bluuebunny/crossref_metadata_2025 huggingface dataset:
Disease allele-dependent small-molecule sensitivities in blood cells from monogenic diabetes
Authors: Shaw Stanley Y. , Blodgett David M. , Ma Maggie S. , Westly Elizabeth C. , Clemons Paul A. , Subramanian Aravind , Schreiber Stuart L.
Published: December 2010

Even as genetic studies identify alleles that influence human disease susceptibility, it remains challenging to understand their functional significance and how they contribute to disease phenotypes. Here, we describe an approach to translate discoveries from human genetics into functional and therapeutic hypotheses by relating human genetic variation to small-molecule sensitivities. We use small-molecule probes modulating a breadth of targets and processes to reveal disease allele-dependent sensitivities, using cells from multiple individuals with an extreme form of diabetes (maturity onset diabetes of the young type 1, caused by mutation in the orphan nuclear receptor HNF4α). This approach enabled the discovery of small molecules that show mechanistically revealing and therapeutically relevant interactions with HNF4α in both lymphoblasts and pancreatic β-cells, including compounds that physically interact with HNF4α. Compounds including US Food and Drug Administration–approved drugs were identified that favorably modulate a critical disease phenotype, insulin secretion from β-cells. This method may suggest therapeutic hypotheses for other nonblood disorders.
Reaction mechanism of
Drosophila
cryptochrome
Authors: Ozturk Nuri , Selby Christopher P. , Annayev Yunus , Zhong Dongping , Sancar Aziz
Published: December 2010

Cryptochrome (CRY) is a blue-light sensitive flavoprotein that functions as the primary circadian photoreceptor in
Drosophila melanogaster
. The mechanism by which it transmits the light signal to the core clock circuitry is not known. We conducted in vitro studies on the light-induced conformational change in CRY and its effect on protein–protein interaction and performed in vivo analysis of the lifetime of the signaling state of the protein to gain some insight into the mechanism of phototransduction. We find that exposure of CRY to blue light induces a conformation similar to that of the constitutively active CRY mutant with a C-terminal deletion (CRYΔ). This light-induced conformation has a half-life of ∼15 min in the dark at 25 °C and is characterized by increased affinity to Jetlag E3 ligase. In vivo analysis reveals that in the
Drosophila
S2 cell line, the signaling state induced by a millisecond light exposure has a half-life of 27 min in the dark at 0 °C during which period it is susceptible to degradation by the ubiquitin-proteasome system. These findings lead to a plausible model for circadian photoreception/phototransduction in
Drosophila
.
miR-29 and miR-30 regulate B-Myb expression during cellular senescence
Authors: Martinez Ivan , Cazalla Demian , Almstead Laura L. , Steitz Joan A. , DiMaio Daniel
Published: December 2010

Cellular senescence is a form of irreversible growth arrest and a major tumor suppressor mechanism. We show here that the miR-29 and miR-30 microRNA families are up-regulated during induced and replicative senescence and that up-regulation requires activation of the Rb pathway. Expression of a reporter construct containing the 3′UTR of the B-Myb oncogene is repressed during senescence, and repression is blocked by mutations in conserved miR-29 and miR-30 binding sites in the B-Myb 3′UTR. In proliferating cells, transfection of miR-29 and miR-30 represses a reporter construct containing the wild-type but not the mutant B-Myb 3′UTR, and repression of the mutant 3′UTR is reinstituted by compensatory mutations in miR-29 and miR-30 that restore binding to the mutant sites. miR-29 and miR-30 introduction also represses expression of endogenous B-Myb and inhibits cellular DNA synthesis. Finally, interference with miR-29 and miR-30 expression inhibits senescence. These findings demonstrate that miR-29 and miR-30 regulate B-Myb expression by binding to its 3′UTR and suggest that these microRNAs play an important role in Rb-driven cellular senescence.
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
Authors: Walter Vonn , Nobel Andrew B. , Wright Fred A.
Published: December 2010

Motivation: DNA copy number gains and losses are commonly found in tumor tissue, and some of these aberrations play a role in tumor genesis and development. Although high resolution DNA copy number data can be obtained using array-based techniques, no single method is widely used to distinguish between recurrent and sporadic copy number aberrations.

Results: Here we introduce Discovering Copy Number Aberrations Manifested In Cancer (DiNAMIC), a novel method for assessing the statistical significance of recurrent copy number aberrations. In contrast to competing procedures, the testing procedure underlying DiNAMIC is carefully motivated, and employs a novel cyclic permutation scheme. Extensive simulation studies show that DiNAMIC controls false positive discoveries in a variety of realistic scenarios. We use DiNAMIC to analyze two publicly available tumor datasets, and our results show that DiNAMIC detects multiple loci that have biological relevance.

Availability: Source code implemented in R, as well as text files containing examples and sample datasets are available at http://www.bios.unc.edu/research/genomic_software/DiNAMIC.

Contact:  vwalter@email.unc.edu; fwright@bios.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bladder Cancer
Authors: Fabricius Michael , Williams Rhian , Rainsbury Paul , McLarty Esther
Published: December 2010

Bladder cancer is the seventh most common cancer in the UK. Survival rates for this disease are favourable, with approximately 60–70% of patients surviving 5 years. This long survival rate means that many GPs will encounter patients being treated for this malignancy. This article provides an overview of the disease and its various treatment modalities.
Suspicious Oral Lesions
Authors: Field Anne , Field Jennifer
Published: December 2010

Patients frequently present to their GP complaining of soreness or ulceration inside their mouth. Some will have noticed signs such as white or red patches; others will be concerned they may have mouth cancer. The majority of lesions that appear on the oral mucosa are benign; however, oral cancer or potentially malignant lesions may present with a similar clinical appearance and therefore a high level of suspicion is required. Late diagnosis of oral cancer results in a lower survival rate and a compromised functional and cosmetic outcome. Early detection and referral of any suspicious oral lesions are therefore essential to improve the outcome following treatment. This article describes the clinical presentation of malignant and potentially malignant oral lesions and reinforces National Institute for Health and Clinical Excellence (NICE) guidelines concerning specialist referral.
Stochastic Process Methods with an Application to Budgetary Data
Authors: Breunig Christian , Jones Bryan D.
Published: December 2010

Political scientists have increasingly focused on causal processes that operate not solely on mean differences but on other stochastic characteristics of the distribution of a dependent variable. This paper surveys important statistical tools used to assess data in situations where the entire distribution of values is of interest. We first outline three broad conditions under which stochastic process methods are applicable and show that these conditions cover many domains of social inquiry. We discuss a variety of visual and analytical techniques, including distributional analysis, direct parameter estimates of probability density functions, and quantile regression. We illustrate the utility of these statistical tools with an application to budgetary data because strong theoretical expectations at the micro- and macrolevel exist about the distributional characteristics for such data. The expository analysis concentrates on three budget series (total, domestic, and defense outlays) of the U.S. government for 1800–2004.
Effects of antibiotics on Chlamydia trachomatis viability as determined by real-time quantitative PCR
Authors: Peuchant Olivia , Duvert Jean Philippe , Clerc Maïthé , Raherison Sophie , Bébéar Christiane , Bébéar Cécile M. , de Barbeyrac Bertille
Published: December 2010

The objective of this study was to determine the effect of antibiotics on Chlamydia trachomatis viability by using a quantitative real-time PCR assay that measured DNA replication and mRNA transcription of the structural omp1 and omp2 genes, 16S rRNA and the groEL1 gene with and without antibiotics. Ofloxacin, moxifloxacin, azithromycin and doxycycline were tested against the serovar D and L2 reference strains and a derivative mutant resistant to fluoroquinolones, L2-OFXR, obtained by in vitro selection. Using DNA quantification, the antibiotic MIC was calculated when the number of DNA copies was equal to that of the chlamydial inoculum at time zero. This method allowed the easy determination of MICs by DNA quantification of the four selected genes and gave similar results to those obtained by immunofluorescence staining without biased interpretation. By using cDNA quantification, the lowest antibiotic concentration for which no RNA was transcribed corresponded to the minimum bactericidal concentration. C. trachomatis still transcribed the16S rRNA and groEL1 genes, even at concentrations well above the MIC, showing a bacteriostatic effect for all antibiotics tested. This method allows the study of antibiotic activity on growth and viability of C. trachomatis by DNA and RNA quantification at the same time without additional cell-culture passaging.
Utility of reverse transcriptase PCR and DNA-PCR in the diagnosis of female genital tuberculosis
Authors: Rana Tanu , Singh Urvashi B. , Kulshrestha Vidushi , Kaushik Amit , Porwal Chhavi , Agarwal Nutan , Kriplani Alka
Published: December 2010

This study was designed to test the utility of mRNA-based RT-PCR to detect viable bacilli, indicating active tubercular involvement, and DNA-PCR to detect present or past infection in the diagnosis of active female genital tuberculosis (TB) infection. A total of 200 subjects with complaints of infertility were enrolled in the study. Multiple sampling was done. One hundred and forty-three endometrial aspirate (EA), 94 peritoneal fluid/peritoneal washing (PF/PW) and six cornual biopsy (CB) specimens were collected for diagnosis using microscopy, culture, RT-PCR and DNA-PCR and results were compared with laparoscopic findings. RT-PCR and culture were concordant [positive in four (2.8 %) EA specimens] signalling sampling from the site of active infection. Smear microscopy showed a poor detection rate while DNA-PCR showed high positivity. Sixty-one (44.85 %) EA specimens, nine (9.57 %) PF/PW specimens and two (33.33 %) CB specimens were positive by DNA-PCR. Genital TB causing infertility (localized or secondary to TB elsewhere) can be picked up early by DNA-PCR, when it can be completely cured prior to the appearance of florid disease.
Clinical presentation and molecular characterization of group B rotaviruses in diarrhoea patients in Bangladesh
Authors: Saiada Farjana , Rahman H. N. Ashiqur , Moni Sayra , Karim M. Manjurul , Pourkarim Mahmoud Reza , Azim Tasnim , Rahman Mustafizur
Published: December 2010

A total of 1106 stool samples collected from diarrhoea patients admitted to Dhaka hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh, during January–December 2008 were analysed for the presence of rotavirus-specific RNA by PAGE. The group B-specific RNA migration pattern was detected in 26 patients (2.4 %) and group A-specific pattern in 259 patients (23.4 %). Clinical data from group A and group B rotavirus-infected patients indicated that episodes did not differ much in the prevalence of diarrhoea, number of stools, outcome or differences in gender. However, abdominal pain was more common in group B rotavirus infections (36 vs 15 %, P=0.02) and the virus was responsible for more severe dehydration compared with group A-infected patients (12 vs 3 %, P=0.04). Sequence analyses of VP4, VP7 and NSP2 indicated that an Indian–Bangladeshi lineage of the virus, which is different from both the prototype (Chinese) lineage and from the animal group B rotaviruses, has been circulating in Bangladesh. Continuous monitoring of group B rotaviruses both in hospitals and in the community will be helpful to determine the true burden of group B rotaviruses.
A case of pulmonary aspergilloma and actinomycosis
Authors: Huang Chen-Wei , Lee Ming-An , Lu Ruey-Hwa , Peng Hui-Chin , Chao Heng-Shen
Published: December 2010

Pulmonary aspergilloma and pulmonary actinomycosis are rare pulmonary infectious diseases. Clinical manifestations of pulmonary aspergilloma and pulmonary actinomycosis include chronic cough, fever, chest pain, haemoptysis and other pathologies, but some patients may be asymptomatic. We report a case of a healthy 33-year-old woman without any underlying diseases, who was admitted to Zhongxing Branch of Taipei City Hospital, Taiwan, for intermittent haemoptysis and right upper chest pain, which had persisted for several months. A chest radiograph revealed a focal consolidation in the right upper lobe (RUL) of the lung, which grew in size over time. A sputum study and bronchoscopy revealed no positive findings, although malignancy could not be ruled out. Thus, the patient received a wedge resection of the RUL lesion. Subsequent, pathological examination demonstrated the presence of pulmonary aspergilloma and pulmonary actinomycosis. The patient's symptoms resolved after resection of the RUL lesion.
Distribution of Chlamydia trachomatis genovars among youths and adults in Brazil
Authors: Machado Ana C. S. , Bandea Claudiu I. , Alves Maria F. C. , Joseph Kahaliah , Igietseme Joseph , Miranda Angélica E. , Guimarães Eleuse M. B. , Turchi Marília D. , Black Carolyn M.
Published: December 2010

Despite a high prevalence of sexually transmittedChlamydia trachomatisinfections in Brazil and other countries in South America, very little is known about the distribution ofC. trachomatisgenovars. In this study, we genotypedC. trachomatisstrains from urine or endocervical specimens collected from 163C. trachomatis-positive female and male youths, and female adults, residing in two different regions of Brazil, the city of Goiânia located in the central part of Brazil, and the city of Vitória in the south-east region.C. trachomatisstrains were genotyped by amplifying and sequencing theompAgene encoding the chlamydial major outer-membrane protein, which is genovar specific. We found nine differentC. trachomatisgenovars: E (39.3 %), F (16.6 %), D (15.9 %), I (8.6 %), J (7.4 %), G (4.9 %), K (3.1 %), H (2.4 %) and B (1.8 %). The distribution of theC. trachomatisgenovars in the two regions of Brazil was similar, and there was no statistically significant association of serovars with age, gender, number of sexual partners or clinical symptoms. The overall distribution ofC. trachomatisgenovars in Brazil appears similar to that found in other regions of the world, where E, D and F are the most common. This supports the notion that, during the last few decades, the overall distribution ofC. trachomatisgenovars throughout the world has been relatively stable.
Rapid and accurate identification of species belonging to the Candida parapsilosis complex by real-time PCR and melting curve analysis
Authors: Hays Constantin , Duhamel Chantal , Cattoir Vincent , Bonhomme Julie
Published: December 2010

Candida parapsilosis is the second most frequent Candida species isolated from blood cultures. Since 2005, C. parapsilosis has been divided into three distinct species based on genetic traits: Candida parapsilosis, Candida metapsilosis and Candida orthopsilosis. The aim of this study was to develop a rapid real-time PCR assay able to distinguish these closely related species via a melting curve analysis. This identification method was optimized by using reference strains and well-characterized clinical isolates of Candida species. A single set of consensus primers was designed to amplify a 184 bp portion of the SADH gene in order to identify species based on the unique melt profile resulting from DNA sequence variations from each species of the complex. PCR products were detected with SYBR Green fluorescent dye and identification was established by melting curve analysis. For validation of the technique, a total of 116 clinical isolates, phenotypically identified as C. parapsilosis, were tested by real-time PCR and results were further compared with PCR-RFLP patterns of the SADH gene, used as the reference method. The melting curve analysis of amplified DNA could differentiate between C. parapsilosis (83.5 °C), C. metapsilosis (82.9 °C) and C. orthopsilosis (82.1 °C), with a sensitivity and specificity comparable to those of the reference method. One hundred and fourteen C. parapsilosis and two C. orthopsilosis isolates were identified among the clinical isolates. This method provides a simple, rapid and reliable identification of species belonging to the C. parapsilosis complex. This novel approach could be helpful for clinical and epidemiological investigations.
Extended-spectrum β-lactamase-producing Gram-negative bacteria causing neonatal sepsis in India in rural and urban settings
Authors: Chandel Dinesh S. , Johnson Judith A. , Chaudhry Rama , Sharma Nidhi , Shinkre Nandita , Parida Sailajanandan , Misra Pravas R. , Panigrahi Pinaki
Published: December 2010

Extended-spectrumβ-lactamase (ESBL)-producing Gram-negative bacilli (GNB) are of increasing clinical concern in all age groups worldwide. Whilst sepsis continues to be the leading cause of morbidity and mortality in Indian neonates in the community, identification of microbiological attributes in this population is lacking. This population-based study enrolled 1738 infants with a diagnosis of clinical sepsis at four participating centres in India. Each study site conducted Bactec blood culture, identified bacterial species by API test and stored isolates at −70 °C. From 252 GNB isolates, 155 (113Klebsiellaspecies, 21Escherichia coliand 21 other) were subjected to drug susceptibility testing, ESBL phenotyping and testing for clonal relatedness of ESBL strains by PFGE. The results demonstrated thatKlebsiellaspecies andE. coliare the most common GNB causes of neonatal sepsis in India, and over one-third are ESBL producers in both community and hospital settings. ESBL-producing strains exhibited frequent co-resistance to aminoglycosides and ciprofloxacin, but remained susceptible to imipenem. PFGE analysis revealed extensive genetic diversity within the ESBL-producing isolates, showing multiple profiles (total of 23). Over 40 % of all ESBL-producing isolates formed three pulsed-field profiles (PFP I–III), with PFP-II being the largest cluster (>20 % of all ESBL-producing isolates), sharing strains from two distant locations. Identification of a common clone at two geographically distant centres indicated that predominant clones with increased virulence may exist, even in the absence of any clear outbreak. The presence of ESBL-producing strains in community infants with no prior history of hospitalization or antibiotic use dictates heightened vigilance and further studies on the ecology of these organisms.
Development of a dry reagent-based triplex PCR for the detection of toxigenic and non-toxigenic Vibrio cholerae
Authors: Chua Ang Lim , Elina Husni Tan , Lim Boon Huat , Yean Chan Yean , Ravichandran Manickam , Lalitha Pattabhiraman
Published: December 2010

Vibrio choleraehas caused severe outbreaks of cholera worldwide with thousands of recorded deaths annually. Molecular diagnosis for cholera has become increasingly important for rapid detection of cholera as the conventional methods are time-consuming and labour intensive. However, traditional PCR tests still require cold-chain transportation and storage as well as trained personnel to perform, which makes them user-unfriendly. The aim of this study was to develop a thermostabilized triplex PCR test for cholera which is in a ready-to-use form and requires no cold chain. The PCR test specifically detects both toxigenic and non-toxigenic strains ofV. choleraebased on the cholera toxin A (ctxA) and outer-membrane lipoprotein (lolB) genes. The thermostabilized triplex PCR also incorporates an internal amplification control that helps to check for PCR inhibitors in samples. PCR reagents and the specific primers were lyophilized into a pellet form in the presence of trehalose, which acts as an enzyme stabilizer. The triplex PCR was validated with 174 bacteria-spiked stool specimens and was found to be 100 % sensitive and specific. The stability of the thermostabilized PCR was evaluated using the Q10method and it was found to be stable for approximately 7 months at 24 °C. The limit of detection of the thermostabilized triplex PCR assay was 2×104c.f.u. at the bacterial cell level and 100 pg DNA at the genomic DNA level, comparable to conventional PCR methods. In conclusion, a rapid thermostabilized triplex PCR assay was developed for detecting toxigenic and non-toxigenicV. choleraewhich requires minimal pipetting steps and is cold chain-free.
Clp-dependent proteolysis of the LexA N-terminal domain in Staphylococcus aureus
Authors: Cohn Marianne T. , Kjelgaard Peter , Frees Dorte , Penadés José R. , Ingmer Hanne
Published: December 2010

The SOS response is governed by the transcriptional regulator LexA and is elicited in many bacterial species in response to DNA damaging conditions. Induction of the SOS response is mediated by autocleavage of the LexA repressor resulting in a C-terminal dimerization domain (CTD) and an N-terminal DNA-binding domain (NTD) known to retain some DNA-binding activity. The proteases responsible for degrading the LexA domains have been identified in Escherichia coli as ClpXP and Lon. Here, we show that in the human and animal pathogen Staphylococcus aureus, the ClpXP and ClpCP proteases contribute to degradation of the NTD and to a lesser degree the CTD. In the absence of the proteolytic subunit, ClpP, or one or both of the Clp ATPases, ClpX and ClpC, the LexA domains were stabilized after autocleavage. Production of a stabilized variant of the NTD interfered with mitomycin-mediated induction of sosA expression while leaving lexA unaffected, and also significantly reduced SOS-induced mutagenesis. Our results show that sequential proteolysis of LexA is conserved in S. aureus and that the NTD may differentially regulate a subset of genes in the SOS regulon.
Yersinia pseudotuberculosis mntH functions in intracellular manganese accumulation, which is essential for virulence and survival in cells expressing functional Nramp1
Authors: Champion Olivia L. , Karlyshev Andrey , Cooper Ian A. M. , Ford Donna C. , Wren Brendan W. , Duffield Melanie , Oyston Petra C. F. , Titball Richard W.
Published: December 2010

Manganese has an important yet undefined role in the virulence of many bacterial pathogens. In this study we confirm that a null mutation in Yersinia pseudotuberculosis mntH reduces intracellular manganese accumulation. An mntH mutant was susceptible to killing by reactive oxygen species when grown under manganese-limited conditions. The mntH mutant was defective in survival and growth in macrophages expressing functional Nramp1, but in macrophages deficient in Nramp the bacteria were able to survive and replicate. In Galleria mellonella, the mntH mutant was attenuated. Taken together, these data suggest a role for manganese in Y. pseudotuberculosis during macrophage intracellular survival, protecting the bacteria from the antimicrobial products released during the respiratory burst.
The nitrogen interaction network in Synechococcus WH5701, a cyanobacterium with two PipX and two PII-like proteins
Authors: Laichoubi Karim Boumediene , Beez Sabine , Espinosa Javier , Forchhammer Karl , Contreras Asunción
Published: December 2010

Nitrogen regulation involves the formation of different types of protein complexes between signal transducers and their transcriptional or metabolic targets. In oxygenic phototrophs, the signal integrator PIIactivates the enzymeN-acetyl-l-glutamate kinase (NAGK) by complex formation. PIIalso interacts with PipX, a protein with a tudor-like domain that mediates contacts with PIIand with the transcriptional regulator NtcA, to which it binds to increase its activity. Here, we use a combination ofin silico, yeast two-hybrid andin vitroapproaches to investigate the nitrogen regulation network ofSynechococcusWH5701, a marine cyanobacterium with two PII(GlnB_A and GlnB_B) and two PipX (PipX_I and PipX_II) proteins. Our results indicate that GlnB_A is functionally equivalent to the canonical PIIprotein fromSynechococcus elongatus. GlnB_A interacted with PipX and NAGK proteins and stimulated NAGK activity, counteracting arginine inhibition. GlnB_B had only a slight stimulatory effect on NAGK activity, but its potential to bind effectors and form heterotrimers inSynechococcusWH5701 indicates additional regulatory functions. PipX_II, and less evidently PipX_I, specifically interacted with GlnB_A and NtcA, supporting a role for bothSynechococcusWH5701 PipX proteins in partner swapping with GlnB_A and NtcA.
TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock in Arabidopsis thaliana
Authors: Giraud Estelle , Ng Sophia , Carrie Chris , Duncan Owen , Low Jasmine , Lee Chun Pong , Van Aken Olivier , Millar A. Harvey , Murcha Monika , Whelan James
Published: December 2010

Diurnal regulation of transcripts encoding proteins located in mitochondria, plastids, and peroxisomes is important for adaptation of organelle biogenesis and metabolism to meet cellular requirements. We show this regulation is related to diurnal changes in promoter activities and the presence of specific cis-acting regulatory elements in the proximal promoter region [TGGGC(C/T)], previously defined as site II elements, and leads to diurnal changes in organelle protein abundances. These site II elements can act both as activators or repressors of transcription, depending on the night/day period and on the number and arrangement of site II elements in the promoter tested. These elements bind to the TCP family of transcriptions factors in Arabidopsis thaliana, which nearly all display distinct diurnal patterns of cycling transcript abundance. TCP2, TCP3, TCP11, and TCP15 were found to interact with different components of the core circadian clock in both yeast two-hybrid and direct protein–protein interaction assays, and tcp11 and tcp15 mutant plants showed altered transcript profiles for a number of core clock components, including LATE ELONGATED HYPOCOTYL1 and PSEUDO RESPONSE REGULATOR5. Thus, site II elements in the promoter regions of genes encoding mitochondrial, plastid, and peroxisomal proteins provide a direct mechanism for the coordination of expression for genes involved in a variety of organellar functions, including energy metabolism, with the time-of-day specific needs of the organism.
Parents evaluation of the processes of care in child rehabilitation: a reliability study of the Norwegian translation of MPOC‐20
Authors: Hagen A.‐K. , Bjorbækmo W. S.
Published: December 2010

Background  The objective was to assess the reliability of the Norwegian translation of the Canadian Measure of Processes of Care‐20 (MPOC‐20) questionnaire for use in child rehabilitation in Norway. MPOC‐20 is a standardized questionnaire with 20 items and 5 scales that assesses to what extent parents experience that the services offered to them and their children are in line with the ideologies and principles of the family‐centred service (FCS).

Methods  The translation of MPOC‐20 was performed according to international standards for translation of questionnaires. A pilot study was carried out with representatives from four patient advocacy organizations. A test–retest reliability study was performed. MPOC‐20 (N) was sent to the participants twice with 2‐ to 6‐week intervals. Participants were 36 parents of 25 children aged 0–18 years. Response rate was 41.8%.

Results  The intraclass correlations (ICCs) for test–retest scores ranged 0.78–0.86. The internal consistency expressed as Cronbach's alpha ranged 0.62–0.93; the score was high for four of the scales and acceptable for the fifth ‘Providing specific information’. These findings strongly suggest that the five scales of MPOC‐20 (N) have good test–retest reliability. Average scores of each scale did not differ significantly between the first and second rating, indicating that the average scores of the ratings are stable.

Conclusions  The Measure of Processes of Care‐20 (N) appears to be reliable and useful in the Norwegian context, and can be recommended for evaluation of the processes of child rehabilitation1 in Norway.
New homozygous SPINK5 mutation, p.Gln333X, in a Turkish pedigree with Netherton syndrome
Authors: Fong K. , Akdeniz S. , Isi H. , Taskesen M. , McGrath J. A. , Lai-Cheong J. E.
Published: December 2010

Netherton syndrome (NS) is a rare autosomal recessive genodermatosis caused by loss-of-function mutations in the SPINK5 gene. The clinical features include congenital ichthyosis, trichorrhexis invaginata and atopy. In this study, we report a new homozygous SPINK5 mutation, p.Gln333X, responsible for NS in affected members of two closely related Turkish families, and provide an overview of the genotype–phenotype correlation in this condition.
Functional characterization of Rho GTPases in Aspergillus niger uncovers conserved and diverged roles of Rho proteins within filamentous fungi
Authors: Kwon Min Jin , Arentshorst Mark , Roos Eelke D. , van den Hondel Cees A. M. J. J. , Meyer Vera , Ram Arthur F. J.
Published: December 2010

Rho GTPases are signalling molecules regulating morphology and multiple cellular functions including metabolism and vesicular trafficking. To understand the connection between polarized growth and secretion in the industrial model organism Aspergillus niger, we investigated the function of all Rho family members in this organism. We identified six Rho GTPases in its genome and used loss‐of‐function studies to dissect their functions. While RhoA is crucial for polarity establishment and viability, RhoB and RhoD ensure cell wall integrity and septum formation respectively. RhoC seems to be dispensable for A. niger. RacA governs polarity maintenance via controlling actin but not microtubule dynamics, which is consistent with its localization at the hyphal apex. Both deletion and dominant activation of RacA (RacG18V) provoke an actin localization defect and thereby loss of polarized tip extension. Simultaneous deletion of RacA and CftA (Cdc42) is lethal; however, conditional overexpression of RacA in this strain can substitute for CftA, indicating that both proteins concertedly control actin dynamics. We finally identified NoxR as a RacA‐specific effector, which however, is not important for apical dominance as reported for A. nidulans but for asexual development. Overall, the data show that individual Rho GTPases contribute differently to growth and morphogenesis within filamentous fungi.
High‐resolution esophageal pressure topography is superior to conventional sleeve manometry for the detection of transient lower esophageal sphincter relaxations associated with a reflux event
Authors: Rohof W. O. A. , Boeckxstaens G. E. E. , Hirsch D. P.
Published: December 2010

Background  Transient lower esophageal sphincter relaxations (TLESRs) are the main mechanism underlying gastro‐esophageal reflux and are detected during manometric studies using well defined criteria. Recently, high‐resolution esophageal pressure topography (HREPT) has been introduced and is now considered as the new standard to study esophageal and lower esophageal sphincter (LES) function. In this study we performed a head‐to‐head comparison between HREPT and conventional sleeve manometry for the detection of TLESRs.

Methods  A setup with two synchronized MMS‐solar systems was used. A solid state HREPT catheter, a water‐perfused sleeve catheter, and a multi intraluminal impedance pH (MII‐pH) catheter were introduced in 10 healthy volunteers (M6F4, age 19–56). Subjects were studied 0.5 h before and 3 h after ingestion of a standardized meal. Tracings were blinded and analyzed by the three authors according to the TLESR criteria.

Key Results  In the HREPT mode 156 TLESRs were scored, vs 143 during sleeve manometry (P = 0.10). Hundred and twenty‐three TLESRs were scored by both techniques. Of all TLESRs (177), 138 were associated with reflux (78%). High‐resolution esophageal pressure topography detected significantly more TLESRs associated with a reflux event (132 vs 119, P = 0.015) resulting in a sensitivity for detection of TLESRs with reflux of 96% compared to 86% respectively. Analysis of the discordant TLESRs associated with reflux showed that TLESRs were missed by sleeve manometry due to low basal LES pressure (N = 5), unstable pharyngeal signal (N = 4), and residual sleeve pressure >2 mmHg (N = 10).

Conclusions & Inferences  The HREPT is superior to sleeve manometry for the detection of TLESRs associated with reflux. However, rigid HREPT criteria are awaited.
Lipid content of terrestrial arthropods in relation to body size, phylogeny, ontogeny and sex
Authors: LEASE HILARY M. , WOLF BLAIR O.
Published: December 2010

Energy storage in arthropods has important implications for survival and reproduction. The lipid content of 276 species of adult arthropods with wet mass in the range 0.2–6.13 g is determined to assess how lipid mass scales with body mass. The relative contribution of lipids to total body mass is investigated with respect to phylogeny, ontogeny and sex. The lipid content of adult insects, arachnids, and arthropods in general shows an isometric scaling relationship with respect to body mass (M) (Marthropod lipid= −1.09 ×Mdry1.01andMarthropod lipid= −1.00 ×Mlean0.98). However, lipid allocation varies between arthropod taxa, as well as with sex and developmental stage within arthropod taxa. Female insects and arachnids generally have higher lipid contents than males, and larval holometabolous insects and juvenile arachnids have higher lipid contents than adults.
Rice interspecies hybrids show precocious or delayed developmental transitions in the endosperm without change to the rate of syncytial nuclear division
Authors: Ishikawa Ryo , Ohnishi Takayuki , Kinoshita Yuki , Eiguchi Mitsugu , Kurata Nori , Kinoshita Tetsu
Published: December 2010

In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested as under‐proliferation or over‐proliferation of endosperm. Recent analyses using crosses between Arabidopsis thaliana and its related species with different ploidy levels have shown that interspecific hybridization causes delayed developmental transition and increased mitotic activity in the endosperm. In this study, we investigated endosperm development in interspecific crosses between diploid Oryza species. In a cross between female O. sativa and male O. punctata, we found that the hybrid endosperm was reduced in size and this cross was associated with precocious developmental transition. By contrast, the cross between O. sativa and O. longistaminata generated enlarged hybrid endosperm at the mid‐point of seed development and this cross was associated with delayed developmental transition. Subsequently, the hybrid endosperm displayed a shriveled appearance at the seed maturation stage. We found that the accumulation of storage products and the expression patterns of several marker genes were also altered in the hybrid endosperm. By contrast, the rate of syncytial mitotic nuclear divisions was not significantly affected. The gene OsMADS87 showed a maternal origin‐specific expression pattern in rice endosperm, in contrast to its Arabidopsis homologue PHERES1, which shows paternal origin‐specific expression. OsMADS87 expression was decreased or increased depending on the type of developmental transition change in the hybrid rice endosperm. Our results indicate that one of the interspecies hybridization barriers in Oryza endosperm is mediated by precocious or delayed developmental alterations and de‐regulation of OsMADS87, without change to the rate of syncytial mitotic nuclear division in the hybrid endosperm.
Small RNAs from MITE‐derived stem‐loop precursors regulate abscisic acid signaling and abiotic stress responses in rice
Authors: Yan Yongsheng , Zhang Yuman , Yang Kun , Sun Zongxiu , Fu Yaping , Chen Xiaoying , Fang Rongxiang
Published: December 2010

Small silencing RNAs (sRNAs) are non‐coding RNA regulators that negatively regulate gene expression by guiding mRNA degradation, translation repression or chromatin modification. Plant sRNAs play crucial roles in various developmental processes, hormone signaling, immune responses and adaptation to a variety of abiotic stresses. miR441 and miR446 were previously annotated as microRNAs (miRNAs) because their precursors can form typical stem‐loop structures, but are not considered as real miRNAs because of inconsistency with some ancillary criteria of the recent guidelines for annotation of plant miRNAs. We tentatively rename them small interfering (si)R441 and siR446, respectively, in this study. It has recently been shown that the precursors of siR441 and siR446 might originate from the miniature inverted‐repeat transposable element (MITE) Stowaway1. In this report, we show that, in contrast with Dicer‐like (DCL)3‐ and RNA‐dependent RNA polymerase (RDR)2‐dependent MITE‐derived ra‐siRNAs, siR441 and siR446 are processed by OsDCL3a but independent of OsRDR2, indicating that siR441 and siR446 are generated from single‐stranded stem‐loop precursors. We also show that abscisic acid (ABA) and abiotic stresses downregulate the expression of siR441 and siR446 but, surprisingly, increase the accumulation of their precursors in rice plants, implying that processing of siRNA precursors is inhibited. We provide evidence to show that this defective processing is due to increased precursor accumulation per se, possibly by intermolecular self‐pairing of the processing intermediate sequences, thus hindering their normal processing. Functional examinations indicate that siR441 and siR446 are positive regulators of rice ABA signaling and tolerance to abiotic stress, possibly by regulating MAIF1 expression.
TFL2/LHP1 is involved in auxin biosynthesis through positive regulation of YUCCA genes
Authors: Rizzardi Kristina , Landberg Katarina , Nilsson Lars , Ljung Karin , Sundås‐Larsson Annika
Published: December 2010

TERMINAL FLOWER2 (TFL2) is the plant homologue of metazoan HETEROCHROMATIN PROTEIN1 (HP1) protein family. It is known that, unlike most HP1 proteins, TFL2 does not primarily localize to heterochromatin; instead it functions in regulation of specific genes in euchromatic regions. We show that the tfl2 mutant has a lower rate of auxin biosynthesis, resulting in low levels of auxin. In line with this, tfl2 mutants have lower levels of expression of auxin response genes and retain an auxin response. The reduced rate of auxin biosynthesis in tfl2 is correlated to the down‐regulation of specific genes in the tryptophan‐dependent auxin biosynthesis pathway, a sub‐set of the YUCCA genes. In vivo, TFL2 is targeted to a number of the YUCCA genes in an auxin‐dependent fashion revealing a role of TFL2 in auxin regulation, probably as a component of protein complexes affecting transcriptional control.
Transcription‐dependence of histone H3 lysine 27 trimethylation at the Arabidopsis polycomb target gene FLC
Authors: Buzas Diana Mihaela , Robertson Masumi , Finnegan E. Jean , Helliwell Chris A.
Published: December 2010

The FLC gene encodes a MADS box repressor of flowering that is the main cause of the late‐flowering phenotype of many Arabidopsis ecotypes. Expression of FLC is repressed by vernalization; maintenance of this repression is associated with the deposition of histone 3 K27 trimethylation (H3K27me3) at the FLC locus. However, whether this increased H3K27me3 is a consequence of reduced FLC transcription or the cause of transcriptional repression is not well defined. In this study we investigate the effect of changes in transcription rate on the abundance of H3K27me3 in the FLC gene body, a chromatin region that includes sequences required to maintain FLC repression following vernalization. We show that H3K27me3 is inversely correlated with transcription across the FLC gene body in a range of ecotypes and mutants with different flowering times. We demonstrate that the FLC gene body becomes marked with H3K27me3 in the absence of transcription. When transcription of the gene body is directed by an inducible promoter, H3K27me3 is removed following activation of transcription and H3K27me3 is added after transcription is decreased. The rate of addition of H3K27me3 to the FLC transgene following inactivation of transcription is similar to that observed in the FLC gene body following vernalization. Our data suggest that reduction of FLC transcription during vernalization leads to an increase of H3K27me3 levels in the FLC gene body that in turn maintains FLC repression.
The intracellular Arabidopsis COPT5 transport protein is required for photosynthetic electron transport under severe copper deficiency
Authors: Garcia‐Molina Antoni , Andrés‐Colás Nuria , Perea‐García Ana , del Valle‐Tascón Secundino , Peñarrubia Lola , Puig Sergi
Published: December 2010

Copper is an essential micronutrient that functions as a redox cofactor in multiple plant processes, including photosynthesis. Arabidopsis thaliana possesses a conserved family of CTR‐like high‐affinity copper transport proteins denoted as COPT1‐5. COPT1, the only family member that is functionally characterized, participates in plant copper acquisition. However, little is known about the function of the other Arabidopsis COPT proteins in the transport and distribution of copper. Here, we show that a functional fusion of COPT5 to the green fluorescent protein localizes in Arabidopsis cells to the prevacuolar compartment. Plants defective in COPT5 do not exhibit any significant phenotype under copper‐sufficient conditions, but their growth is compromised under copper limitation. Under extreme copper deficiency, two independent copt5 knockout mutant lines exhibit severe defects in vegetative growth and root elongation, low chlorophyll content, and impairment in the photosynthetic electron transfer. All these phenotypes are rescued when the wild‐type copy of the COPT5 gene is retransformed into a copt5 knockout line or when copper, but not other metals, are added to the medium. COPT5 is expressed in vascular tissues, with elevated levels in roots. Taken together, these results suggest that COPT5 plays an important role in the plant response to environmental copper scarcity, probably by remobilizing copper from prevacuolar vesicles, which could act as internal stores or recycling vesicles to provide the metal cofactor to key copper‐dependent processes such as photosynthesis.
The Clavata2 genes of pea and Lotus japonicus affect autoregulation of nodulation
Authors: Krusell Lene , Sato Naoto , Fukuhara Izumi , Koch Bjørn E. V. , Grossmann Christina , Okamoto Satoru , Oka‐Kira Erika , Otsubo Yoko , Aubert Grégoire , Nakagawa Tomomi , Sato Shusei , Tabata Satoshi , Duc Gerard , Parniske Martin , Wang Trevor L. , Kawaguchi Masayoshi , Stougaard Jens
Published: December 2010

The number of root nodules developing on legume roots after rhizobial infection is controlled by the plant shoot through autoregulation and mutational inactivation of this mechanism leads to hypernodulation. We have characterised the Pisum sativum (pea) Sym28 locus involved in autoregulation and shown that it encodes a protein similar to the Arabidopsis CLAVATA2 (CLV2) protein. Inactivation of the PsClv2 gene in four independent sym28 mutant alleles, carrying premature stop codons, results in hypernodulation of the root and changes to the shoot architecture. In the reproductive phase sym28 shoots develops additional flowers, the stem fasciates, and the normal phyllotaxis is perturbed. Mutational substitution of an amino acid in one leucine rich repeat of the corresponding Lotus japonicus LjCLV2 protein results in increased nodulation. Similarly, down‐regulation of the Lotus Clv2 gene by RNAi mediated reduction of the transcript level also resulted in increased nodulation. Gene expression analysis of LjClv2 and Lotus hypernodulation aberrant root formation Har1 (previously shown to regulate nodule numbers) indicated they have overlapping organ expression patterns. However, we were unable to demonstrate a direct protein–protein interaction between LjCLV2 and LjHAR1 proteins in contrast to the situation between equivalent proteins in Arabidopsis. LjHAR1 was localised to the plasma membrane using a YFP fusion whereas LjCLV2‐YFP localised to the endoplasmic reticulum when transiently expressed in Nicotiana benthamiana leaves. This finding is the most likely explanation for the lack of interaction between these two proteins.
The significance of anticardiolipin antibody and immunologic abnormality in livedoid vasculitis
Authors: Feng Su‐ying , Jin Pei‐ying , Shao Chang‐geng
Published: December 2010

Objective  To evaluate the significance of anticardiolipin and immunologic abnormality in the livedoid vasculitis (LV).

Methods  30 patients with biopsy‐proven LV and 30 normal controls involved in the study. Indirect immunofluorescence, immunoblot, and ELISA were used for detecting antinuclear antibody (ANA), circulating immune complex, immune globulin, anticardiophospholipin antibody (ACA), and anti‐β2GP1.

Results  ANA was positive in four patients with LV, and among them, two patients were diagnosed as Systemic Lupus Erythematosus (SLE) later. Addition to the two SLE patients, the level of ENA and immunoglobulin were normal in the rest of patients. Anticardiolipin antibodies were present in 13 (43.33%), and β2GP1 was present in nine (30%) of 30 patients. There were significant differences between LV and controls.

Conclusions  ACA is one of important pathogenesis of LV. Numerous heterogeneous coagulation abnormalities and thrombogenesis may involve the LV.
Causes of death among active leprosy patients in China
Authors: Shen Jianping , Liu Musang , Zhou Min , Li Wenzhong
Published: December 2010

We analyzed the causes of death among active leprosy patients in China, to better understand the disease and improve the quality of services, by performing a retrospective study involving 24 provinces of China. Information about patients with active leprosy who were not clinically cured and died between January 1, 2000, and December 31, 2005, was collected by professionals at county levels. A total of 524 deaths were analyzed. The leading cause of death was suicide. There were 86 patients (16%) who died at a mean of 21 ± 19 months after starting multi‐drug therapy (MDT). The second and third leading causes of death were cardiovascular disease and organ failure associated with advanced age, respectively. Two hundred and twenty‐one patients (42%) died within one year of beginning MDT. The second month of MDT was the riskiest for newly treated patients; approximately 20% of patients succumbed to liver failure, 33% to dapsone (diaminodiphenylsulfone/DDS) allergy, and 27% to renal insufficiency during this period. Among 143 deaths related to leprosy, 37 (26%) occurred within three months of starting MDT. We recommend that newly diagnosed patients should be provided with no more than two months of MDT blister packs.