A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites

We describe here a new family of IS which are related to IS1202, originally isolated from Streptococcus pneumoniae in the mid-1990s and previously tagged as an emerging IS family in the ISfinder database. Members of this family have impacted some important properties of their hosts. We describe here another potentially important property of certain family members: specific targeting of xrs recombination sites. The family could be divided into three subgroups based on their transposase sequences and the length on the target repeats (DR) they generate on insertion: subgroup IS1202 (24-29 bp); ISTde1 (15-18 bp); and ISAba32 (5-6 bp). Members of the ISAba32 subgroup were repeatedly found abutting Xer recombinase recombination sites (xrs), separated by an intervening copy of a DR. These xrs sites, present in multiple copies in a number of Acinetobacter plasmids flanking antibiotic resistance genes, were proposed to form a new type of mobile genetic element using the chromosomally-encoded XerCD recombinase for mobility. Transposase alignments identified subgroup-specific indels which may be responsible for the differences in the transposition properties of the three subgroups (i.e. DR length and target specificity). We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of three subgroups, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.

CO-DESIGNED PERSON-CENTERED NARRATIVES FOR PEOPLE WITH ALZHEIMER’S AND RELATED DEMENTIAS

MemoryWell’s professional writers capture and share patient life stories with care teams and families in healthcare settings, with the goal of improving person-centered care. This mixed methods study employs participatory-design methods to assess the feasibility and acceptability of adapting this existing life story service to an acute care setting and implementing stories into the electronic health record (EHR) for older adults with Alzheimer’s and Related Dementias (ADRD). Through in-depth interviews and surveys, we engage patients, family caregivers and care providers to co-design the life story process adaptation and development of EHR wireframes to iterate and pilot in the acute care setting. We will present the co-designed EHR wireframes and data analyzed using qualitative content analysis. Results describe life story utility and potential impacts on outcomes for people with ADRD. Findings from in-depth interviews with 11 providers indicated high feasibility and acceptability, e.g. describing a high likelihood of daily use. Providers shared barriers and facilitators, e.g. time and accessibility, and potential impacts on person-centered care and patient outcomes, e.g. trust, cultural competency, and delirium. Patient and caregiver data collection is underway; one patient and one caregiver have been interviewed out of ten for each respective group. Interviews with all groups have suggested that life stories would be useful for helping patients in unfamiliar and disorienting environments and learning information such as hobbies and interests would be helpful for providers to better understand and engage with patients.

Response from Varani et al. to "Comment on 'the IS6 family, a clinically important group of insertion sequences including IS26' by Ruth M. Hall"

The IS6 family of insertion sequences is a large but coherent group which was originally named to avoid confusion between a number of identical or nearly identical IS that were identified at about the same time and given different names (IS15D, IS26, IS46, IS140, IS160, IS176). The underlying common mechanistic feature of all IS6 family members which have been investigated is that they appear to transpose by replicative transposition and form pseudo compound transposons with the flanking IS in direct repeat and in which associated genes are simply transferred to the target replicon and lost from the donor.

In the accompanying letter Hall raises a number of very serious and wide-ranging criticisms of our recent review article concerning the IS6 family of insertion sequences. She clearly feels that we have undervalued her work and that we question or ignore certain of her in vivo results. This impression is almost certainly the result of the standard of proof we generally apply to mechanistic aspects of transposition where we think it important to identify transposition intermediates including the types of synaptic, strand cleavage and strand transfer complexes involved.

Characterizing Patients after Opioid Taper in a VA Medical Center

To identify potential areas for intervention and gain insight on current practice in patients who are tapered to zero morphine equivalent daily doses (MEDD) through the Pharmacy Pain E-Consult at a Veterans Healthcare System. This was done by describing the types of follow-up care and resources utilized by patients. This project is a retrospective chart review of Veterans with non-cancer pain on chronic-opioid therapy consulted to the pharmacy e-consult service and tapered to 0 MEDD. Descriptive statistics are collected one year pre-taper and one year post-taper. One year post-taper, approximately one-third of the patients were re-started on opioid therapy. However, average MEDD overall was significantly decreased one year post-taper compared to pre-taper. Average pain scores were not significantly different pre-taper compared to post-taper. Non-opioid medications generally increased post-taper. Follow-up with mental health and pain management clinical pharmacy specialists decreased post-taper. Tapering to zero MEDD did not lead to a significant increase in pain one-year post-taper; however, approximately 33% of patients were re-started on opioids within one year post-taper. Average MEDD scores decreased post-taper as expected but with effects on mental health being largely unknown, we believe that further study in this area will help us better support patients.

The IS6 family, a clinically important group of insertion sequences including IS26

The IS6 family of bacterial and archaeal insertion sequences, first identified in the early 1980s, has proved to be instrumental in the rearrangement and spread of multiple antibiotic resistance. Two IS, IS26 (found in many enterobacterial clinical isolates as components of both chromosome and plasmids) and IS257 (identified in the plasmids and chromosomes of gram-positive bacteria), have received particular attention for their clinical impact. Although few biochemical data are available concerning the transposition mechanism of these elements, genetic studies have provided some interesting observations suggesting that members of the family might transpose using an unexpected mechanism. In this review, we present an overview of the family, the distribution and phylogenetic relationships of its members, their impact on their host genomes and analyse available data concerning the particular transposition pathways they may use. We also provide a mechanistic model that explains the recent observations on one of the IS6 family transposition pathways: targeted cointegrate formation between replicons.

Comparing Effectiveness of Gabapentin and Pregabalin in Treatment of Neuropathic Pain: A Retrospective Cohort of Palliative Care Outpatients

Gabapentin and pregabalin are often considered first line treatment options for various neuropathic pain conditions. The purpose of this retrospective cohort study was to compare clinically meaningful pain reduction and other relevant outcomes among patients prescribed either gabapentin or pregabalin at the University of Arkansas for Medical Sciences (UAMS) Palliative Care Clinic (PCC). The primary endpoint was a significant improvement in pain within six months of initiating either gabapentin or pregabalin. Secondary endpoints included the average number of pills per day as documented at last visit in the study period, the incidence of gabapentinoid dose reductions due to adverse effects, and the incidence of discontinuation of a gabapentinoid due to adverse effects. 222 patients were included in the gabapentin group and 30 patients were included in the pregabalin group. There was not a statistically significant difference between the groups in the primary outcome of pain reduction (p = 0.43). Dose reductions due to adverse effects were statistically significantly (p = 0.03) higher in the gabapentin group than the pregabalin group. The average number of pills per day by a patient in the gabapentin group was 1.8 pills higher than the pregabalin group which was statistically significant (p = 0.01). The results of this analysis support the notion that there is no significant difference in meaningful pain reduction with gabapentin versus pregabalin. This study demonstrates that pregabalin may afford better tolerability and lower pill burden compared to gabapentin.

World Small Animal Veterinary Association Global Dental Guidelines

Dental, oral, and maxillofacial diseases are some of the most common problems in small animal veterinary practice. These conditions create significant pain as well as localized and potentially systemic infection. As such, the World Small Animal Veterinary Association (WSAVA) believes that un- and under treated oral and dental diseases pose a significant animal welfare concern. Dentistry is an area of veterinary medicine which is still widely ignored and is subject to many myths and misconceptions. Effective teaching of veterinary dentistry in the veterinary school is the key to progression in this field of veterinary medicine, and to the improvement of welfare for all our patients globally. These guidelines were developed to provide veterinarians with the information required to understand best practices for dental therapy and create realistic minimum standards of care. Using the three-tiered continuing education system of WSAVA, the guidelines make global equipment and therapeutic recommendations and highlight the anaesthetic and welfare requirements for small animal patients. This document contains information on common oral and dental pathologies, diagnostic procedures (an easily implementable and repeatable scoring system for dental health, dental radiography and radiology) and treatments (periodontal therapy, extractions). Further, there are sections on anaesthesia and pain management for dental procedures, home dental care, nutritional information, and recommendations on the role of the universities in improving veterinary dentistry. A discussion of the deleterious effects of anaesthesia free dentistry (AFD) is included, as this procedure is ineffective at best and damaging at worst. Throughout the document the negative effects of undiagnosed and/or treated dental disease on the health and well-being of our patients, and how this equates to an animal welfare issue, is discussed.

Characteristics of Minor Ions and Electrons in Flux Transfer Events Observed by the Magnetospheric Multiscale Mission

In this study, the ion composition of flux transfer events (FTEs) observed within the magnetosheath proper is examined. These FTEs were observed just upstream of the Earth's postnoon magnetopause by the National Aeronautics and Space Administration (NASA) Magnetospheric Multiscale (MMS) spacecraft constellation. The minor ion characteristics are described using energy spectrograms, flux distributions, and ion moments as the constellation encountered each FTE. In conjunction with electron data and magnetic field observations, such observations provide important contextual information on the formation, topologies, and evolution of FTEs. In particular, minor ions, when combined with the field-aligned streaming of electrons, are reliable indicators of FTE topology. The observations are also placed (i) in context of the solar wind magnetic field configuration, (ii) the connection of the sampled flux tube to the ionosphere, and (iii) the location relative to the modeled reconnection line at the magnetopause. While protons and alpha particles were often depleted within the FTEs relative to the surrounding magnetosheath plasma, the He+ and O+ populations showed clear enhancements either near the center or near the edges of the FTE, and the bulk plasma flow directions are consistent with magnetic reconnection northward of the spacecraft and convection from the dayside toward the flank magnetopause.

Comparative Effectiveness of Behavioral Interventions to Prevent or Delay Dementia: One-Year Partner Outcomes

BACKGROUND/OBJECTIVE

Various behavioral interventions are recommended to combat the distress experienced by caregivers of those with cognitive decline, but their comparative effectiveness is poorly understood.

DESIGN/SETTING

Caregivers in a comparative intervention study randomly had 1 of 5 possible interventions suppressed while receiving the other four. Caregivers in a full clinical program received all 5 intervention components. Care partner outcomes in the study group were compared to participants enrolled in a full clinical program.

PARTICIPANTS

Two hundred and seventy-two dyads of persons with amnestic mild cognitive impairment (pwMCI) and care partners enrolled in the comparative intervention study. 265 dyads participated in the full clinical program.

INTERVENTION

Behavioral intervention components included: memory compensation training, computerized cognitive training, yoga, support group, and wellness education. Each was administered for 10 sessions over 2 weeks.

MEASUREMENTS

A longitudinal mixed-effect regression model was used to analyze the effects of the interventions on partner burden, quality of life (QoL), mood, anxiety, and self-efficacy at 12 months follow-up.

RESULTS

At 12 months, withholding wellness education or yoga had a significantly negative impact on partner anxiety compared to partners in the clinical program (ES=0.55 and 0.44, respectively). Although not statistically significant, withholding yoga had a negative impact on partner burden and mood compared to partners in the full clinical program (ES=0.32 and 0.36, respectively).

CONCLUSION

Our results support the benefits of wellness education and yoga for improving partner's burden, mood, and anxiety at one year. Our findings are the first to provide an exploration of the impact of multicomponent interventions in care partners of pwMCI.

Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering

Transposable elements are efficient DNA carriers and thus important tools for transgenesis and insertional mutagenesis. However, their poor target sequence specificity constitutes an important limitation for site-directed applications. The insertion sequence IS608 from Helicobacter pylori recognizes a specific tetranucleotide sequence by base pairing, and its target choice can be re-programmed by changes in the transposon DNA. Here, we present the crystal structure of the IS608 target capture complex in an active conformation, providing a complete picture of the molecular interactions between transposon and target DNA prior to integration. Based on this, we engineered IS608 variants to direct their integration specifically to various 12/17-nt long target sites by extending the base pair interaction network between the transposon and the target DNA. We demonstrate in vitro that the engineered transposons efficiently select their intended target sites. Our data further elucidate how the distinct secondary structure of the single-stranded transposon intermediate prevents extended target specificity in the wild-type transposon, allowing it to move between diverse genomic sites. Our strategy enables efficient targeting of unique DNA sequences with high specificity in an easily programmable manner, opening possibilities for the use of the IS608 system for site-specific gene insertions.

Testing implementation facilitation of a primary care-based collaborative care clinical program using a hybrid type III interrupted time series design: a study protocol

Background

Dissemination of evidence-based practices that can reduce morbidity and mortality is important to combat the growing opioid overdose crisis in the USA. Research and expert consensus support reducing high-dose opioid therapy, avoiding risky opioid-benzodiazepine combination therapy, and promoting multi-modal, collaborative models of pain care. Collaborative care interventions that support primary care providers have been effective in medication tapering. We developed a patient-centered Primary Care-Integrated Pain Support (PIPS) collaborative care clinical program based on effective components of previous collaborative care interventions. Implementation facilitation, a multi-faceted and dynamic strategy involving the provision of interactive problem-solving and support during implementation of a new program, is used to support key organizational staff throughout PIPS implementation. The primary aim of this study is to evaluate the effectiveness of the implementation facilitation strategy for implementing and sustaining PIPS in the Veterans Health Administration (VHA). The secondary aim is to examine the effect of the program on key patient-level clinical outcomes—transitioning to safer regimens and enhancing access to complementary and integrative health treatments. The tertiary aim is to determine the categorical costs and ultimate budget impact of PIPS implementation.

Methods

This multi-site study employs an interrupted time series, hybrid type III design to evaluate the effectiveness of implementation facilitation for a collaborative care clinical program—PIPS—in primary care clinics in three geographically diverse VHA health care systems (sites). Participants include pharmacists and allied staff involved in the delivery of clinical pain management services as well as patients. Eligible patients are prescribed either an outpatient opioid prescription greater than or equal to 90 mg morphine equivalent daily dose or a combination opioid-benzodiazepine regimen. They must also have an upcoming appointment in primary care. The Consolidated Framework for Implementation Research will guide the mixed methods work across the formative evaluation phases and informs the selection of activities included in implementation facilitation. The RE-AIM framework will be used to assess Reach, Effectiveness, Adoption, Implementation, and Maintenance of PIPS.

Discussion

This implementation study will provide important insight into the effectiveness of implementation facilitation to enhance uptake of a collaborative care program in primary care, which targets unsafe opioid prescribing practices.

Electronic supplementary material

The online version of this article (10.1186/s13012-018-0838-2) contains supplementary material, which is available to authorized users.

Surveillance of traffic incident management-related occupational fatalities in Kentucky, 2005-2016

OBJECTIVE

Traffic incidents occurring on roadways require the coordinated effort of multiple responder and recovery entities, including communications, law enforcement, fire and rescue, emergency medical services, hazardous materials, transportation agencies, and towing and recovery. The objectives of this study were to (1) identify and characterize transportation incident management (TIM)-related occupational fatalities; (2) assess concordance of surveillance data sources in identifying TIM occupations, driver vs. pedestrian status, and occupational fatality incident location; and (3) determine and compare U.S. occupational fatality rates for TIM industries.

METHODS

The Kentucky Fatality Assessment and Control Evaluation (FACE) program analyzed 2005-2016 TIM occupational fatality data using multiple data sources: death certificate data, Collision Report Analysis for Safer Highways (CRASH) data, and media reports, among others. Literal text analysis was performed on FACE data, and a multiple linear regression model and SAS proc sgpanel were used to estimate and visualize the U.S. TIM occupational mortality trend lines and confidence bounds.

RESULTS

There were 29 TIM fatalities from 2005 to 2015 in Kentucky; 41% of decedents were in the police protection occupation, and 21% each were in the fire protection and motor vehicle towing industries. Over one half of the TIM decedents were performing work activities as pedestrians when they died. Media reports identified the majority of the occupational fatalities as TIM related (28 of 29 TIM-related deaths); the use of death certificates as the sole surveillance data source only identified 17 of the 29 deaths as TIM related, and the use of CRASH data only identified 4 of the 29 deaths as TIM related. Injury scenario text analysis showed that law enforcement vehicle pursuit, towing and recovery vehicle loading, and disabled vehicle response were particular high-risk activities that led to TIM deaths. Using U.S. data, the motor vehicle towing industry had a significantly higher risk for occupational mortality compared to the fire protection and police protection industries.

CONCLUSIONS

Multiple data sources are needed to comprehensively identify TIM fatalities and to examine the circumstances surrounding TIM fatalities, because no one data source in itself was adequate and undercounted the total number of TIM fatalities. The motor vehicle towing industry, in particular, is at elevated risk for occupational mortality, and targeted mandatory TIM training for the motor vehicle towing industry should be considered. In addition, enhanced law enforcement roadside safety training during vehicle pursuit and apprehension of suspects is recommended.

Use of Methadone to Reverse Opioid Escalation in a Patient With Surgical Pain

Acute pain is a prevalent issue for patients recovering from surgical procedures. Methadone has been recognized as a unique option for treatment of surgical pain due to its multiple mechanisms of analgesia and its potential to decrease tolerance to other opioids. Studies of methadone use in postoperative settings are sparse in part due to safety concerns, such as complex pharmacokinetics, risk of respiratory depression, and association with arrhythmias. In this case study of a 70-year-old male with postsurgical abdominal pain, methadone utilization over a period of 9 days resulted in patient-reported analgesia and aided in de-escalating overall opioid use. More studies are needed to develop guidance on how methadone can be used to relieve pain following surgical procedures.

The Birth and Demise of the ISApl1-mcr-1-ISApl1 Composite Transposon: the Vehicle for Transferable Colistin Resistance

The origin and mobilization of the ~2,609-bp DNA segment containing the mobile colistin resistance gene mcr-1 continue to be sources of uncertainty, but recent evidence suggests that the gene originated in Moraxella species. Moreover mcr-1 can be mobilized as an ISApl1-flanked composite transposon (Tn6330), but many sequences have been identified without ISApl1 or with just a single copy (single ended). To further clarify the origins and mobilization of mcr-1, we employed the Geneious R8 software suite to comprehensively analyze the genetic environment of every complete mcr-1 structure deposited in GenBank as of this writing (September 2017) both with and without associated ISApl1 (n = 273). This revealed that the 2,609-bp mcr-1 structure was likely mobilized from a close relative of a novel species of Moraxella containing a chromosomal region sharing >96% nucleotide identity with the canonical sequence. This chromosomal region is bounded by AT and CG dinucleotides, which have been described on the inside ends (IE) of all intact Tn6330 described to date and represent the ancestral 2-bp target site duplications (TSDs) generated by ISApl1 transposition. We further demonstrate that all mcr-1 structures with just one ISApl1 copy or with no ISApl1 copies were formed by deletion of ISApl1 from the ancestral Tn6330, likely by a process related to the "copy-out-paste-in" transposition mechanism. Finally, we show that only the rare examples of single-ended structures that have retained a portion of the excised downstream ISApl1 including the entire inverted right repeat might be capable of mobilization.IMPORTANCE A comprehensive analysis of all intact mcr-1 sequences in GenBank was used to identify a region on the chromosome of a novel Moraxella species with remarkable homology to the canonical mcr-1 structure and that likely represents the origin of this important gene. These data also demonstrate that all mcr-1 structures lacking one or both flanking ISApl1 were formed from ancestral composite transposons that subsequently lost the insertion sequences by a process of abortive transposition. This observation conclusively shows that mobilization of mcr-1 occurs as part of a composite transposon and that structures lacking the downstream ISApl1 are not capable of mobilization.

Known knowns, known unknowns and unknown unknowns in prokaryotic transposition

Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species. It is not exhaustive. Examples have been chosen to provide encouragement in the continued exploration of the considerable prokaryotic mobilome especially in light of the current threat to public health posed by the spread of multiple Ab^R.

The impact of insertion sequences on bacterial genome plasticity and adaptability

Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.

The "Mental" Health of Canada's Indigenous Children and Youth: Finding New Ways Forward

Focusing, as it is meant to do, on child mental health, this special issue of Healthcare Quarterly singles out for attention a distinctive category of concerns that, when viewed through lenses common to many Indigenous peoples, is arguably better left unmarked. That is, attempts to carve up the world in such a way that health concerns centre on matters of the "mind," on the one hand, and on "physical" ill health, on the other, are expressive of a form of self-understanding that is more consonant with the classic dualisms of traditional, "Western," Cartesian thought (e.g., the mental in counter-distinction to the physical; selves set off against societies), and quite out of place in those more holistic frameworks of understanding favoured by many of the world's Indigenous peoples (Chandler 2010). Why such putative cultural differences might make a difference - or at least a difference in what is written here - is that any account of health matters in which Indigenous people might actually recognize themselves requires, as a constitutive condition of its coherence, a kind of radical reframing - a shift in axes that replaces the arguably "false" dichotomy between mental and physical health with something better approximated by the much-overheard and more broadly inclusive notion of personal and community "well-being."

International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany

The third international conference on Transposable Elements (ICTE) was held 16–19 April 2016 in Saint Malo, France. Organized by the French Transposition Community (Research group of the CNRS: “Mobile genetic elements: from mechanism to populations, an integrative approach”) and the French Society of Genetics, the conference’s goal was to bring together researchers who study transposition in diverse organisms, using multiple experimental approaches. The meeting gathered 180 participants from all around the world. Most of them contributed through poster presentations, invited talks and short talks selected from poster abstracts. The talks were organized into six scientific sessions: “Taming mobile DNA: self and non-self recognition”; “Trans-generational inheritance”; “Mobile DNA genome structure and organization, from molecular mechanisms to applications”; “Remembrance of (retro)transposon past: mobile DNA in genome evolution”; and finally “The yin and the yang of mobile DNA in human health”.

Surviving Time: The Persistence of Identity in This Culture and That

This account is all about how young persons of different cultural stripes work to keep their identities in good repair. Rank-and-file Euro-American adolescents are shown to be steeped in a standard brew of essentialist thought. By contrast, ‘First Nations’ youth commonly adopt a more narrative approach to the problem by weaving together the various threads of their lives into some culturally available fabric. Beyond exploring the relation between the breakdown of such diverse self-warranting practices and youth suicide, the present essay works to bring out possible parallels between such alternative conceptions of personal persistence and various accounts of selfhood and timeconsciousness evident in the course of recent intellectual history.

The Development of Moral Behavior: Continuities and Discontinuities

A conceptual framework and supporting research findings are presented which are intended to contribute to a better understanding of the relationship between moral judgment and moral action. A transactional model, based in part upon the earlier work of Piaget, is outlined. Within this framework, the outcome of moral deliberation is viewed as the joint product of an individual's current level of cognitive complexity and the structural complexity of the moral dilemma which he or she must arbitrate. In this context cognitive development level is assumed to predict concrete behavioral choices whenever individuals are at least as complex as are the moral alternatives which confront them.

In order to test this hypothesis, children at three levels of conceptual maturity were presented with six dilemmas, representing all pairwise combinations of rituals, rules and principles, and were required to formulate specific plans of action to resolve these conflicts. The results are consistent with the hypothesis and show a significant interaction between the structural complexity of moral dilemmas and cognitive complexity of persons who attempt to resolve them.

Electron-scale measurements of magnetic reconnection in space

Magnetic reconnection is a fundamental physical process in plasmas whereby stored magnetic energy is converted into heat and kinetic energy of charged particles. Reconnection occurs in many astrophysical plasma environments and in laboratory plasmas. Using measurements with very high time resolution, NASA's Magnetospheric Multiscale (MMS) mission has found direct evidence for electron demagnetization and acceleration at sites along the sunward boundary of Earth's magnetosphere where the interplanetary magnetic field reconnects with the terrestrial magnetic field. We have (i) observed the conversion of magnetic energy to particle energy; (ii) measured the electric field and current, which together cause the dissipation of magnetic energy; and (iii) identified the electron population that carries the current as a result of demagnetization and acceleration within the reconnection diffusion/dissipation region.

Culture and the Home-Field Disadvantage

The home-field disadvantage refers to the disadvantage inherent in research that takes a particular cultural group as the starting point or standard for research, including cross-cultural research. We argue that home-field status is a serious handicap that often pushes researchers toward deficit thinking, however good the researchers' intentions may be. In this article, we aim to make this home-field bias more explicit and, in doing so, more avoidable. We discuss three often-overlooked disadvantages that result from this home-field status: the problem of marked versus unmarked culture, the problem of homogenous versus heterogeneous culture, and the problem of regression toward the mean. We also recommend four interventions researchers can apply to avoid the home-field disadvantage or, at the least, attenuate its deleterious effects.

Advancing suicide prevention research with rural American Indian and Alaska Native populations

As part of the National Action Alliance for Suicide Prevention's American Indian and Alaska Native (AI/AN) Task Force, a multidisciplinary group of AI/AN suicide research experts convened to outline pressing issues related to this subfield of suicidology. Suicide disproportionately affects Indigenous peoples, and remote Indigenous communities can offer vital and unique insights with relevance to other rural and marginalized groups. Outcomes from this meeting include identifying the central challenges impeding progress in this subfield and a description of promising research directions to yield practical results. These proposed directions expand the alliance's prioritized research agenda and offer pathways to advance the field of suicide research in Indigenous communities and beyond.

The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries

Transposable elements (TEs) are major components of both prokaryotic and eukaryotic genomes and play a significant role in their evolution. In this study, we have identified new prokaryotic DDE transposase families related to the eukaryotic Mutator-like transposases. These genes were retrieved by cascade PSI-Blast using as initial query the transposase of the streptococcal integrative and conjugative element (ICE) TnGBS2. By combining secondary structure predictions and protein sequence alignments, we predicted the DDE catalytic triad and the DNA-binding domain recognizing the terminal inverted repeats. Furthermore, we systematically characterized the organization and the insertion specificity of the TEs relying on these prokaryotic Mutator-like transposases (p-MULT) for their mobility. Strikingly, two distant TE families target their integration upstream σ_A dependent promoters. This allowed us to identify a transposase sequence signature associated with this unique insertion specificity and to show that the dissymmetry between the two inverted repeats is responsible for the orientation of the insertion. Surprisingly, while DDE transposases are generally associated with small and simple transposons such as insertion sequences (ISs), p-MULT encoding TEs show an unprecedented diversity with several families of IS, transposons, and ICEs ranging in size from 1.1 to 52 kb.

Measurement of heat and moisture exchanger efficiency

Deciding between a passive heat and moisture exchanger or active humidification depends upon the level of humidification that either will deliver. Published international standards dictate that active humidifiers should deliver a minimum humidity of 33 mg.l(-1); however, no such requirement exists, for heat and moisture exchangers. Anaesthetists instead have to rely on information provided by manufacturers, which may not allow comparison of different devices and their clinical effectiveness. I suggest that measurement of humidification efficiency, being the percentage moisture returned and determined by measuring the temperature of the respired gases, should be mandated, and report a modification of the standard method that will allow this to be easily measured. In this study, different types of heat and moisture exchangers for adults, children and patients with a tracheostomy were tested. Adult and paediatric models lost between 6.5 mg.l(-1) and 8.5 mg.l(-1) moisture (corresponding to an efficiency of around 80%); however, the models designed for patients with a tracheostomy lost between 16 mg.l(-1) and 18 mg.l(-1) (60% efficiency). I propose that all heat and moisture exchangers should be tested in this manner and percentage efficiency reported to allow an informed choice between different types and models.

Toward 1-mGal accuracy in global marine gravity from CryoSat-2, Envisat, and Jason-1

More than 60% of the Earth's land and shallow marine areas are covered by > 2 km of sediments and sedimentary rocks, with the thickest accumulations on rifted continental margins (Figure 1). Free-air marine gravity anomalies derived from Geosat and ERS-1 satellite altimetry (Fairhead et al., 2001; Sandwell and Smith, 2009; Andersen et al., 2009) outline most of these major basins with remarkable precision. Moreover, gravity and bathymetry data derived from altimetry are used to identify current and paleo-submarine canyons, faults, and local recent uplifts. These geomorphic features provide clues to where to look for large deposits of sediments. While current altimeter data delineate large offshore basins and major structures, they do not resolve some of the smaller geomorphic features and basins (Yale et al., 1998; Fairhead et al., 2001). Improved accuracy and resolution is desirable: to facilitate comparisons between continental margins; as an exploration tool and to permit extrapolation of known structures from well-surveyed areas; to follow fracture zones out of the deep-ocean basin into antecedent continental structures, to define and compare segmentation of margins along strike and identify the position of the continent-ocean boundary; and to study mass anomalies (e.g., sediment type and distribution) and isostatic compensation at continental margins. In this article, we assess the accuracy of a new global marine gravity model based on a wealth of new radar altimetry data and demonstrate that these gravity data are superior in quality to the majority of publicly available academic and government ship gravity data.

Urine concentrations of xanthine, hypoxanthine and uric acid in UK Cavalier King Charles spaniels

OBJECTIVES

Xanthine urolithiasis and asymptomatic xanthinuria have been diagnosed in Cavalier King Charles spaniel dogs suggesting that primary xanthinuria may be a breed-related disorder, although its prevalence remains unclear. The hypothesis of this study was that asymptomatic xanthinuria is common in Cavalier King Charles spaniel dogs.

METHODS

Free catch urine samples were collected from 35 client-owned Cavalier King Charles spaniel dogs and from 24 dogs of other breeds. The purine metabolites were measured by high-performance liquid chromatography. The urine ratios of xanthine/creatinine and hypoxanthine/creatinine were calculated and compared between the two groups of dogs.

RESULTS

The urine concentrations of purine metabolites were not significantly different between the two groups and were very low in both. The urine concentrations of xanthine in all 35 Cavalier King Charles spaniel were markedly lower than in the previously reported case of xanthine urolithiasis in a UK Cavalier King Charles spaniel dog.

CLINICAL SIGNIFICANCE

Asymptomatic xanthinuria was not detected in this UK Cavalier King Charles spaniel population. This data may be used as a reference for urinary purine metabolite concentrations in the dog.

ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB

Transposable elements belonging to the recently identified IS200/IS605 family radically differ from classical insertion sequences in their transposition mechanism by strictly requiring single-stranded DNA substrates. This IS family includes elements encoding only the transposase (TnpA), and others, like ISDra2 from Deinococcus radiodurans, which contain a second gene, tnpB, dispensable for transposition and of unknown function to date. Here, we show that TnpB has an inhibitory effect on the excision and insertion steps of ISDra2 transposition. This inhibitory action of TnpB was maintained when ISDra2 transposition was induced by γ-irradiation of the host cells and required the integrity of its putative zinc finger motif. We also demonstrate the negative role of TnpB when ISDra2 transposition was monitored in a heterologous Escherichia coli host, indicating that TnpB-mediated inhibition does not involve Deinococcus-specific factors. TnpB therefore appears to play a regulatory role in ISDra2 transposition.

The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease

Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. REPs are found in many bacterial species at a high copy number and are important in regulation of certain bacterial functions, such as Integration Host Factor recruitment and mRNA turnover. Although a new clade of putative transposases (RAYTs or TnpA_REP) is often associated with an increase in these repeats, it is not clear how these proteins might have directed amplification of REPs. We report here the structure to 2.6 Å of TnpA_REP from Escherichia coli MG1655 bound to a REP. Sequence analysis showed that TnpA_REP is highly related to the IS200/IS605 family, but in contrast to IS200/IS605 transposases, TnpA_REP is a monomer, is auto-inhibited and is active only in manganese. These features suggest that, relative to IS200/IS605 transposases, it has evolved a different mechanism for the movement of discrete segments of DNA and has been severely down-regulated, perhaps to prevent REPs from sweeping through genomes.

Cotranslational control of DNA transposition: a window of opportunity

Transposable elements are important in genome dynamics and evolution. Bacterial insertion sequences (IS) constitute a major group in number and impact. Understanding their role in shaping genomes requires knowledge of how their transposition activity is regulated and interfaced with the host cell. One IS regulatory phenomenon is a preference of their transposases (Tpases) for action on the element from which they are expressed (cis) rather than on other copies of the same element (trans). Using IS911, we show in vivo that activity in cis was ~200 fold higher than in trans. We also demonstrate that a translational frameshifting pause signal influences cis preference presumably by facilitating sequential folding and cotranslational binding of the Tpase. In vitro, IS911 Tpase bound IS ends during translation but not after complete translation. Cotranslational binding of nascent Tpase permits tight control of IS proliferation providing a mechanistic explanation for cis regulation of transposition involving an unexpected partner, the ribosome.

Exploring bacterial insertion sequences with ISfinder: objectives, uses, and future developments

We describe here the use of the ISfinder database and its associated software. ISfinder was conceived -initially as a comprehensive database for prokaryotic insertion sequences (ISs). It now includes software for visualising complete and partial IS copies in whole genomes (ISbrowser) and for high-quality genome annotation (Insertion Sequence Semi-automatic Genome Annotation).

Inflammatory cytokines regulate endothelial cell survival and tissue repair functions via NF-κB signaling

Inflammation contributes to the development of fibrotic and malignant diseases. We assessed the ability of inflammatory cytokines to modulate endothelial cell survival and functions related to tissue repair/remodeling. Treatment with interleukin (IL)-1β or tumor necrosis factor (TNF)-α (2 ng/mL) led to human pulmonary artery endothelial cells becoming spindle-shaped fibroblast-like cells. However, immunoblot and DNA microarray showed no change in most endothelial and mesenchymal markers. In the presence of IL-1β or TNF-α, cells were resistant to apoptosis induced by deprivation of serum and growth factor, and were more migratory. In addition, cells treated with IL-1β or TNF-α contracted collagen gels more robustly. In contrast, transforming growth factor-β1 did not induce these responses. RNA interference targeting nuclear factor (NF)-κB p65 blocked the effects of IL-1β or TNF-α on cell morphologic change, survival, migration, and collagen gel contraction. These results suggest that endothelial cells may contribute to tissue repair/remodeling via the NF-κB signaling in a milieu of airway inflammation.

Case Series with Endoscopic Findings of a Novel Nasal Irrigation Protocol for Refractory Chronic Rhinosinusitis

Objective: Present an innovative treatment protocol for refractory chronic rhinosinusitis (CRS) in order for practitioners to 1) learn of a new topical treatment regimen, 2) be able to apply this protocol to their own patients, and 3) understand the proposed mechanism of its action.

Method: Case series of 20 patients with refractory CRS treated with a novel topical sinus regimen that included diluted baby shampoo between June 2009 and June 2010 with analysis of patient, disease, and treatment characteristics. Treatment endpoints include subjective improvement of nasal symptoms and objective improvements on nasal endoscopy.

Results: Our novel treatment protocol involves gentamicin 20 mg per 240 mL (8 ounces), Johnson’s Baby Shampoo 1 drop per 240 mL, and pulmicort respules 1 mg per 240 mL. Patients are advised to use 120 mL via a 240 mL squeeze bottle. We then remove the gentamicin, pulmicort, or both, and track patient progress based on symptomatic improvement and improvements seen on nasal endoscopy. All patients had positive response using this treatment protocol after failed medical and surgical management with a variety of other topical and systemic therapies. Two notable cases are presented with endonasal photos to illustrate the positive response achieved using this treatment protocol.

Conclusion: This novel sinus irrigation treatment protocol is effective in the treatment of CRS as documented by subjective improvements in nasal symptoms as well as significant improvement in nasal endoscopic findings. This protocol is well tolerated by patients and should be considered by otolaryngologists and allergists treating refractory CRS.

Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing

Single-stranded (ss) transposition, a recently identified mechanism adopted by members of the widespread IS200/IS605 family of insertion sequences (IS), is catalysed by the transposase, TnpA. The transposase of IS608, recognizes subterminal imperfect palindromes (IP) at both IS ends and cleaves at sites located at some distance. The cleavage sites, C, are not recognized directly by the protein but by short sequences 5′ to the foot of each IP, guide (G) sequences, using a network of canonical (‘Watson–Crick’) base interactions. In addition a set of non-canonical base interactions similar to those found in RNA structures are also involved. We have reconstituted a biologically relevant complex, the transpososome, including both left and right ends and TnpA, which catalyses excision of a ss DNA circle intermediate. We provide a detailed picture of the way in which the IS608 transpososome is assembled and demonstrate that both C and G sequences are essential for forming a robust transpososome detectable by EMSA. We also address several questions central to the organization and function of the ss transpososome and demonstrate the essential role of non-canonical base interactions in the IS608 ends for its stability by using point mutations which destroy individual non-canonical base interactions.

Single-stranded DNA transposition is coupled to host replication

DNA transposition has contributed significantly to evolution of eukaryotes and prokaryotes. Insertion sequences (ISs) are the simplest prokaryotic transposons and are divided into families on the basis of their organization and transposition mechanism. Here, we describe a link between transposition of IS608 and ISDra2, both members of the IS200/IS605 family, which uses obligatory single-stranded DNA intermediates, and the host replication fork. Replication direction through the IS plays a crucial role in excision: activity is maximal when the "top" IS strand is located on the lagging-strand template. Excision is stimulated upon transient inactivation of replicative helicase function or inhibition of Okazaki fragment synthesis. IS608 insertions also exhibit an orientation preference for the lagging-strand template and insertion can be specifically directed to stalled replication forks. An in silico genomic approach provides evidence that dissemination of other IS200/IS605 family members is also linked to host replication.

Gene exchange and the origin of giant viruses

Giant viruses or nucleocytoplasmic large DNA viruses (NCLDVs) infect a wide range of eukaryotic hosts (including, algae, amoebae and metazoans) and show a very large range in genome size (between 100 kb and 1.2 Mb). Here we review some recent results concerning the extensive lateral gene transfer which appears to have occurred during NCLDV evolution. Current data suggest that giant viruses probably originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. A large array of lateral gene transfers from diverse cellular sources, including several families of mobile genetic elements, is probably responsible for the huge diversity of genome size and composition found in extant giant viruses.

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure

DNA rearrangements are important in genome function and evolution. Genetic material can be rearranged inadvertently during processes such as DNA repair, or can be moved in a controlled manner by enzymes specifically dedicated to the task. DNA transposases comprise one class of such enzymes. These move DNA segments known as transposons to new locations, without the need for sequence homology between transposon and target site. Several biochemically distinct pathways have evolved for DNA transposition, and genetic and biochemical studies have provided valuable insights into many of these. However, structural information on transposases - particularly with DNA substrates - has proven elusive in most cases. On the other hand, large-scale genome sequencing projects have led to an explosion in the number of annotated prokaryotic and eukaryotic mobile elements. Here, we briefly review biochemical and mechanistic aspects of DNA transposition, and propose that integrating sequence information with structural information using bioinformatics tools such as secondary structure prediction and protein threading can lead not only to an additional level of understanding but possibly also to testable hypotheses regarding transposition mechanisms. Detailed understanding of transposition pathways is a prerequisite for the long-term goal of exploiting DNA transposons as genetic tools and as a basis for genetic medical applications.

Structure, function, and evolution of the Thiomonas spp. genome

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.

Irradiation-induced Deinococcus radiodurans genome fragmentation triggers transposition of a single resident insertion sequence

Stress-induced transposition is an attractive notion since it is potentially important in creating diversity to facilitate adaptation of the host to severe environmental conditions. One common major stress is radiation-induced DNA damage. Deinococcus radiodurans has an exceptional ability to withstand the lethal effects of DNA–damaging agents (ionizing radiation, UV light, and desiccation). High radiation levels result in genome fragmentation and reassembly in a process which generates significant amounts of single-stranded DNA. This capacity of D. radiodurans to withstand irradiation raises important questions concerning its response to radiation-induced mutagenic lesions. A recent study analyzed the mutational profile in the thyA gene following irradiation. The majority of thyA mutants resulted from transposition of one particular Insertion Sequence (IS), ISDra2, of the many different ISs in the D. radiodurans genome. ISDra2 is a member of a newly recognised class of ISs, the IS200/IS605 family of insertion sequences.

Induction of transposition in prokaryotes under cell stress conditions is potentially important in creating diversity facilitating adaptation to severe environments. In Deinococcus radiodurans, the most radiation-resistant organism known, despite abundance of resident insertion sequences (IS), transposition of a single IS, ISDra2, was found to be strongly induced by irradiation. We show that both steps involved in transposition, IS excision, and insertion, increase significantly following host cell irradiation and, using PCR analysis of genomic DNA, that exposure to γ-irradiation stimulates massive excision of the single genomic ISDra2 copy as a DNA circle and reclosure of the empty site. These events are closely correlated with the initiation of the process leading to genome reassembly from chromosomal fragments, which occurs mainly through a mechanism generating long stretches of single-stranded DNA. Consistent with this, we also demonstrate a requirement for single strand DNA substrates in TnpA-catalysed cleavage and strand transfer in vitro. Since we find no evidence for irradiation-induced expression of the ISDra2 transposase, we infer that transposition is triggered by the increase in its single-strand DNA substrate. The potential impact on genome reassembly and in creating genome host diversity by triggering transposition in this way is discussed.

ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes

Insertion sequences (ISs) are among the smallest and simplest autonomous transposable elements. ISfinder (http://www-is.biotoul.fr/) is a dedicated IS database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. Online tools are gradually being added. At present, it is difficult to visualize the global distribution of ISs in a given bacterial genome. Such information would facilitate understanding of the impact of these small transposable elements on shaping their host genome. Here we describe ISbrowser (http://www-genome.biotoul.fr/ISbrowser.php), an extension to the ISfinder platform and a tool which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes.

Resetting the site: redirecting integration of an insertion sequence in a predictable way

Target site choice is a complex and poorly understood aspect of DNA transposition despite its importance in rational transposon-mediated gene delivery. Though most transposons choose target sites essentially randomly or with some slight sequence or structural preferences, insertion sequence IS608 from Helicobacter pylori, which transposes using single-stranded DNA, always inserts just 3' of a TTAC tetranucleotide. Our results from studies on the IS608 transposition mechanism demonstrated that the transposase recognizes its target site by co-opting an internal segment of transposon DNA and utilizes it for specific recognition of the target sites through base-pairing. This suggested a way to redirect IS608 transposition to novel target sites. As we demonstrate here, we can now direct insertions in a predictable way into a variety of different chosen target sequences, both in vitro and in vivo.