon formation was identified in the mouse adult lung and kidney. In addition, we showed alternative splicing of exons 20, 25 and part of exon 6.

Evolutionary breakpoints on human chromosome 21

Segments of the long arm of human chromosome 21 are conserved, centromere to telomere, in mouse chromosomes 16, 17, and 10. There have been 28 genes identified in human chromosome 21 between TMPRSS2, whose orthologue is the most distal gene mapped to mouse chromosome 16, and PDXK, whose orthologue is the most proximal gene mapped to mouse chromosome 10. Only 6 of these 28 genes have been mapped in mouse, and all are located on chromosome 17. To better define the chromosome 17 segment and the 16 to 17 transition, we used a combination of mouse radiation hybrid panel mapping and physical mapping by mouse: human genomic sequence comparison. We have determined the mouse chromosomal location of an additional 12 genes, predicted the location of 7 more,and defined the endpoints of the mouse chromosome 17 region. The mouse chromosome 16/chromosome 17 evolutionary breakpoint is between human genes ZNF295 and UMODL1, showing there are seven genes in the chromosome 16 segment distal to Tmprss2. The chromosome 17/chromosome 10 breakpoint seems to have involved a duplication of the gene PDXK, which on chromosome 21 lies immediately distal to the KIAA0179 gene. These data suggest that there may be as few as 21 functional genes in the mouse chromosome 17 segment. This information is important for defining existing and constructing more complete mouse models of Down syndrome.

Ts65Dn -- localization of the translocation breakpoint and trisomic gene content in a mouse model for Down syndrome

Fluorescent in situ hybridization (FISH) -- using mouse chromosome paints, probes for the mouse major centromeric satellite DNA, and probes for genes on chromosomes (Chr) 16 and 17 -- was employed to locate the breakpoint in a translocation used to produce a mouse model for Down syndrome. The Ts65Dn trisomy is derived from the reciprocal translocation T(16;17)65Dn. The Ts65Dn mouse carries a marker chromosome containing the distal segment of Chr 16, a region that shows linkage conservation with human Chr 21, and the proximal end of Chr 17. This chromosome confers trisomy for most of the genes in the Chr 16 segment and Ts65Dn mice show many of the phenotypic features characteristic of Down syndrome. We used FISH on metaphase chromosomes from translocation T65Dn/+ heterozygotes and Ts65Dn mice to show that the Chr 17 breakpoint is distal to the heterochromatin of Chr 17, that the Ts65Dn marker chromosome contains a small portion of Chr 17 euchromatin, that the Chr 16 breakpoint lies between the Ncam2 and Gabpa/App genes, and that the Ts65Dn chromosome contains >80% of the human Chr 21 homologs. The significance of this finding is discussed in terms of the utility of this mouse model.

Respiratory health effects from exposure to carbon black: results of the phase 2 and 3 cross sectional studies in the European carbon black manufacturing industry

OBJECTIVES

To assess respiratory morbidity over several cross sectional phases in the European carbon black manufacturing industry.

METHODS

Participants completed an amended (and translated) MRC respiratory morbidity questionnaire with additional questions on previous exposures, job history, etc, and spirometry traces in each phase. Concurrent with the health outcome measures, personal exposure to inhalable dust was measured.

RESULTS

Percentage participation rose from 90% in phase 2 (19 factories) to 95% in phase 3 (16 factories). Exposure dropped slightly between the 2 and 3 phases; as did the prevalence of reporting symptoms. Percentage of predicted lung function volumes exceeded 100% for forced expired volume in 1 second (FEV(1)) and forced vital capacity (FVC), whereas forced mid-expiratory flow (FEF(25%-75%)) and FEV(1)/FVC ratio were below 100% in both phases. The multiple linear and logistic regressions showed that carbon black had a significant effect on lung function and on most respiratory symptoms, respectively.

CONCLUSION

Both current and cumulative exposure to carbon black have a deleterious effect on respiratory morbidity. Due to the drop in exposure between phases 2 and 3, recent exposures seem to have less of an impact on the respiratory morbidity in the workers in phase 3 than those in phase 2.

Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history

One of the evolutionary mechanisms for acquisition of novel functional sequences can be domestication of exogenous retroviruses that have been integrated into the germ line. The whole genome mapping of such elements in various species could reveal differences in positions of the retroviral integration and suggest possible roles of these differences in speciation. Here, we describe the number, locations and sequence features of the human endogenous retrovirus HERV-K (HML-2) long terminal repeat (LTR) sequences on human chromosome 21. We show that their distribution along the chromosome is not only non-random but also roughly correlated with the gene density. Amplification of orthologous LTR sites from a number of primate genomes produced patterns of presence and absence for each LTR sequence and allowed determination of the phylogenetic ages and evolutionary order of appearance of individual LTRs. The identity level and phylogenetic age of the LTRs did not correlate with their map locations. Thus, despite the non-random distribution of LTRs, they have apparently been inserted randomly into the chromosome relative to each other. As evidenced in previous studies of chromosomes 19 and 22, this is a characteristic of HERV-K integration.

Genomic sequence analysis tools: a user's guide

The wealth of information from various genome sequencing projects provides the biologist with a new perspective from which to analyze, and design experiments with, mammalian systems. The complexity of the information, however, requires new software tools, and numerous such tools are now available. Which type and which specific system is most effective depends, in part, upon how much sequence is to be analyzed and with what level of experimental support. Here we survey a number of mammalian genomic sequence analysis systems with respect to the data they provide and the ease of their use. The hope is to aid the experimental biologist in choosing the most appropriate tool for their analyses.

A cohort mortality study of U.K. carbon black workers, 1951-1996

BACKGROUND

Carbon black, a powdered form of elemental carbon is used in the manufacture of rubber products, paints, plastics, and inks. In 1974, the Health and Safety Executive initiated a cohort mortality study on possible carcinogenic effects on carbon black workers.

METHODS

The mortality of a cohort of 1,147 male manual workers from five U.K. factories manufacturing carbon black was investigated for the period 1951-1996. All subjects were employed in the carbon black industry for 12 months or more, and all were first employed before 1975. Limited work histories were used to calculate estimates of individual cumulative exposure to carbon black, using a job-exposure matrix derived by the study team.

RESULTS

Based on serial rates for the general population of England and Wales, significantly elevated mortality was observed in the main study cohort for all causes (Obs 372, Exp 328.7, SMR 113, P < 0.05) and for lung cancer (Obs 61, Exp 35.3, SMR 173, P < 0.001). There were highly elevated lung cancer SMRs at two of the factories, and unexceptional SMRs at the remaining three factories. There was no indication of lung cancer SMRs increasing with period from first employment. Poisson regression analyses failed to find significant trends of lung cancer risks increasing either with cumulative exposure to carbon black (4 levels) or with duration of employment at the participating factories (4 levels).

CONCLUSIONS

Confident interpretation of the elevated SMRs found for lung cancer in two of the factory subcohorts is not possible but the study has been unable to link cumulative exposure to carbon black with elevated risks of lung cancer.

Determinants of inhalable dust exposure in the European carbon black manufacturing industry

A large study to investigate the respiratory health effects of occupational exposure to carbon black in the European carbon black manufacturing industry commenced in 1987. During the study, a large amount of personal occupational exposure data was collected. This article describes the empirical models used to study the determinants of inhalable dust exposure, using data from 16 factories collected in the third and last cross-sectional phase of this study. Information on activities during the measurements was collected using short job category-specific questionnaires. In addition, questionnaires were completed by factory representatives on the implementation of control measures and changes in production process since the first cross-sectional phase. Mixed effects analyses of variance models were used to identify determinants of exposure, while taking into account the within- and between-worker (random) variance components. The results of these models show that, for any job category, factory is a strong predictor of exposure in this industry. These differences could not be explained entirely by factors such as age of the factory or the control measures implemented since the first phase of the study. Surprisingly, implementation of local exhaust ventilation systems had an effect that was counterintuitive; for example, in warehouses where local exhaust ventilation systems had been implemented, higher dust exposure levels were found compared to those where such control measures had not been installed since the first cross-sectional survey. Season appeared to have some effect on exposure for some job titles, with generally relatively low exposures being found in the summer. Finally, a number of activities were identified that caused higher levels of dust exposure, most notably "changing of filters" and "clean-up of carbon black spills."

The sequence of human chromosome 21 and implications for research into Down syndrome

The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of the major mouse models of Down syndrome, suggest how the chromosome sequence may help in understanding the complex Down syndrome phenotype.

Transcription factor GATA-2 gene is located near 3q21 breakpoints in myeloid leukemia

Rearrangements affecting chromosome band 3q21 are observed in a subgroup of patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). However, little is known about the molecular consequences of such aberrations. We therefore established a PAC contig in the 3q21 breakpoint region and identified potential protein coding sequences by exon trapping. One of the exons isolated was from the human GATA-2 gene, which we showed to be transcribed from telomere to centromere. The majority of 3q21 breakpoints are located telomeric to the transcribed portion of this gene in a region that in mice appears to be necessary for proper promoter function. Results of GATA-2 expression analyses in leukemic cell lines as well as primary patient samples are compatible with the hypothesis that 3q21 aberrations contribute to leukemogenesis through deregulation of the hematopoietic transcription factor GATA-2.

Trends in levels of inhalable dust exposure, exceedance and overexposure in the European carbon black manufacturing industry

In an attempt to investigate the relationship between exposure to carbon black and respiratory morbidity, a study of the complete carbon black manufacturing industry in Western Europe was commissioned. As part of this study, a large number of personal inhalable (n=8015) dust exposure measurements was taken during three phases of data collection between 1987 and 1995. Repeated measurements on the same worker were taken in the last two phases, which enabled the estimation of the within- and between-worker components of variance. Simultaneously, the fixed effects of phase and factory were estimated using mixed-effects analysis of variance. The results show that the personal inhalable dust exposure has reduced significantly since the first phase of the study. In addition, the interaction term between phase and factory was significant in most job categories, confirming that the reduction of exposure was not equal across all factories. When all factories were considered together, the probability that the mean exposure of a randomly selected worker (overexposure) or the probability that the exposure on a randomly selected day for a randomly selected worker (exceedance) was higher than 3.5mg m(-3), was 10% or less for all job categories in the last phase. However, when the factories were considered separately, it appeared that the probability of overexposure or exceedance was in excess of 10% for the job categories 'Fitter/Welder', 'Warehouseman' and 'Site crew' for a number of factories. Therefore, even though exposure levels of inhalable dust have dropped considerably across the whole carbon black manufacturing industry in Western Europe, further reductions in exposure levels are required in these areas to make sure that the probability of overexposure and exceedance falls below a level of 10%.

Comparative analysis of the RED1 and RED2 A-to-I RNA editing genes from mammals, pufferfish and zebrafish

One type of RNA editing involves the deamination of adenosine (A) residues to inosines (I) at specific sites in specific pre-mRNAs. These inosines are subsequently read as guanosines by the ribosome, with potentially significant consequences for protein sequence. In mammals, two such A-to-I RNA editases are RED1, which edits some serotonin and glutamate receptors, and RED2, with unidentified substrates. To study the evolutionary conservation among these editases, we have isolated homologous genes from the Japanese pufferfish, Fugu rubripes. Fugu has two genes homologous to Red1 that are similar in size and organization and that show a fivefold compaction relative to the human gene; they differ, however, in their base compositional features. The Fugu gene for RED2 is unusually large, spanning more than 50kb; within the largest intron, there is evidence for a novel gene on the opposite strand. Because of these unusual features, the partial genomic structure was determined for the mouse RED2 gene. A partial cDNA for RED1 was also isolated from zebrafish. Comparisons between fish and between fish and mammals of the protein sequences show that the catalytic domains are highly conserved for each gene, while the RNA-binding domains vary within a single protein in their levels of conservation. Different levels of conservation among domains of different functional roles may reflect differences in editase substrate specificity and/or substrate sequence conservation.

Comparative analysis of the DRADA A-to-I RNA editing gene from mammals, pufferfish and zebrafish

The DRADA gene in mammals encodes an A-to-I RNA editase, an adenosine deaminase that acts on pre-mRNAs to produce site specific inosines. DRADA has been shown to deaminate specific adenosine residues in a subset of glutamate and serotonin receptors, and this editing results in proteins of altered sequences and functional properties. DRADA thus plays a role in creating protein diversity. To study the evolutionary significance of this gene, we have characterized the genomic structure of DRADA from Fugu rubripes, and compared the protein sequences of DRADA from mammals, pufferfish and zebrafish. The DRADA gene from Fugu is three-fold compacted with respect to the human gene, and contains a novel intron within the large second coding exon. DRADA cDNAs were isolated from zebrafish and a second pufferfish, Tetraodon fluviatilis. Comparisons among fish, and between fish and mammals, of the protein sequences show that the catalytic domains are highly conserved for each gene, while the RNA binding domains vary within a single protein in their levels of conservation. Conservation within the Z DNA binding domain has also been assessed. Different levels of conservation among domains of different functional roles may reflect differences in editase substrate specificity and/or substrate sequence conservation.

The DNA sequence of human chromosome 21

Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.

Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21

To establish criteria for and the limitations of novel gene identification, to identify novel genes of potential relevance to Down Syndrome and to investigate features of genome organization, 6. 550kb. In total, 41 novel gene models were predicted, and for a subset of these, RT-PCR experiments helped to verify and refine the models, and were used to assess expression in early development and in adult brain regions of potential relevance to Down syndrome. Results suggest generally low and/or restricted patterns of expression, and also reveal examples of complex alternative processing, especially in brain, that may have important implications for regulation of protein function. Analysis of complete gene structures of the known genes identified a number of very large introns, a number of very short intergenic distances, and at least one potentially bi-directional promoter. At least 3/4 of known genes and 1/2 of predicted genes are associated with CpG islands. For novel genes, three cases of overlapping genes are predicted. Results of these analyses illustrate some of the complexities inherent in mammalian genome organization and some of the limitations of current sequence analysis technologies. They also doubled the number of potential genes within the region.

Gene expression relevant to Down syndrome: problems and approaches

The long arm of human chromosome 21 likely contains several hundred genes. To determine which of these are responsible for specific aspects of the Down Syndrome phenotype, protein functional analysis coupled to phenotypic analysis of transgenic mice will be required. Because such experiments are both time consuming and expensive, prioritizing 21q genes for further studies would be advantageous. Here, we discuss expression analysis, specifically the use of Northern analysis, cDNA array screening and RNA tissue in situ hybridization to assess place and time of expression of forty-two genes. For a subset of these, over expression in normal versus trisomy cell lines and mouse tissues is discussed. Lastly, several examples of alternative processing and their potential for generation of brain specific proteins are described. Together, these experiments give information on time, place and level of expression of a number of 21q genes and suggest some interesting candidates worth further investigation for relevance to Down Syndrome. These data also illustrate the complexities and ambiguities inherent in interpretation and use of expression information.

Risk factors for bronchial hyperresponsiveness in workers exposed to acid anhydrides

Risk factors for bronchial hyperresponsiveness have previously been established in the general community. In settings where occupational asthma is a risk, it has not been established whether occupational sensitization or measures of exposure are important. Bronchial responsiveness to histamine was measured in a cohort of 506 workers exposed to acid anhydrides. Skin-prick tests were performed with conjugates of phthalic, maleic and trimellitic anhydride with human serum albumin and with common inhalant allergens. Employment and smoking histories were recorded. Occupational exposure was measured using personal air samplers and estimates of past exposure made by retrospective exposure assessment. Three hundred and seventy workers (73%) had bronchial responsiveness measured (median age 39 yrs, range 18-77) and 46 (12%) of these were hyperresponsive (provocative dose causing a 20% fall in forced expiratory volume in one second (FEV1; PD20) < or = 8 micromol). Twelve (3%) of these responsive workers had a skin-prick test reaction to an acid anhydride conjugate, 124 (34%) to a common inhalant allergen, and 148 (40%) were current smokers. Multivariate analysis showed that occupational sensitization, sensitization to a common inhalant allergen, age, and pack-years of smoking were independent risk factors for bronchial hyperresponsiveness. Of these only occupational sensitization was completely independent of baseline FEV1. It is concluded that sensitization to acid anhydrides is a significant risk factor for bronchial hyperresponsiveness. However, measures of personal acid anhydride exposure were not associated with bronchial hyperresponsiveness.

Human phosphoribosylformylglycineamide amidotransferase (FGARAT): regional mapping, complete coding sequence, isolation of a functional genomic clone, and DNA sequence analysis

Purines play essential roles in many cellular functions, including DNA replication, transcription, intra- and extra-cellular signaling, energy metabolism, and as coenzymes for many biochemical reactions. The de-novo synthesis of purines requires 10 enzymatic steps for the production of inosine monophosphate (IMP). Defects in purine metabolism are associated with human diseases. Further, many anticancer agents function as inhibitors of the de-novo biosynthetic pathway. Genes or cDNAs for most of the enzymes comprising this pathway have been isolated from humans or other mammals. One notable exception is the phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which encodes the fourth step of this pathway. This gene has been cloned from numerous microorganisms and from Drosophila melanogaster and C. elegans. We report here the identification of a human cDNA containing the coding region of the FGARAT mRNA and the isolation of a P1 clone that contains an intact human FGARAT gene. The P1 clone corrects the purine auxotrophy and protein deficiency of Chinese hamster ovary (CHO) cell mutants (AdeB) deficient in both the activity and the protein for FGARAT. The P1 clone was used to regionally map the FGARAT gene to chromosome region 17p13, a location consistent with our prior assignment of this gene to chromosome 17. A comparison of the DNA sequence of the human FGARAT and FGARAT DNA sequence from 17 other organisms is reported. The isolation of this gene means that DNA clones for all the 10 steps of IMP synthesis have been isolated from humans or other mammals.

Assessment of the sensitivity of the relation between current exposure to carbon black and lung function parameters when using different grouping schemes

BACKGROUND

Equations using variance components in exposure data to predict attenuation and standard error of exposure--response slopes have been published recently. However, to date, no comparisons have been made between results of applying these equations to a real data set with the exposure-response relations estimated directly.

METHODS

Data on lung function parameters and personal inhalable and respirable dust exposure levels from the European carbon black respiratory health study were used. The predicted attenuation and standard error of the relation between current inhalable and respirable dust levels and lung function parameters (FVC and FEV(1)) were calculated for various exposure grouping schemes. These results were compared with the observed exposure-response relations. Workers were grouped by Job Category, the combination of factory and Job Category and five a posteriori created Exposure Groups. In addition, the individual approach was also used, as exposure data were available for each worker.

RESULTS

The rank orders of the coefficients from the regression analyses using the different grouping schemes were similar to those predicted by the equations, although the differences were larger than predicted. When using inhalable dust exposure, the predicted standard errors of the exposure-response slopes were slightly lower than those estimated directly; for respirable dust the predicted standard errors were about a factor two to three smaller than those from the regression analyses. When considering FVC, the predicted exposure-response relations were all statistically significant, whilst the observed relation was only significant when using the five a posteriori Exposure Groups. When reviewing the relations between dust exposure and level of FEV(1), all relations were statistically significant, with the exception of the (observed) relation between respirable dust and FEV(1), when the individual approach was used.

CONCLUSIONS

Using different grouping schemes for estimating exposure can have large effects on the slope and standard error of the exposure-response relation. It is, therefore, important that the effect of the different grouping schemes on the level and precision of the exposure-response slope be estimated. Despite violation of most of the assumptions when applying the equations to predict attenuation and the standard error of the exposure-response slope, the similarities in predicted and observed exposure-response relations and standard errors are indicative of the robustness of these equations. Therefore, the equations appear to be a useful tool in establishing the most efficient way of utilizing exposure measurements.

Benign neoplastic polyp of the caecum as a rare cause of intussusception in adults

Images

Juxta-centromeric region of human chromosome 21 is enriched for pseudogenes and gene fragments

A physical map including four pseudogenes and 10 gene fragments and spanning 500 kb in the juxta-centromeric region of the long arm of human chromosome 21 is presented. cDNA fragments isolated from a selected cDNA library were characterized and mapped to the 831B6 YAC and to two BAC contigs that cover 250 kb of the region. An 85 kb genomic sequence located in the proximal region of the map was analyzed for putative exons. Four pseudogenes were found, including psiIGSF3, psiEIF3, psiGCT-rel whose functional copies map to chromosome 1p13, chromosome 2 and chromosome 22q11, respectively. The TTLL1 pseudogene corresponds to a new gene whose functional copy maps to chromosome 22q13. Ten gene fragments represent novel sequences that have related sequences on different human chromosomes and show 97-100% nucleotide identity to chromosome 21. These may correspond to pseudogenes on chromosome 21 and to functional genes in other chromosomes. The 85 kb genomic sequence was analyzed also for GC content, CpG islands, and repetitive sequence distribution. A GC-poor L isochore spanning 40 kb from satellite 1 was observed in the most centromeric region, next to a GC-rich H isochore that is a candidate region for the presence of functional genes. The pericentric duplication of a 7.8 kb region that is derived from the 22q13 chromosome band is described. We showed that the juxta-centromeric region of human chromosome 21 is enriched for retrotransposed pseudogenes and gene fragments transferred by interchromosome duplications, but we do not rule out the possibility that the region harbors functional genes also.

Haploinsufficiency of CBFA2 causes familial thrombocytopenia with propensity to develop acute myelogenous leukaemia

Familial platelet disorder with predisposition to acute myelogenous leukaemia (FPD/AML, MIM 601399) is an autosomal dominant disorder characterized by qualitative and quantitative platelet defects, and propensity to develop acute myelogenous leukaemia (AML). Informative recombination events in 6 FPD/AML pedigrees with evidence of linkage to markers on chromosome 21q identified an 880-kb interval containing the disease gene. Mutational analysis of regional candidate genes showed nonsense mutations or intragenic deletion of one allele of the haematopoietic transcription factor CBFA2 (formerly AML1) that co-segregated with the disease in four FPD/AML pedigrees. We identified heterozygous CBFA2 missense mutations that co-segregated with the disease in the remaining two FPD/AML pedigrees at phylogenetically conserved amino acids R166 and R201, respectively. Analysis of bone marrow or peripheral blood cells from affected FPD/AML individuals showed a decrement in megakaryocyte colony formation, demonstrating that CBFA2 dosage affects megakaryopoiesis. Our findings support a model for FPD/AML in which haploinsufficiency of CBFA2 causes an autosomal dominant congenital platelet defect and predisposes to the acquisition of additional mutations that cause leukaemia.