Structure of the regulatory domain of the LysR family regulator NMB2055 (MetR-like protein) from Neisseria meningitidis

Copyright @ 2012 International Union of CrystallographyThe crystal structure of the regulatory domain of NMB2055, a putative MetR regulator from Neisseria meningitidis, is reported at 2.5 Å resolution. The structure revealed that there is a disulfide bond inside the predicted effector-binding pocket of the regulatory domain. Mutation of the cysteines (Cys103 and Cys106) that form the disulfide bond to serines resulted in significant changes to the structure of the effector pocket. Taken together with the high degree of conservation of these cysteine residues within MetR-related transcription factors, it is suggested that the Cys103 and Cys106 residues play an important role in the function of MetR regulators.This study is funded by the Medical Research Council, with additional finance from the Biotechnology and Biological Science Research Council

Structure of the PII signal transduction protein of Neisseria meningitidis at 1.85 Ȃ resolution

Copyright @ 2006 International Union of CrystallographyThe PII signal transduction proteins GlnB and GlnK are implicated in the regulation of nitrogen assimilation in Escherichia coli and other enteric bacteria. PII-like proteins are widely distributed in bacteria, archaea and plants. In contrast to other bacteria, Neisseria are limited to a single PII protein (NMB 1995), which shows a high level of sequence identity to GlnB and GlnK from Escherichia coli (73 and 62%, respectively). The structure of the PII protein from N. meningitidis (serotype B) has been solved by molecular replacement to a resolution of 1.85 Ȃ. Comparison of the structure with those of other PII proteins shows that the overall fold is tightly conserved across the whole population of related proteins, in particular the positions of the residues implicated in ATP binding. It is proposed that the Neisseria PII protein shares functions with GlnB/GlnK of enteric bacteria.This study is funded by the Medical Research Council UK and Europe (SPINE) consortium (European Commission Grant No. QLG2-CT-2002-00988)

Structural basis of transcription initiation by RNA polymerase II.

Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

The general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II– TFIIB complex1,2 indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions3,4 enigmatic. Here we report crystal structures of the Pol II–TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4A˚ resolution and of an initially transcribing complex that additionally contains theDNAtemplate and a 6-nucleotide RNAproduct.The structures reveal the entire B-reader and protein– nucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emergingDNA–RNAhybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12–13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors5, and the bacterial initiation factor sigma has TFIIB-like topology1,2 and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function6–8. TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template

The influence of risk factors associated with captive rearing on post-release survival in translocated cirl buntings Emberiza cirlus in the UK

Population decline resulting from agricultural intensification led to contraction of the range of the cirl bunting Emberiza cirlus in the UK to a small area of south Devon. As part of the UK Biodiversity Action Plan for the species, a project to re-establish a population in suitable habitat in Cornwall was undertaken during 2006–2011, in which chicks were removed from the nest in Devon, hand-reared and then delayed-released. The survival of the birds to four time points in the year after release was analysed in relation to the effect of rearing factors, using a multivariable logistic regression model. Individuals with higher body weight at capture were more likely to survive to 1 January and 1 May in the year following release, and individuals released in June and July were more likely to survive than those released in August. Individuals released in 2006 and 2011 had a higher survival rate than those released during 2007–2010. Timing of capture, time spent at each stage in captivity, medication and the detection of parasites in the brood had no significant effect. Immunosuppressive disease, weather factors and predator activity may have led to some of the observed differences in survival. This analysis provides evidence with which to plan future translocation projects for cirl buntings and other passerine birds

Gastric ulcers: malignancy yield and risk stratification for follow-up endoscopy

Background and study aim: Malignant change can occur in gastric ulcer but guideline recommendations for follow-endoscopy (FU-OGD) are conflicting. This study aims to determine rate of malignancy and need for follow-up for gastric ulcers. Patients and methods: Patients with a first diagnosis of gastric ulcer between January 2012 and September 2013 were studied by analyzing endoscopic assessments, dysplasia, and malignancy yield and the influence of risk factors on the likelihood of benign disease. Results: In a cohort of 432 patients with gastric ulcer (53 % male, mean age 65 years) dysplasia or neoplasia were found in 27 (19 adenocarcinomas, 2 cases of dysplasia, 5 lymphomas, 1 melanoma; malignancy yield 6 %). Twenty-five (93 %) cases were diagnosed on first biopsy. The cancer yield of FU-OGD after initially benign biopsy was 0.9 %. Binary logistic regression analysis revealed that endoscopically benign appearance (odds ratio 0.004 95 % CI 0 – 0.576; P = 0.029), benign histology on first biopsy (odds ratio 0 95 % CI 0 – 0.39; P = 0.011) and lower number of ulcers (odds ratio 0.22 (95 % CI 0.05 – 0.99); P = 0.049) were independent predictors of benign disease. All dysplastic and neoplastic cases would have been identified by a combination of initial biopsies plus repeat endoscopy with further biopsies for endoscopically suspicious appearances. Conclusions: In this large cohort 6 % of gastric ulcers were found to be malignant, highlighting the need for all gastric ulcers to be biopsied. The cancer yield of FU-OGD after benign biopsies was low. We have demonstrated that the combination of benign index histology and no endoscopic suspicion of malignancy can predict benign disease. We recommend that all gastric ulcers to be biopsied. Risk stratification could potentially reduce need for FU-OGD

Molecular identification of Sarcocystis wobeseri-like parasites in a new intermediate host species, the white-tailed sea eagle (Haliaeetus albicilla)

A reintroduced white-tailed sea eagle (Haliaeetus albicilla) in moderate body condition was found dead and submitted for post-mortem examination. There were no signs of disease on gross pathological examination. Histopathological examination however revealed the presence of encysted protozoan parasites in pectoral and cardiac muscle sections. Polymerase chain reaction amplification of extracted genomic DNA and sequencing of four regions: the 18S rDNA, 28S rDNA, internal transcribed spacer (ITS) 1, and RNA polymerase B (rpoB) loci, confirmed the presence of a Sarcocystis species in pectoral and cardiac muscle which appeared phylogenetically similar to Sarcocystis wobeseri. This is the first report of S. wobeseri-like infection in a white-tailed sea eagle revealing a new intermediate host species for this parasite

Maintenance of a gluten free diet in coeliac disease: The roles of self-regulation, habit, psychological resources, motivation, support, and goal priority

Introduction: A strict lifelong gluten free diet (GFD) is the only treatment for coeliac disease (CD). Theory-based research has focused predominantly on initiation, rational, and motivational processes in predicting adherence. The aim of this study was to evaluate an expanded collection of theoretical constructs specifically relevant to the maintenance of behaviour change, in the understanding and prediction of GFD adherence. Methods: Respondents with CD (N = 5573) completed measures of GFD adherence, psychological distress, intentions, self-efficacy, and the maintenance-relevant constructs of self-regulation, habit, temptation and intentional and unintentional lapses (cognitive and behavioural consequences of lowered or fluctuating psychological resources and self-control), motivation, social and environmental support, and goal priority, conflict, and facilitation. Correlations and multiple regression were used to determine their influence on adherence, over and above intention and self-efficacy, and how relationships changed in the presence of distress. Results: Better adherence was associated with greater self-regulation, habit, self-efficacy, priority, facilitation, and support; and lower psychological distress, conflict, and fewer self-control lapses (e.g., when busy/stressed). Autonomous and wellbeing-based, but not controlled motivations, were related to adherence. In the presence of distress, the influence of self-regulation and intentional lapses on adherence were increased, while temptation and unintentional lapses were decreased. Discussion: The findings point to the importance of considering intentional, volitional, automatic, and emotional processes in the understanding and prediction of GFD adherence. Behaviour change interventions and psychological support are now needed so that theoretical knowledge can be translated into evidence-based care, including a role for psychologists within the multi-disciplinary treatment team