Genomic consequences associated with Agrobacterium-mediated transformation of plants

Attenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium-mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant-microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long-read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium-mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large-scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.

Impact of war on veteran life span: natural experiment involving combat versus non-combat exposed military personnel

INTRODUCTION

There is still uncertainty around the impact of combat exposure on the life span of war veterans. Therefore we made use of a natural experiment to study the impact on veteran life span of combat versus non-combat exposure in World War II (WW2).

METHODS

The combat-exposed military personnel were derived from a random (10%) sample of the military roll of the 28th (Māori) Battalion from New Zealand. One non-combat cohort was the 15th Reinforcements of this same Battalion, since the war ended before they reached the front line. The other non-combat cohort were Māori personnel who were only involved in Jayforce, which occupied Japan at the end of the WW2. Data on life span were mainly derived from an official repository of birth and death records, but supplemented with other sources, including military files.

RESULTS

When comparing life spans of service veterans, there was no statistically significant reduction for the average life span of the 234 combat-exposed veterans in our sample from the 28th (Māori) Battalion (66.7 years), relative to the Māori veterans from two non-combat cohorts: the 132 personnel in the 15th Reinforcements (67.2 years) and the 147 personnel in Jayforce (66.9 years).

CONCLUSIONS

Despite a very high level of wounding in the combat-exposed group (48%), there were no statistically significant reductions in life span between this group and comparable non-combat exposed veterans. This finding contrasts to life span reductions found in a similar study of New Zealand veterans of WW1.

Regulation of gene editing using T-DNA concatenation

Transformation via Agrobacterium tumefaciens is the predominant method used to introduce exogenous DNA into plant genomes1,2. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in complex concatenated forms3,4, but the mechanisms affecting final T-DNA structure remain unknown. Here we demonstrate that inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase T-DNA copy number by more than 50-fold in Arabidopsis thaliana. These additional T-DNA copies are organized into large concatemers, an effect primarily induced by the long terminal repeats (LTRs) of RTs that can be replicated using non-LTR DNA repeats. We found that T-DNA concatenation is dependent on the activity of the DNA repair proteins MRE11, RAD17 and ATR. Finally, we show that T-DNA concatenation can be used to increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA concatenation for plant gene editing.

Induction of T-DNA amplification by retrotransposon-derived sequences

Transformation via Agrobacterium tumefaciens (Agrobacterium) is the predominant method used to introduce exogenous DNA into plants. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in concatenated forms in plant genomes, but the mechanisms affecting final T-DNA structure remain unknown. In this study, we demonstrate that the inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase transgene copy number by more than 50-fold in Arabidopsis thaliana (Arabidopsis). RT-mediated amplification of T-DNA results in large concatemers in the Arabidopsis genome, which are primarily induced by the long terminal repeats (LTRs) of RTs. T-DNA amplification is dependent on the activity of DNA repair proteins associated with theta-mediated end joining (TMEJ). Finally, we show that T-DNA amplification can increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA amplification for plant gene editing.

Differential lifespan impacts on veterans by war exposure in the First World War

INTRODUCTION

There remains uncertainty around the impact of war on the lifespan of First World War (WW1) veterans. In particular, study comparison groups do not typically consider the 'healthy soldier effect'.

METHODS

We obtained lifespan data on a random sample of 857 war-exposed New Zealand WW1 veterans and compared this with lifespans of a non-war military cohort (n=1039). This comparison was possible as the non-war-cohort arrived in Europe too late to participate in the war, allowing a 'natural experiment' that avoided the 'healthy solider effect'.

RESULTS

The lifespan comparisons indicated lower mean lifespan in the war-exposed veteran cohort compared with the non-war veteran cohort (69.7 vs 71.1 years; p=0.0405). This gap persisted (range: 0.8-1.1 years) but was no longer statistically significant when only considering the non-Māori ethnic grouping (nearly all European/Pākehā personnel), when excluding additional deaths in the immediate postwar period up to 31 December 1923, and when excluding participation in any other wars. This was the case in both analysis of variance and Cox proportional hazards regression adjusting for year of birth and occupational status. Within the war-exposed cohort, there were suggestive patterns of increasing lifespan with increasing occupational status and military rank (eg, 69.5, 70.0 and 70.7 mean years as group-level occupational status progressively increased). There were also stark differences in lifespan of 8.3 years between Māori (Indigenous) and non-Māori veterans (p=0.0083).

CONCLUSIONS

The pattern of reduced lifespan in war-exposed versus non-war-exposed veterans was compatible with a smaller previous New Zealand study with comparable methodology. Veterans who were Māori had significantly lower lifespans than non-Māori veterans. There are a number of feasible avenues to further improve this type of work with existing data sources.

MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression

Flowering of the reference legume Medicago truncatula is promoted by winter cold (vernalization) followed by long-day photoperiods (VLD) similar to winter annual Arabidopsis. However, Medicago lacks FLC and CO, key regulators of Arabidopsis VLD flowering. Most plants have two INHIBITOR OF GROWTH (ING) genes (ING1 and ING2), encoding proteins with an ING domain with two anti-parallel alpha-helices and a plant homeodomain (PHD) finger, but their genetic role has not been previously described. In Medicago, Mting1 gene-edited mutants developed and flowered normally, but an Mting2-1 Tnt1 insertion mutant and gene-edited Mting2 mutants had developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes, and smaller seeds and barrels. Mting2 mutants had reduced expression of activators of flowering, including the FT-like gene MtFTa1, and increased expression of the candidate repressor MtTFL1c, consistent with the delayed flowering of the mutant. MtING2 overexpression complemented Mting2-1, but did not accelerate flowering in wild type. The MtING2 PHD finger bound H3K4me2/3 peptides weakly in vitro, but analysis of gene-edited mutants indicated that it was dispensable to MtING2 function in wild-type plants. RNA sequencing experiments indicated that >7000 genes are mis-expressed in the Mting2-1 mutant, consistent with its strong mutant phenotypes. Interestingly, ChIP-seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutants compared to wild type R108. Overall, our mutant study has uncovered an important physiological role of a plant ING2 gene in development, flowering, and gene expression, which likely involves an epigenetic mechanism.

NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects

BACKGROUND

The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization.

RESULTS

We present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allow their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest.

CONCLUSION AND AVAILABILITY

NODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis . The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE .

The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication

The tail of replication-dependent histone H3.1 varies from that of replication-independent H3.3 at the amino acid located at position 31 in plants and animals, but no function has been assigned to this residue to demonstrate a unique and conserved role for H3.1 during replication. We found that TONSOKU (TSK/TONSL), which rescues broken replication forks, specifically interacts with H3.1 via recognition of alanine 31 by its tetratricopeptide repeat domain. Our results indicate that genomic instability in the absence of ATXR5/ATXR6-catalyzed histone H3 lysine 27 monomethylation in plants depends on H3.1, TSK, and DNA polymerase theta (Pol θ). This work reveals an H3.1-specific function during replication and a common strategy used in multicellular eukaryotes for regulating post-replicative chromatin maturation and TSK, which relies on histone monomethyltransferases and reading of the H3.1 variant.

Experiencing loneliness in parenthood: a scoping review

AIMS

Chronic loneliness is experienced by around a third of parents, but there is no comprehensive review into how, why and which parents experience loneliness. This scoping review aimed to provide insight into what is already known about parental loneliness and give directions for further applied and methodological research.

METHODS

Searches for peer-reviewed articles were undertaken in six databases: PsycINFO, Medline, CINAHL, Embase, Web of Science and Scopus, during May 2019 to February 2020. We searched for English studies which examined loneliness experienced during parenthood, including studies that involved parents with children under 16 years and living at home and excluding studies on pregnancy, childbirth or postbirth hospital care.

RESULTS

From 2566 studies retrieved, 133 were included for analysis. Most studies (n = 80) examined the experience of loneliness in specific groups of parents, for example, teenage parents, parents of a disabled child. Other studies examined theoretical issues (n = 6) or health and wellbeing impacts on parents (n = 16) and their offspring (n = 17). There were 14 intervention studies with parents that measured loneliness as an outcome. Insights indicate that parental loneliness may be different to loneliness experienced in other cohorts. There is evidence that parental loneliness has direct and intergenerational impacts on parent and child mental health. Some parents (e.g. with children with chronic illness or disability, immigrant or ethnic minority parents) also appear to be at increased risk of loneliness although evidence is not conclusive.

CONCLUSION

This work has identified key gaps with further international, comparative and conceptual research needed.

The Candidate Photoperiod Gene MtFE Promotes Growth and Flowering in Medicago truncatula

Flowering time influences the yield and productivity of legume crops. Medicago truncatula is a reference temperate legume that, like the winter annual Arabidopsis thaliana, shows accelerated flowering in response to vernalization (extended cold) and long-day (LD) photoperiods (VLD). However, unlike A. thaliana, M. truncatula appears to lack functional homologs of core flowering time regulators CONSTANS (CO) and FLOWERING LOCUS C (FLC) which act upstream of the mobile florigen FLOWERING LOCUS T (FT). Medicago truncatula has three LD-induced FT-like genes (MtFTa1, MtFTb1, and MtFTb2) with MtFTa1 promoting M. truncatula flowering in response to VLD. Another photoperiodic regulator in A. thaliana, FE, acts to induce FT expression. It also regulates the FT transport pathway and is required for phloem development. Our study identifies a M. truncatula FE homolog Medtr6g444980 (MtFE) which complements the late flowering fe-1 mutant when expressed from the phloem-specific SUCROSE-PROTON SYMPORTER 2 (SUC2) promoter. Analysis of two M. truncatula Tnt1 insertional mutants indicate that MtFE promotes flowering in LD and VLD and growth in all conditions tested. Expression of MtFTa1, MtFTb1, and MtFTb2 are reduced in Mtfe mutant (NF5076), correlating with its delayed flowering. The NF5076 mutant plants are much smaller than wild type indicating that MtFE is important for normal plant growth. The second mutant (NF18291) displays seedling lethality, like strong fe mutants. We searched for mutants in MtFTb1 and MtFTb2 identifying a Mtftb2 knock out Tnt1 mutant (NF20803). However, it did not flower significantly later than wild type. Previously, yeast-two-hybrid assays (Y2H) suggested that Arabidopsis FE interacted with CO and NUCLEAR FACTOR-Y (NF-Y)-like proteins to regulate FT. We found that MtFE interacts with CO and also M. truncatula NF-Y-like proteins in Y2H experiments. Our study indicates that despite the apparent absence of a functional MtCO-like gene, M. truncatula FE likely influences photoperiodic FT expression and flowering time in M. truncatula via a partially conserved mechanism with A. thaliana.

Tokophobia and fear of birth: a workshop consensus statement on current issues and recommendations for future research

Objective: To discuss and develop a statement on the current state of the evidence and opinion in Fear of Childbirth (FoC) and Tokophobia (Tocophobia), and to provide recommendations. Background: A group met in 2019 to discuss the state of clinical and academic knowledge relating to FoC/Tokophobia. Five key areas were agreed as the focus of the meeting. Methods: 12 internationally acknowledged experts, in this or a closely related area (e.g. PTSD) met to discuss their understanding of the evidence for FoC/ Tokophobia and current practice. The consensus described in this paper constitutes the expression of the general opinion of the participants and does not necessarily imply unanimity. Keys points: Work focussed on tokophobia is recent and there remains a wide range of issues, which were addressed in the workshop including complexity in defining prevalence, a theoretical lack of understanding, which creates challenge for robust assessment and the identification of risk factors. An improved aetiological and developmental understanding of the tokophobia is required to underpin appropriate, effective and evidence-based interventions. Evaluation of pathways of care and relevant interventions, should be a focus of future research. Conclusion: Significant gaps remain within the FoC/tokophobia knowledge base. Further research is necessary.

Overexpression of Medicago MtCDFd1_1 Causes Delayed Flowering in Medicago via Repression of MtFTa1 but Not MtCO-Like Genes

Optimizing flowering time is crucial for maximizing crop productivity, but gaps remain in the knowledge of the mechanisms underpinning temperate legume flowering. Medicago, like winter annual Arabidopsis, accelerates flowering after exposure to extended cold (vernalization, V) followed by long-day (LD) photoperiods. In Arabidopsis, photoperiodic flowering is triggered through CO, a photoperiodic switch that directly activates the FT gene encoding a mobile florigen and potent activator of flowering. In Arabidopsis, several CYCLING DOF FACTORs (CDFs), including AtCDF1, act redundantly to repress CO and thus FT expression, until their removal in LD by a blue-light-induced F-BOX1/GIGANTEA (FKF1/GI) complex. Medicago possesses a homolog of FT, MtFTa1, which acts as a strong activator of flowering. However, the regulation of MtFTa1 does not appear to involve a CO-like gene. Nevertheless, work in pea suggests that CDFs may still regulate flowering time in temperate legumes. Here, we analyze the function of Medicago MtCDF genes with a focus on MtCDFd1_1 in flowering time and development. MtCDFd1_1 causes strong delays to flowering when overexpressed in Arabidopsis and shows a cyclical diurnal expression in Medicago with peak expression at dawn, consistent with AtCDF genes like AtCDF1. However, MtCDFd1_1 lacks predicted GI or FKF1 binding domains, indicating possible differences in its regulation from AtCDF1. In Arabidopsis, CDFs act in a redundant manner, and the same is likely true of temperate legumes as no flowering time phenotypes were observed when MtCDFd1_1 or other MtCDFs were knocked out in Medicago Tnt1 lines. Nevertheless, overexpression of MtCDFd1_1 in Medicago plants resulted in late flowering relative to wild type in inductive vernalized long-day (VLD) conditions, but not in vernalized short days (VSDs), rendering them day neutral. Expression of MtCO-like genes was not affected in the transgenic lines, but LD-induced genes MtFTa1, MtFTb1, MtFTb2, and MtSOC1a showed reduced expression. Plants carrying both the Mtfta1 mutation and 35S:MtCDFd1_1 flowered no later than the Mtfta1 plants. This indicates that 35S:MtCDFd1_1 likely influences flowering in VLD via repressive effects on MtFTa1 expression. Overall, our study implicates MtCDF genes in photoperiodic regulation in Medicago by working redundantly to repress FT-like genes, particularly MtFTa1, but in a CO-independent manner, indicating differences from the Arabidopsis model.

The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula

Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.

Perceptions of European medical staff on the facilitators and barriers to physical closeness between parents and infants in neonatal units

Aim

Studies have provided insights into factors that may facilitate or inhibit parent–infant closeness in neonatal units, but none have specifically focused on the perspectives of senior neonatal staff. The aim of this study was to explore perceptions and experiences of consultant neonatologists and senior nurses in five European countries with regard to these issues.

Methods

Six small group discussions and three‐one‐to‐one interviews were conducted with 16 consultant neonatologists and senior nurses representing nine neonatal units from Estonia, Finland, Norway, Spain and Sweden. The interviews explored facilitators and barriers to parent–infant closeness and implications for policy and practice, and thematic analysis was undertaken.

Results

Participants highlighted how a humanising care agenda that enabled parent–infant closeness was an aspiration, but pointed out that neonatal units were at different stages in achieving this. The facilitators and barriers to physical closeness included socio‐economic factors, cultural norms, the designs of neonatal units, resource issues, leadership, staff attitudes and practices and relationships between staff and parents.

Conclusion

Various factors affected parent–infant closeness in neonatal units in European countries. There needs to be the political motivation, appropriate policy planning, legislation and resource allocation to increase measures that support closeness agendas in neonatal units.

MtVRN2 is a Polycomb VRN2-like gene which represses the transition to flowering in the model legume Medicago truncatula

Optimising the timing of flowering contributes to successful sexual reproduction and yield in agricultural plants. FLOWERING LOCUS T (FT) genes, first identified in Arabidopsis thaliana (Arabidopsis), promote flowering universally, but the upstream flowering regulatory pathways can differ markedly among plants. Flowering in the model legume, Medicago truncatula (Medicago) is accelerated by winter cold (vernalisation) followed by long day (LD) photoperiods leading to elevated expression of the floral activator, FT-like gene FTa1. However, Medicago, like some other plants, lacks the activator CONSTANS (CO) and the repressor FLOWERING LOCUS C (FLC) genes which directly regulate FT and are key to LD and vernalisation responses in Arabidopsis. Conversely, Medicago has a VERNALISATION2-LIKE VEFS-box gene (MtVRN2). In Arabidopsis AtVRN2 is a key member of a Polycomb complex involved in stable repression of Arabidopsis FLC after vernalisation. VRN2-like genes have been identified in other eudicot plants, but their function has never been reported. We show that Mtvrn2 mutants bypass the need for vernalisation for early flowering in LD conditions in Medicago. Investigation of the underlying mechanism by transcriptome analysis reveals that Mtvrn2 mutants precociously express FTa1 and other suites of genes including floral homeotic genes. Double-mutant analysis indicates that early flowering is dependent on functional FTa1. The broad significance of our study is that we have demonstrated a function for a VRN2-like VEFS gene beyond the Brassicaceae. In particular, MtVRN2 represses the transition to flowering in Medicago by regulating the onset of expression of the potent floral activator, FTa1.

An integrative review exploring decision-making factors influencing mental health nurses in the use of restraint

WHAT IS KNOWN ON THE SUBJECT?: There is emerging evidence highlighting the counter therapeutic impact of the use of restraint and promoting the minimization of this practice in mental health care. Mental health nurses are often the professional group using restraint and understanding factors influencing their decision-making becomes critical. To date, there are no other published papers that have undertaken a similar broad search to review this topic. WHAT THIS PAPER ADDS TO EXISTING KNOWLEDGE?: Eight emerging themes are identified as factors influencing mental health nurses decisions-making in the use of restraint. The themes are: 'safety for all', 'restraint as a necessary intervention', 'restraint as a last resort', 'role conflict', 'maintaining control', 'staff composition', 'knowledge and perception of patient behaviours', and 'psychological impact'. 'Last resort' appears to be the mantra of acceptable restraint use, although, to date, there are no studies that specifically consider what this concept actually is. WHAT ARE THE IMPLICATIONS FOR PRACTICE?: These findings should be considered in the evaluation of the use of restraint in mental health settings and appropriate strategies placed to support shifting towards restraint minimization. As the concept of 'last resort' is mentioned in many policies and guidelines internationally with no published understanding of what this means, research should prioritize this as a critical next step in restraint minimization efforts.

INTRODUCTION

While mechanical and manual restraint as an institutional method of control within mental health settings may be perceived to seem necessary at times, there is emergent literature highlighting the potential counter-therapeutic impact of this practice for patients as well as staff. Nurses are the professional group who are most likely to use mechanical and manual restraint methods within mental health settings. In-depth insights to understand what factors influence nurses' decision-making related to restraint use are therefore warranted.

AIM

To explore what influences mental health nurses' decision-making in the use of restraint.

METHOD

An integrative review using Cooper's framework was undertaken.

RESULTS

Eight emerging themes were identified: 'safety for all', 'restraint as a necessary intervention', 'restraint as a last resort', 'role conflict', 'maintaining control', 'staff composition', 'knowledge and perception of patient behaviours', and 'psychological impact'. These themes highlight how mental health nurses' decision-making is influenced by ethical and safety responsibilities, as well as, interpersonal and staff-related factors.

CONCLUSION

Research to further understand the experience and actualization of 'last resort' in the use of restraint and to provide strategies to prevent restraint use in mental health settings are needed.

Positive selection in glycolysis among Australasian stick insects

BACKGROUND

The glycolytic pathway is central to cellular energy production. Selection on individual enzymes within glycolysis, particularly phosphoglucose isomerase (Pgi), has been associated with metabolic performance in numerous organisms. Nonetheless, how whole energy-producing pathways evolve to allow organisms to thrive in different environments and adopt new lifestyles remains little explored. The Lanceocercata radiation of Australasian stick insects includes transitions from tropical to temperate climates, lowland to alpine habitats, and winged to wingless forms. This permits a broad investigation to determine which steps within glycolysis and what sites within enzymes are the targets of positive selection. To address these questions we obtained transcript sequences from seven core glycolysis enzymes, including two Pgi paralogues, from 29 Lanceocercata species.

RESULTS

Using maximum likelihood methods a signature of positive selection was inferred in two core glycolysis enzymes. Pgi and Glyceraldehyde 3-phosphate dehydrogenase (Gaphd) genes both encode enzymes linking glycolysis to the pentose phosphate pathway. Positive selection among Pgi paralogues and orthologues predominately targets amino acids with residues exposed to the protein's surface, where changes in physical properties may alter enzyme performance.

CONCLUSION

Our results suggest that, for Lancerocercata stick insects, adaptation to new stressful lifestyles requires a balance between maintaining cellular energy production, efficiently exploiting different energy storage pools and compensating for stress-induced oxidative damage.

Efficacy of dexmedetomidine compared with midazolam for sedation in adult intensive care patients: a systematic review

Patients in Intensive Care Unit (ICU) often require sedatives which commonly include midazolam and the more recently developed α2-receptor agonist, dexmedetomidine. It was our aim to compare the sedative and clinical effectiveness of dexmedetomidine vs midazolam in adults admitted to ICU, using an objective appraisal of randomized control trials. Medline, Embase, SCOPUS, Web of Knowledge, Cinhal, the United States National Library of Medicine, and the Cochrane Database of Systematic Reviews were searched using keywords: 'dexmedetomidine', 'midazolam', and 'intensive care'. These were limited to human studies and adults (>18 yr old). Six randomized controlled trials were found and were critically appraised using a standardized appraisal method. Two papers described the time spent by each intervention group within a specified target sedation range and both found no statistically significant difference between midazolam and dexmedetomidine (P=0.18 and P=0.15). A third paper found no statistically significant difference in the length of time that patients were sedated within a target zone (P=0.445). Two additional pilot studies did not report P values as they were insufficiently statistically powered. A final paper found that, of the eight occasions measured, patients on dexmedetomidine were more often within the target sedation range than patients on midazolam. The sedative benefits of dexmedetomidine vs midazolam remain inconclusive. While some secondary outcomes showed clinical effectiveness of dexmedetomidine, more research is needed to validate the findings of these studies.

Responders to insulin therapy at 18 months in adults with newly diagnosed diabetes: which insulin regimen?

OBJECTIVES

To describe baseline characteristics of responders to insulin therapy (HbA(1c) targets < 58 mmol/mol, 7.5%) at 18 months among adults with newly diagnosed diabetes.

METHODS

A retrospective UK study derived from 479 general practices electronic dataset. We included all adults (age > 18 years) with newly diagnosed diabetes who required insulin therapy within 6 months of diagnosis. The data comprised insulin regimen (long-acting only; premixed insulin only; basal bolus insulin regimen), gender, Townsend quintile, baseline and an 18-month measurement of clinical and biochemical variables. Multiple imputations were undertaken and logistic regression used to assess the effect of covariates.

RESULTS

A total of 1492 patients (aged 19-93 years) were analysed. Means (SD) baseline HbA(1c) and BMI were 10.3% (2.6%) and 29.6 (7.0%), respectively. Following multiple imputation for missing data, logistic regression analysis indicated important covariates to achieve HbA(1c) targets were baseline HbA(1c), lipid lowering therapy, gender and age. Including all covariates, those treated with premixed insulin were 47% more likely to achieve target HbA(1c) at 18 months than those treated with a basal-bolus regimes (adjusted OR 1.47; 95% CI 1.12-1.92, P = 0.006)) and 32% more likely than those treated with long-acting insulin was (adjusted OR 1.32; 95% CI 1.01-1.74, P = 0.044). Those with a higher baseline HbA(1c) level, on lipid-lowering therapy, women and younger patients had a lower response rate. Mean weight gain (SD) was 2.4 kg (8.5 kg) and was not influenced by treatment regimen.

CONCLUSION

The use of premixed insulin regimen among newly diagnosed patients with diabetes appears to be most effective in reaching HbA(1c) target values, independent of other confounders. The appropriate choice of insulin regimen at initiation should therefore take into account various metabolic and psychosocial factors.

Identifying abnormalities in symbiotic development between Trifolium spp. and Rhizobium leguminosarum bv. trifolii leading to sub-optimal and ineffective nodule phenotypes

BACKGROUND AND AIMS

Legumes overcome nitrogen limitations by entering into a mutualistic symbiosis with N(2)-fixing bacteria (rhizobia). Fully compatible associations (effective) between Trifolium spp. and Rhizobium leguminosarum bv. trifolii result from successful recognition of symbiotic partners in the rhizosphere, root hair infection and the formation of nodules where N(2)-fixing bacteroids reside. Poorly compatible associations can result in root nodule formation with minimal (sub-optimal) or no (ineffective) N(2)-fixation. Despite the abundance and persistence of strains in agricultural soils which are poorly compatible with the commercially grown clover species, little is known of how and why they fail symbiotically. The aims of this research were to determine the morphological aberrations occurring in sub-optimal and ineffective clover nodules and to determine whether reduced bacteroid numbers or reduced N(2)-fixing activity is the main cause for the Sub-optimal phenotype.

METHODS

Symbiotic effectiveness of four Trifolium hosts with each of four R. leguminosarum bv. trifolii strains was assessed by analysis of plant yields and nitrogen content; nodule yields, abundance, morphology and internal structure; and bacteroid cytology, quantity and activity.

KEY RESULTS

Effective nodules (Nodule Function 83-100 %) contained four developmental zones and N(2)-fixing bacteroids. In contrast, Sub-optimal nodules of the same age (Nodule Function 24-57 %) carried prematurely senescing bacteroids and a small bacteroid pool resulting in reduced shoot N. Ineffective-differentiated nodules carried bacteroids aborted at stage 2 or 3 in differentiation. In contrast, bacteroids were not observed in Ineffective-vegetative nodules despite the presence of bacteria within infection threads.

CONCLUSIONS

Three major responses to N(2)-fixation incompatibility between Trifolium spp. and R. l. trifolii strains were found: failed bacterial endocytosis from infection threads into plant cortical cells, bacteroid differentiation aborted prematurely, and a reduced pool of functional bacteroids which underwent premature senescence. We discuss possible underlying genetic causes of these developmental abnormalities and consider impacts on N(2)-fixation of clovers.

Infection control practices in facilities for highly infectious diseases across Europe

BACKGROUND

The management of patients with highly infectious diseases (HIDs) is a challenge for healthcare provision requiring a high level of care without compromising the safety of other patients and healthcare workers.

AIM

To study the infection control practice in isolation facilities participating in the European Network for Highly Infectious Diseases (EuroNHID) project.

METHODS

A survey was conducted during 2009 of 48 isolation facilities caring for patients with HIDs in 16 European countries. Checklists and standard evaluation forms were used to collect and interpret data on hand hygiene, routine hygiene and disinfection, and waste management.

FINDINGS

Forty percent of HIDs had no non-hand-operated sinks or alcohol-based antiseptic distributors, while 27% did not have procedures for routine hygiene, final disinfection, or safe discarding of non-disposable objects or equipment. There was considerable variation in the management of waste and in the training of housekeeping personnel. EuroNHID has developed recommendations for hand hygiene, disinfection, routine hygiene, and waste management.

CONCLUSIONS

Most aspects of hand hygiene, routine hygiene and disinfection, and waste management were considered at least partially adequate in the majority of European isolation facilities dedicated for the care of patients with HIDs. But considerable variability was observed, with management of waste and training of housekeeping personnel being generally less satisfactory.

Framing obesity: the framing contest between industry and public health at the New Zealand inquiry into obesity

Drawing on submissions to the 2006-2007 New Zealand Inquiry into Obesity and Type 2 Diabetes, this article outlines how the food and marketing industries (industry) and the public health sector framed the issue of obesity. The analysis revealed that industry framed obesity as a consequence of poor lifestyle choices attributed largely to knowledge, cultural or other character deficits. Industry argued that lack of physical activity rather than increased food consumption was the dominant cause of obesity. In contrast, public health groups positioned obesity as a normal response to an obesogenic environment, characterized by the ubiquitous marketing and availability of low-cost, energy-dense/nutrient-poor foods. For public health groups, increased consumption of energy-dense/nutrient-poor foods was positioned as the dominant cause of obesity. Many public health submitters also suggested that social inequalities contributed to obesity. Industry emphasized education as the key solution to obesity, while public health groups argued for regulation of the activities of the food and marketing industries, and policies to address wider determinants of health and social inequalities. Identifying and documenting these frames, by making transparent the interests of the frame's sponsors, contributes to greater understanding of the wider policy context around obesity and provides useful information for public health advocacy.

A community standard for immunogenomic data reporting and analysis: proposal for a STrengthening the REporting of Immunogenomic Studies statement

Modern high-throughput HLA and KIR typing technologies are generating a wealth of immunogenomic data with the potential to revolutionize the fields of histocompatibility and immune-related disease association and population genetic research, much as SNP-based approaches have revolutionized association research. The STrengthening the REporting of Genetic Association studies (STREGA) statement provides community-based data reporting and analysis standards for genomic disease-association studies, identifying specific areas in which adoption of reporting guidelines can improve the consistent interpretation of genetic studies. While aspects of STREGA can be applied to immunogenomic studies, HLA and KIR research requires additional consideration, as the high levels of polymorphism associated with immunogenomic data pose unique methodological and computational challenges to the synthesis of information across datasets. Here, we outline the principle challenges to consistency in immunogenomic studies, and propose that an immunogenomic-specific analog to the STREGA statement, a STrengthening the REporting of Immunogenomic Studies (STREIS) statement, be developed as part of the 16th International HLA and Immunogenetics Workshop. We propose that STREIS extends at least four of the 22 elements of the STREGA statement to specifically address issues pertinent to immunogenomic data: HLA and KIR nomenclature, data-validation, ambiguity resolution, and the analysis of highly polymorphic genetic systems. As with the STREGA guidelines, the intent behind STREIS is not to dictate the design of immunogenomic studies, but to ensure consistent and transparent reporting of research, facilitating the synthesis of HLA and KIR data across studies.

Crimean-Congo hemorrhagic fever in Europe: current situation calls for preparedness

During the last decade Crimean-Congo hemorrhagic fever (CCHF) emerged and/or re-emerged in several Balkan countries, Turkey, southwestern regions of the Russian Federation, and the Ukraine, with considerable high fatality rates. Reasons for re-emergence of CCHF include climate and anthropogenic factors such as changes in land use, agricultural practices or hunting activities, movement of livestock that may influence host-tick-virus dynamics. In order to be able to design prevention and control measures targeted at the disease, mapping of endemic areas and risk assessment for CCHF in Europe should be completed. Furthermore, areas at risk for further CCHF expansion should be identified and human, vector and animal surveillance be strengthened.

Crimean-Congo hemorrhagic fever in Europe: current situation calls for preparedness

During the last decade Crimean-Congo hemorrhagic fever (CCHF) emerged and/or re-emerged in several Balkan countries, Turkey, southwestern regions of the Russian Federation, and the Ukraine, with considerable high fatality rates. Reasons for re-emergence of CCHF include climate and anthropogenic factors such as changes in land use, agricultural practices or hunting activities, movement of livestock that may influence host-tick-virus dynamics. In order to be able to design prevention and control measures targeted at the disease, mapping of endemic areas and risk assessment for CCHF in Europe should be completed. Furthermore, areas at risk for further CCHF expansion should be identified and human, vector and animal surveillance be strengthened.

Estimating missed government tax revenue from foreign tobacco: survey of discarded cigarette packs

AIM

To clarify the extent of use of foreign (including duty free, foreign normal retail and smuggled) tobacco, and to estimate missed government tax revenue in a geographically isolated country.

METHODS

Discarded cigarette packs were collected on the streets of four cities and six New Zealand towns/rural locations between November 2008 and January 2009.

RESULTS

Out of a total of 1310 packs collected, 42 foreign packs were identified (3.2%, 95% CI 2.4% to 4.3%). Overall, the distribution of packs by country and company was not suggestive of any clustering that might indicate smuggling. At 3.2% of packs being "foreign", the New Zealand government is losing around $36 million per year in tobacco-related tax relative to if all this tobacco was purchased in New Zealand. For various reasons (including that it was not possible to identify packs bought duty free within New Zealand, and other New Zealand survey data indicating duty free product use at 3.8% of packs), the figure reached is probably an underestimate of the true level.

CONCLUSION

The New Zealand government is missing out on revenue that could be used for improving the funding of tobacco control, and smokers are being exposed to cheaper tobacco thus increasing their risk of continuing to smoke. This government and other governments can and should act at the international and national levels to end the sales of duty free tobacco.

Analysis of maternal-offspring HLA compatibility, parent-of-origin and non-inherited maternal effects for the classical HLA loci in type 1 diabetes

AIM

Type 1 diabetes (T1D) is a complex trait for which variation in the classical human leucocyte antigen (HLA) loci within the Major Histocompatibility Complex (MHC) significantly influences disease risk. To date, HLA class II DR-DQ genes confer the strongest known genetic effect in T1D. HLA loci may also influence T1D through additional inherited or non-inherited effects. Evidence for the role of increased maternal-offspring HLA compatibility, and both parent-of-origin (POO) and non-inherited maternal HLA (NIMA) effects in autoimmune disease has been previously established. The current study tested hypotheses that classical HLA loci influence T1D through these mechanisms, in addition to genetic transmission of particular risk alleles.

METHODS

The Type 1 Diabetes Genetics Consortium (T1DGC) cohort was of European descent and consisted of 2271 affected sib-pair families (total n = 11 023 individuals). Class I genes HLA-A, Cw and B, and class II genes HLA-DRB1, DQA1, DQB1, DPA1 and DPB1 were studied. The pedigree disequilibrium test was used to examine transmission of HLA alleles to individuals with T1D. Conditional logistic regression was used to model compatibility relationships between mother-offspring and father-offspring for all HLA loci. POO and NIMA effects were investigated by comparing frequencies of maternal and paternal transmitted and non-transmitted HLA alleles for each locus. Analyses were also stratified by gender of T1D-affected offspring.

RESULTS

Strong associations were observed for all classical HLA loci except for DPA1, as expected. Compatibility differences between mother-offspring and father-offspring were not observed for any HLA loci. Furthermore, POO and NIMA HLA effects influencing T1D were not present.

CONCLUSIONS

Maternal-offspring HLA compatibility, POO and NIMA effects for eight classical HLA loci were investigated. Results suggest that these HLA-related effects are unlikely to play a major role in the development of T1D.

Several loci in the HLA class III region are associated with T1D risk after adjusting for DRB1-DQB1

AIM

Several studies have indicated that genes in the human leucocyte antigen (HLA) region additional to the HLA class II DRB1-DQB1 contribute to type 1 diabetes (T1D) susceptibility. The aim of this study was to assess if markers in the class III Major Histocompatibility Complex (MHC) region are associated with T1D after accounting for linkage disequilibrium (LD) with DRB1-DQB1.

METHODS

We investigated 356 single nucleotide polymorphisms (SNPs) in the class III region covering 1.1 megabases in two subsets of data: 289 Human Biological Data Interchange (HBDI) Caucasian families and 597 additional Caucasian families collected by the Type 1 Diabetes Genetics Consortium (T1DGC). Analysis conditioning on DRB1-DQB1 was performed using the overall conditional genotype method.

RESULTS

Thirteen SNPs replicated in both subsets of the data and showed evidence of an additional effect on disease risk. Although some of the SNPs are in tight LD with each other, at least six of the associations were not because of LD with other class III markers. The strongest association within class III markers was with rs2395106 that maps 5' to the NOTCH4 gene, which has also been implicated in susceptibility to rheumatoid arthritis. The second association was with rs707915 mapping to the MSH5 gene, in a block of six markers significantly associated with T1D after adjusting for LD with DR-DQ. In total, six-independent associations within class III were observed although results were not adjusted for LD with class I.

CONCLUSIONS

Our data confirm that the class III region is involved in T1D susceptibility and suggest that more than one gene in the region is involved.

Killing the canary: the international epidemiology of the homicide of media workers

OBJECTIVES

To describe the international epidemiology of the homicide of media workers, and investigate country-level risk factors.

METHODS

Data on the homicides occurring from 2002 to 2006 were collected and collated from five international databases. Analyses included consideration of seven existing international indices relating to human development, and to the social and political functioning of states.

RESULTS

During the 5-year period, 370 deaths in 54 countries met our definitions of homicides and media workers. Almost all (89%) were nationals of the country in which they died. The annual number of such homicides globally has more than doubled, from 41 in 2002 to 104 in 2006 (including 49 in Iraq in 2006). Less than 25% of the homicides of media workers over the last 5 years have resulted in an arrest or prosecution. Statistically significant associations (p<0.001; Political Terror Scores, OR 1.15; Corruption Perceptions Index, OR 0.53; Overall Failed State Index, OR 1.05; Failed State Index 7, OR 1.52; Failed State Index 9, OR 1.55; Failed State Index 10, OR 1.61) were found on logistic regression between the occurrence of the homicide of media workers in countries and scoring on six of the seven indices associated with country-level sociopolitical development. These indices reflected high levels of political terror and corruption, low government legitimisation, poor human rights, and uncontrolled armed groups. However, in terms of the homicide rate for countries, these associations were significant for only four of the seven indices (the general functionality of government, ability of governments to control armed groups, the level of political terror, and the level of violation of rights).

CONCLUSIONS

The homicide of media workers increased substantially in this 5-year period and was found to be particularly concentrated in selected countries such as Iraq. The authors were able to identify specific sociopolitical risk factors for homicide occurrence, and for homicide rates at the country level.

Public attitudes to laws for smoke-free private vehicles: a brief review

As smoke-free car policy is a frontier domain for tobacco control, attitudes to smoke-free private car laws are briefly reviewed. Medline and Google Scholar searches for the period up to mid-November 2008, from English language sources, were undertaken. Studies were included that contained data from national and subnational populations (eg, in states and provinces), but not for smaller administrative units, eg, cities or councils. Jurisdiction, sample size and survey questions were assessed. One reviewer conducted the data extraction and both authors conducted assessments. A total of 15 relevant studies (from 1988) were identified, set in North America, the UK and Australasia. The available data indicates that, for the jurisdictions with data, there is majority public support for laws requiring cars that contain children to be smoke free. There appears to be an increase over time in this support. In five surveys in 2005 or since (in California, New Zealand and Australia), the support from smokers was 77% or more. The high levels of public (and smoker) support for smoke-free car laws found in the studies to date suggest that this can be a relatively non-controversial tobacco control intervention. Survey series on attitudes to such laws are needed, and surveys in jurisdictions where the issue has not been investigated to date.

The changing epidemiology of infantile hypertrophic pyloric stenosis in Scotland

BACKGROUND

The aetiology of infantile hypertrophic pyloric stenosis (IHPS) has not been fully elucidated. Since the 1990s, a sharp decline in IHPS has been reported in various countries. Recent research from Sweden reported a correlation between falling rates of IHPS and of sudden infant death syndrome (SIDS). This was attributed to a reduction in the number of infants sleeping in the prone position following the "Back to Sleep" campaign.

OBJECTIVES

To describe the changing epidemiology of IHPS in Scotland, to examine the relationship between IHPS and SIDS rates and to examine trends in other factors that may explain the observed reduction in IHPS incidence.

DESIGN

Incidence rates of IHPS and SIDS were derived from routine data and their relationship analysed. Trends in mean maternal age, maternal smoking, mean birth weight and breastfeeding rates were also examined.

SETTING

The whole of Scotland between 1981 and 2004.

RESULTS

IHPS incidence fell from 4.4 to 1.4 per 1000 live births in Scotland between 1981 and 2004. Rates were consistently higher in males, although the overall incidence patterns in males and females were similar. Rates showed a positive relationship with deprivation. The fall in the incidence of IHPS preceded the fall in SIDS by 2 years and the incidence of SIDS displayed less variability than that of IHPS. Significant temporal trends were also observed in other maternal and infant characteristics.

CONCLUSION

There has been a marked reduction in Scotland's IHPS incidence, but this is unlikely to be a consequence of a change in infant sleeping position.

Building capacity for improved veterinary epidemiosurveillance in southern Africa

A workshop to produce recommendations on training requirements for improved epidemiosurveillance of livestock diseases in southern Africa was organised at the Department of Veterinary Tropical Diseases in the Veterinary Faculty of the University of Pretoria. It was attended by 23 persons representing 10 different southern African countries. The majority of the participants were actively involved in veterinary epidemiosurveillance and many of them were members of the SADC Epidemiology and Informatics Subcommittee. Discussions focused on (i) epidemiosurveillance networks and their 2 main components, i.e. (ii) diagnosis and (iii) information flow. The debates were guided by 3 questions; (i) what are the requirements for an effective network, (ii) what cannot be achieved with existing capacity and (iii) how can the current capacity be improved. Workshop participants developed lists of realistic capacity building needs, which were divided into structural needs and training requirements. Structural needs mainly concerned communication means and quality assurance. With regard to training, the need for appropriate continuing education of all actors at the various disease management levels (non-professional, para-professional, professional) was expressed. Special emphasis was put on capacity building at the lowest level, i.e. the livestock owner and the para-professionals at the community level. At the international level, it was felt that special emphasis should be put on building capacity to improve the understanding of international agreements on trade in animals and animal products and to improve the capacity of negotiating such agreements.