bluuebunny/crossref_metadata_2025 huggingface dataset:
Major ampullate spidroins from Euprosthenops australis: multiplicity at protein, mRNA and gene levels
Authors: Rising A. , Johansson J. , Larson G. , Bongcam‐Rudloff E. , Engström W. , Hjälm G.
Published: August 2007

Spider dragline silk possesses extraordinary mechanical properties. It consists of large fibrous proteins called spidroins that display modular structures. It is known to consist of two proteins: the major ampullate spidroin (MaSp) 1 and MaSp2. This study analyses MaSp sequences from the nursery‐web spider Euprosthenops australis. We have identified a previously uncharacterized MaSp2 sequence and a new MaSp‐like spidroin, which display distinct homogenous submotifs within their respective Gly‐rich repeats. Furthermore, a group of MaSp1 cDNA clones show unexpected heterogeneity. Genomic PCR identified several MaSp1 gene variants within individual spiders, which suggests the presence of a gene cluster in E. australis. Finally, the evolution of spidroin genes is discussed in relation to phylogenetic analysis of nonrepetitive C‐terminal domains from diverse species.
Quality of stroke rehabilitation clinical practice guidelines
Authors: Hurdowar Amanda , Graham Ian D. , Bayley Mark , Harrison Margaret , Wood‐Dauphinee Sharon , Bhogal Sanjit
Published: August 2007

Background and purpose  Clinical practice guidelines (CPGs) are systematically developed statements that assist practitioners to provide appropriate evidence‐based care. The purpose of this study was to evaluate the quality of currently published CPGs for stroke care and to examine the reliability and validity of the appraisal of guidelines, research and evaluation (AGREE) instrument.

Methods  Multiple databases and Internet resources were searched for stroke care CPGs. Guidelines included were published in English or French from 1998 to 2004 and developed by a group process. Four appraisers evaluated each CPG using the AGREE instrument. The AGREE consists of 23 items, ranked on a 4‐point Likert scale, that is organized into six domains. A standardized score is calculated separately for each domain and ranges from 0 to 100.

Results  Eight guidelines were identified. The AGREE quality scores were high for the ‘scope and purpose’ domain (mean ± SE = 71.2 ± 5.48, intra‐class correlation (ICC) = 0.66), and ‘clarity and presentation’ (mean ± SE = 70.6 ± 4.43, ICC = 0.66). There was wide variation in ratings of ‘rigour of development’ (mean ± SE = 60.7 ± 7.1, ICC = 0.75) and ‘stakeholder involvement’ (mean ± SE = 52.6 ± 7.14, ICC = 0.89). The ‘editorial independence’ (mean ± SE = 38.1 ± 8.72, ICC = 0.88) and ‘applicability’ (mean ± SE = 35.1 ± 4.93, ICC = 0.75) had the lowest scores.

Conclusions  There is considerable variability in quality of stroke care guidelines but stroke guidelines score higher on the AGREE rigour of development domain than CPGs from other medical fields. The Scottish Intercollegiate Guideline Network, Veterans Affairs/Department of Defence, Royal College of Physicians, and the New Zealand Guidelines Group consistently scored the highest across the domains. Stroke rehabilitation clinicians should consider these results in selecting a guideline. CPG development groups can improve their AGREE scores by considering the cost of implementing their CPGs, pilot testing their CPGs, recording conflict of interest of development panel members and providing tools supporting application of the their CPGs.
Deterministic versus evidence‐based attitude towards clinical diagnosis
Authors: Soltani Akbar , Moayyeri Alireza
Published: August 2007

Generally, two basic classes have been proposed for scientific explanation of events. Deductive reasoning emphasizes on reaching conclusions about a hypothesis based on verification of universal laws pertinent to that hypothesis, while inductive or probabilistic reasoning explains an event by calculation of some probabilities for that event to be related to a given hypothesis. Although both types of reasoning are used in clinical practice, evidence‐based medicine stresses on the advantages of the second approach for most instances in medical decision making. While ‘probabilistic or evidence‐based’ reasoning seems to involve more mathematical formulas at the first look, this attitude is more dynamic and less imprisoned by the rigidity of mathematics comparing with ‘deterministic or mathematical attitude’. In the field of medical diagnosis, appreciation of uncertainty in clinical encounters and utilization of likelihood ratio as measure of accuracy seem to be the most important characteristics of evidence‐based doctors. Other characteristics include use of series of tests for refining probability, changing diagnostic thresholds considering external evidences and nature of the disease, and attention to confidence intervals to estimate uncertainty of research‐derived parameters.
Changes in perceived effect of practice guidelines among primary care doctors
Authors: Cheng Lee , Nieman Linda Z. , Becton James L.
Published: August 2007

Rationale, aims and objectives  Evidence suggests that when doctors use systematically developed clinical practice guidelines they have the potential to improve the safety, quality and value of health care. The purpose of this study was to evaluate recent changes in the perceptions of practice guidelines among US primary care doctors.

Methods  Data were collected from the Community Tracking Survey 1996–97 and 2000–01. All results were weighted and adjusted to reflect the complex survey design.

Results  Over the 5 years, the proportion of primary care doctors who said that practice guidelines had at least a moderate effect on their practice of medicine increased from 45.8% to 60.7%. This increase was nearly equal among primary care doctors of family medicine, internal medicine and paediatrics. In the 2001 survey, a higher perceived effect of practice guidelines was described by female doctors (OR = 1.39, 95% CI 1.19–1.63) and doctors who were practising in a large model group (OR = 1.73; 95% CI 1.04–2.89). Doctors who graduated from medical school within 10 years of the survey were more likely to report that practice guidelines had a positive effect on their practice of medicine than doctors who graduated 10 or more years before the survey.

Conclusion  The perceived effect of practice guidelines on primary care doctors increased over time. Improved dissemination of guidelines and curriculum changes may have led recent primary care graduates to view practice guidelines as more important.
Impact of consensus development conference guidelines on primary care of bronchiolitis: are national guidelines being followed?
Authors: Touzet Sandrine , Réfabert Luc , Letrilliart Laurent , Ortolan Bernard , Colin Cyrille
Published: August 2007

Aim  To measure the impact of French national consensus guidelines on the clinical practices of primary care paediatricians and general practitioners.

Design  Non‐randomized intervention study, with a first survey 1 year before the consensus development conference and a second survey 1 year after.

Intervention  Implementation of bronchiolitis management guidelines through the medical press and the Internet.

Subjects  Paediatricians and general practitioners treating infants 1 year of age and under consulting for a first‐time episode of bronchiolitis.

Results  Ninety‐three doctors and 510 infants were included during the first phase of the study and 96 doctors and 394 infants during the second phase. This study showed a slight increase in adherence to the guidelines for non‐validated drugs (6.6% adherence before and 14.3% after), general advice (29.0% adherence before and 57.1% after) and flow modulation respiratory physical therapy (91.9% adherence before and 98.8% after). Increase in adherence to guidelines for other practices, that is, hospitalization, prescribing antibiotics and complementary examinations, was not statistically significant. Adherence to the guidelines on providing general advice increased the most between the two studies.

Conclusion  The guidelines helped practitioners evolve slightly in their approach to the treatment of bronchiolitis. Non‐validated drugs remain frequently used. Additional resources for implementing the guidelines should be provided to improve primary care doctors’ practices.
Evaluating primary care doctors’ evidence‐based medicine skills in a busy clinical setting
Authors: Shuval Kerem , Shachak Aviv , Linn Shai , Brezis Mayer , Reis Shmuel
Published: August 2007

Rationale, aims and objectives  To date, primary care doctors’ (PCDs) evidence‐based medicine (EBM) skills have rarely been studied. We conducted a cross‐sectional study to evaluate PCDs’ practical EBM skills and to determine risk markers associated with these skills.

Methods  The study sample consisted of 70 PCDs (70.7% response rate) practising in a busy urban setting from a large health maintenance organization. Participants were given a short validated questionnaire gauging attitudes, barriers, online medical resources utilization, as well as demographic and personal characteristics. Additionally, doctors completed an online and written exam evaluating their ability to formulate clinical questions, and retrieve medical information efficiently. Data analysis was performed using both bivariate and multivariate analysis (linear regression).

Results  PCDs found it difficult to formulate clinical questions both in the written and online exam, mostly neglecting to mention the Patient and Comparison components of PICO (patient, intervention, comparison and outcome). Search strategies primarily dispensed with the use of MeSH terms, ignoring appropriate limits. Doctors final scores were low (score = 41.5/100, SD = 16.2). In bivariate analysis clinical experience was negatively correlated with the final score (r = −0.36, P = 0.01), and specialists’ scores were significantly higher than general practitioners’ scores (46.7/100 and 31.5/100 respectively, P < 0.001). In multivariate analysis, doctors specialization was the only statistically significant predictor of the final score (B = 12.74, P = 0.002), while controlling for participating in a prior EBM course.

Conclusions  This study emphasizes the need for enhancing PCDs practical EBM skills. Future research and interventions should focus on this population emphasizing the specific needs of subpopulations (i.e. general practitioners and doctors without previous EBM training).
Medical evidence and health policy: a marriage of convenience? The case of proton pump inhibitors
Authors: Van Driel Mieke L. , Vander Stichele Robert , De Maeseneer Jan , De Sutter An , Christiaens Thierry
Published: August 2007

Rationale  In Belgium, several policies regulating reimbursement of acid suppressant drugs and evidence‐based recommendations for clinical practice were issued in a short period of time, creating a unique opportunity to observe their effect on prescribing.

Aims and objectives  To describe the evolution of prescriptions for acid suppressants and explore the interaction of policies and practice recommendations with prescribing patterns.

Method  Monthly claims‐based data for proton pump inhibitors (PPIs) and H2‐antihistamines by general practitioners, internists and gastroenterologists were obtained from the Belgian national health insurance database (1997–2005). The evolution of reimbursed defined daily doses and expenses after introduction of reimbursement regulations and dissemination of practice recommendations was explored.

Results  Recommendations had no impact on prescribing. All changes can be related to concomitant policies. Lifting reimbursement restrictions for cheaper products did not control growth or save costs in the long term. Only restricting reimbursement of all PPIs managed to curb the growth. We observed an unintended increase of non‐omeprazole PPIs by gastroenterologists.

Conclusions  Reimbursement policies influence prescribing, but their effect can be unintended. A dialogue between policymakers and guideline developers, and evidence‐based policies that are linked to clinical guidelines, could be an effective way to pursue both cost‐containment and quality of care.
No exit? Intellectual integrity under the regime of ‘evidence’ and ‘best‐practices’
Authors: Murray Stuart J. , Holmes Dave , Perron Amélie , Rail Geneviève
Published: August 2007

No exit? Have we arrived at an impasse in the health sciences? Has the regime of ‘evidence’, coupled with corporate models of accountability and ‘best‐practices’, led to an inexorable decline in innovation, scholarship, and actual health care? Would it be fair to speak of a ‘methodological fundamentalism’ from which there is no escape? In this article, we make an argument about intellectual integrity and good faith. We take this risk knowing full well that we do so in a hostile political climate in the health sciences, positioning ourselves against those who quietly but assiduously control the very terms by which the public faithfully understands ‘integrity’ and ‘truth’. In doing so, we offer an honest critique of these definitions and of the systemic power that is reproduced and guarded by the gatekeepers of ‘Good Science’.
Availability and development of guidelines in a tertiary teaching hospital
Authors: Guo Yang , Adelstein Barbara‐Ann , Rubin George L.
Published: August 2007

Objective  The purpose of this study was to review existing guidelines in clinical departments and describe their characteristics, development and implementation at a large teaching hospital in Sydney, Australia.

Methods  The study was undertaken in two stages. First, from September to November 2005, we reviewed and classified documents from eight departments as clinical practice guidelines (CPGs), clinical procedural protocols (technology and technique) or administrative guidelines. We also collected information about the scope, format and target user of the guidelines. Second, from March to June 2006, we interviewed department staff in seven of eight participating departments about the guidelines’ development and implementation. A revised Appraisal of Guidelines Research and Evaluation questionnaire was used to collect data in both stages.

Results  A total of 368 of 509 documents reviewed were classified as CPGs. Almost 90% of the CPGs had five or fewer pages; nearly 80% had no references; and 90% had no application tools. The CPGs had been developed locally by each individual department. The departments used various methods to collect evidence. In six (albeit a different six departments in each case) of seven departments, clinicians’ clinical experience was used in the analysis of the evidence; informal expert consensus was used for formulating recommendations; internal peer review was the major method used to review the guidelines (after drafting); hard copy of guidelines was the major medium used; and provision of educational material was the major implementation strategy.

Conclusions  There was great variation in the number, availability and presentation of guidelines in the departments. There was a lack of standardized methods and narrow skills representation during guideline development.
Teaching evidence‐based practice: the teachers consider the content
Authors: Yousefi‐Nooraie Reza , Rashidian Arash , Keating Jennifer L. , Schonstein Eva
Published: August 2007

Objective  To identify the views of evidence‐based practice (EBP) experts about information that should be included in EBP courses.

Design  A two‐round Delphi process.

Setting and subject  The panel of experts in teaching EBP residing in developed and developing countries identified through purposive and snowball sampling.

Main outcome measures  We developed a list of 49 topics representing key educational topics. The panel scored the importance of topics for inclusion in introductory and advanced courses. In the second round, we sent a summary of results to the panel and asked them to re‐score in light of the group’s responses.

Results  We used email to invite 105 EBP teachers to participate in the study. Fifty‐one people from 15 countries agreed to participate, and 40 completed the second round. We achieved consensus that formulating clinical questions, searching pre‐appraised resources, introduction to systematic reviews and critical appraisal of studies about therapy should be covered earlier in EBP courses while other critical appraisal topics and quantitative decision‐making techniques should be left to more advanced levels.

Conclusion  Experts concur that introductory EBP courses should be simple and certain topics should be avoided. Specifically, critical appraisal and statistical methods should be left to advanced courses.
Mapping the Cochrane evidence for decision making in health care
Authors: El Dib Regina P. , Atallah Álvaro N. , Andriolo Regis B.
Published: August 2007

Rationale and aim  Over the past 12 years, thousands of authors working with the Cochrane Collaboration around the world have produced systematic reviews to reduce uncertainty in health care decision making. We evaluated the conclusions from Cochrane systematic reviews of randomized controlled trials in terms of their recommendations for clinical practice and research.

Methods  In our cross‐sectional study of systematic reviews published in the Cochrane Library, we randomly selected and analysed completed systematic reviews published across all 50 Cochrane Collaborative Review Groups.

Results  We analysed 1016 completed systematic reviews. Of these, 44% concluded that the interventions studied were likely to be beneficial, of which 1% recommended no further research and 43% recommended additional research. Also, 7% of the reviews concluded that the interventions were likely to be harmful, of which 2% did not recommend further studies and 5% recommended additional studies. In total, 49% of the reviews reported that the evidence did not support either benefit or harm, of which 1% did not recommend further studies and 48% recommended additional studies. Overall, 96% of the reviews recommended further research.

Conclusions  Cochrane systematic reviews were about evenly split between those in which the authors concluded that at least one of the interventions was beneficial and those in which the evidence neither supported nor refuted the intervention tested. The Cochrane Collaboration needs to include clinical trial protocol summaries with a study design optimized to answer the relevant research questions.
Psychological variables as correlates of adjustment in mothers of children with intellectual disabilities: cross‐sectional and longitudinal relationships
Authors: Lloyd T. , Hastings R. P.
Published: August 2007

Background  Existing research studies suggest that parenting a child with intellectual disabilities (ID) can be a stressful experience. However, there are few data addressing the question of how or why parents might experience considerable distress. In the present study, psychological variables (acceptance, mindfulness, avoidant coping) are explored that may explain some variance in maternal distress.

Method  Questionnaire data were gathered from mothers of children attending special schools at two time points, 18 months apart (n = 91 at Time 1; n = 57 at Time 2). In addition to measures of the child's functioning, the questionnaire pack included: a measure of acceptance of unwanted thoughts/feelings; a measure of attention to the present (mindfulness); a measure of active avoidance coping; measures of maternal anxiety, depression and stress; and a measure of mothers' positive perceptions of their child.

Results  In cross‐sectional analysis, acceptance was negatively associated with maternal anxiety, depression and stress, such that mothers who were generally more accepting reported fewer psychological adjustment problems. Longitudinal analysis showed that acceptance is bidirectionally related to anxiety and depression. Mindfulness was not significantly related to maternal distress, and avoidance coping was positively cross‐sectionally associated with depression only. There were no associations between psychological variables and maternal positive perceptions.

Conclusions  These data suggest that acceptance, in particular, may be a construct that explains some variance in maternal distress. Further research could focus on the utility of acceptance‐based interventions (e.g. Acceptance and Commitment Therapy) in the support of families with a child with ID.
Microalbuminuria is a negative correlate for cognitive function in older adults with peripheral arterial disease: results from the U.S. National Health and Nutrition Examination Survey 1999–2002
Authors: Kuo H.‐K. , Lin L.‐Y. , Yu Y.‐H.
Published: August 2007

Objectives.  Microalbuminuria (MA) has been increasingly identified as a marker of cardiovascular risk. Although poor cognitive function has been implicated as a sequelae of increased cardiovascular burden, little is known about the association between MA and cognitive function.

Design.  Population‐based cross‐sectional study.

Settings.  National Health and Nutrition Examination Survey 1999–2002 in the USA.

Subjects.  2049 noninstitutionalized adults (≥60 years) with nonmissing values in cognitive test, urinary albumin‐to‐creatinine ratio (UACR) and ankle‐brachial blood pressure index (ABPI) was analysed. Participants with UACR >300 μg mg−1 were excluded.

Main outcome measures.  The UACR, in the unit of μg mg−1, was calculated by dividing the urinary albumin value by the urinary creatinine concentration. MA was defined as UACR between 30 and 300 μg mg−1. Cognitive function was measured by a 2‐min Digit Symbol Substitution Test (DSST). Peripheral artery disease (PAD) was defined as an ABPI <0.9 in either leg.

Results.  Overall speaking, MA was inversely associated with DSST score after controlling for age, sex, race, body mass index and educational level (regression coefficient = −2.8, P = 0.002). There was an effect modification of PAD on the association between MA and the DSST score. Amongst participants with PAD, the DSST score for those with MA was lower than those without MA (β = −6.3, P = 0.003) after multivariate adjustment. Moreover, participants with PAD in the highest quartile of UACR had significantly lower DSST score compared to those in the lowest quartile (β = −8.7, P = 0.001). There was no association between MA and cognitive function amongst participants without PAD. We observed an additive effect of MA and PAD on DSST score. Participants with both MA and PAD had a lower mean DSST score compared to those without both conditions (β = −6.2, P = 0.003).

Conclusions.  The presence of MA or a higher level of urinary albumin excretion was inversely associated with cognitive function in participants with PAD.
Comparison of deaths related to Hepatitis C and AIDS in Scotland
Authors: Palmateer N. E. , Hutchinson S. J. , McLeod A. , Codere G. , Goldberg D. J.
Published: August 2007

Summary.  In resource‐rich countries, the incidence of and mortality from AIDS has fallen dramatically since the introduction of combination antiretroviral therapy. In contrast, developed countries have observed increases in the public health burden associated with the hepatitis C virus (HCV). We compared past and current trends in mortality related to HCV sequelae and HIV/AIDS in Scotland by linking death records with national databases of persons diagnosed with HCV and HIV/AIDS. AIDS‐related deaths increased rapidly during the late‐1980s to mid‐1990s and declined dramatically after 1996. Deaths related to HCV (i.e., viral hepatitis, liver cancer, alcoholic liver disease, or non‐alcoholic liver disease) surpassed the number of AIDS‐related deaths in 1998 and increased at an average annual rate of 10.5% (95% confidence interval = 7–14%) during 1996–2005. The leading underlying cause of HCV‐related deaths was alcoholic liver disease (50% of deaths during 2001–2005). This study highlights the increasing public health burden, vis‐à‐vis mortality, of HCV, when compared with HIV/AIDS in developed countries. Increased diagnosis and treatment of eligible HCV‐infected individuals will be required if we wish to mitigate the future impact of HCV morbidity and mortality.
Genetic adaptation to captivity in species conservation programs
Authors: FRANKHAM RICHARD
Published: August 2007

As wild environments are often inhospitable, many species have to be captive‐bred to save them from extinction. In captivity, species adapt genetically to the captive environment and these genetic adaptations are overwhelmingly deleterious when populations are returned to wild environments. I review empirical evidence on (i) the genetic basis of adaptive changes in captivity, (ii) factors affecting the extent of genetic adaptation to captivity, and (iii) means for minimizing its deleterious impacts. Genetic adaptation to captivity is primarily due to rare alleles that in the wild were deleterious and partially recessive. The extent of adaptation to captivity depends upon selection intensity, genetic diversity, effective population size and number of generation in captivity, as predicted by quantitative genetic theory. Minimizing generations in captivity provides a highly effective means for minimizing genetic adaptation to captivity, but is not a practical option for most animal species. Population fragmentation and crossing replicate captive populations provide practical means for minimizing the deleterious effects of genetic adaptation to captivity upon populations reintroduced into the wild. Surprisingly, equalization of family sizes reduces the rate of genetic adaptation, but not the deleterious impacts upon reintroduced populations. Genetic adaptation to captivity is expected to have major effects on reintroduction success for species that have spent many generations in captivity. This issue deserves a much higher priority than it is currently receiving.
Stability of genetic variance and covariance for reproductive characters in the face of climate change in a wild bird population
Authors: GARANT DANY , HADFIELD JARROD D. , KRUUK LOESKE E. B. , SHELDON BEN C.
Published: August 2007

Global warming has had numerous effects on populations of animals and plants, with many species in temperate regions experiencing environmental change at unprecedented rates. Populations with low potential for adaptive evolutionary change and plasticity will have little chance of persistence in the face of environmental change. Assessment of the potential for adaptive evolution requires the estimation of quantitative genetic parameters, but it is as yet unclear what impact, if any, global warming will have on the expression of genetic variances and covariances. Here we assess the impact of a changing climate on the genetic architecture underlying three reproductive traits in a wild bird population. We use a large, long‐term, data set collected on great tits (Parus major) in Wytham Woods, Oxford, and an ‘animal model’ approach to quantify the heritability of, and genetic correlations among, laying date, clutch size and egg mass during two periods with contrasting temperature conditions over a 40‐year period (1965–1988 [cooler] vs. 1989–2004 [warmer]). We found significant additive genetic variance and heritability for all traits under both temperature regimes. We also found significant negative genetic covariances and correlations between clutch size and egg weight during both periods, and among laying date and clutch size in the colder years only. The overall G matrix comparison among periods, however, showed only a minor difference among periods, thus suggesting that genotype by environment interactions are negligible in this context. Our results therefore suggest that despite substantial changes in temperature and in mean laying date phenotype over the last decades, and despite the large sample sizes available, we are unable to detect any significant change in the genetic architecture of the reproductive traits studied.
The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation
Authors: LI MENG‐HUA , TAPIO ILMA , VILKKI JOHANNA , IVANOVA ZOYA , KISELYOVA TATYANA , MARZANOV NURBY , ĆINKULOV MIRJANA , STOJANOVIĆ SRDJAN , AMMOSOV INNOKENTY , POPOV RUSLAN , KANTANEN JUHA
Published: August 2007

We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian‐based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within‐population differences accounted for ~90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of ‘genetic endemism’, where cattle populations should be given conservation priority. The results will also be of importance for cost‐effective management of their future utilization.
Cross‐species transfer of nuclear microsatellite markers: potential and limitations
Authors: BARBARÁ THELMA , PALMA‐SILVA CLARISSE , PAGGI GECELE M. , BERED FERNANDA , FAY MICHAEL F. , LEXER CHRISTIAN
Published: August 2007

Molecular ecologists increasingly require ‘universal’ genetic markers that can easily be transferred between species. The distribution of cross‐species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross‐species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross‐species transferable markers.
Genetic variation and differentiation in captive and wild zebra finches (Taeniopygia guttata)
Authors: FORSTMEIER WOLFGANG , SEGELBACHER GERNOT , MUELLER JAKOB C. , KEMPENAERS BART
Published: August 2007

The zebra finch (Taeniopygia guttata) is a small Australian grassland songbird that has been domesticated over the past two centuries. Because it is easy to breed in captivity, it has become a widely used study organism, especially in behavioural research. Most work has been conducted on domesticated populations maintained at numerous laboratories in Europe and North America. However, little is known about the extent to which, during the process of domestication, captive populations have gone through bottlenecks in population size, leading to inbred and potentially genetically differentiated study populations. This is an important issue, because (i) behavioural studies on captive populations might suffer from artefacts arising from high levels of inbreeding or lack of genetic variation in such populations, and (ii) it may hamper the comparability of research findings. To address this issue, we genotyped 1000 zebra finches from 18 captive and two wild populations at 10 highly variable microsatellite loci. We found that all captive populations have lost some of the genetic variability present in the wild, but there is no evidence that they have gone through a severe bottleneck, as the average captive population still showed a mean of 11.7 alleles per locus, compared to a mean of 19.3 alleles/locus for wild zebra finches. We found significant differentiation between the captive populations (FST = 0.062). Patterns of genetic similarity closely match geographical relationships, so the most pronounced differences occur between the three continents: Australia, North America, and Europe. By providing a tree of the genetic similarity of the different captive populations, we hope to contribute to a better understanding of variation in research findings obtained by different laboratories.
Molecular analysis of dispersal in giant pandas
Authors: ZHAN X. J. , ZHANG Z. J. , WU H. , GOOSSENS B. , LI M. , JIANG S. W. , BRUFORD M. W. , WEI F. W.
Published: August 2007

Although dispersal in the giant panda (Ailuropoda melanoleuca) is a demographic mechanism which can potentially counteract the negative effect of habitat fragmentation, little is known about dispersal in this species because of difficulties in observing individuals. Using data from faecal microsatellite genotyping, we compared the spatial distribution of giant pandas in two populations and the proximity of relatives in one key population to infer their dispersal pattern. We conclude that giant pandas exhibit female‐biased dispersal because: (i) vAIc (variance of assignment index) for females was significantly larger than for males, suggesting that females comprise both ‘local’ and ‘foreign’ genotypes; (ii) the average spatial distance of related female dyads was significantly larger than that of males; (iii) largerr(relatedness),FST(genetic variance among populations) andmAIc(mean of assignment index) values were found in males using the software FSTAT, although the differences were not significant; (iv) males set up territories neighbouring to their birth place; (v) significant population structure using microsatellites with a concomitant lack of mitochondrial structure was found in a previous study, possibly indicating more extensive female dispersal; and (vi) female‐biased dispersal was strongly supported by evidence from concomitant ecological studies. Considering previous ecological data and life‐history characteristics of the giant panda, female‐biased dispersal is most likely to be due to competition for birth dens among females, inbreeding avoidance and enhancing inclusive fitness among related males.
Structural similarity between the DnaA‐binding proteins HobA (HP1230) from Helicobacter pylori and DiaA from Escherichia coli
Authors: Natrajan Ganesh , Hall David R. , Thompson Alex C. , Gutsche Irina , Terradot Laurent
Published: August 2007

In prokaryotes, DNA replication is initiated by the binding of DnaA to the oriC region of the chromosome to load the primosome machinery and start a new replication round. Several proteins control these events in Escherichia coli to ensure that replication is precisely timed during the cell cycle. Here, we report the crystal structure of HobA (HP1230) at 1.7 Å, a recently discovered protein that specifically interacts with DnaA protein from Helicobacter pylori (HpDnaA). We found that the closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. Remarkably, SIS proteins share strong sequence homology with DiaA from E. coli; yet, HobA and DiaA share no sequence homology. Thus, by solving the structure of HobA, we unexpectedly discovered that HobA is a H. pylori structural homologue of DiaA. By comparing the structure of HobA to a homology model of DiaA, we identified conserved, surface‐accessible residues that could be involved in protein–protein interaction. Finally, we show that HobA specifically interacts with the N‐terminal part of HpDnaA. The structural homology between DiaA and HobA strongly supports their involvement in the replication process and these proteins could define a new structural family of replication regulators in bacteria.
Polyhead formation in phage P22 pinpoints a region in coat protein required for conformational switching
Authors: Parent Kristin N. , Suhanovsky Margaret M. , Teschke Carolyn M.
Published: August 2007

Eighteen single amino acid substitutions in phage P22 coat protein cause temperature‐sensitive folding defects (tsf). Three intragenic global suppressor (su) substitutions (D163G, T166I and F170L), localized to a flexible loop, rescue the folding of several tsf coat proteins. Here we investigate the su substitutions in the absence of the original tsf substitutions. None of the su variant coat proteins displayed protein folding defects. Individual su substitutions had little effect on phage production in vivo; yet double and triple combinations resulted in a cold‐sensitive (cs) phenotype, consistent with a defect in assembly. During virus assembly and maturation, conformational switching of capsid subunits is required when chemically identical capsid subunits form an icosahedron. Analysis of double‐ and triple‐su phage‐infected cell lysates by negative‐stain electron microscopy reveals an increase in aberrant structures at the cs temperature. In vitro assembly of F170L coat protein causes production of polyheads, never seen before in phage P22. Purified procapsids composed of all of the su coat proteins showed defects in expansion, which mimics maturation in vitro. Our results suggest that a previously identified surface‐exposed loop in coat protein is critical in conformational switching of subunits during both procapsid assembly and maturation.
Oxidative folding of small Tims is mediated by site‐specific docking onto Mia40 in the mitochondrial intermembrane space
Authors: Sideris Dionisia P. , Tokatlidis Kostas
Published: August 2007

Oxidative folding in the mitochondrial intermembrane space (IMS) is crucial for the import of certain cysteine‐rich IMS proteins. The essential proteins Mia40 and Erv1 are key components for this mechanism functioning as a disulphide protein cascade that is functionally linked to the respiratory chain by shuttling electrons onto CytC. The subunits of the chaperone complex Tim9–Tim10 require Mia40 for their biogenesis. Previously, it was shown that the four cysteines of Tim10 are crucial for folding and assembly, that they are connected intramolecularly into an inner and an outer disulphide bridge, and that the inner disulphide has a more prominent role in these processes. Here we show that interaction with Mia40 is a site‐specific event: (i) the N‐terminal first cysteine of the precursor is crucial for docking onto Mia40 via a mixed disulphide; (ii) release is triggered by disulphide pairing of the C‐terminal cysteine onto the N‐terminal one; and (iii) formation of the inner disulphide between the second and third cysteines apparently precedes the release reaction and is critical for assembly with Tim9. The Tim10–Mia40 interaction is independent of divalent cations, any other mitochondrial proteins or membranes, and is shown to occur efficiently in organello and in vitro.
A huge filamentary structure at z= 0.55 and star formation histories of galaxies at z < 1
Authors: Tanaka Masayuki , Hoshi Takako , Kodama Tadayuki , Kashikawa Nobunari
Published: August 2007

We report a definitive confirmation of a large-scale structure around the super rich cluster CL0016+1609 at z= 0.55. We made spectroscopic follow-up observations with Faint Object Camera and Spectrograph (FOCAS) on Subaru along the large filamentary structure identified in our previous photometric studies, including some subclumps already found by other authors. We have confirmed the physical connection of the huge filament extending over 20h−170 Mpc in the north–south (NS) direction hosting the main cluster and several clumps aligned in a chain-like structure. We have also confirmed a physical association of a new filament extending from the main cluster to the east, which was newly discovered by us. Based on a simple energy argument, we show that it is likely that most of the clumps are bound to the main CL0016 cluster. Given its spatial extent and richness, this structure is surely one of the most prominent confirmed structures ever identified in the distant Universe, which then serves as an ideal laboratory to examine the environmental variation of galaxy properties. We draw star formation histories of galaxies from the composite spectra of red galaxies in field, group and cluster environments. Combining the results from our previous studies, we find that red galaxies in groups at z∼ 0.8 and red field galaxies at z∼ 0.5 show strong Hδ absorption lines for their D4000 indices. These are the environments in which we observed the on-going build-up of the colour–magnitude relation in our previous photometric analyses. The strong Hδ absorption lines observed in their composite spectra imply that their star formation is truncated on a relatively short time-scale in these relatively low density environments. We suggest that galaxy–galaxy interactions are the most likely physical driver of the truncation of star formation and thus responsible for the build-up of the colour–magnitude relation since z∼ 1.
Identification of a 150 bp cis‐acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant
Authors: GIRIN THOMAS , LEJAY LAURENCE , WIRTH JUDITH , WIDIEZ THOMAS , PALENCHAR PETER M , NAZOA PATRICIA , TOURAINE BRUNO , GOJON ALAIN , LEPETIT MARC
Published: August 2007

The Arabidopsis thaliana AtNRT2.1 gene, which encodes a NO3‐ transporter involved in high‐affinity uptake by the roots, is a molecular target of several mechanisms responsible for the regulation of root NO3‐ acquisition by the N status of the plant. All levels of AtNRT2.1 expression (promoter activity, transcript level, protein accumulation, transport activity) are coordinately up‐regulated in the presence of NO3‐, and repressed by downstream N metabolites. Transgenic plants expressing the GUS reporter gene under the control of upstream sequences of AtNRT2.1 have been studied to identify elements targeted by these two regulatory mechanisms. A 150 bp sequence located upstream of the TATA box that is required for both stimulation by NO3‐ and repression by N metabolites of the promoter has been identified. This sequence is able to confer these two regulations to a minimal promoter. Split‐root experiments indicate that the stimulation of the chimaeric promoter by NO3‐ occurs only at the local level, whereas its repression by N metabolites is mediated by a systemic signal spread to the whole plant. The activity of the cis‐acting 150 bp element is also regulated by sucrose supply to the roots, suggesting a possible interaction between N and C signalling within this short region. Accordingly, multiple motifs potentially involved in regulations by N and/or C status are identified within this sequence by bioinformatic approaches. This is the first report of such a cis‐acting element in higher plants.
A red algal bloom in the aftermath of the Marinoan Snowball Earth
Authors: Elie Marcel , Nogueira Afonso C.R. , Nédélec Anne , Trindade Ricardo I.F. , Kenig Fabien
Published: August 2007

Organic matter from the cap dolostones overlying the Marinoan‐age glacigenic diamictites of the Araras Group, Amazon craton, has been studied to reconstruct the post‐glacial ecosystem. Molecular fossils indicate that the post‐Marinoan ecosystem was marked by an apparent decline in marine algal diversity. The proliferation of red algae may be explained by environmental changes, such as a massive nutrient input accompanying continental weathering after the ice thaw and a dimer light penetrating sea water due to the drowning of the platform. In addition, the presence of green sulphur bacteria indicates that sea water was stratified with an anoxic (possibly euxinic, i.e. sulphidic) layer at the water–sediment interface. Sulphur cycling probably occurred at the redox boundary as suggested by the recognition of active sulphate reduction. This observation supports a microbially induced model for the formation of the cap dolostones.
Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos
Authors: Alonso Ana P. , Goffman Fernando D. , Ohlrogge John B. , Shachar‐Hill Yair
Published: August 2007

The efficiency with which developing sunflower embryos convert substrates into seed storage reserves was determined by labeling embryos with [U‐14C6]glucose or [U‐14C5]glutamine and measuring their conversion to CO2, oil, protein and other biomass compounds. The average carbon conversion efficiency was 50%, which contrasts with a value of over 80% previously observed in Brassica napus embryos (Goffman et al., 2005), in which light and the RuBisCO bypass pathway allow more efficient conversion of hexose to oil. Labeling levels after incubating sunflower embryos with [U‐14C4]malate indicated that some carbon from malate enters the plastidic compartment and contributes to oil synthesis. To test this and to map the underlying pattern of metabolic fluxes, separate experiments were carried out in which embryos were labeled to isotopic steady state using [1‐13C1]glucose, [2‐13C1]glucose, or [U‐13C5]glutamine. The resultant labeling in sugars, starch, fatty acids and amino acids was analyzed by NMR and GC‐MS. The fluxes through intermediary metabolism were then quantified by computer‐aided modeling. The resulting flux map accounted well for the labeling data, was in good agreement with the observed carbon efficiency, and was further validated by testing for agreement with gas exchange measurements. The map shows that the influx of malate into oil is low and that flux through futile cycles (wasting ATP) is low, which contrasts with the high rates previously determined for growing root tips and heterotrophic cell cultures.
Epidemiology of rhinitis in Portugal: evaluation of the intermittent and the persistent types
Authors: Todo‐Bom A. , Loureiro C. , Almeida M. M. , Nunes C. , Delgado L. , Castel‐Branco G. , Bousquet J.
Published: August 2007

Background:  The prevalence of rhinitis is rapidly increasing in recent years and has become a major public health problem in developed countries. A new classification of allergic rhinitis has been proposed by the allergic rhinitis and its impact on asthma group. In this study we aimed to evaluate the prevalence of rhinitis, including different rhinitis subtypes and to describe the severity, rate of diagnosis and use of medication in this pathology.

Methods:  A cross‐sectional, population‐based study including 6859 questionnaire responses was performed.

Results:  The estimated prevalence of rhinitis was 26.1% (48% for intermittent vs 52% for persistent rhinitis). Only about one‐third of the rhinitis cases (31.9%) had done skin prick tests (35.3% for persistent rhinitis vs 21.5% for intermittent rhinitis: P < 0.001) or had medication prescribed in the last year (34%), (35.6% for persistent rhinitis vs 20.1% for intermittent rhinitis : P < 0.001). The prevalence of rhinitis was higher in women (28.2 vs 22.2%; P < 0.001). Intermittent/persistent rhinitis showed the following percentages : ≤25 years (65.6 vs 34.5, P = 0.001); 25–65 years (50.2 vs 49.5) ≥ 65 years (52.1vs 47.9).

The estimated prevalence of rhino conjunctivitis was 18.4%. In a severity scale from 0 to 10, the mean value was 6.1 points (6.4 for persistent rhinitis vs 4.8 for intermittent rhinitis: P < 0.001).

Conclusion:  A significant prevalence of rhinitis and rhino conjunctivitis was identified in all age groups. The severity, the frequency and duration of the symptoms which classify the persistent type should be considered to establish a more effective treatment and improve the quality of life of the patients with rhinitis.