bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel APC mutations in Czech and Slovak FAP families: clinical and genetic aspects
Authors: Stekrova Jitka , Sulova Martina , Kebrdlova Vera , Zidkova Katerina , Kotlas Jaroslav , Ilencikova Denisa , Vesela Kamila , Kohoutova Milada
Published: May 2007

Background

Germline mutations in the adenomatous polyposis gene (APC) result in familial adenomatous polyposis (FAP). FAP is an autosomal dominantly inherited disorder predisposing to colorectal cancer. Typical FAP is characterized by hundreds to thousands of colorectal adenomatous polyps and by several extracolonic manifestations. An attenuated form of polyposis (AFAP) is characterized by less than 100 adenomas and later onset of the disease.

Methods

Here, we analyzed the APC gene for germline mutations in 59 Czech and 15 Slovak FAP patients. In addition, 50 apparently APC mutation negative Czech probands and 3 probands of Slovak origin were screened for large deletions encompassing the APC gene. Mutation screening was performed using denaturing gradient gel electrophoresis and/or protein truncation test. DNA fragments showing an aberrant electrophoretic banding pattern were sequenced. Screening for large deletions was performed by multiplex ligation dependent probe amplification. The extent of deletions was analyzed using following microsatellite markers: D5S299, D5S82, D5S134 and D5S346.

Results

In the set of Czech and Slovak patients, we identified 46 germline mutations among 74 unrelated probands. Total mutation capture is 62,2% including large deletions. Thirty seven mutations were detected in 49 patients presenting a classical FAP phenotype (75,5%) and 9 mutations in 25 patients with attenuated FAP (36%). We report 20 novel germline APC mutations and 3 large deletions (6%) encompassing the whole-gene deletions and/or exon 14 deletion. In the patients with novel mutations, correlations of the mutation localization are discussed in context of the classical and/or attenuated phenotype of the disease.

Conclusion

The results of the molecular genetic testing are used both in the establishment of the predictive diagnosis and in the clinical management of patients. In some cases this study has also shown the difficulty to classify clinically between the classical and the attenuated form of FAP according to the established criteria. Interfamilial and/or intrafamilial phenotype variability was also confirmed in some cases which did not fit well with predicted genotype-phenotype correlation. All these findings have to be taken into consideration both in the genetic counselling and in the patient care.
Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy
Authors: Nishiyama Atsushi , Takeshima Yasuhiro , Saiki Kayoko , Narukage Akiko , Oyazato Yoshinobu , Yagi Mariko , Matsuo Masafumi
Published: May 2007

Background

Myostatin is a negative regulator of skeletal muscle growth. Truncating mutations in the myostatin gene have been reported to result in gross muscle hypertrophy. Duchenne muscular dystrophy (DMD), the most common lethal muscle wasting disease, is a result of an absence of muscle dystrophin. Although this disorder causes a rather uniform pattern of muscle wasting, afflicted patients display phenotypic variability. We hypothesized that genetic variation in myostatin is a modifier of the DMD phenotype.

Methods

We analyzed 102 Japanese DMD patients for mutations in the myostatin gene.

Results

Two polymorphisms that are commonly observed in Western countries, p.55A>T and p.153K>R, were not observed in these Japanese patients. An uncommon polymorphism of p.164E>K was uncovered in four cases; each patient was found to be heterozygous for this polymorphism, which had the highest frequency of the polymorphism observed in the Japanese patients. Remarkably, two patients were found to be heterozygous for one of two novel missense mutations (p.95D>H and p.156L>I). One DMD patient carrying a novel missense mutation of p.95D>H was not phenotypically different from the non-carriers. The other DMD patient was found to carry both a novel mutation (p.156L>I) and a known polymorphism (p.164E>K) in one allele, although his phenotype was not significantly modified. Any nucleotide change creating a target site for micro RNAs was not disclosed in the 3' untranslated region.

Conclusion

Our results indicate that heterozygous missense mutations including two novel mutations did not produce an apparent increase in muscle strength in Japanese DMD cases, even in a patient carrying two missense mutations.
Up-regulation of expression and lack of 5' CpG island hypermethylation of p16 INK4ain HPV-positive cervical carcinomas
Authors: Ivanova Tatiana A , Golovina Daria A , Zavalishina Larisa E , Volgareva Galina M , Katargin Alexey N , Andreeva Yulia Y , Frank Georgy A , Kisseljov Fjodor L , Kisseljova Natalia P
Published: May 2007

Background

High risk type human papilloma viruses (HR-HPV) induce carcinomas of the uterine cervix by expressing viral oncogenes E6 and E7. Oncogene E7 of HR-HPV disrupts the pRb/E2F interaction, which negatively regulates the S phase entry. Expression of tumor suppressor p16ink4a drastically increases in majority of HR-HPV associated carcinomas due to removal of pRb repression. The p16ink4a overexpression is an indicator of an aberrant expression of viral oncogenes and may serve as a marker for early diagnostic of cervical cancer. On the other hand, in 25–57% of cervical carcinomas hypermethylation of the p16 INK4a promoter has been demonstrated using a methylation-specific PCR, MSP. To evaluate a potential usage of the p16 INK4a 5' CpG island hypermethylation as an indicator of tumor cell along with p16ink4a overexpression, we analyzed the methylation status of p16 INK4a in cervical carcinomas

Methods

Methylation status of p16 INK4a was analyzed by MSP and by bisulfite-modified DNA sequencing. The expression of p16ink4a was analyzed by RT-PCR and by immunohistochemical technique.

Results

The extensive methylation within p16 INK4a 5' CpG island was not detected either in 13 primary cervical carcinomas or in 5 cancer cell lines by bisulfite-modified DNA sequencing (including those that were positive by MSP in our hands). The number and distribution of rare partially methylated CpG sites did not differ considerably in tumors and adjacent normal tissues. The levels of the p16 INK4a mRNA were increased in carcinomas compared to the normal tissues independently of the number of partially methylated CpGs within 5'CpG island. The transcriptional activation of p16 INK4a was accompanied by p16ink4a cytoplasmic immunoreactivity in the majority of tumor cells and presence of a varied number of the p16 positive nuclei in different tumors.

Conclusion

Hypermethylaion of the p16INK4a 5' CpG island is not a frequent event in HR-HPV-positive cervical carcinomas and cannot be an effective marker of cancer cells with up-regulated expression of p16ink4a. Our data confirm other previous studies claiming specific p16INK4a up-regulation in the majority of cervical carcinomas at both the protein and mRNA levels. Cytoplasmic accumulation of p16ink4a is a feature of cervical carcinomas.
Vinorelbine plus 3-weekly trastuzumab in metastatic breast cancer: a single-centre phase 2 trial
Authors: De Maio Ermelinda , Pacilio Carmen , Gravina Adriano , Morabito Alessandro , Di Rella Francesca , Labonia Vincenzo , Landi Gabriella , Nuzzo Francesco , Rossi Emanuela , Silvestro Pasqualina , Botti Gerardo , Di Bonito Maurizio , Curcio Maria Pia , Formichelli Franca , La Vecchia Franca , Staiano Maria , Maurea Nicola , D'Aiuto Giuseppe , D'Aiuto Massimiliano , Thomas Renato , Signoriello Giuseppe , Perrone Francesco , de Matteis Andrea
Published: May 2007

Background

After two studies reporting response rates higher than 70% in HER2-positive metastatic breast cancer with weekly trastuzumab and vinorelbine, we planned a phase 2 study to test activity of the same combination, with trastuzumab given every 3 weeks.

Methods

Patients with HER2-positive metastatic breast cancer (3+ at immunohistochemistry or positive at fluorescence in situ hybridization), PS ≤2, normal left-ventricular ejection fraction (LVEF) and no more than one chemotherapy line for metastatic disease were eligible. Vinorelbine (30 mg/m2) was given on days 1&8 every 21 and trastuzumab (8 mg/kg day 1, then 6 mg/kg) every 21 days). A single-stage phase 2 design, with p0 = 0.45, p1 = 0.65, type I and II error = 0.10, was applied; 22 objective responses were required in 39 patients.

Results

From Nov 2002 to May 2005, 50 patients were enrolled, with a median age of 54 years (range 31–81). Among 40 patients eligible for response assessment, there were 7 complete and 13 partial responses (overall response rate 50%; 95% exact CI 33.8–66.2); 11 patients had disease stabilization, lasting more than 6 months in 10 cases. Response rate did not vary according to patients and tumor characteristics, type and amount of previous chemotherapy. Within the whole series, median progression-free survival was 9.6 months (95% CI 7.3–12.3), median overall survival 22.7 months (95% CI 19.5-NA). Fifteen patients (30%) developed brain metastases at a median time of 12 months (range 1–25). There was one toxic death due to renal failure in a patient receiving concomitant pamidronate. Twenty-three patients (46%) had grade 3–4 neutropenia, 2 (4%) grade 3 anemia, 4 (8%) febrile neutropenia. Two patients stopped treatment because of grade 2 decline of LVEF and one patient because of grade 2 liver toxicity concomitant with a grade 1 decline of LVEF. One patient stopped trastuzumab after 50 cycles because of grade 1 decline of LVEF.

Conclusion

Although lower than in initial studies, activity of 3-weekly trastuzumab plus vinorelbine fell within the range of results reported with weekly schedules. Toxicity was prevalently manageable. This combination is safe and active for metastatic breast cancer patients who received adjuvant taxanes with anthracyclines.
Clinical benefit of readministration of gefitinib for initial gefitinib-responders with non-small cell lung cancer
Authors: Yokouchi Hiroshi , Yamazaki Koichi , Kinoshita Ichiro , Konishi Jun , Asahina Hajime , Sukoh Noriaki , Harada Masao , Akie Kenji , Ogura Shigeaki , Ishida Takashi , Munakata Mitsuru , Dosaka-Akita Hirotoshi , Isobe Hiroshi , Nishimura Masaharu
Published: May 2007

Background

Gefitinib, an oral agent of epidermal growth factor receptor tyrosine kinase inhibitor, has a certain efficacy against non-small cell lung cancer (NSCLC). Several predictive factors of gefitinib sensitivity have been well described. However, few studies have investigated the clinical features of gefitinib-responders. In the present study, we analyzed the response and disease progression of primary and metastatic lesions to gefitinib in responders and the results of gefitinib readministration following temporary cessation of gefitinib upon progression of initial gefitinib treatment and other treatments.

Method

We retrospectively evaluated the clinical courses of 27 NSCLC patients who received gefitinib and achieved either a complete or partial response.

Results

The best-response rate and disease-control rate against the initial chemotherapy for the gefitinib-responders were 27.3% and 77.3%, respectively. Favorable efficacy was observed in the primary lesion and metastases to the lung, liver and brain, while there was no obvious effect on bone metastasis. The primary lesion and intrapulmonary metastasis were the sites of major recurrence. Median progression-free survival was 13.8 months, median duration of gefitinib treatment was 17.0 months and median overall survival was 29.2 months. Some of the patients who experienced disease progression after responding to gefitinib were again sensitive to readministration of gefitinib following temporary cessation of gefitinib and other treatments.

Conclusion

Patients may still be expected to have prolonged survival if they once responded to gefitinib and then underwent various subsequent treatments followed by readministration of gefitinib. These findings might provide valuable information for the management of gefitinib-responders.
Identification of a robust gene signature that predicts breast cancer outcome in independent data sets
Authors: Korkola James E , Blaveri Ekaterina , DeVries Sandy , Moore Dan H , Hwang E Shelley , Chen Yunn-Yi , Estep Anne LH , Chew Karen L , Jensen Ronald H , Waldman Frederic M
Published: May 2007

Background

Breast cancer is a heterogeneous disease, presenting with a wide range of histologic, clinical, and genetic features. Microarray technology has shown promise in predicting outcome in these patients.

Methods

We profiled 162 breast tumors using expression microarrays to stratify tumors based on gene expression. A subset of 55 tumors with extensive follow-up was used to identify gene sets that predicted outcome. The predictive gene set was further tested in previously published data sets.

Results

We used different statistical methods to identify three gene sets associated with disease free survival. A fourth gene set, consisting of 21 genes in common to all three sets, also had the ability to predict patient outcome. To validate the predictive utility of this derived gene set, it was tested in two published data sets from other groups. This gene set resulted in significant separation of patients on the basis of survival in these data sets, correctly predicting outcome in 62–65% of patients. By comparing outcome prediction within subgroups based on ER status, grade, and nodal status, we found that our gene set was most effective in predicting outcome in ER positive and node negative tumors.

Conclusion

This robust gene selection with extensive validation has identified a predictive gene set that may have clinical utility for outcome prediction in breast cancer patients.
Nectin-4 is a new histological and serological tumor associated marker for breast cancer
Authors: Fabre-Lafay Stéphanie , Monville Florence , Garrido-Urbani Sarah , Berruyer-Pouyet Carole , Ginestier Christophe , Reymond Nicolas , Finetti Pascal , Sauvan Richard , Adélaïde José , Geneix Jeannine , Lecocq Eric , Popovici Cornel , Dubreuil Patrice , Viens Patrice , Gonçalves Anthony , Charafe-Jauffret Emmanuelle , Jacquemier Jocelyne , Birnbaum Daniel , Lopez Marc
Published: May 2007

Introduction

Breast cancer is a complex and heterogeneous disease at the molecular level. Evolution is difficult to predict according to classical histoclinical prognostic factors. Different studies highlight the importance of large-scale molecular expression analyses to improve taxonomy of breast cancer and prognostic classification. Identification of new molecular markers that refine this taxonomy and improve patient management is a priority in the field of breast cancer research.

Nectins are cell adhesion molecules involved in the regulation of epithelial physiology. We present here Nectin-4/PVRL4 as a new histological and serological tumor associated marker for breast carcinoma.

Methods

Expression of Nectin-4 protein was measured on a panel of 78 primary cells and cell lines from different origins and 57 breast tumors by FACS analysis and immunohistochemistry (IHC), respectively. mRNA expression was measured by quantitative PCR.

Serum Nectin-4 was detected by ELISA and compared with CEA and CA15.3 markers, on panels of 45 sera from healthy donors, 53 sera from patients with non-metastatic breast carcinoma (MBC) at diagnosis, and 182 sera from patients with MBC. Distribution of histological/serological molecular markers and histoclinical parameters were compared using the standard Chi-2 test.

Results

Nectin-4 was not detected in normal breast epithelium. By contrast, Nectin-4 was expressed in 61% of ductal breast carcinoma vs 6% in lobular type. Expression of Nectin-4 strongly correlated with the basal-like markers EGFR, P53, and P-cadherin, and negatively correlated with the luminal-like markers ER, PR and GATA3. All but one ER/PR-negative tumors expressed Nectin-4. The detection of Nectin-4 in serum improves the follow-up of patients with MBC: the association CEA/CA15.3/Nectin-4 allowed to monitor 74% of these patients compared to 67% with the association CEA/CA15.3. Serum Nectin-4 is a marker of disease progression, and levels correlate with the number of metastases (P= 0.038). Serum Nectin-4 is also a marker of therapeutic efficiency and correlates, in 90% of cases, with clinical evolution.

Conclusion

Nectin-4 is a new tumor-associated antigen for breast carcinoma. Nectin-4 is a new bio-marker whose use could help refine breast cancer taxonomy and improve patients' follow-up. Nectin-4 emerges as a potential target for breast cancer immunotherapy.
Experimental based experiences with the introduction of a water safety plan for a multi-located university clinic and its efficacy according to WHO recommendations
Authors: Dyck Alexander , Exner Martin , Kramer Axel
Published: May 2007

Background

Due to the high number of immunosuppressed and other predisposed patients hospitals have to control and ensure the microbiological water quality. The origin for the occurrence of pathogenic microorganisms in water pipes is the formation of biofilm.

Methods

For the permanent control of water safety a water safety plan (WSP) was realized as recommended by the WHO following the principle "search and destroy". The WSP is based on an established HACCP concept due to the special focus. The most important measures include the concept for sample taking depending on patient risk. 3 different categories) are distinguished: risk area1 (high infection risk), risk 2 (moderate infection risk), and risk area 3 (not increased infection risk). Additionally to the threshold value of the German law for the quality of drinking water (TrinkwV) three more limiting values were defined (warning, alert, and worst case) for immediate risk adapted reaction. Additional attention has to be focussed on lavatory sinks, which are an open bacterial reservoir. Therefore continuous disinfecting siphons were installed as part of the WSP in high risk areas.

If extended technical equipment is not available, especially for immunocompromised patients the following measures are easy to realize: boiled (or sun exposed) water for nursing procedures as well alimentary use, no showering.

Results

Comparing data over 3 years the microbial water quality was significantly improved resulting in no new case of nosocomial Legionella pneumoniae and decrease in neonatal sepsis.

Conclusion

According to average situations with highly contaminated water system the management must be defined with implementation of water task force, immediate providing of special equipment, information of patients and staff and control of the water quality, an example for successful decontamination of the hospital within 24 hours is given.
The presence of a booster phenomenon among contacts of active pulmonary tuberculosis cases: a retrospective cohort
Authors: Salles Cristiane G , Ruffino-Netto Antonio , Lapa-e-Silva Jose R , Kritski Afranio L , Cailleaux-Cesar Michelle , Queiroz-Mello Fernanda C , Conde Marcus B
Published: May 2007

Background

Assuming a higher risk of latent tuberculosis (TB) infection in the population of Rio de Janeiro, Brazil, in October of 1998 the TB Control Program of Clementino Fraga Filho Hospital (CFFH) routinely started to recommend a two-step tuberculin skin test (TST) in contacts of pulmonary TB cases in order to distinguish a boosting reaction due to a recall of delayed hypersensitivity previously established by infection with Mycobacterium tuberculosis (M.tb) or BCG vaccination from a tuberculin conversion. The aim of this study was to assess the prevalence of boosted tuberculin skin tests among contacts of individuals with active pulmonary tuberculosis (TB).

Methods

Retrospective cohort of TB contacts ≥ 12 years old who were evaluated between October 1st, 1998 and October 31st 2001. Contacts with an initial TST ≤ 4 mm were considered negative and had a second TST applied after 7–14 days. Boosting reaction was defined as a second TST ≥ 10 mm with an increase in induration ≥ 6 mm related to the first TST. All contacts with either a positive initial or repeat TST had a chest x-ray to rule out active TB disease, and initially positive contacts were offered isoniazid preventive therapy. Contacts that boosted did not receive treatment for latent TB infection and were followed for 24 months to monitor the development of TB. Statistical analysis of dichotomous variables was performed using Chi-square test. Differences were considered significant at a p < 0.05.

Results

Fifty four percent (572/1060) of contacts had an initial negative TST and 79% of them (455/572) had a second TST. Boosting was identified in 6% (28/455). The mean age of contacts with a boosting reaction was 42.3 ± 21.1 and with no boosting was 28.7 ± 21.7 (p = 0.01). Fifty percent (14/28) of individuals whose test boosted met criteria for TST conversion on the second TST (increase in induration ≥ 10 mm). None of the 28 contacts whose reaction boosted developed TB disease within two years following the TST.

Conclusion

The low number of contacts with boosting and the difficulty in distinguishing boosting from TST conversion in the second TST suggests that the strategy of two-step TST testing among contacts of active TB cases may not be useful. However, this conclusion must be taken with caution because of the small number of subjects followed.
Stroke risk perception among participants of a stroke awareness campaign
Authors: Kraywinkel Klaus , Heidrich Jan , Heuschmann Peter U , Wagner Markus , Berger Klaus
Published: May 2007

Background

Subjective risk factor perception is an important component of the motivation to change unhealthy life styles. While prior studies assessed cardiovascular risk factor knowledge, little is known about determinants of the individual perception of stroke risk.

Methods

Survey by mailed questionnaire among 1483 participants of a prior public stroke campaign in Germany. Participants had been informed about their individual stroke risk based on the Framingham stroke risk score. Stroke risk factor knowledge, perception of lifetime stroke risk and risk factor status were included in the questionnaire, and the determinants of good risk factor knowledge and high stroke risk perception were identified using logistic regression models.

Results

Overall stroke risk factor knowledge was good with 67–96% of the participants recognizing established risk factors. The two exceptions were diabetes (recognized by 49%) and myocardial infarction (57%). Knowledge of a specific factor was superior among those affected by it. 13% of all participants considered themselves of having a high stroke risk, 55% indicated a moderate risk. All major risk factors contributed significantly to the perception of being at high stroke risk, but the effects of age, sex and education were non-significant. Poor self-rated health was additionally associated with high individual stroke risk perception.

Conclusion

Stroke risk factor knowledge was high in this study. The self perception of an increased stroke risk was associated with established risk factors as well as low perception of general health.
Improving return-to-work after childbirth: design of the Mom@Work study, a randomised controlled trial and cohort study
Authors: Stomp-van den Berg Suzanne GM , van Poppel Mireille NM , Hendriksen Ingrid JM , Bruinvels David J , Uegaki Kimi , de Bruijne Martine C , van Mechelen Willem
Published: May 2007

Background

Many women suffer from health problems after giving birth, which can lead to sick leave. About 30% of Dutch workers are on sick leave after maternity leave. Structural contact of supervisors with employees on maternity leave, supported by early medical advice of occupational physicians, may increase the chances of return-to-work after maternity leave. In addition, to understand the process of sick leave and return-to-work after childbirth it is important to gain insight into which factors hinder return-to-work after childbirth, as well, as which prognostic factors lead to the development of postpartum health complaints. In this paper, the design of the Mom@Work study is described.

Methods

The Mom@Work study is simultaneously a randomised controlled trial and a cohort study. Pregnant women working for at least 12 hours a week at one of the 15 participating companies are eligible to participate. The supervisors of these pregnant employees are randomised at 35 weeks pregnancy into the intervention group or control group. During maternity leave, supervisors in the intervention group contact their employee six weeks after delivery using a structured interview. When employees do not expect to return to their jobs at the end of their scheduled maternity leave due to health problems, the supervisor offers early support of the occupational physician. Supervisors in the control group have no structural contact with their employees during maternity leave. Measurements take place at 30 weeks pregnancy and at 6, 12, 24 and 52 weeks postpartum. In addition, cost data are collected. For the RCT, primary outcome measures are sick leave and return-to-work, and secondary outcome measures are costs, health, satisfaction with intervention and global feelings of recovery. Outcome measures for the cohort are pregnancy-related pelvic girdle pain, fatigue and depression. Finally, a number of prognostic factors for return-to-work and for the development of complaints will be measured.

Discussion

The Mom@Work study will provide important information about return-to-work of employees after giving birth. Results will give insight in prognosis of postpartum sick leave and complaints. Also, the role of supervisors and occupational physicians in successful return-to-work after childbirth will be clarified.
Association of toll-interacting protein gene polymorphisms with atopic dermatitis
Authors: Schimming Tobias T , Parwez Qumar , Petrasch-Parwez Elisabeth , Nothnagel Michael , Epplen Joerg T , Hoffjan Sabine
Published: May 2007

Background

Atopic dermatitis (AD) is a common inflammatory skin disorder, affecting up to 15% of children in industrialized countries. Toll-interacting protein (TOLLIP) is an inhibitory adaptor protein within the toll-like receptor (TLR) pathway, a part of the innate immune system that recognizes structurally conserved molecular patterns of microbial pathogens, leading to an inflammatory immune response.

Methods

In order to detect a possible role of TOLLIP variation in the pathogenesis of AD, we screened the entire coding sequence of the TOLLIP gene by SSCP in 50 AD patients. We identified an amino acid exchange in exon 6 (Ala222Ser) and a synonymous variation in exon 4 (Pro139Pro). Subsequently, these two variations and four additional non-coding polymorphisms (-526 C/G, two polymorphisms in intron 1 and one in the 3'UTR) were genotyped in 317 AD patients and 224 healthy controls.

Results

The -526G allele showed borderline association with AD in our cohort (p = 0.012; significance level after correction for multiple testing 0.0102). Haplotype analysis did not yield additional information. Evaluation of mRNA expression by quantitative real-time polymerase chain reaction in six probands with the CC and six with the GG genotype at the -526 C/G locus did not reveal significant differences between genotypes.

Conclusion

Variation in the TOLLIP gene may play a role in the pathogenesis of AD. Yet, replication studies in other cohorts and populations are warranted to confirm these association results.
High level expression of soluble glycoproteins in the allantoic fluid of embryonated chicken eggs using a Sendai virus minigenome system
Authors: Corral Teresa , Ver Lorena S , Mottet Geneviève , Cano Olga , García-Barreno Blanca , Calder Lesley J , Skehel John J , Roux Laurent , Melero José A
Published: May 2007

Background

Embryonated chicken eggs have been used since the mid-20th century to grow a wide range of animal viruses to high titers. However, eggs have found so far only limited use in the production of recombinant proteins. We now describe a system, based on a Sendai virus minigenome, to produce large amounts of heterologous viral glycoproteins in the allantoic cavity of embryonated eggs.

Results

Soluble forms of human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV) fusion (F) proteins, devoid of their transmembrane and cytoplasmic domains, were produced in allantoic fluids using the Sendai minigenome system. The first step was rescuing in cell cultures Sendai virus minigenomes encoding the proteins of interest, with the help of wild type Sendai virus. The second step was propagating such recombinant defective viruses, together with the helper virus, in the allantoic cavity of chicken embryonated eggs, and passage to optimize protein production. When compared with the production of the same proteins in the culture supernatant of cells infected with vaccinia recombinants, the yield in the allantoic fluid was 5–10 fold higher. Mutant forms of these soluble proteins were easily constructed by site-directed mutagenesis and expressed in eggs using the same approach.

Conclusion

The simplicity and economy of the Sendai minigenome system, together with the high yield achieved in the allantoic fluid of eggs, makes it an attractive method to express soluble glycoproteins aimed for structural studies.
Complex interplay between intrinsic and extrinsic drivers of long-term survival trends in southern elephant seals
Authors: de Little Siobhan C , Bradshaw Corey JA , McMahon Clive R , Hindell Mark A
Published: May 2007

Background

Determining the relative contribution of intrinsic and extrinsic factors to fluctuations in population size, trends and demographic composition is analytically complex. It is often only possible to examine the combined effects of these factors through measurements made over long periods, spanning an array of population densities or levels of food availability. Using age-structured mark-recapture models and datasets spanning five decades (1950–1999), and two periods of differing relative population density, we estimated age-specific probabilities of survival and examined the combined effects of population density and environmental conditions on juvenile survival of southern elephant seals at Macquarie Island.

Results

First-year survival decreased with density during the period of highest population size, and survival increased during years when the Southern Oscillation Index (SOI) anomaly (deviation from a 50-year mean) during the mother's previous foraging trip to sea was positive (i.e., El Niño). However, when environmental stochasticity and density were considered together, the effect of density on first-year survival effectively disappeared. Ignoring density effects also leads to models placing too much emphasis on the environmental conditions prevailing during the naïve pup's first year at sea.

Conclusion

Our analyses revealed that both the state of the environment and population density combine to modify juvenile survival, but that the degree to which these processes contributed to the variation observed was interactive and complex. This underlines the importance of evaluating the relative contribution of both the intrinsic and extrinsic factors that regulate animal populations because false conclusions regarding the importance of population regulation may be reached if they are examined in isolation.
Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for α-keto acid binding
Authors: Gonin Sophie , Arnoux Pascal , Pierru Bénédicte , Lavergne Jérôme , Alonso Béatrice , Sabaty Monique , Pignol David
Published: May 2007

Background

The import of solutes into the bacterial cytoplasm involves several types of membrane transporters, which may be driven by ATP hydrolysis (ABC transporters) or by an ion or H+ electrochemical membrane potential, as in the tripartite ATP-independent periplasmic system (TRAP). In both the ABC and TRAP systems, a specific periplasmic protein from the ESR family (Extracytoplasmic Solute Receptors) is often involved for the recruitment of the solute and its presentation to the membrane complex. In Rhodobacter sphaeroides, TakP (previously named SmoM) is an ESR from a TRAP transporter and binds α-keto acids in vitro.

Results

We describe the high-resolution crystal structures of TakP in its unliganded form and as a complex with sodium-pyruvate. The results show a limited "Venus flytrap" conformational change induced by substrate binding. In the liganded structure, a cation (most probably a sodium ion) is present and plays a key role in the association of the pyruvate to the protein. The structure of the binding pocket gives a rationale for the relative affinities of various ligands that were tested from a fluorescence assay. The protein appears to be dimeric in solution and in the crystals, with a helix-swapping structure largely participating in the dimer formation. A 30 Å-long water channel buried at the dimer interface connects the two ligand binding cavities of the dimer.

Conclusion

The concerted recruitment by TakP of the substrate group with a cation could represent a first step in the coupled transport of both partners, providing the driving force for solute import. Furthermore, the unexpected dimeric structure of TakP suggests a molecular mechanism of solute uptake by the dimeric ESR via a channel that connects the binding sites of the two monomers.
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect
Authors: Jang Hyunbum , Ma Buyong , Nussinov Ruth
Published: May 2007

Background

Protegrin-1 (PG-1) is known as a potent antibiotic peptide; it prevents infection via an attack on the membrane surface of invading microorganisms. In the membrane, the peptide forms a pore/channel through oligomerization of multiple subunits. Recent experimental and computational studies have increasingly unraveled the molecular-level mechanisms underlying the interactions of the PG-1 β-sheet motifs with the membrane. The PG-1 dimer is important for the formation of oligomers, ordered aggregates, and for membrane damaging effects. Yet, experimentally, different dimeric behavior has been observed depending on the environment: antiparallel in the micelle environment, and parallel in the POPC bilayer. The experimental structure of the PG-1 dimer is currently unavailable.

Results

Although the β-sheet structures of the PG-1 dimer are less stable in the bulk water environment, the dimer interface is retained by two intermolecular hydrogen bonds. The formation of the dimer in the water environment implies that the pathway of the dimer invasion into the membrane can originate from the bulk region. In the initial contact with the membrane, both the antiparallel and parallel β-sheet conformations of the PG-1 dimer are well preserved at the amphipathic interface of the lipid bilayer. These β-sheet structures illustrate the conformations of PG-1 dimer in the early stage of the membrane attack. Here we observed that the activity of PG-1 β-sheets on the bilayer surface is strongly correlated with the dimer conformation. Our long-term goal is to provide a detailed mechanism of the membrane-disrupting effects by PG-1 β-sheets which are able to attack the membrane and eventually assemble into the ordered aggregates.

Conclusion

In order to understand the dimeric effects leading to membrane damage, extensive molecular dynamics (MD) simulations were performed for the β-sheets of the PG-1 dimer in explicit water, salt, and lipid bilayers composed of POPC lipids. Here, we studied PG-1 dimers when organized into a β-sheet motif with antiparallel and parallel β-sheet arrangements in an NCCN packing mode. We focus on the conformations of PG-1 dimers in the lipid bilayer, and on the correlation between the conformations and the membrane disruption effects by PG-1 dimers. We investigate equilibrium structures of the PG-1 dimers in different environments in the early stage of the dimer invasion. The dimer interface of the antiparallel β-sheets is more stable than the parallel β-sheets, similar to the experimental observation in micelle environments. However, we only observe membrane disruption effects by the parallel β-sheets of the PG-1 dimer. This indicates that the parallel β-sheets interact with the lipids with the β-sheet plane lying obliquely to the bilayer surface, increasing the surface pressure in the initial insertion into the lipid bilayer. Recent experimental observation verified that parallel PG-1 dimer is biologically more active to insert into the POPC lipid bilayer.
The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3
Authors: Casares Salvador , AB Eiso , Eshuis Henk , Lopez-Mayorga Obdulio , van Nuland Nico AJ , Conejero-Lara Francisco
Published: May 2007

Background

SH3 domains are small protein modules of 60–85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the α-spectrin SH3 domain (Spc-SH3).

Results

Here we present the high-resolution structure of the complex between the R21A mutant of Spc-SH3 and p41 derived from NMR data. Thermodynamic parameters of binding of p41 to both WT and R21A Spc-SH3 were measured by a combination of isothermal titration and differential scanning calorimetry. Mutation of arginine 21 to alanine in Spc-SH3 increases 3- to 4-fold the binding affinity for p41 due to elimination at the binding-site interface of the steric clash produced by the longer arginine side chain. Amide hydrogen-deuterium experiments on the free and p41-bound R21A Spc-SH3 domain indicate that binding elicits a strong reduction in the conformational flexibility of the domain. Despite the great differences in the thermodynamic magnitudes of binding, the structure of the R21A Spc-SH3:P41 complex is remarkably similar to that of the Abl-SH3:P41 complex, with only few differences in protein-ligand contacts at the specificity pocket. Using empirical methods for the prediction of binding energetics based on solvent-accessible surface area calculations, the differences in experimental energetics of binding between the two complexes could not be properly explained only on the basis of the structural differences observed between the complexes. We suggest that the experimental differences in binding energetics can be at least partially ascribed to the absence in the R21A Spc-SH3:P41 complex of several buried water molecules, which have been proposed previously to contribute largely to the highly negative enthalpy and entropy of binding in the Abl-SH3:P41 complex.

Conclusion

Based on a deep structural and thermodynamic analysis of a low and high affinity complex of two different SH3 domains with the same ligand p41, we underline the importance of taking into account in any effective strategy of rational design of ligands, factors different from the direct protein-ligand interactions, such as the mediation of interactions by water molecules or the existence of cooperative conformational effects induced by binding.
A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding
Authors: Stanley Will A , Pursiainen Niko V , Garman Elspeth F , Juffer André H , Wilmanns Matthias , Kursula Petri
Published: May 2007

Background

The C-terminal tetratricopeptide (TPR) repeat domain of Pex5p recognises proteins carrying a peroxisomal targeting signal type 1 (PTS1) tripeptide in their C-terminus. Previously, structural data have been obtained from the TPR domain of Pex5p in both the liganded and unliganded states, indicating a conformational change taking place upon cargo protein binding. Such a conformational change would be expected to play a major role both during PTS1 protein recognition as well as in cargo release into the peroxisomal lumen. However, little information is available on the factors that may regulate such structural changes.

Results

We have used a range of biophysical and computational methods to further analyse the conformational flexibility and ligand binding of Pex5p. A new crystal form for the human Pex5p C-terminal domain (Pex5p(C)) was obtained in the presence of Sr2+ ions, and the structure presents a novel conformation, distinct from all previous liganded and apo crystal structures for Pex5p(C). The difference relates to a near-rigid body movement of two halves of the molecule, and this movement is different from that required to reach a ring-like conformation upon PTS1 ligand binding. The bound Sr2+ ion changes the dynamic properties of Pex5p(C) affecting its conformation, possibly by making the Sr2+-binding loop – located near the hinge region for the observed domain motions – more rigid.

Conclusion

The current data indicate that Pex5p(C) is able to sample a range of conformational states in the absence of bound PTS1 ligand. The domain movements between various apo conformations are distinct from those involved in ligand binding, although the differences between all observed conformations so far can be characterised by the movement of the two halves of Pex5p(C) as near-rigid bodies with respect to each other.
Infection rates associated with epidural indwelling catheters for seven days or longer: systematic review and meta-analysis
Authors: Ruppen Wilhelm , Derry Sheena , McQuay Henry J , Moore R Andrew
Published: May 2007

Background

To determine infection rate with use of epidural catheters in place for seven days or more.

Methods

Systematic review and pooled analysis of observational studies.

Results

Twelve studies with 4,628 patients (median 197 patients) provided information, of which nine (4,334 patients) were published after 1990. Eight studies (3,893 patients) were retrospective, and four studies (735 patients) prospective. Electronic searches identified three studies and searching reference lists nine.

There were 257 catheter-related infections in total, of which 211 were superficial and 57 deep, giving rates of 6.1%, 4.6% and 1.2% respectively. Ten of the 12 studies had deep infection rates of 2% or less. The incidence of deep infection was 1 per 2391 days of treatment, or 0.4 per 1000 catheter treatment days. In nine studies (1503 patients), predominantly in cancer, and with average catheter duration of 74 days, the deep infection rate was 2.8%. The proportion of patients with infection of any type was higher in cancer patients with longer catheter duration. Limited numbers of events meant that no reliable estimate of the impact of prospective and retrospective design could be made. There appeared to be a relationship between catheter duration and infection rate from this and other recent estimates. Four of 57 (7%) patients with deep infection died.

Conclusion

The best estimate is that one person in 35 with an epidural catheter in place for 74 days for relief of cancer pain can be expected to have a deep epidural infection, and that about 1 in 500 may die of infection-related causes. This is a most uncertain estimate given the limited nature of the evidence.
Rosai-Dorfman Disease: A previously unreported association with Sickle Cell Disease
Authors: Stebbing Claire , van der Walt Jon , Ramadan Ghada , Inusa Baba
Published: May 2007

Background

Rosai-Dorfman Disease is an uncommon benign systemic histio-proliferative disease. This is the first time the disease, although more common in people of African descent, is described in association with Sickle cell disease.

Case presentation

A Nigerian boy born started a complex medical history with post-natal anemia of unknown origin. Subsequently he was diagnosed with Sickle Cell Anemia (Hb SS). At age 3 during a routine review, he was noted to have generalised massive lymphadenopathy. He had further reoccurrences of this lymphadenopathy, but investigations did not reveal the cause until age five. At this point, because of the progressive lymph node enlargement, a biopsy was performed, and he was diagnosed with Rosai-Dorfman Disease. Since that time, the child has had further episodes of intermittent massive lymphadenopathy, particularly associated with Sickle Crisis. His medical history has been further complicated by development of complications from Sickle Cell Disease, cardiomyopathy and an autoimmune hemolytic anemia with multiple alloantibodies.

Conclusion

This case for the first time presents the co-existence of two diseases, of increased prevalence in those of African descent, but to date not described in the literature to occur concurrently.
Feasibility and results of a randomised pilot-study of pre-discharge occupational therapy home visits
Authors: Lannin Natasha Anne , Clemson Lindy , McCluskey Annie , Lin Chung-Wei Christine , Cameron Ian D , Barras Sarah
Published: May 2007

Background

Pre-discharge home visits aim to maximise independence in the community. These visits involve assessment of a person in their own home prior to discharge from hospital, typically by an occupational therapist. The therapist may provide equipment, adapt the home environment and/or provide education. The aims of this study were to investigate the feasibility of a randomised controlled trial in a clinical setting and the effect of pre-discharge home visits on functional performance in older people undergoing rehabilitation.

Methods

Ten patients participating in an inpatient rehabilitation program were randomly assigned to receive either a pre-discharge home visit (intervention), or standard practice in-hospital assessment and education (control), both conducted by an occupational therapist. The pre-discharge home visit involved assessment of the older person's function and environment, and education, and took an average of 1.5 hours. The hospital-based interview took an average of 40 minutes. Outcome data were collected by a blinded assessor at 0, 2, 4, 8 and 12 weeks. Outcomes included performance of activities of daily living, reintegration to community living, quality of life, readmission and fall rates.

Results

Recruitment of 10 participants was slow and took three months. Observed performance of functional abilities did not differ between groups due to the small sample size. Difference in activities of daily living participation, as recorded by the Nottingham Extended Activities of Daily Living scale, was statistically significant but wide confidence intervals and low statistical power limit interpretation of results.

Conclusion

Evaluation of pre-discharge home visits by occupational therapists in a rehabilitation setting is feasible, but a more effective recruitment strategy for a main study is favored by application of a multi-centre setting.