bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light Modulates Metabolic Pathways and Other Novel Physiological Traits in the Human Pathogen Acinetobacter baumannii
Authors: Müller Gabriela L. , Tuttobene Marisel , Altilio Matías , Martínez Amezaga Maitena , Nguyen Meaghan , Cribb Pamela , Cybulski Larisa E. , Ramírez María Soledad , Altabe Silvia , Mussi María Alejandra 
Published: March 2017

ABSTRACTLight sensing in chemotrophic bacteria has been relatively recently ascertained. In the human pathogenAcinetobacter baumannii, light modulates motility, biofilm formation, and virulence through the blue-light-sensing-using flavin (BLUF) photoreceptor BlsA. In addition, light can induce a reduction in susceptibility to certain antibiotics, such as minocycline and tigecycline, in a photoreceptor-independent manner. In this work, we identified new traits whose expression levels are modulated by light in this pathogen, which comprise not only important determinants related to pathogenicity and antibiotic resistance but also metabolic pathways, which represents a novel concept for chemotrophic bacteria. Indeed, the phenylacetic acid catabolic pathway and trehalose biosynthesis were modulated by light, responses that completely depend on BlsA. We further show that tolerance to some antibiotics and modulation of antioxidant enzyme levels are also influenced by light, likely contributing to bacterial persistence in adverse environments. Also, we present evidence indicating that surfactant production is modulated by light. Finally, the expression of whole pathways and gene clusters, such as genes involved in lipid metabolism and genes encoding components of the type VI secretion system, as well as efflux pumps related to antibiotic resistance, was differentially induced by light. Overall, our results indicate that light modulates global features of theA. baumanniilifestyle.IMPORTANCEThe discovery that nonphototrophic bacteria respond to light constituted a novel concept in microbiology. In this context, we demonstrated that light could modulate aspects related to bacterial virulence, persistence, and resistance to antibiotics in the human pathogenAcinetobacter baumannii. In this work, we present the novel finding that light directly regulates metabolism in this chemotrophic bacterium. Insights into the mechanism show the involvement of the photoreceptor BlsA. In addition, tolerance to antibiotics and catalase levels are also influenced by light, likely contributing to bacterial persistence in adverse environments, as is the expression of the type VI secretion system and efflux pumps. Overall, a profound influence of light on the lifestyle ofA. baumanniiis suggested to occur.
Control of Recombination Directionality by the Listeria Phage A118 Protein Gp44 and the Coiled-Coil Motif of Its Serine Integrase
Authors: Mandali Sridhar , Gupta Kushol , Dawson Anthony R. , Van Duyne Gregory D. , Johnson Reid C. 
Published: March 2017

ABSTRACT

The serine integrase of phage A118 catalyzes integrative recombination between
attP
on the phage and a specific
attB
locus on the chromosome of
Listeria monocytogenes
, but it is unable to promote excisive recombination between the hybrid
attL
and
attR
sites found on the integrated prophage without assistance by a recombination directionality factor (RDF). We have identified and characterized the phage-encoded RDF Gp44, which activates the A118 integrase for excision and inhibits integration. Gp44 binds to the C-terminal DNA binding domain of integrase, and we have localized the primary binding site to be within the mobile coiled-coil (CC) motif but distinct from the distal tip of the CC that is required for recombination. This interaction is sufficient to inhibit integration, but a second interaction involving the N-terminal end of Gp44 is also required to activate excision. We provide evidence that these two contacts modulate the trajectory of the CC motifs as they extend out from the integrase core in a manner dependent upon the identities of the four
att
sites. Our results support a model whereby Gp44 shapes the Int-bound complexes to control which
att
sites can synapse and recombine.

IMPORTANCE
Serine integrases mediate directional recombination between bacteriophage and bacterial chromosomes. These highly regulated site-specific recombination reactions are integral to the life cycle of temperate phage and, in the case of
Listeria monocytogenes
lysogenized by A118 family phage, are an essential virulence determinant. Serine integrases are also utilized as tools for genetic engineering and synthetic biology because of their exquisite unidirectional control of the DNA exchange reaction. Here, we identify and characterize the recombination directionality factor (RDF) that activates excision and inhibits integration reactions by the phage A118 integrase. We provide evidence that the A118 RDF binds to and modulates the trajectory of the long coiled-coil motif that extends from the large carboxyl-terminal DNA binding domain and is postulated to control the early steps of recombination site synapsis.
Use of a Phosphorylation Site Mutant To Identify Distinct Modes of Gene Repression by the Control of Virulence Regulator (CovR) in Streptococcus pyogenes
Authors: Horstmann Nicola , Sahasrabhojane Pranoti , Yao Hui , Su Xiaoping , Shelburne Samuel A. 
Published: March 2017

ABSTRACT
Control of the virulence regulator/sensor kinase (CovRS) two-component system (TCS) serves as a model for investigating the impact of signaling pathways on the pathogenesis of Gram-positive bacteria. However, the molecular mechanisms by which CovR, an OmpR/PhoB family response regulator, controls virulence gene expression are poorly defined, partly due to the labile nature of its aspartate phosphorylation site. To better understand the regulatory effect of phosphorylated CovR, we generated the phosphorylation site mutant strain 10870-CovR-D53E, which we predicted to have a constitutive CovR phosphorylation phenotype. Interestingly, this strain showed CovR activity only for a subset of the CovR regulon, which allowed for classification of CovR-influenced genes into D53E-regulated and D53E-nonregulated groups. Inspection of the promoter sequences of genes belonging to each group revealed distinct promoter architectures with respect to the location and number of putative CovR-binding sites. Electrophoretic mobility shift analysis demonstrated that recombinant CovR-D53E protein retains its ability to bind promoter DNA from both CovR-D53E-regulated and -nonregulated groups, implying that factors other than mere DNA binding are crucial for gene regulation. In fact, we found that CovR-D53E is incapable of dimerization, a process thought to be critical to OmpR/PhoB family regulator function. Thus, our global analysis of CovR-D53E indicates dimerization-dependent and dimerization-independent modes of CovR-mediated repression, thereby establishing distinct mechanisms by which this critical regulator coordinates virulence gene expression.

IMPORTANCE
Streptococcus pyogenes
causes a wide variety of diseases, ranging from superficial skin and throat infections to life-threatening invasive infections. To establish these various disease manifestations,
Streptococcus pyogenes
requires tightly coordinated production of its virulence factor repertoire. Here, the response regulator CovR plays a crucial role. As an OmpR/PhoB family member, CovR is activated by phosphorylation on a conserved aspartate residue, leading to protein dimerization and subsequent binding to operator sites. Our transcriptome analysis using the monomeric phosphorylation mimic mutant CovR-D53E broadens this general notion by revealing dimerization-independent repression of a subset of CovR-regulated genes. Combined with promoter analyses, these data suggest distinct mechanisms of CovR transcriptional control, which allow for differential expression of virulence genes in response to environmental cues.
Preserved glucagon-like peptide-1 responses to oral glucose, but reduced incretin effect, insulin secretion and sensitivity in young Asians with type 2 diabetes mellitus
Authors: Yeow Toh Peng , Pacini Giovanni , Tura Andrea , Hor Chee Peng , Lim Shueh Lin , Tan Florence Hui Sieng , Tong Chin Voon , Hong Janet Yeow Hua , Md Zain Fuziah , Holst Jens Juul , Wan Mohamud Wan Nazaimoon 
Published: March 2017

ObjectiveYouth onset type 2 diabetes mellitus (YT2DM) is a globally rising phenomenon with substantial Asians representation. The understanding of its pathophysiology is derived largely from studies in the obese African-American and Caucasian populations, while studies on incretin effect are scarce. We examined the insulin resistance, β-cell function (BC), glucagon-like peptide (GLP)-1 hormone and incretin effect in Asian YT2DM.Research design and methodsThis case–control study recruited 25 Asian YT2DM and 15 healthy controls, matched for gender, ethnicity and body mass index. Serum glucose, insulin, C peptide and GLP-1 were sampled during 2-hour oral glucose tolerance tests (OGTTs) and 1-hour intravenous glucose tolerance tests (IVGTTs). Insulin sensitivity was derived from the Quantitative Insulin Sensitivity Check Index (QUICKI), Oral Glucose Insulin Sensitivity Index (OGIS) in OGTT and surrogate index of SI from the minimal model (calculated SI, CSI). Acute insulin response (AIR) was obtained from IVGTT. Total BC was computed as incremental area under the curve of insulin/incremental area under the curve of glucose, during OGTT (BCOG) and IVGTT (BCIV), respectively. Disposition index (DI) was calculated using the product of insulin sensitivity and insulin secretion. GLP-1 response to oral glucose was calculated as incremental area under the curve of GLP-1 (ΔAUCGLP-1). Per cent incretin effect was estimated as 100×(BCOG−BCIV)/BCOG).ResultsThe YT2DM had marked impairment in BC (>80% reduction in AIR and BCOG, p<0.001) and lower QUICKI (p<0.001), OGIS (p<0.001) and CSI (p=0.015) compared with controls. There was no difference in GLP-1 at all time points and ΔAUCGLP-1but the per cent incretin effect was reduced in the YT2DM compared with controls (12.1±8.93 vs 70.0±4.03, p<0.001).ConclusionsAsian YT2DM showed similar GLP-1 response to oral glucose as controls but reduced incretin effect, BC and insulin sensitivity. The lack of compensatory mechanisms, as shown by the DI may be partly ascribed to the impaired incretin effect, similar to that of adult T2DM.Trial registration numberNMRR-12-1042-13254.
Kids in Communities Study (KiCS) study protocol: a cross-sectional mixed-methods approach to measuring community-level factors influencing early child development in Australia
Authors: Goldfeld Sharon , Villanueva Karen , Tanton Robert , Katz Ilan , Brinkman Sally , Woolcock Geoffrey , Giles-Corti Billie 
Published: March 2017

IntroductionHealthy childhood development in the early years is critical for later adult health and well-being. Early childhood development (ECD) research has focused primarily on individual, family and school factors, but largely ignored community factors. The Kids in Communities Study (KiCS) will test and investigate community-level influences on child development across Australia.Methods and analysisCross-sectional mixed-methods study exploring community-level effects in 25 Australian local communities; selection based on community socioeconomic status (SES) and ECD using the Australian Early Development Census (AEDC), a population measure of child development, to create a local community ‘diagonality type’, that is, those performing better or worse (off-diagonal), or as expected (on-diagonal) on the AEDC relative to their SES. Data collection includes stakeholder interviews, parent and service provider focus groups, and surveys with general community residents and service providers, mapping of neighbourhood design and local amenities and services, analysis of policy documents, and the use of existing sociodemographic and early childhood education and care data. Quantitative data will be used to test associations between local community diagonality type, and ECD based on AEDC scores. Qualitative data will provide complementary and deeper exploration of these same associations.Ethics and disseminationThe Royal Children's Hospital Human Research Ethics Committee approved the study protocol (#30016). Further ethics approvals were obtained from State Education and Health departments and Catholic archdioceses where required. ECD community-level indicators will eventually be derived and made publically available. Findings will be published in peer-reviewed journals, community reports, websites and policy briefs to disseminate results to researchers, and key stakeholders including policymakers, practitioners and (most importantly) the communities involved.
Use of standard risk screening and assessment forms to prevent harm to older people in Australian hospitals: a mixed methods study
Authors: Redley Bernice , Raggatt Michelle 
Published: March 2017

BackgroundStandard risk screening and assessment forms are frequently used in strategies to prevent harm to older people in hospitals. Little is known about good practices for their use.ObjectiveScope the preventable harms addressed by standard forms used to screen and assess older people and how standard forms are operationalised in hospitals across Victoria, Australia.MethodsMixed methods study: (1) cross-sectional audit of the standard risk screening and assessment forms used to assess older people at 11 health services in 2015; (2) nine focus groups with a purposive sample of 69 participants at 9 health services. Descriptive analysis examined the number of items on forms, preventable harms assessed and sources of duplication. Qualitative thematic analysis of focus group data identified themes explaining issues commonly affecting how health services used the forms.Results152 standard assessment forms from 11 Victorian health services included over 3700 items with 17% duplicated across multiple forms. Assessments of skin integrity and mobility loss (including falls) were consistently included in forms; however, nutrition, cognitive state, pain and medication risks were inconsistent; and continence, venous thromboembolism risk and hospital acquired infection from invasive devices were infrequent. Qualitative analyses revealed five themes explaining issues associated with current use of assessment forms: (1) comprehensive assessment of preventable harms; (2) burden on staff and the older person, (3) interprofessional collaboration, (4) flexibility to individualise care and (5) information management. Examples of good practice were identified.ConclusionsCurrent use of standard risk screening and assessment forms is associated with a high burden and gaps in assessment of several common preventable harms that can increase risk to older people in hospital. Improvement should focus on streamlining forms, increased guidance on interventions to prevent harm and facilitating front-line staff to manage complex decisions.
The barriers associated with emergency medical service use for acute coronary syndrome: the awareness and influence of an Australian public mass media campaign
Authors: Cartledge Susie , Finn Judith , Straney Lahn , Ngu Phillip , Stub Dion , Patsamanis Harry , Shaw James , Bray Janet 
Published: March 2017

BackgroundEmergency medical services (EMS) transport to hospital is recommended in acute coronary syndrome (ACS) guidelines, but only half of patients with ACS currently use EMS. The recent Australian Warning Signs campaign conducted by the Heart Foundation addressed some of the known barriers against using EMS. Our aim was to examine the influence of awareness of the campaign on these barriers in patients with ACS.MethodsInterviews were conducted with patients admitted to an Australian tertiary hospital between July 2013 and April 2014 with a diagnosis of ACS. Patient selection criteria included: aged 35–75 years, competent to provide consent, English speaking, not in residential care and medically stable. Multivariable logistic regression was used to examine factors associated with EMS use.ResultsOnly 54% of the 199 patients with ACS interviewed used EMS for transport to hospital. Overall 64% of patients recalled seeing the campaign advertising, but this was not associated with increased EMS use (52.0%vs56.9%, p=0.49) or in the barriers against using EMS. A large proportion of patients (43%) using other transport thought it would be faster. Factors associated with EMS use for ACS were: age >65 years, ST-elevation myocardial infarction, a sudden onset of pain and experiencing vomiting.ConclusionIn medically stable patients with ACS, awareness of the Australian Warning Signs campaign was not associated with increased use of EMS or a change in the barriers for EMS use. Future education strategies could emphasise the clinical role that EMS provide in ACS.
Lifestyle medicine course for family medicine residents: preliminary assessment of the impact on knowledge, attitudes, self-efficacy and personal health
Authors: Malatskey Lilach , Bar Zeev Yael , Tzuk-Onn Adva , Polak Rani 
Published: March 2017

ABSTRACTPurposeThe WHO estimates that by 2020 two-thirds of the diseases worldwide will be the result of unhealthy lifestyle habits. Less than half of primary care physician graduates feel prepared to give lifestyle behaviour counselling. Our objective was to evaluate the impact of lifestyle medicine (LM) course on self-reported knowledge, attitudes, self-efficacy and health behaviour of family medicine residents.MethodsBased on the Israeli syllabus for the study of LM, we delivered five face to face 20 H courses. Pre/post data were collected by knowledge, attitudes, self-efficacy and personal health survey:ResultsA total of 112 family medicine residents participated in one of the five courses, of which 91 (81.3%) filled both pre and post surveys. Participates showed an improvement in self-reported knowledge and capacity to manage patients in regard to smoking, weight management and physical activity. An improvement was noted in personal health behaviour of overweight participant’s in regard to self-reported physical activity.ConclusionsA comprehensive LM syllabus based course has a positive impact on family medicine residents LM counselling abilities. We suggest that LM course should be considered as a potential permanent addition to the family medicine residency programme.
An indium tin oxide metasurface filter for terahertz applications: Design, fabrication, and characterization
Authors: Nebioğlu Mehmet Ali , Takan Taylan , Altan Hakan , Demirhan Yasemin , Alaboz Hakan , Özyüzer Lütfi , Sabah Cumali 
Published: March 2017

In this paper, using a cross-shaped complementary Indium Tin Oxide (ITO)-based metasurface design, the transmission of THz radiation is shown to be filtered within the 3 dB level from maximum in the frequency range of interest ([Formula: see text][Formula: see text]333 GHz). Various metasurface structures primarily composed of cross-shaped openings with a 400 micron unit cell size are patterned on top of 1750 micron thick fused silica substrates. They are patterned using UV lithography methods after the films were grown using DC sputtering. The fabricated structures were characterized using Terahertz Time Domain Spectroscopy (THz-TDS) measurement technique. The measured transmission agrees well with the simulation of the structure for four different samples with different geometries. These results suggest that metasurface and/or metamaterial patterns based on ITO in visibly transparent media can be utilized for filtering of frequencies in the long wavelength spectrum. These types of filters can be very useful in the near future for THz communication and security applications.
Distinct Afatinib Resistance Mechanisms Identified in Lung Adenocarcinoma Harboring an EGFR Mutation
Authors: Yamaoka Toshimitsu , Ohmori Tohru , Ohba Motoi , Arata Satoru , Murata Yasunori , Kusumoto Sojiro , Ando Koichi , Ishida Hiroo , Ohnishi Tsukasa , Sasaki Yasutsuna 
Published: March 2017

Abstract
EGFR tyrosine kinase inhibitors (TKI) are associated with significant responses in non–small cell lung cancer (NSCLC) patients harboring EGFR-activating mutations. However, acquired resistance to reversible EGFR-TKIs remains a major obstacle. In particular, although the second-generation irreversible EGFR-TKI afatinib is currently used for treating NSCLC patients, the mechanisms underlying acquired afatinib resistance remain poorly understood. Here, heterogeneous mechanisms of acquired resistance were identified following long-term exposure to increasing doses of afatinib in EGFR-mutant lung adenocarcinoma PC-9 cells. Notably, three resistant cell lines, PC-9AFR1, PC-9AFR2, and PC-9AFR3 (AFR1, AFR2, and AFR3, respectively) employed distinct mechanisms for avoiding EGFR inhibition, with increased EGFR expression being detected in all resistant cell lines. Moreover, an activating EGFR mutation was partially lost in AFR1 and AFR2 cells. AFR1 cells exhibited afatinib resistance as a result of wild-type KRAS amplification and overexpression; however, these cells showed a progressive decrease and eventual loss of the acquired KRAS dependence, as well as resensitization to afatinib, following a drug holiday. Meanwhile, AFR2 cells exhibited increased expression of insulin-like growth factor-binding protein 3 (IGFBP3), which promoted insulin-like growth factor 1 receptor (IGF1R) activity and subsequent AKT phosphorylation, thereby indicating a potential bypass signaling pathway associated with IGFR1. Finally, AFR3 cells harbored the secondary EGFR mutation T790M. Our findings constitute the first report showing acquired wild-type KRAS overexpression and attenuation of afatinib resistance following a drug holiday.
Implications: The heterogeneous mechanisms of afatinib resistance should facilitate the development of more effective therapeutic strategies for NSCLC patients. Mol Cancer Res; 15(7); 915–28. ©2017 AACR.
Identification of a DNA Damage–Induced Alternative Splicing Pathway That Regulates p53 and Cellular Senescence Markers
Authors: Chen Jing , Crutchley John , Zhang Dadong , Owzar Kouros , Kastan Michael B. 
Published: March 2017

AbstractCellular responses to DNA damage are critical determinants of cancer development and aging-associated pathogenesis. Here, we identify and characterize a DNA-damage response (DDR) pathway that regulates alternative splicing of numerous gene products, including the human tumor suppressor TP53, and controls DNA damage–induced cellular senescence. In brief, ionizing radiation (IR) inhibits the activity of SMG1, a phosphoinositide-3-kinase-like kinase family member, reducing the binding of SMG1 to a specific region near exon 9 of p53 precursor mRNA and promoting the binding of ribosomal protein L26 (RPL26) to p53 pre-mRNA. RPL26, in turn, is required for the recruitment of the serine/arginine-rich splicing factor SRSF7 to p53 pre-mRNA and generation of alternatively spliced p53β RNA. Disruption of this pathway via selective knockout of p53β by CRISPR/Cas9 or downregulation of pathway constituents significantly reduces IR-induced senescence markers, and cells lacking p53β expression fail to transcriptionally repress negative regulators of cellular senescence and aging.Significance: We identified a new component of the DDR pathway that regulates alternative splicing of messenger RNAs, including human TP53 mRNA. Modulation of this regulatory pathway affects DNA-damage induction of cellular senescence markers. Cancer Discov; 7(7); 766–81. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 653