Automated management of gene discovery projects

The paper reports on programs, organization and Hypertext Mark-up Language (HTML) presentation provided by the Hierarchical Automated Gene Identification System (HAGIS) designed for managing sequencing projects.

AVAILABILITY

On request from the authors.

CONTACT

st23646@ggr.co.uk

Deaths and injuries due to unexploded ordnance (UXO) in northern Lao PDR (Laos)

Xieng Khousang province in Lao PDR (Laos) is one of the most heavily bombed areas on earth due to the secret bombing during the Vietnam war. This study presents the community-based cumulative incidence of injuries related to unexploded ordnance (UXO) after the war. The data were collected by one of the UK based non-governmental organizations, Mines Advisory Group (MAG). Three districts in the province, reported to have the largest UXO load, were studied. Nearly half of the injuries and deaths involved children below age 15. The case-fatality rate was not different among children and adults. Males were significantly more likely to die of UXO injuries than females. We believe that UXO is an important public health problem in Laos for the following reasons: (1) 22 years after the end of the war, an average of one injury still occurs every other day (2) there is a high incidence among children below age 15 (3) the case-fatality rate is high (4) most injuries involve multiple fragments which usually require complex surgical and medical management skills.

Accretion rate of cosmic spherules measured at the South Pole

Micrometeorites are terrestrially collected, extraterrestrial particles smaller than about 1 mm, which account for most of the mass being accreted to the Earth. Compared with meteorites, micrometeorites more completely represent the Earth-crossing meteoroid complex and should include fragments of asteroids, comets, Mars and our Moon, as well as pre-solar and interstellar grains. Previous measurements of the flux of micrometeoroids that survive to the Earth's surface have large uncertainties owing to the destruction of particles by weathering, inefficiencies in magnetic collection or separation techniques, low particle counts, poor age constraint or highly variable concentrating processes. Here we describe an attempt to circumvent these problems through the collection of thousands of well preserved and dated micrometeorites from the bottom of the South Pole water well, which supplies drinking water for the Scott-Amundsen station. Using this collection, we have determined precise estimates of the flux and mass distribution for 50-700-microm cosmic spherules (melted micrometeorites). Allowing for the expected abundance of unmelted micrometeorites in the samples, our results indicate that about 90% of the incoming mass of submillimetre particles evaporates during atmospheric entry. Our data indicate the loss of glass-rich and small stony spherules from deep-sea deposits, and they provide constraints for models describing the survival probability of micrometeoroids.

19F-NMR and directly coupled HPLC-NMR-MS investigations into the metabolism of 2-bromo-4-trifluoromethylaniline in rat: a urinary excretion balance study without the use of radiolabelling

1. The metabolic fate and urinary excretion of 2-bromo-4-trifluoromethylaniline has been studied in rat using 19F-NMR spectroscopic and directly coupled HPLC-NMR-MS methods. The compound was dosed to Sprague-Dawley rats (50 mg kg-1, i.p.) and urine collected over 0-8, 8-24 and 24-48 h post-dosing. 2. A total urinary recovery of 53.5 +/- 7.0% of the dose was achieved up to 48 h after dosing. The major metabolite in the urine was identified as 2-amino-3-bromo-5-trifluoromethylphenylsulphate accounting for a total of 35.7 +/- 6.2% of the dose. 3. Further metabolites detected were 2-bromo-4-trifluoromethylphenylhydroxylamine-1V-glucuronide (9.7 +/- 0.2% of the dose), 2-bromo-4-trifluoromethylaniline-N-glucuronide (3.0 +/- 0.3%) and 2-amino-3-bromo-5-trifluoromethylphenylglucuronide (2-St 0-4). Minor metabolites, including 2-bromo-4-trifluoromethylphenylhydroxylamine-O-glucuronide, 2-amino-3-bromo-5-trifluoromethylphenol and 2-bromo-4-trifluoromethylphenylsulphamate, in total accounted for 2.3 +/- 0.9% of the dose. 4. Directly coupled HPLC-NMR-MS and 19F-NMR spectroscopy proved to be efficient techniques for the unequivocal and rapid determination of the urinary metabolic fate and excretion balance of fluorinated xenobiotics without the need for radiolabelling.

Comorbid panic disorder and major depression: implications for cognitive-behavioral therapy

Panic disorder and major depression frequently coexist, yet the implications of comorbidity for psychological treatments have rarely been studied. The objective of this study was to evaluate whether pretreatment comorbidity of major depression affects the outcome of cognitive-behavioral treatment (CBT) of panic disorder. Thirty-seven clients who met diagnostic criteria for both panic and major depression participated in 10 sessions of individual CBT for panic. Treatment outcome was contrasted with the outcome of 53 clients having only panic disorder who received the same treatment. The co-occurrence of depression did not adversely affect CBT for panic. These results have implications for clinical practice and theoretical implications for the nature of the relationship between panic and depression.

Identification of the low density lipoprotein receptor-binding site in apolipoprotein B100 and the modulation of its binding activity by the carboxyl terminus in familial defective apo-B100

Familial defective apolipoprotein B100 (FDB) is caused by a mutation of apo-B100 (R3500Q) that disrupts the receptor binding of low density lipoproteins (LDL), which leads to hypercholesterolemia and premature atherosclerosis. In this study, mutant forms of human apo-B were expressed in transgenic mice, and the resulting human recombinant LDL were purified and tested for their receptor-binding activity. Site-directed mutagenesis and other evidence indicated that Site B (amino acids 3,359-3,369) binds to the LDL receptor and that arginine-3,500 is not directly involved in receptor binding. The carboxyl-terminal 20% of apo-B100 is necessary for the R3500Q mutation to disrupt receptor binding, since removal of the carboxyl terminus in FDB LDL results in normal receptor-binding activity. Similarly, removal of the carboxyl terminus of apo-B100 on receptor-inactive VLDL dramatically increases apo-B-mediated receptor-binding activity. We propose that the carboxyl terminus normally functions to inhibit the interaction of apo-B100 VLDL with the LDL receptor, but after the conversion of triglyceride-rich VLDL to smaller cholesterol-rich LDL, arginine-3,500 interacts with the carboxyl terminus, permitting normal interaction between LDL and its receptor. Moreover, the loss of arginine at this site destabilizes this interaction, resulting in receptor-binding defective LDL.

The hierarchic structure of fears

Contemporary theories of fears (and phobias) suggest two kinds of etiologic factors; those common to all fears (factors influencing fear-proneness) and factors specific to particular fears (e.g. specific learning experiences). There also may be etiologic factors of intermediate specificity; factors common to some but not all fears. The present article describes this hierarchic model of fears, which proposes that fears (and phobias) arise from a hierarchy of causal factors, ranging from specific to general. The model is supported by factor-analytic studies of fear inventories and behavioural-genetic studies of twins. However, further research is needed to clarify the number of levels, and to identify environmental, psychobiological, and genetic factors at each level of the causal hierarchy. The hierarchic model of fears represents a call for research. It encourages researchers to take a broad view of etiology by considering factors at various levels of causal specificity.

The structure of posttraumatic stress symptoms

Posttraumatic stress disorder, as defined by the Diagnostic and Statistical Manual of Mental Disorders (3rd ed., rev. and 4th ed.; American Psychiatric Association, 1987, 1994, respectively), is characterized by 17 symptoms, descriptively clustered into 3 groups: (a) intrusions, (b) hyperarousal, and (c) avoidance and numbing. The present study sought to identify the basic dimensions (factors) that underlie these symptoms. Two samples were assessed: 103 victims of motor vehicle accidents and 419 United Nations peacekeepers deployed in Bosnia. A principal axis factor analysis was conducted for each sample. In each sample, 2 correlated factors were obtained, which were very similar across samples. Factor 1 was labeled Intrusions and Avoidance, and Factor 2 represented Hyperarousal and Numbing. These factors loaded on a single higher order factor. The higher order factor accounted for 13% to 38% of variance in symptom severity, and the lower order factors accounted for an additional 8% to 9% of variance. If the authors assume that each factor corresponds to a distinct mechanism (R. B. Cattell, 1978), then the results suggest that posttraumatic stress reactions arise from a general mechanism, with contributions from 2 specific mechanisms.

Adolescents' perceptions of family responsibility-taking

A scale was developed to solicit adolescents' perceptions of their family responsibility-taking (defined as helping out and being supportive). Four hundred adolescents were administered this scale together with self-report measures of intimacy with parents and peers as well as other psychological variables (self-esteem, depression, risk-taking, and drug use). The results revealed that adolescents who felt they assumed more family responsibility reported less depression, more intimate relationships with their parents, and higher self-esteem.

Anxiety sensitivity: multiple dimensions and hierarchic structure

Anxiety sensitivity (AS) is the fear of anxiety-related sensations, based on beliefs that these sensations have harmful consequences. AS is thought to play an important role as a diathesis for anxiety disorders, particularly panic disorder. Recent evidence suggests that AS has a hierarchical structure, consisting of multiple lower-order factors, which load on a single higher-order factor. If each factor corresponds to a discrete mechanism, then the results suggest that AS arises from a hierarchic arrangement of mechanisms. A problem with previous studies is that they were based on the 16-item Anxiety Sensitivity Index (ASI), which may not contain enough items to reveal the type and number of lower-order factors. Accordingly, we developed the 60-item Anxiety Sensitivity Profile, which was administered to 349 university students. Factor analyses revealed four lower-order factors: (1) Fear of respiratory symptoms, (2) fear of cognitive dyscontrol, (3) fear of gastrointestinal symptoms, and (4) fear of cardiac symptoms. These loaded on a single higher-order factor. The lower-order factors shared variance with the higher-order factor, but also contained unique variance. Thus, the results suggest that AS is the product of a general factor, with independent contributions from four specific factors.

The needs of caregivers

Caring for elderly mentally ill people impacts on many aspects of informal caregivers' lives. Respite care is one of the few strategies aimed directly at caregivers and its benefits have been well documented. As part of a wider strategy review of continuing care and respite care for the growing elderly population in an inner London health authority we focused specifically on the needs of caregivers and their elderly dependants with a diagnosis of dementia. A focus group was organised in order to elicit caregivers' perspectives on caring and their views on local services. This component of our overall review highlights the importance of investing further in informal caregivers who, to date, have successfully prevented a large number of admissions to continuing care facilities.

Labor pain is reduced by massage therapy

Twenty-eight women were recruited from prenatal classes and randomly assigned to receive massage in addition to coaching in breathing from their partners during labor, or to receive coaching in breathing alone (a technique learned during prenatal classes). The massaged mothers reported a decrease in depressed mood, anxiety and pain, and showed less agitated activity and anxiety and more positive affect following the first massage during labor. In addition, the massaged mothers had significantly shorter labors, a shorter hospital stay and less postpartum depression.

Two hepatic enhancers, HCR.1 and HCR.2, coordinate the liver expression of the entire human apolipoprotein E/C-I/C-IV/C-II gene cluster

We show that the liver-specific expression of all four genes in the human apolipoprotein (apo) E/C-I/C-IV/C-II gene cluster in transgenic mice is determined by the coordinate action of two distinct hepatic control regions (HCR). These enhancers are positioned 15 kilobases (kb) (HCR.1) and 26 kb (HCR.2) downstream of the apoE gene. To investigate the action of each HCR, transgenic mice were generated with a 70-kb human genomic fragment that contained the complete apoE gene cluster or with this fragment modified by the specific deletion of HCR.1, HCR.2, or both HCR domains. Hepatic expression of all four apolipoprotein genes was observed in transgenic mice in which either HCR.1 or HCR.2 was deleted, but no transgene expression was found in the liver in the absence of both HCR domains. The overall patterns of transgene expression suggested that HCR.2 was the dominant element for apoC-IV and apoC-II expression and that HCR.1 was dominant for the apoE/C-I expression. No liver-specific transcriptional activity was identified for the proximal promoter of any gene in the cluster; all liver-specific activity was associated with HCR.1 and HCR.2. Thus, the HCRs of the apoE gene cluster constitute unique regulatory domains for determining the requirements for apolipoprotein gene expression in the liver.

Educational intervention strategies for children with visual impairments with emphasis on retinopathy of prematurity

Young children with retinopathy of prematurity have many intervention needs. This article discusses the possible causes of retinopathy of prematurity and possible educational problems experienced by these children. In addition, possible intervention strategies are suggested in the areas of language development, social interaction, self-help skills, orientation and mobility, and educational technology as they relate to the needs of young children with retinopathy of prematurity.

A normative study of the maintenance of wakefulness test (MWT)

The maintenance of wakefulness test (MWT) is a daytime polysomnographic procedure which quantifies wake tendency by measuring the ability to remain awake during soporific circumstances. We present normative data based on 64 healthy subjects (27 males and 37 females) who adhered to uniform MWT procedural conditions including polysomnographic montage, illuminance level, seating position, room temperature, meal timing, and subject instructions. When allowed a maximum trial duration of 40 min, subjects' mean sleep latency to the first epoch of sustained sleep was 35.2 +/- 7.9 min. The lower normal limit, defined as two standard deviations below the mean, was 19.4 min. Calculation of data on the basis of a maximum trial duration of 20 min and sleep latency to the first appearance of brief sleep (a microsleep episode or one epoch of any stage of sleep) yielded a mean sleep latency of 18.1 +/- 3.6 min and a lower normal limit of 10.9 min. Sleep latency scores were significantly higher than those previously reported in patients with disorders of excessive somnolence. Therefore, the MWT appears to be a useful procedure in differentiating groups with normal daytime wake tendency from those with impaired wake tendency and in identifying individuals with pathologic inability to remain awake under soporific circumstances.

The effects of respiratory alkalosis and acidosis on net bicarbonate flux along the rat loop of Henle in vivo

We have studied the effects of acute respiratory alkalosis (ARALK, hyperventilation) and acidosis (ARA, 8% CO2), chronic respiratory acidosis (CRA; 10% CO2 for 7-10 days), and subsequent recovery from CRA breathing air on loop of Henle (LOH) net bicarbonate flux (JHCO3) by in vivo tubule microperfusion in anesthetized rats. In ARALK blood, pH increased to 7.6, and blood bicarbonate concentration ([HCO3-]) decreased from 29 to 22 mM. Fractional urinary bicarbonate excretion (FEHCO3) increased threefold, but LOH JHCO3 was unchanged. In ARA, blood pH fell to 7.2, and blood [HCO3-] rose from 28 to 34 mM; FEHCO3 was reduced to < 0.1%, but LOH JHCO3 was unaltered. In CRA, blood pH fell to 7.2, and blood [HCO3-] increased to > 50 mM, whereas FEHCO3 decreased to < 0.1%. JHCO3 was reduced by approximately 30%. Bicarbonaturia occurred when CRA rats breathed air, yet LOH JHCO3 increased (by 30%) to normal. These results suggest that LOH JHCO3 is affected by the blood-to-tubule lumen [HCO3-] gradient and HCO3- backflux. When the usual perfusing solution at 20 nl/min was made HCO3- free, mean JHCO3 was -34.5 +/- 4.4 pmol/min compared with 210 +/- 28.1 pmol/min plus HCO3-. When a low-NaCl perfusate (to minimize net fluid absorption) containing mannitol and acetazolamide (2 x 10(-4) M, to abolish H(+)-dependent JHCO3) was used, JHCO3 was -112.8 +/- 5.6 pmol/min. Comparable values for JHCO3 at 10 nl/min were -35.9 +/- 5.8 and -72.5 +/- 8.8 pmol/min, respectively. These data indicate significant backflux of HCO3-along the LOH, which depends on the blood-to-lumen [HCO3-] gradient; in addition to any underlying changes in active acid-base transport mechanisms, HCO3- permeability and backflux are important determinants of LOH JHCO3 in vivo.

Cognitive restructuring in the treatment of social phobia. Efficacy and mode of action

Cognitive restructuring (CR) is commonly used to treat social phobia, although its contribution to treatment efficacy has not been established. CR requires the person to think about and discuss feared social events with his or her therapist and thus entails some degree of exposure to social stimuli. CR also is thought to enhance the efficacy of therapeutic exposure exercises (EXP). Four predictions were tested based on this model: Relative to a control intervention matched for the exposure inherent in CR, CR is more effective in (1) reducing social phobia, (2) reducing negative social cognitions, (3) increasing positive cognitions, and (4) enhancing the effects of subsequent EXP. People with generalized social phobia (N = 60) were randomly assigned to CR followed by EXP or to a control intervention followed by EXP. Support was found for predictions 1 to 3, but not 4.

Transgenic mice expressing human ApoB95 and ApoB97. Evidence that sequences within the carboxyl-terminal portion of human apoB100 are important for the assembly of lipoprotein

The structural features of apolipoprotein (apo) B that are important for its covalent linkage to apo(a) to form lipoprotein(a) (Lp(a)) are incompletely understood. Although apoB100 cysteine 4326 is required for the disulfide linkage with apo(a), other structural features, aside from a single free cysteine residue, must be important for apoB's initial interaction with apo(a) and for facilitating the formation of the disulfide bond. To determine if sequences carboxyl-terminal to cysteine 4326 affect the efficiency of Lp(a) formation, we used "pop-in, pop-out" gene targeting in a human apoB yeast artificial chromosome to introduce nonsense mutations into exon 29 of the apoB gene. The mutant yeast artificial chromosomes, which coded for the truncated versions of human apoB, apoB95, and apoB97, were then used to express these mutant forms of apoB in transgenic mice. As judged by in vitro assays of Lp(a) formation, apoB95 (4330 amino acids) formed a small amount of Lp(a) but did so slowly. In contrast, apoB97 (4397 amino acids) formed Lp(a) rapidly, although not quite as rapidly as the full-length apoB100 (4536 amino acids). These results were supported by an analysis of double-transgenic mice expressing both human apo(a) and either apoB95 or apoB97. In mice expressing both apoB95 and apo(a), there was only a trace amount of Lp(a) in the plasma, and most of the apo(a) was free, whereas in mice expressing both apoB97 and apo(a), virtually all of the apo(a) was bound to apoB97 in the form of Lp(a). These results show that sequences carboxyl-terminal to apoB95 (amino acids 4331-4536) are not absolutely required for Lp(a) formation, but this segment of the apoB molecule, particularly residues 4331-4397, is necessary for the efficient assembly of Lp(a).

Expression of the neonatal Fc receptor, FcRn, on human intestinal epithelial cells

Maternal IgG is transferred to the suckling mouse and rat through a major histocompatibility complex (MHC) class I-related Fc receptor (FcRn) on the brush border of the proximal small intestine. We have previously described a site on the epithelial surface of the human fetal intestine with IgG binding characteristics similar to FcRn. We report here the identification by reverse transcriptase polymerase chain reaction amplification and sequencing of the human orthologue of rat and mouse FcRn in tissue obtained from human fetal and adult intestine. FcRn protein was detected in adult human intestine by western blot. Immunohistochemical studies of sections of human intestine show that the FcRn is localized mostly to the epithelial cells, where it is in the apical region. These data suggest that the binding of IgG previously seen in the fetal intestine is due to the presence of FcRn. Potential roles for this MHC class I-like Fc receptor in the human intestine include the transfer of passive immunity, induction of oral tolerance, and immunosurveillance.

Dual role of a dileucine motif in insulin receptor endocytosis

Two leucines (Leu986 and Leu987) have recently been shown to take part in the control of human insulin receptor (HIR) internalization (Renfrew-Haft, C., Klausner, R. D., and Taylor, S. I. (1994) J. Biol. Chem. 269, 26286-26294). The aim of the present study was to further investigate the exact mechanism of this control process. Constitutive and insulin-induced HIR internalizations were studied biochemically and morphologically in NIH 3T3 cells overexpressing either a double alanine (amino acid residues 986-987) mutant HIR (HIR AA1) or HIR truncated at either amino acid residue 981 (HIR Delta981) or 1000 (HIR Delta1000). Data collected indicate that: (a) the three mutant HIR show a reduced association with microvilli as compared with HIR wild-type; (b) the two receptors containing the dileucine motif (HIR WT and HIR Delta1000) show the highest propensity to associate with clathrin-coated pits, independently of kinase activation; (c) the two receptors lacking the dileucine motif but containing two tyrosine-based motifs, previously described as participating in clathrin-coated pit segregation, associate with these surface domains with a lower affinity than the two others, (d) in the presence of the kinase domain, an unmasking of the tyrosine-based motifs mediated by kinase activation is required. These results indicate that the dileucine motif is not sufficient by itself, but participates in anchoring HIR on microvilli and that another sequence, located downstream from position 1000 is crucial for this event. This dileucine motif also plays a role in HIR segregation in clathrin-coated pits. This latter function is additive with that of the tyrosine-based motifs but the role of the dileucine motif predominates. Eventually, the clathrin-coated pit anchoring function of the dileucine motif is independent of receptor kinase activation in contrast to the tyrosine-based motifs.

A new dynamic tool to perform assembly of expressed sequence tags (ESTs)

MOTIVATION

Expressed Sequence Tags (ESTs) are short single-pass DNA sequences obtained from either ends of cDNA clones. To exploit these sequences efficiently, a dynamic Web-tool has been developed which uses these data to perform fast virtual cloning of cDNAs.

RESULTS

Starting with a query sequence, the user is able to identify related ESTs and extend the sequence of interest step by step, possibly to a full-length transcript. Graphical views of the clustering are used to monitor the progress of a particular 'cloning' project. Potential open reading frames are detected by positional base preference, and hyperlinks to other Worldwide Web sites allows the user to retrieve information relevant to each EST in a cluster (e.g. sequence traces, clone size, plate position). Apart from cDNA cloning, this tool also provides a mechanism for collating gene families and polymorphism sites.