Different genome stability proteins underpin primed and naïve adaptation in E. coli CRISPR-Cas immunity

CRISPR-Cas is a prokaryotic immune system built from capture and integration of invader DNA into CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, termed ‘Adaptation’, which is dependent on Cas1 and Cas2 proteins. In Escherichia coli, Cascade-Cas3 degrades invader DNA to effect immunity, termed ‘Interference’. Adaptation can interact with interference (‘primed’), or is independent of it (‘naïve’). We demonstrate that primed adaptation requires the RecG helicase and PriA protein to be present. Genetic analysis of mutant phenotypes suggests that RecG is needed to dissipate R-loops at blocked replication forks. Additionally, we identify that DNA polymerase I is important for both primed and naive adaptation, and that RecB is needed for naïve adaptation. Purified Cas1-Cas2 protein shows specificity for binding to and nicking forked DNA within single strand gaps, and collapsing forks into DNA duplexes. The data suggest that different genome stability systems interact with primed or naïve adaptation when responding to blocked or collapsed invader DNA replication. In this model, RecG and Cas3 proteins respond to invader DNA replication forks that are blocked by Cascade interference, enabling DNA capture. RecBCD targets DNA ends at collapsed forks, enabling DNA capture without interference. DNA polymerase I is proposed to fill DNA gaps during spacer integration

Assessment of healthcare worker protocol deviations and self-contamination during personal protective equipment donning and doffing

OBJECTIVETo evaluate healthcare worker (HCW) risk of self-contamination when donning and doffing personal protective equipment (PPE) using fluorescence and MS2 bacteriophage.DESIGNProspective pilot study.SETTINGTertiary-care hospital.PARTICIPANTSA total of 36 HCWs were included in this study: 18 donned/doffed contact precaution (CP) PPE and 18 donned/doffed Ebola virus disease (EVD) PPE.INTERVENTIONSHCWs donned PPE according to standard protocols. Fluorescent liquid and MS2 bacteriophage were applied to HCWs. HCWs then doffed their PPE. After doffing, HCWs were scanned for fluorescence and swabbed for MS2. MS2 detection was performed using reverse transcriptase PCR. The donning and doffing processes were videotaped, and protocol deviations were recorded.RESULTSOverall, 27% of EVD PPE HCWs and 50% of CP PPE HCWs made ≥1 protocol deviation while donning, and 100% of EVD PPE HCWs and 67% of CP PPE HCWs made ≥1 protocol deviation while doffing (P=.02). The median number of doffing protocol deviations among EVD PPE HCWs was 4, versus 1 among CP PPE HCWs. Also, 15 EVD PPE protocol deviations were committed by doffing assistants and/or trained observers. Fluorescence was detected on 8 EVD PPE HCWs (44%) and 5 CP PPE HCWs (28%), most commonly on hands. MS2 was recovered from 2 EVD PPE HCWs (11%) and 3 CP PPE HCWs (17%).CONCLUSIONSProtocol deviations were common during both EVD and CP PPE doffing, and some deviations during EVD PPE doffing were committed by the HCW doffing assistant and/or the trained observer. Self-contamination was common. PPE donning/doffing are complex and deserve additional study.Infect Control Hosp Epidemiol 2017;38:1077–1083</jats:sec

Estimating the total incidence of kidney failure in australia including individuals who are not treated by dialysis or transplantation

Background: To date, incidence data for kidney failure in Australia have been available for only those who start renal replacement therapy (RRT). Information about the total incidence of kidney failure, including non-RRT-treated cases, is important to help understand the burden of kidney failure in the community and the characteristics of patients who die without receiving treatment

A Multi-Code Analysis Toolkit for Astrophysical Simulation Data

The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet these challenges, and in order to open up new avenues for collaboration between users of multiple simulation platforms, we present yt (available at http://yt.enzotools.org/), an open source, community-developed astrophysical analysis and visualization toolkit. Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to astrophysical simulation codes. While originally designed for handling Enzo's structure adaptive mesh refinement (AMR) data, yt has been extended to work with several different simulation methods and simulation codes including Orion, RAMSES, and FLASH. We report on its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation and topologically-connected isocontour identification. Furthermore, we discuss the underlying algorithms yt uses for processing and visualizing data, and its mechanisms for parallelization of analysis tasks.Comment: 18 pages, 6 figures, emulateapj format. Resubmitted to Astrophysical Journal Supplement Series with revisions from referee. yt can be found at http://yt.enzotools.org

Why and When Beliefs Change

Why people do or do not change their beliefs has been a long-standing puzzle. Sometimes people hold onto false beliefs despite ample contradictory evidence; sometimes they change their beliefs without sufficient reason. Here, we propose that the utility of a belief is derived from the potential outcomes associated with holding it. Outcomes can be internal (e.g., positive/negative feelings) or external (e.g., material gain/loss), and only some are dependent on belief accuracy. Belief change can then be understood as an economic transaction in which the multidimensional utility of the old belief is compared against that of the new belief. Change will occur when potential outcomes alter across attributes, for example because of changing environments or when certain outcomes are made more or less salient

Congenital duodenal obstruction in the UK: a population-based study

Objective Congenital duodenal obstruction (CDO) comprising duodenal atresia or stenosis is a rare congenital anomaly requiring surgical correction in early life. Identification of variation in surgical and postoperative practice in previous studies has been limited by small sample sizes. This study aimed to prospectively estimate the incidence of CDO in the UK, and report current management strategies and short-term outcomes. Design Prospective population-based, observational study for 12 months from March 2016. Setting Specialist neonatal surgical units in the UK. Main outcome measures Incidence of CDO, associated anomalies and short-term outcomes. Results In total, 110 cases were identified and data forms were returned for 103 infants giving an estimated incidence of 1.22 cases per 10 000 (95% CI 1.01 to 1.49) live births. Overall, 59% of cases were suspected antenatally and associated anomalies were seen in 69%. Operative repair was carried out mostly by duodenoduodenostomy (76%) followed by duodenojejunostomy (15%). Postoperative feeding practice varied with 42% having a trans-anastomotic tube placed and 88% receiving parenteral nutrition. Re-operation rate related to the initial procedure was 3% within 28 days. Two infants died within 28 days of operation from unrelated causes. Conclusion This population-based study of CDO has shown that the majority of infants have associated anomalies. There is variation in postoperative feeding strategies which represent opportunities to explore the effects of these on outcome and potentially standardise approach. Short-term outcomes are generally good

What Do Unions Do for Economic Performance?

Twenty years have passed since Freeman and Medoff's What Do Unions Do? This essay assesses their analysis of how unions in the U.S. private sector affect economic performance - productivity, profitability, investment, and growth. Freeman and Medoff are clearly correct that union productivity effects vary substantially across workplaces. Their conclusion that union effects are on average positive and substantial cannot be sustained, subsequent evidence suggesting an average union productivity effect near zero. Their speculation that productivity effects are larger in more competitive environments appears to hold up, although more evidence is needed. Subsequent literature continues to find unions associated with lower profitability, as noted by Freeman and Medoff. Unions are found to tax returns stemming from market power, but industry concentration is not the source of such returns. Rather, unions capture firm quasi-rents arising from long-lived tangible and intangible capital and from firm-specific advantages. Lower profits and the union tax on asset returns leads to reduced investment and, subsequently, lower employment and productivity growth. There is little evidence that unionization leads to higher rates of business failure. Given the decline in U.S. private sector unionism, I explore avenues through which individual and collective voice might be enhanced, focusing on labor law and workplace governance defaults. Substantial enhancement of voice requires change in the nonunion sector and employer as well as worker initiatives. It is unclear whether labor unions would be revitalized or further marginalized by such an evolution

Treatment for Vestibular Disorders: How Does Your Physical Therapist Treat Dizziness Related to Vestibular Problems?

Dizziness is very common, but it is never normal. Dizziness can make performing daily activities, work, and walking difficult. Many people get dizzy when they turn their head, which can cause problems with walking and makes people more likely to fall. Most of the time dizziness is not from a life-threatening disease. Often dizziness is because of a disorder of the vestibular (or inner ear balance) system. People can get vestibular disorders from infections in the ear, problems with the immune system, medications that harm the inner ear, and rarely from diabetes or stroke because of a lack of blood flow to the inner ear. Stress, poor sleep, migraines, overdoing some activities, and feeling sad can increase symptoms. New guidelines for the treatment of vestibular disorders were published in the April 2016 issue of the Journal of Neurologic Physical Therapy. The guideline describes which exercises are best to treat the dizziness and balance problems commonly seen with an inner ear disorder