A genomic approach to gene fusion technology

Gene expression profiling provides powerful analyses of transcriptional responses to cellular perturbation. In contrast to DNA array-based methods, reporter gene technology has been underused for this application. Here we describe a genomewide, genome-registered collection of Escherichia coli bioluminescent reporter gene fusions. DNA sequences from plasmid-borne, random fusions of E. coli chromosomal DNA to a Photorhabdus luminescens luxCDABE reporter allowed precise mapping of each fusion. The utility of this collection covering about 30% of the transcriptional units was tested by analyzing individual fusions representative of heat shock, SOS, OxyR, SoxRS, and cya/crp stress-responsive regulons. Each fusion strain responded as anticipated to environmental conditions known to activate the corresponding regulatory circuit. Thus, the collection mirrors E. coli's transcriptional wiring diagram. This genomewide collection of gene fusions provides an independent test of results from other gene expression analyses. Accordingly, a DNA microarray-based analysis of mitomycin C-treated E. coli indicated elevated expression of expected and unanticipated genes. Selected luxCDABE fusions corresponding to these up-regulated genes were used to confirm or contradict the DNA microarray results. The power of partnering gene fusion and DNA microarray technology to discover promoters and define operons was demonstrated when data from both suggested that a cluster of 20 genes encoding production of type I extracellular polysaccharide in E. coli form a single operon.

Violence risk prediction. Clinical and actuarial measures and the role of the Psychopathy Checklist

BACKGROUND

Violence risk prediction is a priority issue for clinicians working with mentally disordered offenders.

AIMS

To review the current status of violence risk prediction research.

METHOD

Literature search (Medline). Key words: violence, risk prediction, mental disorder.

RESULTS

Systematic/structured risk assessment approaches may enhance the accuracy of clinical prediction of violent outcomes. Data on the predictive validity of available clinical risk assessment tools are based largely on American and North American studies and further validation is required in British samples. The Psychopathy Checklist appears to be a key predictor of violent recidivism in a variety of settings.

CONCLUSIONS

Violence risk prediction is an inexact science and as such will continue to provoke debate. Clinicians clearly need to be able to demonstrate the rationale behind their decisions on violence risk and much can be learned from recent developments in research on violence risk prediction.

Effect of hand sanitizer use on elementary school absenteeism

BACKGROUND

Several studies have indicated a connection between handwashing and illness-related absenteeism in school settings. The difficulty of ensuring consistent and effective handwashing among student populations has also been noted. The purpose of this study was to assess the effectiveness of the use of an alcohol gel hand sanitizer in the classroom to help decrease the illness-related absentee rate for elementary school students.

METHODS

This study involved 5 individual school districts, 16 individual schools, and more than 6000 students in Delaware, Ohio, Tennessee, and California. Individual schools in each district were paired into product and control groups. In the product group schools, an alcohol gel hand sanitizer was used by the students and staff when entering and leaving the classroom. Absenteeism due to infection was recorded, and the data were statistically analyzed.

RESULTS

The overall reduction in absenteeism due to infection in the schools included in this study was 19.8% for schools that used an alcohol gel hand sanitizer compared with the control schools (P <.05). Data from the school system with the largest teacher population (n = 246) showed that teacher absenteeism decreased 10.1% (trend) in the schools where sanitizer was used.

CONCLUSION

Elementary school absenteeism due to infection is significantly reduced when an alcohol gel hand sanitizer is used in the classroom as part of a hand hygiene program.

Recovery from hip fracture in eight areas of function

BACKGROUND

This report describes changes in eight areas of functioning after a hip fracture, identifies the point at which maximal levels of recovery are reached in each area, and evaluates the sequence of recuperation across multiple functional domains. METHODS. Community-residing hip fracture patients (n = 674) admitted to eight hospitals in Baltimore, Maryland, 1990-1991 were followed prospectively for 2 years from the time of hospitalization. Eight areas of function (i.e., upper and lower extremity physical and instrumental activities of daily living; gait and balance; social, cognitive, and affective function) were measured by personal interview and direct observation during hospitalization at 2, 6, 12, 18, and 24 months. Levels of recovery are described in each area, and time to reach maximal recovery was estimated using Generalized Estimating Equations and longitudinal data.

RESULTS

Most areas of functioning showed progressive lessening of dependence over the first postfracture year, with different levels of recovery and time to maximum levels observed for each area. New dependency in physical and instrumental tasks for those not requiring equipment or human assistance prefracture ranged from as low as 20.3% for putting on pants to as high as 89.9% for climbing five stairs. Recuperation times were specific to area of function, ranging from approximately 4 months for depressive symptoms (3.9 months), upper extremity function (4.3 months), and cognition (4.4 months) to almost a year for lower extremity function (11.2 months).

CONCLUSIONS

Functional disability following hip fracture is significant, patterns of recovery differ by area of function, and there appears to be an orderly sequence by which areas of function reach their maximal levels.

Closed interlocking nailing of humeral shaft fractures with the Russell-Taylor nail

OBJECTIVE

To assess the role of the Russell-Taylor humeral nail in the treatment of humeral shaft fractures.

STUDY DESIGN

Retrospective with a mean radiologic and clinical follow-up at thirty-two months.

SETTING

University teaching hospital.

PATIENTS

Total of thirty-seven patients treated with the Russell-Taylor humeral nail.

INTERVENTION

All patients were treated with the Russell-Taylor humeral nail inserted in an antegrade fashion.

OUTCOME MEASURES

Radiologic union and shoulder function in terms of pain, power, range of movement, and activities of daily living.

RESULTS

There were four established nonunions and four cases of delayed union (time to union > four months). Age of patient was the only predictor of nonunion. There was one infection and one intraoperative fracture. Two prominent proximal screws required removal, and one nail was removed after union because of impingement. Three patients required manipulation under anesthesia to improve shoulder movement. At review, six patients had residual poor shoulder function as per Constant score, four attributable to shoulder stiffness and two to residual pain.

CONCLUSION

The authors' findings indicate a significant rate of delayed or nonunion in the elderly patient. When the high rate of union with conservative treatment is considered, the indications and rationale for intramedullary humeral nailing should be clearly defined.

Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling

Comparative sequence analysis complements experimental methods for the determination of RNA three-dimensional structure. This approach is based on the concept that different sequences within the same gene family form similar higher-order structures. The large number of rRNA sequences with sufficient variation, along with improved covariation algorithms, are providing us with the opportunity to identify new base triples in 16S rRNA. The three-dimensional conformations for one of our strongest candidates involving U121 (C124:G237) and/or U121 (U125:A236) (Escherichia coli sequence and numbering) are analyzed here with different molecular modeling tools. Molecular modeling shows that U121 interacts with C124 in the U121 (C124:G237) base triple. This arrangement maintains isomorphic structures for the three most frequent sequence motifs (approximately 93% of known bacterial and archaeal sequences), is consistent with chemical reactivity of U121 in E. coli ribosomes, and is geometrically favorable. Further, the restricted set of observed canonical (GU, AU, GC) base-pair types at positions 124:237 and 125:236 is consistent with the fact that the canonical base-pair sets (for both base pairs) that are not observed in nature prevent the formation of the 121 (124:237) base triple. The analysis described here serves as a general scheme for the prediction of specific secondary and tertiary structure base pairing where there is a network of correlated base changes.

Devescovinid trichomonad with axostyle-based rotary motor ("Rubberneckia"): taxonomic assignment as Caduceia versatilis sp. nov

An amitochondriate trichomonad cell of the family Devescovinidae (Class Parabasalia), helped demonstrate the fluid model of lipoprotein cell membranes. This wood-ingesting symbiont in the hindgut of the dry wood-eating termite Cryptotermes cavifrons is informally known to cell biologists as "Rubberneckia". As the microtubular axo-style complex generates force causing clockwise movement of the entire anterior portion of the cell at the shear zone the protist displays "head" rotation. Studies by phase contrast and videomicroscopy of live cells, of whole mounts by scanning, and thin sections by transmission electron microscopy extend the observations of Tamm and Tamm [24-26] and Tamm [19-23]. Habitat, cell shape, size, nuclear features, parabasal apparatus and other morphological details permit the assignment of "Rubberneckia" to Kirby's cosmopolitan genus Caduceia. This large-sized devescovinid has distinctive parabasal gyres, an axostylar rotary, motor, and regularly-associated nonflagellated, fusiform and flagellated rod epibiotic surface bacteria. In addition to regularly aligned epibionts intranuclear and endocytoplasmic bacteria are abundant and hydrogenosomes are Present. "Rubberneckia" is compared here to the other seven species of Caduceia. Since it is clearly sufficiently distinctive to warrant new species status, we named it C. versatilis.

Distant metastases in ovarian cancer: association with p53 mutations

Distant metastases are unusual occurrences at presentation and during the progression of epithelial ovarian cancer. There are no good clinical predictors of this phenomenon. Because p53 dysfunction is common in ovarian cancer, we chose to investigate whether specific types of mutations predicted a predisposition to distant metastasis. We hypothesized that the complete absence of intact p53 protein as seen with p53 null mutations may be associated with an enhanced tendency to develop distant metastatic disease. The complete coding sequence of 130 tumor DNA samples was screened for p53 mutations by single-strand conformational polymorphism analysis. Abnormal single-strand conformational polymorphism findings were correlated with the specific DNA sequence abnormalities and outcome. Ninety-four (72%) tumors carried p53 mutations. Sixty-two were missense mutations, and 32 were null mutations (6 nonsense mutations, 23 frameshift mutations, and 3 splice-site mutations). Twenty-eight patients were found to have distant metastases (pericardium, brain, parenchymal liver, spleen, or lung) either at presentation or during the course of their treatment. Distant metastases were nearly 8-fold more common in patients whose tumors carried a null mutation (66%) than in those with either missense mutations (8%) or wild-type p53 (8%; P<0.001). When a null mutation was present, 25% of the tumors were associated with distant metastases at initial diagnosis. No individual with wild-type p53 or a missense mutation in the tumor presented with distant metastasis. Tumors with null mutations were more likely to be associated with lymph node metastasis (P = 0.003), advanced stage (stage III/IV; P<0.001) and high grade (grade II/III; P<0.001), at presentation. These tumors progressed with distant metastases more swiftly than did tumors with either missense mutations (mean, 1.18 versus 2.71 years; P = 0.04) or wild-type p53 (3.57 years; P = 0.015). In contrast to the popular dogma, distant metastases in ovarian cancer do not necessarily result from prolonged treatment of disease. They may be predicted to occur early in the disease course due to a specific molecular genetic abnormality: null mutation of the p53 tumor suppressor gene. These findings need to be carefully considered when choosing between regional versus systemic treatment modalities.

New experimental and computational approaches to the analysis of gene expression

Public and private EST (Expressed Sequence Tag) programs provide access to a large number of ESTs from a number of plant species, including Arabidopsis, corn, soybean, rice, wheat. In addition to the homology of each EST to genes in GenBank, information about homology to all other ESTs in the data base can be obtained. To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries, from different tissues, developmental stages or induction conditions. This quantitation of message levels is quite accurate for highly expressed messages and, unlike conventional Northern blots, allows comparison of expression levels between different genes. Lists of most highly expresses genes in different libraries can be compiled. Also, if EST data is available for cDNA libraries derived from different developmental stages, gene expression profiles across development can be assembled. We present an example of such a profile for soybean seed development. Gene expression data obtained from Electronic Northern analysis can be confirmed and extended beyond the realm of highly expressed genes by using high density DNA arrays. The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the tissue of interest. Two-color fluorescent labeling allows accurate mRNA ratio measurements. We are currently using the DNA array technology to study chemical induction of gene expression and the biosynthesis of oil, carbohydrate and protein in developing seeds.

A cluster of ABA-regulated genes on Arabidopsis thaliana BAC T07M07

Arabidopsis thaliana BAC T07M07 encoding the abscisic acid-insensitive 4 (ABI4) locus has been sequenced completely. It contains a 95,713-bp insert and 24 predicted genes. Most putative genes were confirmed by gel-based RNA profiling and a cluster of ABA-regulated genes was identified. One of the 24 genes, designated PP2C5, encodes a putative protein phosphatase 2C. The encoded protein was expressed in Escherichia coli, and its enzyme activity in vitro was confirmed.

Health status of juvenile offenders. A survey of young offenders appearing before the juvenile courts

This paper reports on the health needs of a sample of juvenile offenders appearing before a Manchester Court during the month of August 1992. Of the 192 subjects interviewed (74% of those listed), 19% had significant medical problems, 42% a history of substance abuse and 7% psychiatric problems requiring further treatment. Substantial numbers (26%) engaged in a variety of dangerous behaviours. Custodial remands were common (21%), particularly in those with multiple psychosocial difficulties.

New experimental and computational approaches to the analysis of gene expression

Public and private EST (Expressed Sequence Tag) programs provide access to a large number of ESTs from a number of plant species, including Arabidopsis, corn, soybean, rice, wheat. In addition to the homology of each EST to genes in GenBank, information about homology to all other ESTs in the data base can be obtained. To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries, from different tissues, developmental stages or induction conditions. This quantitation of message levels is quite accurate for highly expressed messages and, unlike conventional Northern blots, allows comparison of expression levels between different genes. Lists of most highly expresses genes in different libraries can be compiled. Also, if EST data is available for cDNA libraries derived from different developmental stages, gene expression profiles across development can be assembled. We present an example of such a profile for soybean seed development. Gene expression data obtained from Electronic Northern analysis can be confirmed and extended beyond the realm of highly expressed genes by using high density DNA arrays. The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the tissue of interest. Two-color fluorescent labeling allows accurate mRNA ratio measurements. We are currently using the DNA array technology to study chemical induction of gene expression and the biosynthesis of oil, carbohydrate and protein in developing seeds.

Knowledge and attitudes of health-care providers toward cancer pain management: a comparison of physicians, nurses, and pharmacists in the state of New Hampshire

The knowledge and attitudes toward cancer pain management of physicians, nurses, and pharmacists in the state of New Hampshire were examined through the use of a statewide survey. Many of the providers who completed the survey, and thus indicated that they treated patients with cancer pain on a regular basis, were not pain or oncology specialists. Most of these providers were quite well informed about the fundamentals of cancer pain management. Approximately 90% of providers in all three groups were not concerned about addiction among cancer patients. Yet, there was a small percentage of providers who responded in less than optimal ways to items dealing with opioid pharmacology, pain assessment, and the importance of pain relief. Comparison of responses among provider groups indicated that nurses were the most knowledgeable and pharmacists the least knowledgeable about pain assessment. Physicians were the most knowledgeable regarding opioid pharmacology but seemed the least committed to providing optimal pain relief. Further analysis identified a small group of physicians that included a disproportionately high percentage of family practitioners and surgeons who consistently responded in less than optimal ways to items dealing with the importance of pain relief. The results of this study indicate a continuing need for broad-based educational programs in cancer pain management and for new initiatives focused on practitioners who see relatively few cancer patients and may have difficulty accessing traditional educational programs.

Construction of an approximately 2 Mb contig in the region around 80 cM of Arabidopsis thaliana chromosome 2

A method for construction of bacterial artificial chromosome (BAC) contigs from a yeast artificial chromosome (YAC) physical map is described. An approximately 2 Mb contig, consisting of two large BAC contigs linked by a small YAC, has been assembled in the region around 80 cM of Arabidopsis thaliana chromosome 2. Clones from this contig will facilitate gene isolation in the region and can be used directly as substrates for DNA sequencing.

Effects of Ixodes scapularis and Borrelia burgdorferi on modulation of the host immune response: induction of a TH2 cytokine response in Lyme disease-susceptible (C3H/HeJ) mice but not in disease-resistant (BALB/c) mice

Previous studies have demonstrated that both Ixodes scapularis saliva and Borrelia burgdorferi antigens modulated lymphokines and monokines in vitro. The studies presented here were designed to delineate the role of I. scapularis and B. burgdorferi in modulation of the host immune response in vivo. Infestation of C3H/HeJ mice with infected I. scapularis resulted in an up regulation of IL-4 as early as 8 days after tick infestation, while the levels of T helper cell type 1 (TH1) cytokines, interleukin-2 (IL-2) and gamma interferon (IFN-gamma), were significantly decreased by days 10 to 12. In contrast, the cytokine profile of BALB/c mice exposed to infected nymphal ticks resulted in only transient alterations in IL-4, IL-2, and IFN-gamma production throughout a 12-day period postinfestation. Although the IL-10 level was elevated in both C3H/HeJ and BALB/c mice infested with infected nymphal ticks, no significant difference in the levels of IL-10 was noted between the mouse strains. Flow-cytometric analysis demonstrated increases in the numbers of splenic B-cell and CD4+ lymphocytes in C3H/HeJ but not BALB/c mice exposed to infected ticks. Cell depletion experiments with C3H/HeJ mice demonstrated that CD4+ cells were the sole producers of IFN-gamma and IL-10 while both CD4+ and CD8+ splenocytes contributed to the production of IL-2 and IL-4. These findings suggest that B and CD4+ splenocytes are activated, increase in number, and produce a polarized TH2 response in C3H/HeJ mice exposed to infected I. scapularis. Given that C3H/HeJ mice are susceptible to Lyme disease and the initial TH2 polarization is not evident in BALB/c mice, effective control of this response may have ramifications for spirochete transmission in vivo.

Identification of sites in domain I of perlecan that regulate heparan sulfate synthesis

Perlecan is primarily a heparan sulfate containing proteoglycan found in all basement membranes. Rotary shadowed images of perlecan show it to contain three glycosaminoglycan (GAG) side chains extending from one end of its core protein. Domain I is at the N terminus of perlecan and contains three closely spaced Ser-Gly-Asp sequences that may serve in GAG attachment. We evaluated the serines in these three sequences for GAG attachment by preparing a cDNA construct encoding for the N-terminal half (domains I, II, and III) of perlecan and then a series of constructs containing deletions and mutations within domain I of the domain I/II/III construct, expressing these constructs in COS-7 cells, and then analyzing the recombinant product for GAG side chains and GAG type. The results showed that all three serine residues in the Ser-Gly-Asp sequences in domain I can accept both chondroitin and heparan sulfate side chains but that a cluster of acidic residues N-terminal to these sequences is the primary determinant responsible for targeting these sites for heparan sulfate. Furthermore, there are two elements that can enhance heparan sulfate synthesis at a targeted site: 1) the presence of a the SEA module in the C-terminal region of domain I and 2) the presence of multiple acceptors in close proximity. These results indicate that the proportion of heparan and chondroitin sulfate at any one site in domain I of perlecan is regulated by multiple factors.

Flea (Siphonaptera:Ceratophyllidae, hystrichopsyllidae) and tick (Acarina:Ixodidae) control on wood rats using host-targeted liquid permethrin in bait tubes

The efficacy of a liquid permethrin-treated bait tube controlling fleas and ticks on Mexican wood rats, Neotoma mexicana Baird, was evaluated during a 1-yr study in north-central Colorado. Results indicated that the bait tubes were effective for reducing flea and tick infestations on wood rats. The effects of treatment persisted throughout the study, despite the fact that bait tubes were replenished with bait and permethrin only during the first 4 mo (4 replenishments). Our results suggest that these bait tubes provide an effective, economical, and environmentally acceptable means of controlling vectors of flea or tick-borne diseases, although slight modifications of the basic bait tube design might be required to maintain the effectiveness of the tube under different ecological conditions.

The psychosocial characteristics of juvenile sexual offenders referred to an adolescent forensic service in the UK

Criminal statistics indicate that a high percentage of sexual offences are committed by perpetrators under the age of 18 years. Descriptive data based on a retrospective case note study of 121 juvenile sexual offender referrals to an adolescent forensic unit are presented. The results suggest that adolescents commit an array of offences and present with generalized adjustment difficulties. Conduct disorder was the most common diagnosis, while rates of mental illness were lower than in earlier studies. Abused as opposed to non-abused offenders experienced more dysfunctional upbringings and demonstrated higher rates of personal disturbance. Theoretical and treatment implications are discussed in relation to the available literature on adolescent sexual offending.

An evaluation of precaution-based approaches as EMF policy tools in community environments

This paper explores the use of precaution-based approaches as policy tools when responding to concerns about power-frequency electric and magnetic fields (EMF) in community environments. The combination of public concern and scientific uncertainty about potential health impacts from exposure to EMF challenges society to adopt EMF policies that balance the benefits of electric power against the possibility that some aspect of the use of electricity may be harmful. Inappropriate policy responses can undermine the economics of society's use of electricity and have other adverse consequences on public health. These adverse consequences result from the inappropriate diversion of scarce public and private resources. Precaution-based approaches are rooted in individual concepts of common sense and can be an effective component of a comprehensive set of EMF policy options. Precaution-based approaches do not replace science-based policy options and should only be used when the available science-based guidelines are not applicable. The application of these approaches should balance the real and expected costs and benefits of taking or not taking action. Given our current scientific knowledge, actions taken to reduce EMF exposure should necessarily be low cost because the expected benefits are uncertain. Society also needs to avoid adopting EMF policies that could incur high costs from distorting resources from other, more important, personal and public health priorities.