bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Clostridium difficile Dlt Pathway Is Controlled by the Extracytoplasmic Function Sigma Factor σ
V
in Response to Lysozyme
Authors: Woods Emily C. , Nawrocki Kathryn L. , Suárez Jose M. , McBride Shonna M. 
Published: April 2016

ABSTRACT

Clostridium difficile
(also known as
Peptoclostridium difficile
) is a major nosocomial pathogen and a leading cause of antibiotic-associated diarrhea throughout the world. Colonization of the intestinal tract is necessary for
C. difficile
to cause disease. Host-produced antimicrobial proteins (AMPs), such as lysozyme, are present in the intestinal tract and can deter colonization by many bacterial pathogens, and yet
C. difficile
is able to survive in the colon in the presence of these AMPs. Our prior studies established that the Dlt pathway, which increases the surface charge of the bacterium by addition of
d
-alanine to teichoic acids, is important for
C. difficile
resistance to a variety of AMPs. We sought to determine what genetic mechanisms regulate expression of the Dlt pathway. In this study, we show that a
dlt
null mutant is severely attenuated for growth in lysozyme and that expression of the
dltDABC
operon is induced in response to lysozyme. Moreover, we found that a mutant lacking the extracytoplasmic function (ECF) sigma factor σ
V
does not induce
dlt
expression in response to lysozyme, indicating that σ
V
is required for regulation of lysozyme-dependent
d
-alanylation of the cell wall. Using reporter gene fusions and 5′ RACE (rapid amplification of cDNA ends) analysis, we identified promoter elements necessary for lysozyme-dependent and lysozyme-independent
dlt
expression. In addition, we observed that both a
sigV
mutant and a
dlt
mutant are more virulent in a hamster model of infection. These findings demonstrate that cell wall
d
-alanylation in
C. difficile
is induced by lysozyme in a σ
V
-dependent manner and that this pathway impacts virulence
in vivo
.
DAP12 Inhibits Pulmonary Immune Responses to Cryptococcus neoformans
Authors: Heung Lena J. , Hohl Tobias M. 
Published: April 2016

ABSTRACTCryptococcus neoformansis an opportunistic fungal pathogen that is inhaled into the lungs and can lead to life-threatening meningoencephalitis in immunocompromised patients. Currently, the molecular mechanisms that regulate the mammalian immune response to respiratory cryptococcal challenge remain poorly defined. DAP12, a signaling adapter for multiple pattern recognition receptors in myeloid and natural killer (NK) cells, has been shown to play both activating and inhibitory roles during lung infections by different bacteria and fungi. In this study, we demonstrate that DAP12 plays an important inhibitory role in the immune response toC. neoformans. Infectious outcomes in DAP12−/−mice, including survival and lung fungal burden, are significantly improved compared to those in C57BL/6 wild-type (WT) mice. We find that eosinophils and macrophages are decreased while NK cells are increased in the lungs of infected DAP12−/−mice. In contrast to WT NK cells, DAP12−/−NK cells are able to repressC. neoformansgrowthin vitro. Additionally, DAP12−/−macrophages are more highly activated than WT macrophages, with increased production of tumor necrosis factor (TNF) and CCL5/RANTES and more efficient uptake and killing ofC. neoformans. These findings suggest that DAP12 acts as a brake on the pulmonary immune response toC. neoformansby promoting pulmonary eosinophilia and by inhibiting the activation and antifungal activities of effector cells, including NK cells and macrophages.
Azospirillum brasilense Chemotaxis Depends on Two Signaling Pathways Regulating Distinct Motility Parameters
Authors: Mukherjee Tanmoy , Kumar Dhivya , Burriss Nathan , Xie Zhihong , Alexandre Gladys 
Published: April 2016

ABSTRACT

The genomes of most motile bacteria encode two or more chemotaxis (Che) systems, but their functions have been characterized in only a few model systems.
Azospirillum brasilense
is a motile soil alphaproteobacterium able to colonize the rhizosphere of cereals. In response to an attractant, motile
A. brasilense
cells transiently increase swimming speed and suppress reversals. The Che1 chemotaxis pathway was previously shown to regulate changes in the swimming speed, but it has a minor role in chemotaxis and root surface colonization. Here, we show that a second chemotaxis system, named Che4, regulates the probability of swimming reversals and is the major signaling pathway for chemotaxis and wheat root surface colonization. Experimental evidence indicates that Che1 and Che4 are functionally linked to coordinate changes in the swimming motility pattern in response to attractants. The effect of Che1 on swimming speed is shown to enhance the aerotactic response of
A. brasilense
in gradients, likely providing the cells with a competitive advantage in the rhizosphere. Together, the results illustrate a novel mechanism by which motile bacteria utilize two chemotaxis pathways regulating distinct motility parameters to alter movement in gradients and enhance the chemotactic advantage.

IMPORTANCE
Chemotaxis provides motile bacteria with a competitive advantage in the colonization of diverse niches and is a function enriched in rhizosphere bacterial communities, with most species possessing at least two chemotaxis systems. Here, we identify the mechanism by which cells may derive a significant chemotactic advantage using two chemotaxis pathways that ultimately regulate distinct motility parameters.
Functional Characterization of a Novel Member of the Amidohydrolase 2 Protein Family, 2-Hydroxy-1-Naphthoic Acid Nonoxidative Decarboxylase from Burkholderia sp. Strain BC1
Authors: Pal Chowdhury Piyali , Basu Soumik , Dutta Arindam , Dutta Tapan K. 
Published: April 2016

ABSTRACT

The gene encoding a nonoxidative decarboxylase capable of catalyzing the transformation of 2-hydroxy-1-naphthoic acid (2H1NA) to 2-naphthol was identified, recombinantly expressed, and purified to homogeneity. The putative gene sequence of the decarboxylase (
hndA
) encodes a 316-amino-acid protein (HndA) with a predicted molecular mass of 34 kDa. HndA exhibited high identity with uncharacterized amidohydrolase 2 proteins of various
Burkholderia
species, whereas it showed a modest 27% identity with γ-resorcylate decarboxylase, a well-characterized nonoxidative decarboxylase belonging to the amidohydrolase superfamily. Biochemically characterized HndA demonstrated strict substrate specificity toward 2H1NA, whereas inhibition studies with HndA indicated the presence of zinc as the transition metal center, as confirmed by atomic absorption spectroscopy. A three-dimensional structural model of HndA, followed by docking analysis, identified the conserved metal-coordinating and substrate-binding residues, while their importance in catalysis was validated by site-directed mutagenesis.

IMPORTANCE
Microbial nonoxidative decarboxylases play a crucial role in the metabolism of a large array of carboxy aromatic chemicals released into the environment from a variety of natural and anthropogenic sources. Among these, hydroxynaphthoic acids are usually encountered as pathway intermediates in the bacterial degradation of polycyclic aromatic hydrocarbons. The present study reveals biochemical and molecular characterization of a 2-hydroxy-1-naphthoic acid nonoxidative decarboxylase involved in an alternative metabolic pathway which can be classified as a member of the small repertoire of nonoxidative decarboxylases belonging to the amidohydrolase 2 family of proteins. The strict substrate specificity and sequence uniqueness make it a novel member of the metallo-dependent hydrolase superfamily.
Impact of a social network-based intervention promoting diabetes self-management in socioeconomically deprived patients: a qualitative evaluation of the intervention strategies
Authors: Vissenberg C , Stronks K , Nijpels G , Uitewaal P J M , Middelkoop B J C , Kohinor M J E , Hartman M A , Nierkens V 
Published: April 2016

ObjectiveThere is a need for effective interventions that improve diabetes self-management (DSM) among socioeconomically deprived patients with type 2 diabetes. The group-based intervention Powerful Together with Diabetes (PTWD) aimed to increase social support for DSM and decrease social influences hindering DSM (eg, peer pressure, social norms) in patients living in deprived neighbourhoods. Through a qualitative process evaluation, this paper aims to study whether this intervention changed social support and social influences, and which elements of the intervention contributed to this.MethodsThe intervention group (IG) was compared with a standard group-based educational intervention (control group, CG). 27 qualitative in-depth interviews with participants (multiethnic sample) and 24 interviews with group leaders were conducted. Interviews were coded and analysed using MAXQDA according to framework analysis.ResultsPatients in the IG experienced more emotional support from group members and more instrumental and appraisal support from relatives than those in the CG. Also, they were better able to recognise and cope with influences that hinder their DSM, exhibited more positive norms towards DSM and increased their priority regarding DSM and their adherence. Finally, the engagement in DSM by relatives of participants increased. Creating trust between group members, skills training, practising together and actively involving relatives through action plans contributed to these changes.ConclusionsA group-based intervention aimed at creating trust, practising together and involving relatives has the potential to increase social support and diminish social influences hindering DSM in socioeconomically deprived patients with diabetes. Promising elements of the intervention were skills training and providing feedback using role-playing exercises in group sessions with patients, as well as the involvement of patients' significant others in self-management tasks, and actively involving them in making an action plan for self-management. These positive results justify the value of further evaluating the effectiveness of this intervention in a larger sample.Trial registration numberNTR1886, Results.
Research priorities for shoulder surgery: results of the 2015 James Lind Alliance patient and clinician priority setting partnership
Authors: Rangan Amar , Upadhaya Sheela , Regan Sandra , Toye Francine , Rees Jonathan L 
Published: April 2016

ObjectiveTo run a UK based James Lind Alliance Priority Setting Partnership for ‘Surgery for Common Shoulder Problems’.SettingThis was a nationally funded and conducted process. It was organised from a musculoskeletal research centre and Biomedical Research Unit in Oxford.ParticipantsUK shoulder patients, carers and clinicians, involved in treating patients with shoulder pain and shoulder problems that might require surgery.InterventionsThese were national electronic and paper surveys capturing treatment uncertainties that are important to shoulder patients, carers and clinicians.Outcome measuresThe outcomes relevant to this study were the survey results and rankings.ResultsThe process took 18 months to complete, with 371 participants contributing 404 in scope questions. The James Lind process then produced a final 10 research priorities and uncertainties that relate to the scope of ‘Surgery for Common Shoulder Problems’.ConclusionsThe final top 10 UK research priorities have been produced and are now being disseminated to partner organisations and funders to guide funding of shoulder research for the next 5–10 years on topics that are important to patients, their carers and clinicians.
Appropriateness of Omeprazole Prescribing in Quebec’s Senior Population
Authors: Grégoire Jean-Pierre , Moisan Jocelyne , Chabot Isabelle , Gaudet Michel 
Published: April 2016

BACKGROUND: Prescribing omeprazole for the treatment of digestive disorders accounts for an important part of the costs in Quebec’s drug benefit plan. In July 1993, the Quebec drug program listed omeprazole, with restriction, in its formulary. On January 1, 1994, this restriction was lifted; since then, omeprazole has been listed in the regular provincial formulary.OBJECTIVE: To describe the appropriateness of initial omeprazole prescribing in the ambulatory senior population of Quebec in the 27 months after being listed without restriction.SUBJECTS AND METHODS: A retrospective population-based cohort study was performed using prescription and medical services claims databases of the Quebec drug program. Data were extracted for elderly patients who received their first omeprazole prescription between July 1, 1994 and March 31, 1996. RESULTS: Among the 47,140 first-time users of omeprazole identified, 7516 (15.9%) had had an endoscopy in the previous six months, 2308 (4.9%) were given an antimicrobial agent and omeprazole simultaneously, and 22,730 (48.2%) received omeprazole after prior use of an H2receptor antagonist (H2RA) or a prokinetic drug. A total of 26,525 (56.3%) first-time users were prescribed omeprazole based on at least one of the three criteria listed above. Among these users, 729 (2.8%) received an H2RA concurrently with omeprazole. Altogether, 25,796 (54.7%) first-time users received omeprazole appropriately.CONCLUSIONS: Although reimbursement for omeprazole prescriptions has not been restricted in Quebec since January 1, 1994, it was prescribed appropriately for elderly patients in the majority of cases studied.
An Analysis of an Inflammatory Bowel Disease Practise in an Urban Community Hospital
Authors: Adam David , Adam Jonathan , Price Howard 
Published: April 2016

OBJECTIVES: To review an individual community gastroenterologist’s experience with inflammatory bowel disease (IBD). The aspects studied were distribution of disease, need for hospital admission, immunosuppressants, systemic steroids, and surgery and its indications. The incidence of cancer was also reviewed.PATIENTS AND METHODS: The charts of all IBD patients (n=373) seen between 1993 and 1996 by an individual gastroenterologist in an urban community hospital were reviewed for the aforementioned information. Patients seen during this period may have been diagnosed with IBD before or during the period of 1993 to 1996.RESULTS: Of the 373 patients, 219 had Crohn’s disease (CD) and 154 had ulcerative colitis (UC). The most common age of onset for both groups was 20 to 29 years. Distal UC and distal Crohn’s colitis patients rarely required surgery, hospitalization, systemic steroids or immunosuppressants. Eighty per cent of patients with small bowel CD and 51% of those with ileocolonic CD required at least one operation. Of the UC patients, 10.4% required surgery. Of the UC patients undergoing surveillance for cancer, none developed cancer but one developed significant dysplasia.CONCLUSIONS: In both CD and UC the site of the inflammation plays a major role in determining the need for hospitalization, surgery, systemic steroids and immunosuppressants. Distal UC, the most common form of UC in this group of patients, is a very benign disease. Of all forms of IBD, small bowel CD had the greatest need for hospitalization, surgery and systemic steroids.
Ly6E/K Signaling to TGFβ Promotes Breast Cancer Progression, Immune Escape, and Drug Resistance
Authors: AlHossiny Midrar , Luo Linlin , Frazier William R. , Steiner Noriko , Gusev Yuriy , Kallakury Bhaskar , Glasgow Eric , Creswell Karen , Madhavan Subha , Kumar Rakesh , Upadhyay Geeta 
Published: April 2016

Abstract
Stem cell antigen Sca-1 is implicated in murine cancer stem cell biology and breast cancer models, but the role of its human homologs Ly6K and Ly6E in breast cancer are not established. Here we report increased expression of Ly6K/E in human breast cancer specimens correlates with poor overall survival, with an additional specific role for Ly6E in poor therapeutic outcomes. Increased expression of Ly6K/E also correlated with increased expression of the immune checkpoint molecules PDL1 and CTLA4, increased tumor-infiltrating T regulatory cells, and decreased natural killer (NK) cell activation. Mechanistically, Ly6K/E was required for TGFβ signaling and proliferation in breast cancer cells, where they contributed to phosphorylation of Smad1/5 and Smad2/3. Furthermore, Ly6K/E promoted cytokine-induced PDL1 expression and activation and binding of NK cells to cancer cells. Finally, we found that Ly6K/E promoted drug resistance and facilitated immune escape in this setting. Overall, our results establish a pivotal role for a Ly6K/E signaling axis involving TGFβ in breast cancer pathophysiology and drug response, and highlight this signaling axis as a compelling realm for therapeutic invention. Cancer Res; 76(11); 3376–86. ©2016 AACR.
T-cell Landscape in a Primary Melanoma Predicts the Survival of Patients with Metastatic Disease after Their Treatment with Dendritic Cell Vaccines
Authors: Vasaturo Angela , Halilovic Altuna , Bol Kalijn F. , Verweij Dagmar I. , Blokx Willeke A.M. , Punt Cornelis J.A. , Groenen Patricia J.T.A. , van Krieken J. Han J.M. , Textor Johannes , de Vries I. Jolanda M. , Figdor Carl G. 
Published: April 2016

Abstract
Tumor-infiltrating lymphocytes appear to be a predictor of survival in many cancers, including cutaneous melanoma. We applied automated multispectral imaging to determine whether density and distribution of T cells within primary cutaneous melanoma tissue correlate with survival of metastatic melanoma patients after dendritic cell (DC) vaccination. CD3+ T cell infiltration in primary tumors from 77 metastatic melanoma patients was quantified using the ratio of intratumoral versus peritumoral T-cell densities (I/P ratio). Patients with longer survival after DC vaccination had stronger T-cell infiltration than patients with shorter survival in a discovery cohort of 19 patients (P = 0.000026) and a validation cohort of 39 patients (P = 0.000016). I/P ratio was the strongest predictor of survival in a multivariate analysis including M substage and serum lactate dehydrogenase level. To evaluate I/P ratio as a predictive biomarker, we analyzed 19 chemotherapy-treated patients. Longer survival times of DC-vaccinated compared with chemotherapy-treated patients was observed for high (P = 0.000566), but not low (P = 0.154) I/P ratios. In conclusion, T-cell infiltration into primary melanoma is a strong predictor of survival after DC vaccination in metastatic melanoma patients who, on average, started this therapy several years after primary tumor resection. The infiltration remains predictive even after adjustment for late-stage prognostic markers. Our findings suggest that the I/P ratio is a potential predictive biomarker for treatment selection. Cancer Res; 76(12); 3496–506. ©2016 AACR.
Secretome Signature Identifies ADAM17 as Novel Target for Radiosensitization of Non–Small Cell Lung Cancer
Authors: Sharma Ashish , Bender Sabine , Zimmermann Martina , Riesterer Oliver , Broggini-Tenzer Angela , Pruschy Martin N. 
Published: April 2016

Abstract
Purpose: Ionizing radiation (IR) induces intracellular signaling processes as part of a treatment-induced stress response. Here we investigate IR-induced ADAM17 activation and the role of ADAM17-shed factors for radiation resistance in non–small cell lung cancer.
Experimental Design: Large-scale secretome profiling was performed using antibody arrays. Secretion kinetics of ADAM17 substrates was determined using ELISA across multiple in vitro and in vivo models of non–small cell lung cancer. Clonogenic survival and tumor xenograft assays were performed to determine radiosensitization by ADAM17 inhibition.
Results: On the basis of a large-scale secretome screening, we investigated secretion of auto- or paracrine factors in non–small cell lung cancer in response to irradiation and discovered the ADAM17 network as a crucial mediator of resistance to IR. Irradiation induced a dose-dependent increase of furin-mediated cleavage of the ADAM17 proform to active ADAM17, which resulted in enhanced ADAM17 activity in vitro and in vivo. Genetic or pharmacologic targeting of ADAM17 suppressed IR-induced shedding of secreted factors, downregulated ErbB signaling in otherwise cetuximab-resistant target cells, and enhanced IR-induced cytotoxicity. The combined treatment modality of IR with the ADAM17 inhibitor TMI-005 resulted in a supra-additive antitumor response in vivo demonstrating the potential of ADAM17 targeting in combination with radiotherapy.
Conclusions: Radiotherapy activates ADAM17 in non–small cell lung cancer, which results in shedding of multiple survival factors, growth factor pathway activation, and IR-induced treatment resistance. We provide a sound rationale for repositioning ADAM17 inhibitors as short-term adjuvants to improve the radiotherapy outcome of non–small cell lung cancer. Clin Cancer Res; 22(17); 4428–39. ©2016 AACR.
Autophagy Inhibition Dysregulates TBK1 Signaling and Promotes Pancreatic Inflammation
Authors: Yang Shenghong , Imamura Yu , Jenkins Russell W. , Cañadas Israel , Kitajima Shunsuke , Aref Amir , Brannon Arthur , Oki Eiji , Castoreno Adam , Zhu Zehua , Thai Tran , Reibel Jacob , Qian Zhirong , Ogino Shuji , Wong Kwok K. , Baba Hideo , Kimmelman Alec C. , Pasca Di Magliano Marina , Barbie David A. 
Published: April 2016

Abstract
Autophagy promotes tumor progression downstream of oncogenic KRAS, yet also restrains inflammation and dysplasia through mechanisms that remain incompletely characterized. Understanding the basis of this paradox has important implications for the optimal targeting of autophagy in cancer. Using a mouse model of cerulein-induced pancreatitis, we found that loss of autophagy by deletion of Atg5 enhanced activation of the IκB kinase (IKK)-related kinase TBK1 in vivo, associated with increased neutrophil and T-cell infiltration and PD-L1 upregulation. Consistent with this observation, pharmacologic or genetic inhibition of autophagy in pancreatic ductal adenocarcinoma cells, including suppression of the autophagy receptors NDP52 or p62, prolonged TBK1 activation and increased expression of CCL5, IL6, and several other T-cell and neutrophil chemotactic cytokines in vitro. Defective autophagy also promoted PD-L1 upregulation, which is particularly pronounced downstream of IFNγ signaling and involves JAK pathway activation. Treatment with the TBK1/IKKϵ/JAK inhibitor CYT387 (also known as momelotinib) not only inhibits autophagy, but also suppresses this feedback inflammation and reduces PD-L1 expression, limiting KRAS-driven pancreatic dysplasia. These findings could contribute to the dual role of autophagy in oncogenesis and have important consequences for its therapeutic targeting. Cancer Immunol Res; 4(6); 520–30. ©2016 AACR.