bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural studies of Saccharomyces cerevesiae mitochondrial NADP‐dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction
Authors: Peng Yingjie , Zhong Chen , Huang Wei , Ding Jianping 
Published: June 2008

AbstractIsocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into α‐ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP‐IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca2+, which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP‐IDHs reveal that eukaryotic NADP‐IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118–124 and residues 284–287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi‐closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca2+ in the pseudo‐Michaelis complex or with NADPH, AKG, and Ca2+ in the product state. The conformational changes of eukaryotic NADP‐IDHs are quite different from those of Escherichia coli NADP‐IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP‐IDHs is more complex than that of EcIDH, and involves more fine‐tuned conformational changes.
The structure of “defective in induced resistance” protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein
Authors: Lascombe Marie‐Bernard , Bakan Bénédicte , Buhot Nathalie , Marion Didier , Blein Jean‐Pierre , Larue Valéry , Lamb Chris , Prangé Thierry 
Published: June 2008

AbstractScreening of transfer DNA (tDNA) tagged lines of Arabidopsis thaliana for mutants defective in systemic acquired resistance led to the characterization of dir1‐1 (defective in induced resistance [systemic acquired resistance, SAR]) mutant. It has been suggested that the protein encoded by the dir1 gene, i.e., DIR1, is involved in the long distance signaling associated with SAR. DIR1 displays the cysteine signature of lipid transfer proteins, suggesting that the systemic signal could be lipid molecules. However, previous studies have shown that this signature is not sufficient to define a lipid transfer protein, i.e., a protein capable of binding lipids. In this context, the lipid binding properties and the structure of a DIR1–lipid complex were both determined by fluorescence and X‐ray diffraction. DIR1 is able to bind with high affinity two monoacylated phospholipids (dissociation constant in the nanomolar range), mainly lysophosphatidyl cholines, side‐by‐side in a large internal tunnel. Although DIR1 shares some structural and lipid binding properties with plant LTP2, it displays some specific features that define DIR1 as a new type of plant lipid transfer protein. The signaling function associated with DIR1 may be related to a specific lipid transport that needs to be characterized and to an additional mechanism of recognition by a putative receptor, as the structure displays on the surface the characteristic PxxP structural motif reminiscent of SH3 domain signaling pathways.
The structure of a fibril‐forming sequence, NNQQNY, in the context of a globular fold
Authors: Guo Zhefeng , Eisenberg David 
Published: June 2008

AbstractNumerous human disorders are associated with the formation of protein fibrils. The fibril‐forming capacity of a protein has been found in recent studies to be determined by a short segment of residues that forms a dual β‐sheet, called a steric zipper, in the spine of the fibril. The question arises as to whether a fibril‐forming segment, when inserted within the sequence of a globular protein, will invariably cause the protein to form fibrils. Here we investigate this question by inserting the known fibril‐forming segment NNQQNY into the globular enzyme, T7 endonuclease I. From earlier studies, we know that in its fibril form, NNQQNY is in an extended conformation. We first found that the inserted NNQQNY stimulates fibril formation of T7 endonuclease I in solution. Thus NNQQNY within T7 endonuclease I can exist in an extended conformation, capable of forming the steric zipper in the core of a fibril. We also found that T7 endonuclease I folds into a decamer that does not form fibrils. We determined the structure of the decamer by X‐ray crystallography, finding an unusual oligomer without point group symmetry, and finding that the NNQQNY segments within the decamer adopt two twisted conformations, neither is apparently able to fibrillize. We conclude that twisting of fibril forming sequences from the fully extended conformation, imposed by the context of their placement in proteins, can interfere with fibril formation.
Association of BLV infection profiles with alleles of the BoLA‐DRB3.2 gene
Authors: Juliarena M. A. , Poli M. , Sala L. , Ceriani C. , Gutierrez S. , Dolcini G. , Rodríguez E. M. , Mariño B. , Rodríguez‐Dubra C. , Esteban E. N. 
Published: June 2008

SummaryBovine leukaemia virus (BLV) causes lymphosarcoma and persistent lymphocytosis (PL). Some MHC class II gene polymorphisms have been associated with resistance and susceptibility to the development of lymphosarcoma and PL, as well as with a reduced number of circulating BLV‐infected lymphocytes. Previously, 230 BLV‐infected Holstein cattle were classified into two infection profiles characterized by low and high proviral loads (LPL and HPL respectively). Here, the influence of the polymorphism at the BoLA‐DRB3.2* gene of these animals was examined. After genotyping, the association between the BoLA‐DRB3.2* alleles and the BLV infection profile was determined as the odds ratio (OR). Two subtypes of allele *11 were identified (ISAG*0901 and *0902). Allele ISAG*0902 showed a stronger association with the LPL profile (OR = 8.24; P < 0.0001) than allele *11 itself (OR = 5.82; P < 0.0001). Allele ISAG*1701 (*12) also showed significant association with the LPL profile (OR = 3.46; P < 0.0055). Only one allele, ISAG*1501 or 03 (*16), showed significant association with HPL (OR = 0.36; P < 0.0005). The DRB3.2* alleles were assigned to three categories: resistant (R), susceptible (S) and neutral (N). Based on their DRB3 genotypes, cattle were classified as homozygous or heterozygous. The RR and RN genotypes were associated with the LPL profile, while the SS and NS genotypes were associated with the HPL profile. The RS genotype could not be associated with any particular profile. Our results show that allele ISAG*0902 appears to be the best BLV resistance marker in Holstein cattle.
Development of a sufficient design for estimation of fluconazole pharmacokinetics in people with HIV infection
Authors: Roos Juliana F. , Kirkpatrick Carl M. J. , Tett Susan E. , McLachlan Andrew J. , Duffull Stephen B. 
Published: June 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Optimal design is being employed more frequently to help reduce the number of samples taken per patient, the number of patients and number of doses to be given within a study.• In doing this the economic and patient resources required to conduct a population pharmacokinetic or pharmacokinetic–pharmacodynamic study are reduced. WHAT THIS STUDY ADDS • This is the first time that healthy volunteer data (e.g. from Phase I) have been used to develop an optimal design that is to be conducted in a population with different characteristics due to disease (e.g. Phase II).AIMS To assess an optimal design that is sufficient to gain precise estimates of the pharmacokinetic (PK) parameters for fluconazole in people with HIV infection.METHODS Two studies were identified, the first in healthy volunteers and the second in HIV patients. The investigators (J.F.R. and S.B.D.) were blinded to the second study results. The healthy volunteer study was modelled and a design was found to estimate the PK parameters. The design was evaluated by comparison of the standard errors of the parameters and the predictive performance of the optimal design. The predictive performance was assessed by comparing model predictions against observed concentrations for two models. The first model, termed ‘sufficient design’, was developed from data extracted from the HIV study that corresponded to the optimal design. The second model, termed ‘HIV outcome model’, by modelling all the data from the HIV study.RESULTS An optimal design HIV study was developed which had considerably fewer blood samples and dosing arms compared with the actual HIV study. The optimized design performed as well as the actual HIV study in terms of parameter precision. The performance of the design, described as the precision (mg l−1)2 (95% confidence interval) of the predicted concentrations to the actual concentrations for the ‘sufficient design’ and ‘HIV outcome model’ models were: 0.63 (0.40, 0.87) and 0.56 (0.32, 0.79), respectively.CONCLUSION This study demonstrates how data from healthy volunteers can be utilized via optimal design methodology to design a successful study in the target population.
A limited sampling strategy for tacrolimus in renal transplant patients
Authors: Mathew Binu S. , Fleming Denise H. , Jeyaseelan Visalakshi , Chandy Sujith J. , Annapandian V. M. , Subbanna P. K. , John George T. 
Published: June 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Tacrolimus trough concentration is being currently used for dose individualization.• Limited sampling strategies (LSS) have been developed and validated for renal transplant patients.• Earlier literature has suggested that measurement of tacrolimus AUC is more reliable than trough with respect to both rejection and nephrotoxicity. WHAT THIS STUDY ADDS • Four thousand renal transplants take place annually in India, with many patients prescribed tacrolimus in combination with mycophenolate and steroid.• In this study a LSS with two points, i.e. trough and 1.5 h postdose was developed and validated to estimate AUC0–12.• The added benefit of only a single additional sample with completion of blood collection in 1.5 h and minimum additional cost makes this a viable LSS algorithm in renal transplant patients.• In patients having tacrolimus trough concentrations outside the recommended range (<3 and >10 ng ml−1 in the treatment protocol in our institution) or having side‐effects in spite of trough concentrations in the desired range, we can estimate AUC using this LSS for a better prediction of exposure.AIMSTo develop and validate limited sampling strategy (LSS) equations to estimate area under the curve (AUC0–12) in renal transplant patients.METHODSTwenty‐nine renal transplant patients (3–6 months post transplant) who were at steady state with respect to tacrolimus kinetics were included in this study. The blood samples starting with the predose (trough) and collected at fixed time points for 12 h were analysed by microparticle enzyme immunoassay. Linear regression analysis estimated the correlations of tacrolimus concentrations at different sampling time points with the total measured AUC0–12. By applying multiple stepwise linear regression analysis, LSS equations with acceptable correlation coefficients (R2), bias and precision were identified. The predictive performance of these models was validated by the jackknife technique.RESULTSThree models were identified, all with R2 ≥ 0.907. Two point models included one with trough (C0) and 1.5 h postdose (C1.5), another with trough and 4 h postdose. Increasing the number of sampling time points to more than two increased R2 marginally (0.951 to 0.990). After jackknife validation, the two sampling time point (trough and 1.5 h postdose) model accurately predicted AUC0–12. Regression coefficient R2 = 0.951, intraclass correlation = 0.976, bias [95% confidence interval (CI)] 0.53% (−2.63, 3.69) and precision (95% CI) 6.35% (4.36, 8.35).CONCLUSIONThe two‐point LSS equation [AUC0–12 = 19.16 + (6.75.C0) + (3.33.C1.5)] can be used as a predictable and accurate measure of AUC0–12 in stable renal transplant patients prescribed prednisolone and mycophenolate.
Pathogenic ATM mutations occur rarely in a subset of multiple myeloma patients
Authors: Austen Belinda , Barone Giancarlo , Reiman Anne , Byrd Philip J. , Baker Claire , Starczynski Jane , Nobbs Michael C. , Murphy Raymond P. , Enright Helen , Chaila Elijah , Quinn John , Stankovic Tatjana , Pratt Guy , Taylor A. Malcolm R. 
Published: June 2008

SummaryAtaxia Telangiectasia (A‐T) patients have biallelic inactivation of the ATM gene and exhibit a 200‐fold‐increased frequency of lymphoid tumours. ATM mutations have been found in a number of adult lymphoid malignancies but there is no data on the occurrence of ATM mutations in multiple myeloma tumours. The purpose of our work was to investigate the occurrence of ATM mutations in multiple myeloma and to this end we screened 45 sporadic cases for ATM mutations using denaturing high‐performance liquid chromatography analysis and DNA sequencing. Pathogenic ATM mutations were identified in 2/45 of the myelomas compared with a published estimate of ATM mutant allele frequency in the UK population of 2/521 (P = 0·033). One was the missense mutation 7181C>T which was then modelled in an expression system and the S2394L protein shown to have no ATM kinase activity. The second myeloma had the pathogenic ATM splice site mutation IVS40‐1G>C leading to loss of exon 41. We also report a 48‐year‐old ataxia telangiectasia patient who developed multiple myeloma. Taken together our study suggests that ATM mutation may play a role in the pathogenesis of a subset of multiple myelomas.
The small glycine‐rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana
Authors: Streitner Corinna , Danisman Selahattin , Wehrle Franziska , Schöning Jan C. , Alfano James R. , Staiger Dorothee 
Published: June 2008

SummaryThe RNA binding protein AtGRP7 is part of a circadian slave oscillator in Arabidopsis thaliana that negatively autoregulates its own mRNA, and affects the levels of other transcripts. Here, we identify a novel role for AtGRP7 as a flowering‐time gene. An atgrp7‐1 T‐DNA mutant flowers later than wild‐type plants under both long and short days, and independent RNA interference lines with reduced levels of AtGRP7, and the closely related AtGRP8 protein, are also late flowering, particularly in short photoperiods. Consistent with the retention of a photoperiodic response, the transcript encoding the key photoperiodic regulator CONSTANS oscillates with a similar pattern in atgrp7‐1 and wild‐type plants. In both the RNAi lines and in the atgrp7‐1 mutant transcript levels for the floral repressor FLC are elevated. Conversely, in transgenic plants ectopically overexpressing AtGRP7, the transition to flowering is accelerated mainly in short days, with a concomitant reduction in FLC abundance. The late‐flowering phenotype of the RNAi lines is suppressed by introducing the flc‐3 loss‐of‐function mutation, suggesting that AtGRP7 promotes floral transition, at least partly by downregulating FLC. Furthermore, vernalization overrides the late‐flowering phenotype. Retention of both the photoperiodic response and vernalization response are features of autonomous pathway mutants, suggesting that AtGRP7 is a novel member of the autonomous pathway.
Cutaneous rhinosporidiosis presents with recurrent nasal philtrum mass in southern Turkey
Authors: Ağırdır Bülent V. , Derin Alper T. , Özbilim Gülay , Akman Ayse 
Published: June 2008

AbstractWe report a case of cutaneous rhinosporidiosis localized in the nasal philtrum. The patient's complaints started 3 months prior to being seen in our clinics. Ear, nose, and throat examination showed the presence of a polypoid lesion filling the right nostril. Complete surgical resection of the polypoid lesion provided a temporary relief as the patient developed the same lesion atin 6 weeks post‐operation. The appearance and the recurrence pattern have led us to determine whether this lesion was rhinosporidiosis. Histopathological examination confirmed rhinosporidiosis. Finally, we performed complete resection followed by cauterization of the base of the mass. The infection has been reported in hot, tropical climates, and endemic zones of India and Sri Lanka. To our knowledge there is no reported case of rhinosporidiosis from southern Turkey within the subtropical Mediterranean climatic area.
Body mass index is a stronger predictor of alanine aminotransaminase levels than alcohol consumption
Authors: Adams Leon A , Knuiman Matthew W , Divitini Mark L , Olynyk John K 
Published: June 2008

AbstractBackground and Aims:  The relative effects of obesity compared to alcohol on liver injury are uncertain. We examined their effects on alanine aminotransferase (ALT) and gamma glutamyltransferase (GGT) levels in a population‐based cohort.Methods:  Adult residents (2610: 1326 males, 1284 females) from Busselton, Australia, participated in a cross‐sectional survey determining alcohol intake as determined by a validated questionnaire, anthropometric measurements and serum analysis. Alcohol consumption was classified as never, light (<140 g/week), moderate (140–420 g/week) or heavy (>420 g/week).Results:  The majority of subjects were either overweight (41%) or obese (17%). A minority of subjects were moderate (25%) or heavy drinkers (4%). Body mass index (BMI) and waist circumference were strongly associated with ALT and GGT (P < 0.0001 for all tests). Alcohol consumption was modestly associated with ALT in females (P = 0.01) but not in males (P = 0.9). In contrast, GGT was significantly associated with alcohol in both genders (P < 0.0005). The risk of an elevated ALT was seven‐fold higher with obesity but only two‐fold higher with moderate or heavy alcohol use. Obesity accounted for half of all elevated ALT levels in the cohort, whereas alcohol excess was responsible for less than 10%. No synergistic effect was observed between BMI or waist circumference and alcohol on ALT or GGT (P > 0.2 for all tests).Conclusions:  Excess weight is more common than excessive alcohol consumption in the community and confers a greater risk of elevated aminotransaminase levels.
Liver disease and the renin–angiotensin system: Recent discoveries and clinical implications
Authors: Lubel John S , Herath Chandana B , Burrell Louise M , Angus Peter W 
Published: June 2008

AbstractThe renin–angiotensin system (RAS) is a key regulator of vascular resistance, sodium and water homeostasis and the response to tissue injury. Historically, angiotensin II (Ang II) was thought to be the primary effector peptide of this system. Ang II is produced predominantly by the effect of angiotensin converting enzyme (ACE) on angiotensin I (Ang I). Ang II acts mainly through the angiotensin II type‐1 receptor (AT1) and, together with ACE, these components represent the ‘classical’ axis of the RAS. Drug therapies targeting the RAS by inhibiting Ang II formation (ACE inhibitors) or binding to its receptor (angiotensin receptor blockers) are now in widespread clinical use and have been shown to reduce tissue injury and fibrosis in cardiac and renal disease independently of their effects on blood pressure. In 2000, two groups using different methodologies identified a homolog of ACE, called ACE2, which cleaves Ang II to form the biologically active heptapeptide, Ang‐(1–7). Conceptually, ACE2, Ang‐(1–7), and its putative receptor, themasreceptor represent an ‘alternative’ axis of the RAS capable of opposing the often deleterious actions of Ang II. Interestingly, ACE inhibitors and angiotensin receptor blockers increase Ang‐(1–7) production and it has been proposed that some of the beneficial effects of these drugs are mediated through upregulation of Ang‐(1–7) rather than inhibition of Ang II production or receptor binding. The present review focuses on the novel components and pathways of the RAS with particular reference to their potential contribution towards the pathophysiology of liver disease.
Chromoscopic endomicroscopy: In vivo cellular resolution imaging of the colorectum
Authors: Smith Lesley‐Ann , Tiffin Nick , Thomson Mike , Cross Simon S , Hurlstone David P 
Published: June 2008

AbstractAdvances in imaging technology and engineering have now permitted functional integration of a confocal endomicroscope into the distal tip of a conventional video colonoscope enabling imaging of the surface epithelium and the underlying lamina propria during ongoing video endoscopy. For the first time, the endoscopist is now able to resolve the surface and subsurface mucosa at cellular resolution in vivo and in real time. A new era in endoscopic imaging has therefore begun – histoendoscopy. In addition to providing a high‐accuracy in vivo optical biopsy tool for the differentiation between benign hyperplasia, intra‐epithelial neoplasia and carcinoma in sporadic cohorts, endomicroscopy with targeted biopsies has now been shown to increase the yield of intra‐epithelial neoplasia complicating ulcerative colitis. Furthermore, recent data examining endomicroscopic molecular ex vivo imaging using anti‐CD44v6 antibody has identified aberrant crypt foci based on their surface molecular expression. Receptor overexpression in vivo in humans may, in the near future, be exploited for the diagnosis of inflammation, neoplasia and in predicting targeted molecular therapy. Endomicroscopy will be key to this immuno‐imaging interface. Within the present review, we discuss the current clinical evidence in support of confocal endomicroscopy and explore the new diagnostic possibilities for this technology.
V4 Total laparoscopic restorative proctocolectomy for ulcerative colitis
Authors: Sagar P. M. , Gonsalves S. J. , Brayshaw I. , Williams G. 
Published: June 2008

Introduction:  Laparoscopic ileal pouch‐anal anastomosis (IPAA) has been shown to be a safe and feasible technique for patients with ulcerative colitis refractory to medical management and familial polyposis. We aim to demonstrate our technique of total laparoscopic proctocolectomy with intracorporeal pouch‐anal anastomosis with specific reference to intaroperative tricks of the trade.Patient and Methods:  The patient is a 16‐year‐old male with ulcerative colitis. The video demonstrates a total laparoscopic proctocolectomy and formation of a (J) ileal pouch anal anastomosis. A standard colonic mobilisation of the colon was performed with the use of the Goldfinger retractor to aid vessel division and the use of the harmonic scalpel for mesenteric division apart from the transverse mesocolon where the ligasure was employed. The right colon was only mobilised after complete mesenteric division of the left & transverse colon to prevent looping. The rectum, once mobilised to the pelvic floor, was divided in the AP direction with the endoGIA. Techniques to prevent twisting of the pouch and inadvertent twisting of the proximal small bowel are demonstrated. The video also highlights the importance of positioning the patient and use of 0 and 30 degree scopes. A technique to tackle a defect in the anal stump is also described.Conclusion:  The technique of laparoscopic IPAA adheres to the principles of open pouch surgery but we await the development of more suitable laparoscopic staplers to aid the clinician in division of the anorectal junction.