bluuebunny/crossref_metadata_2025 huggingface dataset:
The paradox of journalistic representation of the other
Authors: Leung Christine C. M. , Huang Yu
Published: October 2007

This paper primarily looks at one of the essential aspects of global (usually western) journalists' praxis of covering and depicting the other (generally the non-western). Content analysis of quantitative and qualitative attributes of media coverage of the SARS outbreak with regard to China and Vietnam from newspapers in five countries, including the Washington Post (USA), The Times (UK), the Sydney Morning Herald (Australia), the Globe & Mail (Canada), the Straits Times (Singapore), Newsweek and online news was undertaken. Findings show that while the western news coverage on China corroborated the image of the other in an unfavorable light, Vietnam was not portrayed as the negative other. Differences in China's and Vietnam's handling of SARS have affected their news coverage by the media. Both internal forces and external factors, interplaying and often competing, have contributed to the dynamic process of news coverage and image construction in the international media.
American election night and the journalism of assertion
Authors: Marriott Stephanie
Published: October 2007

The past few decades have seen a number of transformations in both the form and the content of American television news. This article examines the consequences of these shifts for the coverage of the presidential election nights in 2000 and 2004 on the American networks and cable news channels, with particular reference to Kovach and Rosenstiel's (1999) notion of a journalism of assertion. It discusses the changes put in place by broadcasters following widespread criticism of their performance in 2000. The article offers clear evidence that the broadcasters were more circumspect in 2004 in their initial calling of states, but argues that with respect to the interpretative reportage which followed these calls, a range of institutional, cultural and ideological factors ensured that significant elements of the broadcasts remained unchanged.
The process of sample recruitment: an ethnostatistical perspective
Authors: Thomas Michelle , Bloor Michael , Frankland Jane
Published: October 2007

This article draws on the authors' fieldwork experiences in four different research studies to address the gap in the methodological literature on the practical activities of sample recruitment. Boundaries between ineligibility and refusal are considered along with the `emotional labour' required during the recruitment process. In particular, the article aims to draw attention to the necessary indeterminacies in the recruitment process to show how the practical reasoning and situated action of researchers in the field critically determine the constitution of the study sample and the recruitment rate. It is concluded that, while no rules can adequately specify the process of recruitment, more resources, particularly to allow team recruitment, would reduce researcher stress and allow greater quality control.
Reflexive accounts about qualitative interviewing within the context of educational policy in North Cyprus
Authors: Mertkan-Ozünlü Sefika
Published: October 2007

Located within policy studies and politics of education in North Cyprus, this article is a medium through which methodological quandaries about reflexive accounts of qualitative interviewing arise in a dialogic fashion within the arena of education reform. Relying primarily on field notes, it explores the two-way management and negotiation of identity work, its effects on data gathering, and the public and private sides of interviewing. The researcher, present author, argues through numerous examples that both interviewees and the interviewer are actively engaged in identity crafting. These co-constructed identities influence the data-gathering process and the emerging intersubjective narratives of lived experiences in social worlds. She also makes a case that reflexive accounts of identity work are intersubjective, co-constructed identities are not genuinely knowable and the identity work is not genuinely comprehensible.
Ethnic-matching in qualitative research: reversing the gaze on `white others' and `white' as `other'
Authors: Hoong Sin Chih
Published: October 2007

Writings on inter-racial/ethnic research tend to posit `nonwhite' as the researched `other'. There is scant literature dealing with `others' within whiteness or treating whiteness itself as an `other'. This article draws on the experience of a project looking at the quality of life of older people in Britain to illuminate often implicit assumptions underpinning the practice of ethnic-matching in qualitative research by reversing the research gaze. By examining the procedures involved in matching majority and minority ethnic researchers to a range of `white' respondents, this article unveils the often unscrutinized values and assumptions of certain sets of practice in qualitative research that can influence the process and products of research. Reversing the `ethnic' research gaze can help to illuminate new perspectives on the construction of otherness and positionalities within research. While this article looks at the influence of ethnicity on the research process, it acknowledges that ethnicity may not always be the primary social signifier and may also intersect with a range of other identifiers such as age, gender, class and geography.
Embodiment, academics, and the audit culture: a story seeking consideration
Authors: Sparkes Andrew C.
Published: October 2007

In response to the plea by Pelias (2004) for a methodology of the heart, this article presents a story about the embodied struggles of an academic at a university that is permeated by an audit culture. It is based on informal interviews with academics at various universities in England and selected personal experiences. Thus, the constructive process is inspired by partial happenings, fragmented memories, echoes of conversations, whispers in corridors, fleeting glimpses of myriad reflections seen through broken glass, and multiple layers of fiction and narrative imaginings. Methodological issues abound in the telling and showing but, quite rightly, remain dormant on this occasion. In the end, the story simply asks for your consideration.
Conducting a campaign to improve hand hygiene in non-acute health care
Authors: Weaving P.
Published: October 2007

In 2004 the National Patient Safety Agency launched the cleanyourhands campaign to improve hand hygiene in acute NHS trusts in England and Wales through the provision of near patient alcohol hand-rub combined with regularly refreshed prompts. Calls have been made since the campaign started for it to be extended to non-acute healthcare, but the diversity of services and settings in the non-acute sector presents many challenges to successful implementation.
Mapping the research aspirations for the ICNA
Authors: Prieto J. , Hodgson G. , Williams D. , Hughes J. , Loveday H. ,   ICNA Research and Development Group
Published: October 2007

The need for evidence-based infection prevention and control practice necessitates ensuring research capacity and capability to deliver this agenda. This paper reports the findings of a research mapping exercise to identify current research activity and perceived need for support among members of the ICNA. These findings provide insights into how the ICNA research and development group can support practitioners in this field.
The MMR vaccine controversy — winners, losers, impact and challenges
Authors: MacDonald P.F.
Published: October 2007

One of the biggest challenges to professionals involved in immunisation delivery in recent years has been the controversy surrounding the safety of the measles, mumps and rubella (MMR) vaccine. This article explores the history of the vaccine, the controversy and its impact on uptake rates. In discussion potential winners and losers are considered with the conclusion being that there are very few winners among the affected healthcare professionals, children, parents, the NHS and UK government .
Hand hygiene compliance: universally better post-contact than pre-contact in healthcare workers in the UK and Australia
Authors: Bahal A. , Karamchandani D. , Fraise A.P. , McLaws M.L.
Published: October 2007

Objective: To establish whether post-patient contact hand hygiene practice is universally higher than pre-patient contact in two highly resourced countries.

Methods: Observations of medical and nursing staffs' hand hygiene compliance were made by the same observers in two different hospitals in Sydney and Birmingham, in both intensive care units (ICU) and surgical wards, using a standardised data collection tool. Results: Hand hygiene rates pre- and post-patient contact were low for both nurses and doctors in Sydney and Birmingham, with the exception of Sydney ICU doctors (pre-contact 74.8% and post-contact 75.7%, p=0.868). Post-contact compliance was low but significantly better than pre-contact in Sydney ICU nurses (41.3% versus 59.6% p<0.0001), surgical ward nurses (14.9% versus 29.6%, p=0.0019) and Sydney surgeons (10.2% versus 30.2%, p<0.0001). Post-contact compliance rates were low but higher than pre-contact in Birmingham ICU nurses (33.1% versus 52.2%, p=0.0011) and doctors (29.3% versus 70.1%, p<0.0001) but not in the Birmingham surgical ward (nurses: 42.6% versus 43.4%, p=0.89; surgeons: 39.6% versus 48.4%, p=0.187). Handwashing on removal of gloves was extremely low (1.7% to 16.6%), regardless of city, specialties or clinical staff.

Conclusion: The pattern of post-contact compliance and non-compliance associated with glove use strongly suggests hand hygiene practice in both countries is primarily self-protective rather than a patient safety centred practice.
Building Police—Youth Relationships: The Importance of Procedural Justice
Authors: Hinds Lyn
Published: October 2007

A consistent body of research shows that a key reason that adults support police is that they view them as legitimate. This paper adds to the small number of studies to explore factors that influence young people's judgments of police legitimacy. Using data from a written survey of 14 to 16 year-old high school students, findings show that young people's attitudes toward police legitimacy are positively linked to police use of procedural justice. Prior negative contact with police is significantly associated with young people's judgments of lower police legitimacy. Implications for building better police-youth relationships are discussed.
Being Black and in Trouble: The Role of Self-perception in the Offending Behaviour of Black Youth
Authors: Apena Feyishola
Published: October 2007

Young black people in British society are often linked with images of criminality and delinquency. This study aimed to investigate self-perception in young black male offenders. Semi-structured interviews were conducted with eight participants and included questions relating to family background and perceptions of society and themselves. A group discussion was also undertaken to elaborate further on topics raised in the interviews. A `grounded theory' approach was used to analyse the data and ten key themes emerged, which included: the importance of black history; ability to define their ethnic background; normal levels of self-esteem; negative representations of black people and lack of a role model. The methodological limitations in this study are discussed. Notwithstanding these, however, the findings suggest that racial identity is an important part of self-perception for black young offenders and it is recommended that this needs to be taken into consideration when working with young black people in the criminal justice system.
Ecologists and the experimental landscape: the nature of science at the US Department of Energy's Savannah River Site
Authors: Kirsch Scott
Published: October 2007

Although ecological conceptions of nature remain among the most authoritative in the world today, cultural geographers of landscape have paid little attention to the continuing salience of landscape as an object and scale of analysis in landscape and ecosystems ecology. That this object — a naturalized landscape of dynamic and multi-scalar systems and flows, not fixity — has been constructed, disproportionately, from some of the most technological of spaces, compels us to look more closely at the ways that specific natures circulate to inform general principles and ideas. This article explores how ecologists and other environmental scientists have turned the buffer zone surrounding the US Department of Energy's Savannah River Site, a former plutonium and tritium production plant, into an experimental landscape, with all the proprietary qualities embodied in the latter term. The study brings together a genealogy of the site as a space for scientific ecology with interviews conducted with contemporary environmental scientists based there, focusing chiefly on the work of scientists at the Savannah River Ecology Laboratory. By investigating the nature of agency, institution building, and representational practices in the making of an experimental, ecological landscape, the article also raises questions about how, at the Savannah River Site and elsewhere, the work of environmental science relates to the productive processes going on around it.
A subspecies no more? A mouse, its unstable taxonomy, and western riparian resource conflict
Authors: Crifasi Robert R.
Published: October 2007

The Preble's meadow jumping mouse ( Zapus hudsonius preblei) and issues surrounding its listing as a federally threatened species provide a contemporary case study that contributes insights toward the construction of nature and the social construction of science. Designating the mouse as a subspecies and the attack on its taxonomic validity illustrates the contentious and uneven transfer of biological knowledge from the field of taxonomy to the public realm of environmental politics, regional development and species conservation. Listing the mouse set off a process where federal, state, and local governments, plus dozens of others spent millions of dollars and an extraordinary amount of time in a chaotic and often contentious mouse conservation effort. From naming the mouse to listing it under the Endangered Species Act (ESA), the author traces a chain of events that has affected both the landscape and institutions along the Colorado and Wyoming Front Range. This article shows how and why a political struggle over land use transformed into a scientific debate over taxonomy. It describes how economic forces and ideological perspectives influence taxonomists and the names they give plants and animals. In the western US, taxonomists are becoming key actors in struggles over access to riparian resources. The author discusses how using single species listings under the ESA as a tool to combat urban sprawl or to influence land use decisions undermine political support for both the ESA and other species conservation efforts.
Shooting space, tracking time: the city from animated photography to vernacular relativity
Authors: Clarke David B. , Doel Marcus A.
Published: October 2007

The article reflects on the visualization of the city in the late 1890s and early 1900s, with reference to English animated photography and film: two media that are intimately related in terms of technology but worlds apart in terms of form. While both animated photography and film shared an elective affinity with the city, each was drawn to the urban environment for different reasons. Anima-photographers were particularly concerned with the movement and pace of the city and endeavoured to capture the `true motion' of such a dynamic space. Film, by contrast, began to probe the `optical unconscious' of urban space as a way of drawing out its undisclosed potential. Consequently, concerns with rendering `true motion' gave way to an appreciation of modernity's `vernacular relativity', especially in the form of montage. It was this shift that enabled filmmakers to re-engineer space and time, developing all manner of editing techniques with which to rearticulate the world. Hence the revolutionary potential of film. To demonstrate the significance of this shift, two recent projects that rework animated photographs taken in the 1890s and 1900s are explored: Patrick Keiller's The City of the Future (2005), which splices together a number of animated photographs to create a work of narrative cinema; and Gustav Deutsch's Welt Spiegel Kino ( World Mirror Cinema) (2005), which uses archival panning shots of city squares as the basis for a hypertextual montage. The article concludes by outlining the specificity of the ways in which animated photography and film, respectively, envisage the city.
New Developments in Ionomer Technology for Film Applications
Authors: Morris Barry A.
Published: October 2007

Ethylene based ionomers have been used in film applications for many years. Ionic associations formed by neutralizing ethylene-acid copolymers with metal salts, typically sodium or zinc, give these ionomers a unique combination of low seal initiation temperature and high melt strength, clarity, stiffness, toughness, and oil and grease resistance that make them outstanding heat seal resins. New properties can be achieved by manipulating the nature and strength of the ionic associations. Examples of two new developments are described. The first is an ethylene ionomer that when blended with standard polyolefins such as PE or PP imparts permanent antistatic properties. The second is a new family of ionomers that have high gas permeability, which is important for a number of packaging film applications.
A New Class of High-Performance Compostable Plastic Bags and Can Liners
Authors: Ruiz Frank A.
Published: October 2007

Heritage Bag Company has developed compostable bags and liners, which are produced from composites utilizing polymer and mineral materials technology of Heritage Plastics, Inc. This product line is based on proprietary blends of different biodegradable polymers which have been modified using mineral reinforcement technology to produce a readily extrudable polymer composite. This modification yields polymers that can be readily processed for end-use products such as films and bags with characteristics very similar to those obtained with higher α-olefin LLDPE resins, yet which meet the degradability requirements of ASTM D 6400-04.
Development of New Ionomers With Novel Gas Permeation Properties
Authors: Chen John C.
Published: October 2007

Ethylene ionomers, such as Surlyn® from DuPont, have been the premium sealant materials for packaging applications due to their excellent seal strength and process robustness. The ethylene ionomers exhibit their unique property characteristics because they form a network morphology. In this article new ethylene ionomers will be discussed. Their versatile compositions and the unique morphology will be described together with enhanced gas permeability properties.
Film Processability, Morphology, and Properties of Polyamide-6/Low Density Polyethylene Blends
Authors: López-Barrón C.R. , Robledo-Ortiz J.R. , Rodrigue D. , González-Núñez R.
Published: October 2007

The processing, morphology, and tensile properties of blown films prepared from polyamide-6 (PA6) and low density polyethylene (LDPE) blends with and without compatibilizer (Surlyn® 9020) are studied. The results indicate that the presence of PA6 and a compatibilizer has a great influence on blend rheology as well as mechanical and barrier properties of LDPE films where the morphology of the dispersed phase (PA6) plays an important role. In this study, film morphology is controlled mainly by variations in draw ratio and bubble pressure. It is shown that biaxial orientation of the films explains the anisotropic behavior of the mechanical properties and improved barrier properties due to the production of a lamellar structure.
Novel PET Nanocomposites of Interest in Food Packaging Applications and Comparative Barrier Performance With Biopolyester Nanocomposites
Authors: Sanchez-Garcia M.D. , Gimenez E. , Lagaron J.M.
Published: October 2007

Poly(ethylene terephthalate) (PET) is one of the polymers most widely used in the packaging industry. However, it is highly desirable to enhance its barrier properties for applications, such as carbonated drinks and other rigid and flexible packaging applications. The nanocomposites route offers unique possibilities to enhance the properties of this material, provided that adequate thermally resistant and legislation complying nanoadditives are used. This study presents novel PET nanocomposites with enhanced barrier properties to oxygen, water, and limonene based on a new specifically developed food-contact-complying highly swollen montmorillonite grade, and, furthermore, presents and discusses morphological data. Moreover, given the current interest in the packaging industry to replace this material by other biopolyesters, a comparative barrier performance of PET nanocomposites versus that of biopolymers, such as poly(lactic acid) (PLA), polyhydroxyalkanoates (PHB, PHBV), and polycaprolactones (PCL) and their corresponding nanocomposites is also reported.
An immune escape screen reveals Cdc42 as regulator of cancer susceptibility to lymphocyte-mediated tumor suppression
Authors: Marques Celio A. , Hähnel Patricia S. , Wölfel Catherine , Thaler Sonja , Huber Christoph , Theobald Matthias , Schuler Martin
Published: October 2007

Adoptive cellular immunotherapy inducing a graft-versus-tumor (GVT) effect is the therapeutic mainstay of allogeneic hematopoietic stem cell transplantation (ASCT) for high-risk leukemias. Autologous immunotherapies using vaccines or adoptive transfer of ex vivo–manipulated lymphocytes are clinically explored in patients with various cancer entities. Main reason for failure of ASCT and cancer immunotherapy is progression of the underlying malignancy, which is more prevalent in patients with advanced disease. Elucidating the molecular mechanisms contributing to immune escape will help to develop strategies for the improvement of immunologic cancer treatment. To this end, we have undertaken functional screening and expression cloning of factors mediating resistance to antigen-specific cytotoxic T lymphocytes (CTLs). We have identified Cdc42, a GTPase regulating actin dynamics and growth factor signaling that is highly expressed in invasive cancers, as determinator of cancer cell susceptibility to antigen-specific CTLs in vitro and adoptively transferred immune effectors in vivo. Cdc42 prevents CTL-induced apoptosis via mitogen-activated protein kinase (MAPK) signaling and posttranscriptional stabilization of Bcl-2. Pharmacologic inhibition of MAPK/extracellular signal–regulated kinase (ERK) kinase (MEK) overcomes Cdc42-mediated immunoresistance and activation of Bcl-2 in vivo. In conclusion, Cdc42 signaling contributes to immune escape of cancer. Targeting Cdc42 may improve the efficacy of cancer immunotherapies.
Deletion of 3 residues from the C-terminus of MCFD2 affects binding to ERGIC-53 and causes combined factor V and factor VIII deficiency
Authors: Nyfeler Beat , Kamiya Yukiko , Boehlen Françoise , Yamamoto Kazuo , Kato Koichi , de Moerloose Philippe , Hauri Hans-Peter , Neerman-Arbez Marguerite
Published: October 2007

Combined factor V and factor VIII deficiency (F5F8D) is a rare, autosomal recessive coagulation disorder. F5F8D is genetically linked to mutations in the transmembrane lectin ERGIC-53 and its soluble interaction partner MCFD2. The ERGIC-53/MCFD2 protein complex functions as transport receptor of coagulation factors V and VIII by mediating their export from the endoplasmic reticulum (ER). Here, we studied a F5F8D patient who was found to be a compound heterozygote for 2 novel mutations in MCFD2: a large deletion of 8.4 kb eliminating the 5′UTR of the gene and a nonsense mutation resulting in the deletion of only 3 amino acids (ΔSLQ) from the C-terminus of MCFD2. Biochemical and structural analysis of the ΔSLQ mutant demonstrated impaired binding to ERGIC-53 due to modification of the 3-dimensional structure of MCFD2. Our results highlight the importance of the ERGIC-53/MCFD2 protein interaction for the efficient secretion of coagulation factors V and VIII.
Simian virus 40 vectors for pulmonary gene therapy
Authors: Eid Luminita , Bromberg Zohar , EL-Latif Mahmoud Abd , Zeira Evelyn , Oppenheim Ariella , Weiss Yoram G
Published: October 2007

Background

Sepsis remains the leading cause of death in critically ill patients. One of the primary organs affected by sepsis is the lung, presenting as the Acute Respiratory Distress Syndrome (ARDS). Organ damage in sepsis involves an alteration in gene expression, making gene transfer a potential therapeutic modality. This work examines the feasibility of applying simian virus 40 (SV40) vectors for pulmonary gene therapy.

Methods

Sepsis-induced ARDS was established by cecal ligation double puncture (2CLP). SV40 vectors carrying the luciferase reporter gene (SV/luc) were administered intratracheally immediately after sepsis induction. Sham operated (SO) as well as 2CLP rats given intratracheal PBS or adenovirus expressing luciferase served as controls. Luc transduction was evaluated by in vivo light detection, immunoassay and luciferase mRNA detection by RT-PCR in tissue harvested from septic rats. Vector abundance and distribution into alveolar cells was evaluated using immunostaining for the SV40 VP1 capsid protein as well as by double staining for VP1 and for the surfactant protein C (proSP-C). Immunostaining for T-lymphocytes was used to evaluate the cellular immune response induced by the vector.

Results

Luc expression measured by in vivo light detection correlated with immunoassay from lung tissue harvested from the same rats. Moreover, our results showed vector presence in type II alveolar cells. The vector did not induce significant cellular immune response.

Conclusion

In the present study we have demonstrated efficient uptake and expression of an SV40 vector in the lungs of animals with sepsis-induced ARDS. These vectors appear to be capable of in vivo transduction of alveolar type II cells and may thus become a future therapeutic tool.
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments
Authors: Robinson Mark D , De Souza David P , Keen Woon Wai , Saunders Eleanor C , McConville Malcolm J , Speed Terence P , Likić Vladimir A
Published: October 2007

Background

Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies.

Results

A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites.

Conclusion

We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed.
Functional genomic delineation of TLR-induced transcriptional networks
Authors: Elkon Ran , Linhart Chaim , Halperin Yonit , Shiloh Yosef , Shamir Ron
Published: October 2007

Background

The innate immune system is the first line of defense mechanisms protecting the host from invading pathogens such as bacteria and viruses. The innate immunity responses are triggered by recognition of prototypical pathogen components by cellular receptors. Prominent among these pathogen sensors are Toll-like receptors (TLRs). We sought global delineation of transcriptional networks induced by TLRs, analyzing four genome-wide expression datasets in mouse and human macrophages stimulated with pathogen-mimetic agents that engage various TLRs.

Results

Combining computational analysis of expression profiles and cis-regulatory promoter sequences, we dissected the TLR-induced transcriptional program into two major components: the first is universally activated by all examined TLRs, and the second is specific to activated TLR3 and TLR4. Our results point to NF-κB and ISRE-binding transcription factors as the key regulators of the universal and the TLR3/4-specific responses, respectively, and identify novel putative positive and negative feedback loops in these transcriptional programs. Analysis of the kinetics of the induced network showed that while NF-κB regulates mainly an early-induced and sustained response, the ISRE element functions primarily in the induction of a delayed wave. We further demonstrate that co-occurrence of the NF-κB and ISRE elements in the same promoter endows its targets with enhanced responsiveness.

Conclusion

Our results enhance system-level understanding of the networks induced by TLRs and demonstrate the power of genomics approaches to delineate intricate transcriptional webs in mammalian systems. Such systems-level knowledge of the TLR network can be useful for designing ways to pharmacologically manipulate the activity of the innate immunity in pathological conditions in which either enhancement or repression of this branch of the immune system is desired.
Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria
Authors: Zhang Xiaowen , Zhao Fangqing , Guan Xiangyu , Yang Yu , Liang Chengwei , Qin Song
Published: October 2007

Background

Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution.

Results

286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains.

Conclusion

The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.
Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
Authors: Lavín José L , Kiil Kristoffer , Resano Ohiana , Ussery David W , Oguiza José A
Published: October 2007

Background

Pseudomonas syringaeis a widespread bacterial plant pathogen, and strains ofP. syringaemay be assigned to different pathovars based on host specificity among different plant species. The genomes ofP. syringaepv.syringae(Psy) B728a, pv.tomato(Pto) DC3000 and pv.phaseolicola(Pph) 1448A have been recently sequenced providing a major resource for comparative genomic analysis. A mechanism commonly found in bacteria for signal transduction is the two-component system (TCS), which typically consists of a sensor histidine kinase (HK) and a response regulator (RR).P. syringaerequires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions.

Results

Based on the genomic data, pattern searches with Hidden Markov Model (HMM) profiles have been used to identify putative HKs and RRs. The genomes ofPsyB728a,PtoDC3000 andPph1448A were found to contain a large number of genes encoding TCS proteins, and a core of complete TCS proteins were shared between these genomes: 30 putative TCS clusters, 11 orphan HKs, 33 orphan RRs, and 16 hybrid HKs. A close analysis of the distribution of genes encoding TCS proteins revealed important differences in TCS proteins among the threeP. syringaepathovars.

Conclusion

In this article we present a thorough analysis of the identification and distribution of TCS proteins among the sequenced genomes ofP. syringae. We have identified differences in TCS proteins among the threeP. syringaepathovars that may contribute to their diverse host ranges and association with plant hosts. The identification and analysis of the repertoire of TCS proteins in the genomes ofP. syringaepathovars constitute a basis for future functional genomic studies of the signal transduction pathways in this important bacterial phytopathogen.
Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Authors: Bergholz Teresa M , Wick Lukas M , Qi Weihong , Riordan James T , Ouellette Lindsey M , Whittam Thomas S
Published: October 2007

Background:

Global patterns of gene expression of Escherichia coli K-12 during growth transitions have been deeply investigated, however, comparable studies of E. coli O157:H7 have not been explored, particularly with respect to factors regulating virulence genes and genomic islands specific to this pathogen. To examine the impact of growth phase on the dynamics of the transcriptome, O157:H7 Sakai strain was cultured in MOPS minimal media (0.1% glucose), RNA harvested at 10 time points from early exponential to full stationary phase, and relative gene expression was measured by co-hybridization on high-density DNA microarrays. Expression levels of 14 genes, including those encoding Shiga toxins and other virulence factors associated with the locus of enterocyte effacement (LEE), were confirmed by Q-PCR.

Results:

Analysis of variance (R/MAANOVA, Fs test) identified 442 (36%) of 1239 O157-specific ORFs and 2110 (59%) of 3647 backbone ORFs that changed in expression significantly over time. QT cluster analysis placed 2468 of the 2552 significant ORFs into 12 groups; each group representing a distinct expression pattern. ORFs from the largest cluster (n = 1078) decreased in expression from late exponential to early stationary phase: most of these ORFs are involved in functions associated with steady state growth. Also represented in this cluster are ORFs of the TAI island, encoding tellurite resistance and urease activity, which decreased ~4-fold. Most ORFs of the LEE pathogenicity island also decreased ~2-fold by early stationary phase. The ORFs encoding proteins secreted via the LEE encoded type III secretion system, such as tccP and espJ, also decreased in expression from exponential to stationary phase. Three of the clusters (n = 154) comprised genes that are transiently upregulated at the transition into stationary phase and included genes involved in nutrient scavenging. Upregulated genes with an increase in mRNA levels from late exponential to early stationary phase belonged to one cluster (n = 923) which includes genes involved in stress responses (e.g. gadAB, osmBC, and dps). These transcript levels remained relatively high for > 3 h in stationary phase. The Shiga toxin genes (stx 1AB and stx 2B) were significantly induced after transition into stationary phase.

Conclusion:

Expression of more than 300 O157-specific ORFs, many implicated in virulence of the O157 pathogen, was modulated in a growth dependent manner. These results provide a baseline transcriptional profile that can be compared to patterns of gene expression of this important foodborne pathogen under adverse environmental conditions.
Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms
Authors: Mellmann Alexander , Weniger Thomas , Berssenbrügge Christoph , Rothgänger Jörg , Sammeth Michael , Stoye Jens , Harmsen Dag
Published: October 2007

Background

For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that this region also reflects long-term epidemiology. However, no automated and objective algorithm existed to cluster different repeat regions. In this study, the Based Upon Repeat Pattern (BURP) implementation that is a heuristic variant of the newly described EDSI algorithm was investigated to infer the clonal relatedness of different spa types.

For calibration of BURP parameters, 400 representative S. aureus strains with different spa types were characterized by MLST and clustered using eBURST as "gold standard" for their phylogeny. Typing concordance analysis between eBURST and BURP clustering (spa-CC) were performed using all possible BURP parameters to determine their optimal combination. BURP was subsequently evaluated with a strain collection reflecting the breadth of diversity of S. aureus (JCM 2002; 40:4544).

Results

In total, the 400 strains exhibited 122 different MLST types. eBURST grouped them into 23 clonal complexes (CC; 354 isolates) and 33 singletons (46 isolates). BURP clustering of spa types using all possible parameter combinations and subsequent comparison with eBURST CCs resulted in concordances ranging from 8.2 to 96.2%. However, 96.2% concordance was reached only if spa types shorter than 8 repeats were excluded, which resulted in 37% excluded spa types. Therefore, the optimal combination of the BURP parameters was "exclude spa types shorter than 5 repeats" and "cluster spa types into spa-CC if cost distances are less than 4" exhibiting 95.3% concordance to eBURST. This algorithm identified 24 spa-CCs, 40 singletons, and excluded only 7.8% spa types. Analyzing the natural population with these parameters, the comparison of whole-genome micro-array groupings (at the level of 0.31 Pearson correlation index) and spa-CCs gave a concordance of 87.1%; BURP spa-CCs vs. manually grouped spa types resulted in 95.7% concordance.

Conclusion

BURP is the first automated and objective tool to infer clonal relatedness from spa repeat regions. It is able to extract an evolutionary signal rather congruent to MLST and micro-array data.
The adhesion molecule Necl-3/SynCAM-2 localizes to myelinated axons, binds to oligodendrocytes and promotes cell adhesion
Authors: Pellissier François , Gerber Alan , Bauer Christoph , Ballivet Marc , Ossipow Vincent
Published: October 2007

Background

Cell adhesion molecules are plasma membrane proteins specialized in cell-cell recognition and adhesion. Two related adhesion molecules, Necl-1 and Necl-2/SynCAM, were recently described and shown to fulfill important functions in the central nervous system. The purpose of the work was to investigate the distribution, and the properties of Necl-3/SynCAM-2, a previously uncharacterized member of the Necl family with which it shares a conserved modular organization and extensive sequence homology.

Results

We show that Necl-3/SynCAM-2 is a plasma membrane protein that accumulates in several tissues, including those of the central and peripheral nervous system. There, Necl-3/SynCAM-2 is expressed in ependymal cells and in myelinated axons, and sits at the interface between the axon shaft and the myelin sheath. Several independent assays demonstrate that Necl-3/SynCAM-2 functionally and selectively interacts with oligodendrocytes. We finally prove that Necl-3/SynCAM-2 is a bona fide adhesion molecule that engages in homo- and heterophilic interactions with the other Necl family members, leading to cell aggregation.

Conclusion

Collectively, our manuscripts and the works on Necl-1 and SynCAM/Necl-2 reveal a complex set of interactions engaged in by the Necl proteins in the nervous system. Our work also support the notion that the family of Necl proteins fulfils key adhesion and recognition functions in the nervous system, in particular between different cell types.
Costs and consequences of treatment for mild gestational diabetes mellitus – evaluation from the ACHOIS randomised trial
Authors: Moss John R , Crowther Caroline A , Hiller Janet E , Willson Kristyn J , Robinson Jeffrey S ,   The Australian Carbohydrate Intolerance Study in Pregnant Women (ACHOIS) Trial Group
Published: October 2007

Background

Recommended best practice is that economic evaluation of health care interventions should be integral with randomised clinical trials. We performed a cost-consequence analysis of treating women with mild gestational diabetes mellitus by dietary advice, blood glucose monitoring and insulin therapy as needed compared with routine pregnancy care, using patient-level data from a multi-centre randomised clinical trial.

Methods

Women with a singleton pregnancy who had mild gestational diabetes diagnosed by an oral glucose-tolerance test between 24 and 34 weeks' gestation and their infants were included. Clinical outcomes and outpatient costs derived from all women and infants in the trial. Inpatient costs derived from women and infants attending the hospital contributing the largest number of enrolments (26.1%), and charges to women and their families derived from a subsample of participants from that hospital (in 2002 Australian dollars). Occasions of service and health outcomes were adjusted for maternal age, ethnicity and parity. Analysis of variance was used with bootstrapping to confirm results. Primary clinical outcomes were serious perinatal complications; admission to neonatal nursery; jaundice requiring phototherapy; induction of labour and caesarean delivery. Economic outcome measures were outpatient and inpatient costs, and charges to women and their families.

Results

For every 100 women with a singleton pregnancy and positive oral glucose tolerance test who were offered treatment for mild gestational diabetes mellitus in addition to routine obstetric care, $53,985 additional direct costs were incurred at the obstetric hospital, $6,521 additional charges were incurred by women and their families, 9.7 additional women experienced induction of labour, and 8.6 more babies were admitted to a neonatal nursery. However, 2.2 fewer babies experienced serious perinatal complication and 1.0 fewer babies experienced perinatal death. The incremental cost per additional serious perinatal complication prevented was $27,503, per perinatal death prevented was $60,506 and per discounted life-year gained was $2,988.

Conclusion

It is likely that the general public in high-income countries such as Australia would find reductions in perinatal mortality and in serious perinatal complications sufficient to justify additional health service and personal monetary charges. Over the whole lifespan, the incremental cost per extra life-year gained is highly favourable.

Trial Registration

Australian Clinical Trials Registry ACTRN12606000294550
Reliability of lumbar spinal palpation, range of motion, and determination of position
Authors: Troke Michael , Schuit Dale , Petersen Cheryl M
Published: October 2007

Background

The study purposes were to investigate the level of agreement of palpation of lumbar spinous processes between examiners, test-retest repeatability of lumbar spine range of motion, and the reliability of upright position measures in asymptomatic subjects.

Methods

The modified CA 6000 spinal motion apparatus with a new skin fixation system was used by three operators for the test-retest spine measurements (3 days apart), and to obtain measures at one session of spinal position. Mean ranges of motion in all planes for 22 asymptomatic subjects were reported using the Intra-class Correlation Coefficient.

Results

Overall, differences in palpation agreement for lumbar segments occurred in three subjects and did not affect range of motion values. For upright spinal position, ICC (2,3) values for sagittal, coronal, and horizontal plane positions were 0.96, 0.80, and 0.98 respectively. There were statistically significant differences between examiners for position values, determined by the Bonferroni t-test (p < 0.05), but the magnitude of the differences were 2 degrees or less, and not considered clinically important.

Conclusion

Results suggest that lumbar spinal motion measurements and position determination between different operators can be consistent particularly if utilizing the modified instrument. Static lumbar position also appears to be recorded reliably between different operators. Results justify progression to multi-center lumbar research using the modified CA 6000 and the work is considered relevant to medical clinicians working with spinal dysfunction, surgical interventions, or occupational health.