An investigation into the role of optineurin in macrophage-mediated acute antibacterial response in inflammatory bowel disease.

Crohn’s disease (CD) is now recognised to be due to defective host responses to bacteria in genetically susceptible individuals. Others in our research group previously found defective neutrophil recruitment, bacterial clearance and monocyte-derived macrophage (MDM) proinflammatory cytokine secretion in CD. To investigate the defective cytokine secretion, we performed transcriptomic analysis and identified reduced MDM optineurin (OPTN) expression in 10% CD patients. Here, I show that macrophages stimulated with E. coli, bacterial Toll-like and NOD-like receptor ligands upregulate OPTN, a Golgi complex protein that regulates vesicle transport. In vitro, Optn-/- bone marrow-derived macrophages (BMDM) stimulated with E. coli secrete significantly lower levels of proinflammatory TNF and IL6 cytokines, which is normalised to wildtype levels on addition of lysosomal function inhibitors. In vivo, Optn-/- mice develop a more severe Citrobacter colitis with greater mortality, an early defective neutrophil recruitment to the bowel and lower levels of serum proinflammatory cytokines. The Optn-/- mice also demonstrated a similar phenotype of defective neutrophil recruitment and lower serum proinflammatory cytokines in an E. coli-induced peritonitis. These results indicate that the low OPTN expression originally identified in CD macrophages has likely contributed to an attenuated antibacterial response, which potentially led to the development of bowel inflammation

Critical role of the disintegrin metalloprotease ADAM-like Decysin-1 (ADAMDEC1) for intestinal immunity and inflammation

BACKGROUND AND AIMS: ADAM (A Disintegrin And Metalloproteinase) is a family of peptidase proteins, which have diverse roles in tissue homeostasis and immunity. Here, we study ADAM-like Decysin-1 (ADAMDEC1) a unique member of the ADAM family. ADAMDEC1 expression is restricted to the macrophage/dendritic cell populations of the gastrointestinal tract and secondary lymphoid tissue. The biological function of ADAMDEC1 is unknown but it has been hypothesised to play a role in immunity. The identification of reduced ADAMDEC1 expression in Crohn's disease patients has provided evidence of a potential role in bowel inflammation. METHODS: Adamdec1(-/-) mice were exposed to dextran sodium sulphate or infected orally with Citrobacter rodentium or Salmonella typhimurium The clinical response was monitored. RESULTS: The loss of Adamdec1 rendered mice more susceptible to the induction of bacterial and chemical induced colitis, as evidenced by increased neutrophil infiltration, greater IL-6 and IL-1β secretion, more weight loss and increased mortality. In the absence of Adamdec1, greater numbers of Citrobacter rodentium were found in the spleen, suggestive of a breakdown in mucosal immunity which resulted in bacteraemia. CONCLUSION: In summary, Adamdec1 protects the bowel from chemical and bacterial insults, failure of which may predispose to Crohn's disease

Optineurin deficiency contributes to impaired cytokine secretion and neutrophil recruitment in bacteria driven colitis.

Crohn's disease (CD) is associated with delayed neutrophil recruitment and bacterial clearance at sites of acute inflammation as a result of impaired secretion of proinflammatory cytokines by macrophages. To investigate the impaired cytokine secretion, we performed transcriptomic analysis in macrophages and identified a subgroup of CD patients with low expression of the autophagy receptor optineurin (OPTN). Here we clarified the role of OPTN deficiency in macrophage cytokine secretion, models of bacteria driven colitis and peritonitis in mice and zebrafish Salmonella infection. OPTN deficient bone-marrow derived macrophages (BMDM) stimulated with heat-killed E. coli secreted less proinflammatory TNF and IL6 cytokines despite similar gene transcription, which normalised with lysosomal and autophagy inhibitors suggesting that TNF is mistrafficked to lysosomes via bafilomycin A dependent pathways in the absence of OPTN. OPTN deficient mice were more susceptible to Citrobacter colitis and E. coli peritonitis with reduced levels of proinflammatory TNF in serum, diminished neutrophil recruitment to sites of acute inflammation and greater mortality. Optn knockdown zebrafish infected with Salmonella also had higher mortality. OPTN plays a role in acute inflammation and neutrophil recruitment, potentially via defective macrophage proinflammatory cytokine secretion, which suggests that diminished OPTN expression in humans may increase the risk of developing CD

Prediction of photoperiodic regulators from quantitative gene circuit models

Photoperiod sensors allow physiological adaptation to the changing seasons. The external coincidence hypothesis postulates that a light-responsive regulator is modulated by a circadian rhythm. Sufficient data are available to test this quantitatively in plants, though not yet in animals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their lightsensitive proteins are thought to form an external coincidence sensor. We use 40 timeseries of molecular data to model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, the models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modelling makes this complexity explicit and may thus contribute to crop improvement

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

High frequency of pathogenic non-founder germline mutations in BRCA1 and BRCA2 in families with breast and ovarian cancer in a founder population

Funding Information: This work was supported by State Research Program “Biomedicine for the public health (BIOMEDICINE)” project 5 “Personalised cancer diagnostics and treatment effectiveness evaluation”. Publisher Copyright: © 2018 The Author(s).Background: Pathogenic BRCA1 founder mutations (c.4035delA, c.5266dupC) contribute to 3.77% of all consecutive primary breast cancers and 9.9% of all consecutive primary ovarian cancers. Identifying germline pathogenic gene variants in patients with primary breast and ovarian cancer could significantly impact the medical management of patients. The aim of the study was to evaluate the rate of pathogenic mutations in the 26 breast and ovarian cancer susceptibility genes in patients who meet the criteria for BRCA1/2 testing and to compare the accuracy of different selection criteria for second-line testing in a founder population. Methods: Fifteen female probands and 1 male proband that met National Comprehensive Cancer Network (NCCN) criteria for BRCA1/2 testing were included in the study and underwent 26-gene panel testing. Fourteen probands had breast cancer, one proband had ovarian cancer, and one proband had both breast and ovarian cancer. In a 26-gene panel, the following breast and/or ovarian cancer susceptibility genes were included: ATM, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, FAM175A, MEN1, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53, and XRCC2. All patients previously tested negative for BRCA1 founder mutations. Results: In 44% (7 out of 16) of tested probands, pathogenic mutations were identified. Six probands carried pathogenic mutations in BRCA1, and one proband carried pathogenic mutations in BRCA2. In patients, a variant of uncertain significance was found in BRCA2, RAD50, MRE11A and CDH1. The Manchester scoring system showed a high accuracy (87.5%), high sensitivity (85.7%) and high specificity (88.9%) for the prediction of pathogenic non-founder BRCA1/2 mutations. Conclusion: A relatively high incidence of pathogenic non-founder BRCA1/2 mutations was observed in a founder population. The Manchester scoring system predicted the probability of non-founder pathogenic mutations with high accuracy.publishersversionPeer reviewe

A cross-sectional evidence-based review of pharmaceutical promotional marketing brochures and their underlying studies: Is what they tell us important and true?

BACKGROUND: A major marketing technique used by pharmaceutical companies is direct-to-physician marketing. This form of marketing frequently employs promotional marketing brochures, based on clinical research, which may influence how a physician prescribes medicines. This study's objective was to investigate whether or not the information in promotional brochures presented to physicians by pharmaceutical representatives is accurate, consistent, and valid with respect to the actual studies upon which the promotional brochures are based. METHODS: Physicians in five clinics were asked to consecutively collect pharmaceutical promotional brochures and to send them all to a centralized location. The brochures for any class of medication were collected on a continuous basis until 20 distinct promotional brochures were received by a central location. Once the brochure was received, the corresponding original study was obtained. Two blinded reviewers performed an evidence-based review of the article, comparing data that was printed on the brochure to what was found in the original study. RESULTS: Among the 20 studies, 75% of the studies were found to be valid, 80% were funded by the pharmaceutical company, 60% of the studies and the corresponding brochures presented patient-oriented outcomes, and 40% were compared to another treatment regimen. Of the 19 brochures that presented the data as graphs, 4 brochures presented a relative risk reduction while only 1 brochure presented an absolute risk reduction. 15% of the promotional marketing brochures presented data that was different from what was in the original published study. CONCLUSION: Given the present findings, physicians should be cautious about drawing conclusions regarding a medication based on the marketing brochures provided by pharmaceutical companies

Fundamental movement skills are more than run, throw and catch: The role of stability skills.

Introduction In motor development literature fundamental movement skills are divided into three constructs: locomotive, object control and stability skills. Most fundamental movement skills research has focused on children's competency in locomotor and object control skills. The first aim of this study was to validate a test battery to assess the construct of stability skills, in children aged 6 to 10 (M age = 8.2, SD = 1.2). Secondly we assessed how the stability skills construct fitted into a model of fundamental movement skill. Method The Delphi method was used to select the stability skill battery. Confirmatory factor analysis (CFA) was used to assess if the skills loaded onto the same construct and a new model of FMS was developed using structural equation modelling. Results Three postural control tasks were selected (the log roll, rock and back support) because they had good face and content validity. These skills also demonstrated good predictive validity with gymnasts scoring significantly better than children without gymnastic training and children from a high SES school performing better than those from a mid and low SES schools and the mid SES children scored better than the low SES children (all p < .05). Inter rater reliability tests were excellent for all three skills (ICC = 0.81, 0.87, 0.87) as was test retest reliability (ICC 0.87-0.95). CFA provided good construct validity, and structural equation modelling revealed stability skills to be an independent factor in an overall FMS model which included locomotor (r = .88), object control (r = .76) and stability skills (r = .81). Discussion This study provides a rationale for the inclusion of stability skills in FMS assessment. The stability skills could be used alongside other FMS assessment tools to provide a holistic assessment of children's fundamental movement skills. Copyright

The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly

Public health administrators do not have effective models to predict excess influenza-associated mortality and monitor viral changes associated with it. This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan's influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. A negative binomial model was developed to estimate Taiwan's monthly influenza-associated mortality among the elderly. We calculated three winter and annual excess influenza-associated mortalities [pneumonia and influenza (P&I), respiratory and circulatory, and all-cause] from the 1999–2000 through the 2006–2007 influenza seasons. Obtaining influenza virus sequences from the months/years in which death from P&I was excessive, we investigated molecular variation in vaccine-mismatched influenza viruses by comparing hemagglutinin 1 (HA1) of the circulating and vaccine strains. We found that the higher the isolation rate of A (H3N2) and vaccine-mismatched influenza viruses, the greater the monthly P&I mortality. However, this significant positive association became negative for higher matching of A (H3N2) and public health efforts with post-SARS effect. Mean excess P&I mortality for winters was significantly higher before 2003 than after that year [mean ± S.D.: 1.44±1.35 vs. 0.35±1.13, p = 0.04]. Further analysis revealed that vaccine-matched circulating influenza A viruses were significantly associated with lower excess P&I mortality during post-SARS winters (i.e., 2005–2007) than during pre-SARS winters [0.03±0.06 vs. 1.57±1.27, p = 0.01]. Stratification of these vaccine-matching and post-SARS effect showed substantial trends toward lower elderly excess P&I mortalities in winters with either mismatching vaccines during the post-SARS period or matching vaccines during the pre-SARS period. Importantly, all three excess mortalities were at their highest in May, 2003, when inter-hospital nosocomial infections were peaking. Furthermore, vaccine-mismatched H3N2 viruses circulating in the years with high excess P&I mortality exhibited both a lower amino acid identity percentage of HA1 between vaccine and circulating strains and a higher numbers of variations at epitope B. Our model can help future decision makers to estimate excess P&I mortality effectively, select and test virus strains for antigenic variation, and evaluate public health strategy effectiveness

The chlorosome: a prototype for efficient light harvesting in photosynthesis

Three phyla of bacteria include phototrophs that contain unique antenna systems, chlorosomes, as the principal light-harvesting apparatus. Chlorosomes are the largest known supramolecular antenna systems and contain hundreds of thousands of BChl c/d/e molecules enclosed by a single membrane leaflet and a baseplate. The BChl pigments are organized via self-assembly and do not require proteins to provide a scaffold for efficient light harvesting. Their excitation energy flows via a small protein, CsmA embedded in the baseplate to the photosynthetic reaction centres. Chlorosomes allow for photosynthesis at very low light intensities by ultra-rapid transfer of excitations to reaction centres and enable organisms with chlorosomes to live at extraordinarily low light intensities under which no other phototrophic organisms can grow. This article reviews several aspects of chlorosomes: the supramolecular and molecular organizations and the light-harvesting and spectroscopic properties. In addition, it provides some novel information about the organization of the baseplate