A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data

The 16S rRNA gene (16S rDNA) is currently the most widely used gene for estimating the evolutionary history of prokaryotes, To date, there are more than 30 000 16S rDNA sequences available from the core databases, GenBank, EMBL and DDBJ, This great number may cause a dilemma when composing datasets for phylogenetic analysis, since the choice and number of reference organisms are known to affect the resulting tree topology. A group of sequences appearing monophyletic in one dataset may not be so in another. This can be especially problematic when establishing the relationships of distantly related sequences at the division (phylum) level. In this study, a multiple-outgroup approach to resolving division-level phylogenetic relationships is suggested using 16S rDNA data. The approach is illustrated by two case studies concerning the monophyly of two recently proposed bacterial divisions, OP9 and OP10.

Characterization of a novel gene, STAG1/PMEPA1, upregulated in renal cell carcinoma and other solid tumors

Using differential display-polymerase chain reaction, we identified a novel gene sequence, designated solid tumor-associated gene 1 (STAG1), that is upregulated in renal cell carcinoma (RCC). The full-length cDNA (4839 bp) encompassed the recently reported androgen-regulated prostatic cDNA PMEPA1 and so we refer to this gene as STAG1/PMEPA1, Two STAG1/PMEPA1 mRNA transcripts of approximately 2.7 an 5 kb, with identical coding regions but variant 3' untranslated regions, were predominantly expressed in normal prostate tissue and at lower levels in the ovary. The expression of this gene was upregulated in 87% of RCC samples and also was upregulated in stomach and rectal adenocarcinomas. In contrast, STAG1/PMEPA1 expression was barely detectable in leukemia and lymphoma samples, Analysis of expressed sequence tag databases showed that STAG1/PMEPA1 also was expressed in pancreatic, endometrial, and prostatic adenocarcinomas. The STAG1/PMEPA1 cDNA encodes a 287-amino-acid protein containing a putative transmembrane domain and motifs that suggest that it may bind src homology 3- and tryptophan tryptophan domain-containing proteins. This protein shows 67% identity to the protein encoded by the chromosome 18 open reading frame 1 gene. Translation of STAG1/PMEPA1 mRNA in vitro showed two products of 36 and 39 kDa, respectively, suggesting that translation may initiate at more than one site. Comparison to genomic clones showed that STAG1/PMEPA1 was located on chromosome 20q13 between microsatellite markers D20S183 and D20S173 and spanned four exons and three introns. The upregulation of this gene in several solid tumors indicated that it may play an important role in tumorigenesis. (C) 2001 Wiley-Liss, Inc.

Characterization of the mouse hnRNP A2/B1/B0 gene and identification of processed pseudogenes

The mouse hnRNP A2/B1/B0 gene has been cloned using a PCR-based strategy and sequenced. Analysis of this sequence showed that the gene organization closely follows that of the human orthologue with 12 exons and 11 introns. The hnRNP A2/B1/B0 gene gives rise to four splice variants through alternative splicing of exons 2 and 9. RT-PCR assays indicated that all splice variants were expressed in mouse brain, skin, and stomach tissues of varying ages, although their ratios to one another varied with age and tissue type. We also identified a small subset of all polyadenylated splice variants that included intron 11, which shows 94% sequence identity between human and mouse. Several processed pseudogenes were identified in the mouse genome. A search of the mouse genome databases located five pseudogenes, four of. which are presumed to be non-functional because of the presence of premature stop codons, large deletions or rearrangements within the coding region. The fifth, which possesses putative promoter elements and has a coding sequence identical to that of the hnRNP A2 mRNA, variant, may be functional. (C) 2002 Elsevier Science B.V. All rights reserved.

In vivo DNA electrotransfer

The use of electrotransfer for DNA delivery to prokaryotic cells, and eukaryotic cells in vitro, has been well known and widely used for many years. However, it is only recently that electric fields have been used to enhance DNA transfer to animal cells in vivo, and this is known as DNA electrotransfer or in vivo DNA electroporation. Some of the advantages of this method of somatic cell gene transfer are that it is a simple method that can be used to transfer almost any DNA construct to animal cells and tissues in vivo; multiple constructs can be co-transfected; it is equally applicable to dividing and nondividing cells; the DNA of interest does not need to be subeloned into a specific viral transfer vector and there is no need for the production of high titre viral stocks; and, as no viral genes are expressed there is less chance of an adverse immunologic reaction to vector sequences. The ease with which efficient in vivo gene transfer can be achieved with in vivo DNA electrotransfer is now allowing genetic analysis to be applied to a number of classic animal model systems where transgenic and embryonic stem cell techniques are not well developed, but for which a wealth of detailed descriptive embryological information is available, or surgical manipulation is much more feasible. As well as exciting applications in developmental biology, in vivo DNA electrotransfer is also being used to transfer genes to skeletal muscle and drive expression of therapeutically active proteins, and to examine exogenous gene and protein function in normal adult cells situated within the complex environment of a tissue and organ system in vivo. Thus, in effect providing the in vivo equivalent of the in vitro transient transfection assay. As the widespread use of in vivo electroporation has really only just begun, it is likely that the future will hold many more applications for this technology in basic research, biotechnology and clinical research areas.

A review of guidelines and standards for telemedicine

We conducted a review to establish the range and scope of current telemedicine guidelines and standards. Published guidelines were identified by searching the Medline and Telemedicine Information Exchange (TIE) databases, and by performing a Google search using the term 'telemedicine guidelines'. Three types of guidelines were identified, namely clinical, operational and technical. Clinical guidelines included those for teleradiology, telepsychiatry, home telenursing, minor injuries telemedicine, surgical telemedicine, teledermatology and telepathology. Operational guidelines included those for email communication, Internet access and videoconferencing. Technical guidelines included those from the American Telemedicine Association and the US Office for the Advancement of Telehealth. The main standards relevant to telemedicine include those of the International Telecommunication Union and the DICOM standard. The scarcity of guidelines and standards suggests that telemedicine is not yet near to routine use. If an international telemedicine organization were to take responsibility for defining guidelines, under the direction of clinicians with appropriate telemedicine experience, this might speed up their development.

How well do general practitioners deliver palliative care? A systematic review

General practitioners (GPs) deliver the majority of palliative care to patients in the last year of life. This article seeks to examine the nature of GP care, perceptions of the GPs themselves and others of that care, the adequacy of palliative care training, issues relating to accessibility of GPs to palliative care patients, and strategies that may be of use in encouraging more effective delivery of palliative care by GPs. Medline and PubMed databases from 1966 to 2000 were searched, and 135 references identified. Sixty-six of these described studies relevant to GP palliative care. GPs value this part of their work. Most of the time, patients appreciate the contribution the GP makes to palliative care particularly if the GP is accessible, takes time to listen, allows patient and carer to ventilate their feelings, and is seen to be making efforts made regarding symptom relief. However, reports from bereaved relatives suggest that palliative care is performed less well in the community than in other settings. GPs express discomfort about their competence to perform palliative care adequately. They tend to miss symptoms which are not treatable by them, or which are less common. However, with appropriate specialist support and facilities, GPs have been shown to deliver sound and effective care. GP comfort working with specialist teams increases with exposure to this form of patient management, as does the understanding of the potential other team members have in contributing to the care of the patient. Formal arrangements engaging GPs to work with specialist teams have been shown to improve functional outcomes, patient satisfaction, improve effective use of resources and improve effective physician behaviour in other areas of medicine. Efforts by specialist services to develop formal involvement of GPs in the care of individual patients, may be an effective method of improving GP palliative care skills and appreciation of the roles specialist services can play.

Does primary medical practitioner involvement with a specialist team improve patient outcomes? A systematic review.

Patients with chronic or complex medical or psychiatric conditions are treated by many practitioners, including general practitioners (GPs). Formal liaison between primary and specialist is often assumed to offer benefits to patients The aim of this study was to assess the efficacy of formal liaison of GPs with specialist service providers on patient health outcomes, by conducting a systematic review of the published literature in MEDLINE, EMBASE, PsychINFO, CINAHL and Cochrane Library databases using the following search terms family physicians': synonyms of 'patient care planning', 'patient discharge' and 'patient care team'; and synonyms of 'randomised controlled trials'. Seven studies were identified, involving 963 subjects and 899 controls. most health outcomes were unchanged, although some physical and functional health outcomes were improved by formal liaison between GPs and specialist services, particularly among chronic mental illness patients. Some health outcomes worsened during the intervention. Patient retention rates within treatment programmes improved with GP involvement, as did patient satisfaction. Doctor (GP and specialist) behaviour changed, with reports of more rational use of resources and diagnostic tests, improved clinical skills, more frequent use of appropriate treatment strategies, and more frequent clinical behaviours designed to detect disease complications Cost effectiveness could not be determined. In conclusion, formal liaison between GPs and specialist services leaves most physical health outcomes unchanged, but improves functional outcomes in chronically mentally ill patients. It may confer modest long-term health benefits through improvements in patient concordance with treatment programmes and more effective clinical practice.

Carbamazepine augmentation for schizophrenia: How good is the evidence?

Background: Augmentation strategies in schizophrenia treatment remain an important issue because despite the introduction of several new antipsychotics, many patients remain treatment resistant. The aim of this study was to undertake a systematic review and meta-analysis of the safety and efficacy of one frequently used adjunctive compound: carbamazepine. Data sources and study selection: Randomized controlled trials comparing carbamazopine (as a sole or as an adjunctive compound) with placebo or no intervention in participants with schizophrenia or schizoaffective disorder were searched for by accessing 7 electronic databases, cross-referencing publications cited in pertinent studies, and contacting drug companies that manufacture carbamazepine. Method: The identified studies were independently inspected and their quality assessed by 2 reviewers, Because the study results were generally incompletely reported, original patient data were requested from the authors; data were received for 8 of the 10 randomized controlled trials included in the present analysis, allowing for a reanalysis of the primary data. Dichotomous variables were analyzed using the Mantel-Haenszel odds ratio and continuous data were analyzed using standardized mean differences, both specified with 95% confidence intervals. Results: Ten studies (total N = 283 subjects) were included. Carbamazepine was not effective in preventing relapse in the only randomized controlled trial that compared carbamazepine monotherapy with placebo. Carbamazepine tended to be less effective than perphenazine in the only trial comparing carbamazepine with an antipsychotic. Although there was a trend indicating a benefit from carbamazepine as an adjunct to antipsychotics, this trend did not reach statistical significance. Conclusion: At present, this augmentation strategy cannot be recommended for routine use. The most promising targets for future trials are patients with excitement, aggression, and schizoaffective disorder bipolar type.

Conserved modularity and potential for alternate splicing in mouse and human Slit genes

The vertebrate Slit gene family currently consists of three members;Slit1,Slit2 and Slit3. Each gene encodes a protein containing multiple epidermal growth factor and leucine rich repeat motifs, which are likely to have importance in cell-cell interactions. In this study, we sought to fully define and characterise the vertebrate Slit gene family. Using long distance PCR coupled with in silico mapping, we determined the genomic structure of all three Slit genes in mouse and man. Analysis of EST and genomic databases revealed no evidence of further Slit family members in either organism. All three Slit genes were encoded by 36 (Slit3) or 37 (Slit1 and Slit2) exons covering at least 143 kb or 183 kb of mouse or human genomic DNA respectively. Two additional potential leucine-rich repeat encoding exons were identified within intron 12 of Slit2. These could be inserted in frame, suggesting that alternate splicing may occur in Slit2 A search for STS sequences within human Slit3 anchored this gene to D5S2075 at the 5' end (exon 4) and SGC32449 within the 3' UTR, suggesting that Slit3 may cover greater than 693 kb. The genomic structure of all Slit genes demonstrated considerable modularity in the placement of exon-intron boundaries such that individual leucine-rich repeat motifs were encoded by individual 72 by exons. This further implies the potential generation of multiple Slit protein isoforms varying in their number of repeat units. cDNA library screening and EST database searching verified that such alternate splicing does occur.

Mouse proteome analysis

A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteornes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins

A review of peer support in the context of cancer

Peer support interventions for people with cancer, their families, and friends have been widely used throughout the world. The present study reviewed the research literature on psychosocial oncology over the past decade to assess the prevalence and contribution of articles on peer support. Using CD-Rom databases, 25 articles were retrieved for review. In each article, patients or their family members were the target group for supportive interventions, which were primarily for the delivery of peer support and included either a qualitative or quantitative evaluation of the program. A definitional taxonomy for peer support interventions, which identified eight discrete settings, was derived from three key dimensions: style of supervision, interpersonal context, and mode of delivery. The studies suggested that peer support programs help by providing emotional and informational support from the perspective of shared personal experience. However, a paucity of research-particularly randomized controlled trials-was noted. The reasons may include inherent difficulties in isolating for study what is essentially a naturalistically occurring interpersonal dynamic from the complex social and community contexts from which it emanates. The authors discuss the gap between practice and theory in this area and recommend a broader and more inclusive view of supportive care for people with cancer. (C) 2003 by The Haworth Press, Inc. All rights reserved.

A coupled knowledge-based expert system for design of liquid-retaining structures

This paper describes a coupled knowledge-based system (KBS) for the design of liquid-retaining structures, which can handle both the symbolic knowledge processing based on engineering heuristics in the preliminary synthesis stage and the extensive numerical crunching involved in the detailed analysis stage. The prototype system is developed by employing blackboard architecture and a commercial shell VISUAL RULE STUDIO. Its present scope covers design of three types of liquid-retaining structures, namely, a rectangular shape with one compartment, a rectangular shape with two compartments and a circular shape. Through custom-built interactive graphical user interfaces, the user is directed throughout the design process, which includes preliminary design, load specification, model generation, finite element analysis, code compliance checking and member sizing optimization. It is also integrated with various relational databases that provide the system with sectional properties, moment and shear coefficients and final member details. This system can act as a consultant to assist novice designers in the design of liquid-retaining structures with increase in efficiency and optimization of design output and automated record keeping. The design of a typical example of the liquid-retaining structure is also illustrated. (C) 2003 Elsevier B.V All rights reserved.