Characterization of mycobacteriophage Adephagia cytotoxic proteins.

Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin-antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.

Preloading with drugs before entry to the nighttime entertainment district: presentation, intoxication rates, and effects of police presence during assessment.

BACKGROUND: Past research has either focused on alcohol or drug preloading before a night out, but not on the interaction between them. With increased risks of harm through interaction effects, we wished to build upon previous research in this area. We sought to determine who drug preloads, why do people engage in this practice, what drug/s are people using, and how inebriated they are as they enter the NED. Additionally, we examined what impact varying levels of police presence has on the collections of sensitive data in this context. METHODS: We captured estimates of drug and alcohol preloading from 4723 people entering nighttime entertainment districts (NEDs) in Queensland, Australia. Data collection occurred under three varying conditions of police presence (i.e., no police present, police present but not engaging with participants, and police engaging with participants). RESULTS: People who admitted to preloading drugs were found to be younger in age than non-drug admitters, more likely to be male than female, use one type of drug (mostly stimulants) rather than multiple (if we exclude alcohol), significantly more intoxicated upon arrival, and more subjectively affected from their use of alcohol and drugs as Breath Approximated Alcohol Concertation levels increased. People were more likely to admit having used drugs in the absence of police, but this had only a small effect. CONCLUSIONS: People who drug preload are a vulnerable subset of the youth population that is susceptible to experiencing harms in this context. As they drink more alcohol, they experience higher affects than those who do not report to also take drugs. Police engagement through service rather than force may mitigate some risks. Further enquiry is needed to better understand those who engage in this practice and to have quick, cheap, objective tests of what drugs these people are using.

Pre-Loading with Drugs before Entering the Nighttime Entertainment District: A Scoping Review.

Background: Nighttime entertainment districts attract many people who pre-load with alcohol and other substances before entering licensed venues. Despite the harms and dangers associated with both alcohol pre-loading and drug use respectively, there is a paucity of research on drug and polysubstance pre-loading. Objectives: The primary objectives of this scoping review are to systematically map out the body of existing literature on drug and polysubstance pre-loading, discuss methodological potentials and pitfalls in field-based research, identify gaps in knowledge, and derive practical implications and opportunities for future research. Methods: Using the PRISMA (ScR) guidelines, we conducted a search of Medline, PsycINFO, Embase, Scopus, CINAHL, Social Services Abstracts, Sociological Abstracts, and Web of Science databases. We followed this up by conducting an author and citation analysis of relevant articles. Results: Of the 632 data sources identified, 338 articles were reviewed after removing duplicates. Overall, only nine articles were included and thematically analyzed. In our review and analysis of the literature, we find people who drug pre-load to be a particularly vulnerable subset of the population. We also posit that the point-of-entry design has greater sensitivity than the commonly used portal-in design. From this, we also draw attention to various time points where field-based researchers can provide intervention. Conclusions: Given the high prevalence of young adults engaging in the behavior, clinicians should consider pre-loading behaviors when assessing for risk and vulnerability. Field-based research would elucidate the full breadth and scope of the growing pre-loading phenomenon and the dangers associated with this practice.

This is the rhythm of the night: Examining the phases of a night-out on preloading motivations and intentions to backload.

BACKGROUND: Field research into the preloading phenomena has rarely examined how patrons move and transition into target events. We conceptualised three phases of the night (PotN) - entering, within and leaving - which a patron can be intercepted by a research group. Our research tested the differences between the PotN on preloading, preloading motivations and alcohol consuming behaviours in a popular night-time entertainment district (NED). METHODS: The sample comprised 1,585 young-adult patrons (934 Men, 651 Women; ages 18-27 years) collected in a cross-sectional design over three PotN. We measured the patron's preloading motivations, current alcohol intoxication and backloading intentions between three different phases of a night-out on Thursday, Friday and Saturday nights, from 9:00p.m. - 4:00 a.m. in Brisbane NEDs (Queensland, Australia). RESULTS: The phases contributed to a difference in preloading rates - one that decreased over the night (p <.001). Between the phases, the motivation of 'saving money' (≈45%) decreased as a reason for preloading and to 'socialise' (≈20%) increased. Enhancement-based preloading motivations (i.e., 'enjoy the feeling' and 'get drunk') were related to increased alcohol intoxication and backloading intentions at different PotN. However, 'saving money' motivations were also associated with a decrease in alcohol intoxication and backloading intentions (i.e., planning to return home to continue alcohol consumption). CONCLUSIONS: Preloading is valued highly by patrons when proximal to the actual preloading. There is a difference between the PotN on preloading rates, preloading motivations, intentions to backload and drinking outcomes as patrons shift from preloading, to entering the NED, to eventually leaving.

Complete Genome Sequences of the Novel Cluster BP Phages Infecting Streptomyces sanglieri, AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra.

The Streptomyces sanglieri bacteriophages AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra form a novel actinobacteriophage cluster, BP. These siphoviruses have circularly permuted genomes with an average size of 37,700 bp and a GC content of 71%. Each genome contains approximately 58 protein-coding genes, with no tRNAs.

Instructional Models for Course-Based Research Experience (CRE) Teaching.

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

A Proposal for a Taxonomy of Pre-Loading.

Background: Pre-loading of alcohol and other drugs has become a prevalent start to nights out in many countries. Studies into pre-loading have been using different operational definitions and descriptions, leading to confusion and debate in the research literature. Purpose/Objective: We wish to propose a full taxonomy so that research into preloading, of any substances, can be specific and standardized. Methods: We address this problem by analyzing (1) terminology used throughout the literature, (2) the evolving nature of this phenomenon, and (3) the operational components comprising this substance use practice. Additionally, we provide a context and rationale for how we view pre-loading in relation to the broader event-level session. Results: Our results propose a full operational definition and taxonomy of pre-loading to be used, and built upon, by researchers. We also provide a visual representation of pre-loading within an event-level session and provide a method to facilitate consistency across cultures. Conclusions: We propose that this system will lead to greater specificity and higher reliability in the interpretation of research results.

Genomic diversity of bacteriophages infecting Microbacterium spp.

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Exploring patient preferences for involvement in medication management in hospitals.

AIM: The aim of this study was to identify patient preferences for involvement in medication management during hospitalization. DESIGN: A qualitative descriptive study. METHODS: This is a study of 20 inpatients in two medical and two surgical wards at an academic health science centre in Melbourne, Australia. Semi-structured interviews were recorded and analysed using content analysis. FINDINGS: Three themes were identified: (a) 'understanding the medication' established large variation in participants' understanding of their pre-admission medication and current medication; (b) 'ownership of medication administration' showed that few patients had considered an alternative to their current regimen; only some were interested in taking more control; and (c) 'supporting discharge from hospital' showed that most patients desired written medication instructions to be explained by a health professional. Family involvement was important for many. CONCLUSION: There was significant diversity of opinion from participants about their involvement in medication management in hospital. Patient preferences for inclusion need to be identified on admission where appropriate. Education about roles and responsibilities of medication management is required for health professionals, patients and families to increase inclusion and engagement across the health continuum and support transition to discharge. IMPACT STATEMENT: Little is known about patient preferences for participation in medication administration and hospital discharge planning. Individual patient understanding of and interest in participation in medication administration varies. In accordance with individual patient preferences, patients need to be included more effectively and consistently in their own medication management when in hospital.

Nurses' decision-making, practices and perceptions of patient involvement in medication administration in an acute hospital setting.

AIMS: To describe nurses' decision-making, practices and perceptions of patient involvement in medication administration in acute hospital settings. BACKGROUND: Medication errors cause unintended harm to patients. Nurses have a major role in ensuring patient safety in medication administration practices in hospital settings. Investigating nurses' medication administration decision-making and practices and their perceptions of patient involvement, may assist in developing interventions by revealing how and when to involve patients during medication administration in hospital. DESIGN: A descriptive exploratory study design. METHODS: Twenty nurses were recruited from two surgical and two medical wards of a major metropolitan hospital in Australia. Each nurse was observed for 4 hr, then interviewed after the observation. Data were collected over six months in 2015. Observations were captured on an electronic case report form; interviews were audio-recorded and transcribed verbatim. Data were analysed using descriptive statistics and content and thematic analysis. RESULTS: Ninety-five medication administration episodes, of between two and eight episodes per nurse, were observed. A total of 56 interruptions occurred with 26 of the interruptions being medication related. Four major themes emerged from the interviews: dealing with uncertainty; facilitating, framing and filtering information; managing interruptions and knowing and involving patients. CONCLUSION: Nurses work in complex adaptive systems that change moment by moment. Acknowledging and understanding the cognitive workload and complex interactions are necessary to improve patient safety and reduce errors during medication administration. Knowing and involving the patient is an important part of a nurses' medication administration safety strategies.

Fuel-cell breathalyser use for field research on alcohol intoxication: an independent psychometric evaluation.

BACKGROUND: Several field studies have used fuel-cell breathalysers (FCB) to investigate the prevalence of alcohol intoxication. However, there is a lack of evidence evaluating the psychometric properties of these breathalysers outside of the forensic disciplines. METHODS: The current research describes four studies designed that assess the reliability and validity of portable platinum FCBs for research on alcohol intoxication. Utilising the Alcolizer LE5 breathalyser and, to a lesser degree, the Lifeloc FC-20 and the Lion Intoxilyzer 8000, each study sampled patrons frequenting popular night-time entertainment districts with varying levels of alcohol intoxication. RESULTS: Study one and two found excellent test-retest reliability and inter-instrument reliability for FCBs. Study three and four provided evidence to support the convergent validity of the two FCBs (the LE5 with the FC20), and with an evidential breathalyser (i.e., the Lion Intoxilyzer 8000; EB). DISCUSSION: A 93-97% agreement rate between breathalyser readings was found across the four studies. Portable FCB are recommended as a reliable and valid instrument for research designs requiring quick alcohol intoxication estimations in large populations. Strategies to enhance reliable and valid readings are provided for field researchers.

Complete Genome Sequences of 44 Arthrobacter Phages.

We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae, Myoviridae, and Podoviridae) are represented.

Eight Genome Sequences of Cluster BE1 Phages That Infect Streptomyces Species.

Cluster BE1 Streptomyces bacteriophages belong to the Siphoviridae, with genome sizes over 130 kbp, and they contain direct terminal repeats of approximately 11 kbp. Eight newly isolated closely related cluster BE1 phages contain 43 to 48 tRNAs, one transfer-messenger RNA (tmRNA), and 216 to 236 predicted open reading frames (ORFs), but few of their genes are shared with other phages, including those infecting Streptomyces species.

Genome Sequences of Five Streptomyces Bacteriophages Forming Cluster BG.

Cluster BG of the actinobacteriophage was formed upon discovery of five novel bacteriophages isolated by enrichment from their host, Streptomyces griseus subsp. griseus strain ATCC 10137. Four members of this cluster (BabyGotBac, Maih, TP1605, and YDN12) share over 89% average nucleotide identity, while the other (Xkcd426) has only 72% similarity to other cluster members.

Prophage-mediated defence against viral attack and viral counter-defence.

Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.

Development, Validation, and Application of the Microbiology Concept Inventory.

If we are to teach effectively, tools are needed to measure student learning. A widely used method for quickly measuring student understanding of core concepts in a discipline is the concept inventory (CI). Using the American Society for Microbiology Curriculum Guidelines (ASMCG) for microbiology, faculty from 11 academic institutions created and validated a new microbiology concept inventory (MCI). The MCI was developed in three phases. In phase one, learning outcomes and fundamental statements from the ASMCG were used to create T/F questions coupled with open responses. In phase two, the 743 responses to MCI 1.0 were examined to find the most common misconceptions, which were used to create distractors for multiple-choice questions. MCI 2.0 was then administered to 1,043 students. The responses of these students were used to create MCI 3.0, a 23-question CI that measures students' understanding of all 27 fundamental statements. MCI 3.0 was found to be reliable, with a Cronbach's alpha score of 0.705 and Ferguson's delta of 0.97. Test item analysis demonstrated good validity and discriminatory power as judged by item difficulty, item discrimination, and point-biserial correlation coefficient. Comparison of pre- and posttest scores showed that microbiology students at 10 institutions showed an increase in understanding of concepts after instruction, except for questions probing metabolism (average normalized learning gain was 0.15). The MCI will enable quantitative analysis of student learning gains in understanding microbiology, help to identify misconceptions, and point toward areas where efforts should be made to develop teaching approaches to overcome them.

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology.

Misconceptions, or alternative conceptions, are incorrect understandings that students have incorporated into their prior knowledge. The goal of this study was the identification of misconceptions in microbiology held by undergraduate students upon entry into an introductory, general microbiology course. This work was the first step in developing a microbiology concept inventory based on the American Society for Microbiology's Recommended Curriculum Guidelines for Undergraduate Microbiology. Responses to true/false (T/F) questions accompanied by written explanations by undergraduate students at a diverse set of institutions were used to reveal misconceptions for fundamental microbiology concepts. These data were analyzed to identify the most difficult core concepts, misalignment between explanations and answer choices, and the most common misconceptions for each core concept. From across the core concepts, nineteen misconception themes found in at least 5% of the coded answers for a given question were identified. The top five misconceptions, with coded responses ranging from 19% to 43% of the explanations, are described, along with suggested classroom interventions. Identification of student misconceptions in microbiology provides a foundation upon which to understand students' prior knowledge and to design appropriate tools for improving instruction in microbiology.

Genome Sequences of Streptomyces Phages Amela and Verse.

Amela and Verse are two Streptomyces phages isolated by enrichment on Streptomyces venezuelae (ATCC 10712) from two different soil samples. Amela has a genome length of 49,452, with 75 genes. Verse has a genome length of 49,483, with 75 genes. Both belong to the BD3 subcluster of Actinobacteriophage.

Comparison of medication policies to guide nursing practice across seven Victorian health services.

Objectives The objective of this paper is to review and compare the content of medication management policies across seven Australian health services located in the state of Victoria. Methods The medication management policies for health professionals involved in administering medications were obtained from seven health services under one jurisdiction. Analysis focused on policy content, including the health service requirements and regulations governing practice. Results and Conclusions The policies of the seven health services contained standard information about staff authorisation, controlled medications and poisons, labelling injections and infusions, patient self-administration, documentation and managing medication errors. However, policy related to individual health professional responsibilities, single- and double-checking medications, telephone orders and expected staff competencies varied across the seven health services. Some inconsistencies in health professionals' responsibilities among medication management policies were identified. What is known about the topic? Medication errors are recognised as the single most preventable cause of patient harm in hospitals and occur most frequently during administration. Medication management is a complex process involving several management and treatment decisions. Policies are developed to assist health professionals to safely manage medications and standardise practice; however, co-occurring activities and interruptions increase the risk of medication errors. What does this paper add? In the present policy analysis, we identified some variation in the content of medication management policies across seven Victorian health services. Policies varied in relation to medications that require single- and double-checking, as well as by whom, nurse-initiated medications, administration rights, telephone orders and competencies required to check medications. What are the implications for practitioners? Variation in medication management policies across organisations is highlighted and raises concerns regarding consistency in governance and practice related to medication management. Lack of practice standardisation has previously been implicated in medication errors. Lack of intrajurisdictional concordance should be addressed to increase consistency. Inconsistency in expectations between healthcare services may lead to confusion about expectations among health professionals moving from one healthcare service to another, and possibly lead to increased risk of medication errors.