Search

Background Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Results A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within ‘Hongyang’ The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned ‘Hort16A’ cDNAs and comparing with the predicted protein models for Red5 and both the original ‘Hongyang’ assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised ‘Hongyang’ annotation, respectively, compared with 90.9% to the Red5 models. Conclusions Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4656-3) contains supplementary material, which is available to authorized users.

Accessible summary Social support has positive and negative dimensions, each of which has been associated with mental health outcomes. Social networks can also serve as sources of distress and conflict. This paper reviews journal articles published during the last 24 years to provide a consolidated summary of the role of social support and social conflict on immigrant women's mental health. The review reveals that social support can help immigrant women adjust to the new country, prevent depression and psychological distress, and access care and services. When social support is lacking or social networks act as a source of conflict, it can have negative effects on immigrant women's mental health. It is crucial that interventions, programmes, and services incorporate strategies to both enhance social support as well as reduce social conflict, in order to improve mental health and well-being of immigrant women. Abstract Researchers have documented the protective role of social support and the harmful consequences of social conflict on physical and mental health. However, consolidated information about social support, social conflict, and mental health of immigrant women in Canada is not available. This scoping review examined literature from the last 24 years to understand how social support and social conflict affect the mental health of immigrant women in Canada. We searched MEDLINE, PsycINFO, CINAHL, Healthstar, and EMBASE for peer-reviewed publications focusing on mental health among immigrant women in Canada. Thirty-four articles that met our inclusion criteria were reviewed, and are summarized under the following four headings: settlement challenges and the need for social support; social support and mental health outcomes; social conflict and reciprocity; and social support, social conflict, and mental health service use. The results revealed that social support can have a positive effect on immigrant women's mental health and well-being, and facilitate social inclusion and the use of health services. When social support is lacking or social networks act as a source of conflict, it can have negative effects on immigrant women's mental health. The results also highlighted the need for health services to be linguistically-appropriate and culturally-safe, and provide appropriate types of care and support in a timely manner in order to be helpful to immigrant women.

This article emerges from a scoping review of over two decades of relevant literature on immigrants' access to mental health services in Canada. Key online databases were searched to explore the gaps and opportunities for improving access to mental health services using a review framework provided by Arksey and O'Malley (Int J Soc Res Methodol 8:19-32, 2005). Immigrants and refugees came from diverse religious and cultural backgrounds and had complex mental health-related concerns that were not currently being adequately addressed by existing services. The major barriers to the utilization of mental health services included: those related to the uptake of existing health information and services; those that were related to the process of immigrant settlement; and barriers related to availability of appropriate services. A thematic analysis of the range of recommendations that emerge from these studies for improvement of research, practice and policy is provided.

Motivation Knowledge of haplotypes, i.e. phased and ordered marker alleles on a chromosome, is essential to answer many questions in genetics and genomics. By generating short pieces of DNA sequence, high-throughput modern sequencing technologies make estimation of haplotypes possible for single individuals. In polyploids, however, haplotype estimation methods usually require deep coverage to achieve sufficient accuracy. This often renders sequencing-based approaches too costly to be applied to large populations needed in studies of Quantitative Trait Loci. Results We propose a novel haplotype estimation method for polyploids, TriPoly, that combines sequencing data with Mendelian inheritance rules to infer haplotypes in parent-offspring trios. Using realistic simulations of both short and long-read sequencing data for banana (Musa acuminata) and potato (Solanum tuberosum) trios, we show that TriPoly yields more accurate progeny haplotypes at low coverages compared to existing methods that work on single individuals. We also apply TriPoly to phase Single Nucleotide Polymorphisms on chromosome 5 for a family of tetraploid potato with 2 parents and 37 offspring sequenced with an RNA capture approach. We show that TriPoly haplotype estimates differ from those of the other methods mainly in regions with imperfect sequencing or mapping difficulties, as it does not rely solely on sequence reads and aims to avoid phasings that are not likely to have been passed from the parents to the offspring. Availability and implementation TriPoly has been implemented in Python 3.5.2 (also compatible with Python 2.7.3 and higher) and can be freely downloaded at https://github.com/EhsanMotazedi/TriPoly. Supplementary information Supplementary data are available at Bioinformatics online.

Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy. During kiwifruit development SVP2 has a role in growth inhibition, with high-chill kiwifruit Actinidia deliciosa transgenic lines overexpressing SVP2 showing suppressed bud outgrowth. Transcriptomic analyses of these plants suggests that SVP2 mimics the well-documented abscisic acid (ABA) effect on the plant dehydration response. To corroborate the growth inhibition role of SVP2 in kiwifruit development at the molecular level, we analysed the genome-wide direct targets of SVP2 using chromatin immunoprecipitation followed by high-throughput sequencing in kiwifruit A. chinensis. SVP2 was found to bind to at least 297 target sites in the kiwifruit genome, and potentially modulates 252 genes that function in a range of biological processes, especially those involved in repressing meristem activity and ABA-mediated dehydration pathways. In addition, our ChIP-seq analysis reveals remarkable conservation in mechanism of action between SVP genes of taxonomically distant plant species.

Cerebral ischemia has been clearly demonstrated after traumatic brain injury (TBI); however, neuroprotective therapies have not focused on improvement of the cerebral microcirculation. Blood soluble drag-reducing polymers (DRP), prepared from high molecular weight polyethylene oxide, target impaired microvascular perfusion by altering the rheological properties of blood and, until our recent reports, has not been applied to the brain. We hypothesized that DRP improve cerebral microcirculation and oxygenation after TBI. DRP were studied in healthy and traumatized rat brains and compared to saline controls. Using in-vivo two-photon laser scanning microscopy over the parietal cortex, we showed that after TBI, nanomolar concentrations of intravascular DRP significantly enhanced microvascular perfusion and tissue oxygenation in peri-contusional areas, preserved blood–brain barrier integrity and protected neurons. The mechanisms of DRP effects were attributable to reduction of the near-vessel wall cell-free layer which increased near-wall blood flow velocity, microcirculatory volume flow, and number of erythrocytes entering capillaries, thereby reducing capillary stasis and tissue hypoxia as reflected by a reduction in NADH. Our results indicate that early reduction in CBF after TBI is mainly due to ischemia; however, metabolic depression of contused tissue could be also involved.

During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid, AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis &times, A. eriantha) &times, A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

This article analyses the problem-solving networks of young refugee women from Somalia between the ages of 13 and 19 through the concepts of ‘muted voice’ and ‘silence’. Based on life history interviews and participant observation with young refugee women living in the Eastleigh neighbourhood of Nairobi in 2011 and 2012, it investigates the ways in which young Somali women exercise their individual agency through carefully selected strategies of silence and muted voice as conscious forms of agency. The research finds that they rarely use their voice in naming and speaking out about their daily hardships, meaning they do not practice the obvious forms of agency that ‘voice’ implies. Instead, these young women gained strength and personal power through their network-type relationships with other young refugee women in the form of ‘muted voice’, meaning they exhibited a strategic capacity to determine when to speak and when to remain silent in the face of the daily oppression they experience, usually at the ...

Cold storage (2–4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS. A distance matrix for potato clones based on glucose levels after cold storage was constructed and compared to distance matrices constructed using RNA-seq gene expression data. Congruence between glucose and gene expression distance matrices was tested for each gene. Correlation between glucose and gene expression was also tested. Seventy-three genes were found that had significant p values in the congruence and correlation tests. Twelve genes from the list of 73 genes also had a high correlation between glucose and gene expression as measured by Nanostring nCounter. The gene annotations indicated functions in protein degradation, nematode resistance, auxin transport, and gibberellin response. These 12 genes were used to build models for prediction of CIS using multiple linear regression. Nine linear models were constructed that used different combinations of the 12 genes. An F-box protein, cellulose synthase, and a putative Lax auxin transporter gene were most frequently used. The findings of this study demonstrate the utility of gene expression profiles in predictive diagnostics for severity of CIS.

In the early 1990s, Rwanda was devastated by civil war and genocide. From April to July 1994, an interim government lead by ethnic Hutu extremists implemented the systematic murder of almost three-quarters of Rwanda’s ethnic Tutsi minority as well as ethnic Hutu who did not support the plan for genocide. The genocide of at least 500,000 ethnic Tutsi took place in the context of a civil war that began in October 1990, when the then-rebel Rwandan Patriotic Front (RPF) entered Rwanda from its base in Uganda. The genocide ended in mid-July with the RPF’s total victory. It too committed widespread and systematic murder of ethnic Hutu civilians before and during the 1994 genocide. Owing to its gravity, the Rwandan genocide generated intense international interest, which, in turn, shapes how foreign authors have understood its causes and consequences. Initial comment immediately following the genocide often identified “ethnic hatred” or “tribalism” as its root cause. Among nonspecialist and popular writing on the genocide, the idea of tribalism as a root cause remains pervasive today. Scholars, journalists, and human rights agencies have sought to debunk the notion that ethnic hatred is what drove the 1994 genocide—addressing the “tribalism” argument is a central theme in academic and popular literatures. The literature on Rwanda’s post-genocide reconstruction and reconciliation policies is more polarized, divided generally between those who praise the government for its economic growth and human development policies and those who criticize its human rights record. Much of the literature on the Rwandan genocide is published in English, which marks a break from the predominantly French-language scholarly literature on Rwanda before 1994. The lack of pre-genocide literature in English means that many well-intentioned and capable authors have sometimes failed to address the historically relevant details so essential to understanding Rwandan society. Lack of historical depth also means that some authors rely on politicized interpretations of ethnicity and statehood that, in turn, legitimate the current RPF government’s interpretation of how the genocide happened, and what needs to be done to rebuild the country. This matters because of Rwanda’s highly politicized research environment, which has, in turn, created a polarized post-genocide literature that praises or pillories the ruling RPF. Acknowledging this politicized terrain matters because it shapes what is written on Rwanda, and who is able or willing to do so. See also the separate Oxford Bibliographies article Rwanda.

Current treatments for traumatic brain injury (TBI) have not focused on improving microvascular perfusion. Drag-reducing polymers (DRP), linear, long-chain, blood-soluble, nontoxic macromolecules, may offer a new approach to improving cerebral perfusion by primary alteration of the fluid dynamic properties of blood. Nanomolar concentrations of DRP have been shown to improve hemodynamics in animal models of ischemic myocardium and ischemic limb, but have not yet been studied in the brain. We recently demonstrated that DRP improved microvascular perfusion and tissue oxygenation in a normal rat brain. We hypothesized that DRP could restore microvascular perfusion in hypertensive brain after TBI. Using in vivo two-photon laser scanning microscopy we examined the effect of DRP on microvascular blood flow and tissue oxygenation in hypertensive rat brains with and without TBI. DRP enhanced and restored capillary flow, decreased microvascular shunt flow, and, as a result, reduced tissue hypoxia in both nontraumatized and traumatized rat brains at high intracranial pressure. Our study suggests that DRP could constitute an effective treatment for improving microvascular flow in brain ischemia caused by high intracranial pressure after TBI.

In planta the enzymatic activity of apoplastic and vacuolar invertases is controlled by inhibitory proteins. Although these invertase inhibitors (apoplastic and vacuolar forms) have been implicated as contributing to resistance to cold-induced sweetening (CIS) in tubers of potato (Solanum tuberosum L.), there is a lack of information on the structure and allelic diversity of the apoplastic invertase inhibitor genes. We have PCR-isolated and sequenced the alleles of the apoplastic invertase inhibitor gene (Stinh1) from three tetraploid potato genotypes: 1021/1 (a genotype with very high tolerance to CIS), 'Karaka' and 'Summer Delight' (two cultivars that are highly susceptible to CIS). In total, five alleles were identified in these genotypes, of which four (Stinh1-c, Stinh1-d, Stinh1-e, Stinh1-f) were novel. An analysis of allele diversity was conducted by incorporating previously published sequences of apoplastic invertase inhibitors from potato. Eight alleles were assessed for sequence polymorphism in the two exons and the single hypervariable intron. Contrary to the hypervariable intron, only 65 single nucleotide polymorphisms were observed in the exons, of which 42 confer amino acid substitutions. Phylogenetic analysis of amino acid sequences indicates that the alleles of the invertase inhibitor are highly conserved amongst members of the Solanaceae family.

Awareness of the sexual exploitation of children and adolescents is growing in the United States. Yet, very few studies have examined successful treatment options and outcomes for this population. In response to this gap, this descriptive case study provides a brief history of treatment programs for sexually exploited adolescent girls at a residential treatment center in New England, followed by detailed information about the admission process, treatment protocol, daily life, and outcomes of the most recent group home program. Compared with an earlier treatment program at the same facility, during its first year of operation this group home had a 78% decrease in the number of young women who failed to complete treatment goals due to running away, hospitalization or incarceration (p =

Comparing pre- and post-genocide Rwanda, this article argues that clear continuities exist between the regimes of Juvénal Habyarimana and Paul Kagame. Both have projected a remarkably similar image of ‘benevolent leadership’. Presenting themselves as harbingers of an ‘improved’ or ‘new’ Rwanda, both leaderships have claimed to be best able and willing to guide Rwanda along the right path to peace, security, ethnic unity and development. ‘Benevolent leadership’ in both periods has also served as a tool to try and shape regime relationships with international and domestic audiences. Internationally, each government has worked to promote Rwanda and its authorities as a good development partner. Domestically, these projections have served to establish norms of order and obedience. We argue that projections of ‘benevolent leadership’ have been a tool designed to win over the international community and discipline the Rwandan population.

��� This article argues that the gacaca courts represent the darker side of transitional justice in seeking to impose a specific form of justice and reconciliation on its intended beneficiaries –Rwandans who lived through the violence of the genocide. My purpose is to illuminate the formal structures of power that shape individual participation before the gacaca courts to nuance the general consensus that local justice is better than its international counterpart. Analysis of the power dynamics behind Rwanda’s gacaca courts not only illustrates the near-total state control of the process, but also provides a bottom-up analysis that centres the lived-through experiences of violence of those individuals who survived it as a critical, yet largely absent, component of the transitional justice toolkit –of national and international actors alike. While international donors and diplomats recognize that implementing an effective transitional justice strategy is a formidable challenge given the intimacy, scale and sheer brutality of the 1994 genocide, they fail to appreciate adequately the power relations that structure individual participation in traditional justice mechanisms like gacaca –which they praise as a model for other post-conflict societies to emulate in re-establishing the rule of law through trust, truth telling and access to justice for all (UN-OHRLLS 2006: 130). An impressive body of literature heralds the gacaca courts as a viable alternative to punitive, procedural, Western-style justice (for example, Clark 2010; Longman 2006; Meyerstein 2007; Venter 2007). These glowing assessments are based on the idea that gacaca is a local, traditional and restorative judicial mechanism– rather than on the way that the gacaca process, as a key part of a broader regime of state power defined by the post-genocide government’s policy of national unity and reconciliation, actually plays out in the lives of ordinary people. While it is currently fashionable among many scholars of transitional justice to praise locally forged and culturally relative justice as more effective and legitimate, such claims are made without knowing nearly enough about the broader power dynamics that influence local justice mechanisms like gacaca. Without a local-level perspective, grounded in the individual lived experiences of participants in the gacaca processes, the darker side of how the courts work in practice at the level of the everyday person is hidden from view. This is because international academics and journalists laud the outcomes of gacaca–ending impunity and promoting reconciliation –as national policy accomplishments rather than recognizing gacaca as central to a state-run legal system that produces

Residential treatment for troubled adolescents continues to generate controversy. Youth may improve during treatment, but are these gains sustained upon return to the community? We explore this question by analyzing outcome data collected at three months and one year post-discharge for 49 adolescent girls discharged from long-term programs at a residential treatment center in Massachusetts. Qualitative data reveals the range of post-discharge challenges experienced by adolescents and their families. Quantitative data shows a 77% reduction in restrictive level of care placements comparing the year before admission to the year after discharge (p < .001). This success rate suggests that improvements accomplished during long-term residential treatment are sustained by a majority of adolescent girls up to at least one year post-discharge. We will also discuss the process we used to collect outcome data and its impact on our agency staff and clientele.

The government in post-genocide Rwanda stakes its moral claim to legitimacy on a policy of national unity and reconciliation, claiming to create a ‘Rwanda for all Rwandans’. This article investigates peasant resistance to this policy. Focusing on everyday acts of resistance among the rural poor, it demonstrates that despite the appearance of widespread popular support, many peasant Rwandans consider the various mechanisms of national unity and reconciliation to be unjust and illegitimate. Obedience to the dictates of the policy of national unity is frequently tactical, rather than sincere, as peasants employ various strategies to avoid participation. Through a focus on everyday acts of resistance, the article reveals how the post-genocide state through the policy of national unity and reconciliation seeks to depoliticize peasant people by orchestrating public performances and by closing off the possibility for individuals to join together to organize politically.

Resume Cet article se penche les gestes quotidiens de resistance des Rwandais ordinaires vis-a-vis de la politique d’unite nationale et de reconciliation mise en place par le gouvernement a la suite du genocide. Il suit trois formes de resistance au quotidien – le positionnement en marge, le conformisme irreverent, le mutisme detache, adoptees par certains lorsqu’ils interagissent, evitent ou se confrontent aux exigences etatiques liees cette politique. L’article conclut que, pour certains Rwandais, cette politique ne produit qu’un semblant d’unite et de reconciliation au quotidien.

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas

David E. Kiwuwa has written an ambitious book that seeks to theorize transitions from war to democratic governance in deeply divided ethnic societies. To do so, he employs the case-study method to ...

1 In this article, we untangle the relationships among law, power and justice as they impact on the lives of ordinary Rwandans brought into contact with the state and local officials through the gacaca process. Drawing on 37 life-history interviews conducted in 2006, we find that gacaca reinforces a particular version of postgenocide justice that renders the average Rwandan citizen largely powerless over individual processes of reconciliation while serving to maintain a climate of fear and insecurity in their everyday lives. Locating the Rwandan case more broadly, we caution that a preoccupation with harmonizing traditional justice with international standards must look beyond forms of legality. While gacaca may be legally acceptable in a harmonized way, it is both a product and a producer of relations of state power that operate to impact negatively on conflict-affected individuals who bear the brunt of government-led initiatives to promote justice and reconciliation.

Research with people in highly politicized research settings illuminates the gap between the images that most African governments strive to represent and the sociopolitical realities of everyday life. This article discusses the opportunities and challenges of doing research in postgenocide Rwanda and is a useful resource for researchers contemplating their own projects under such conditions, whether in Rwanda or elsewhere. It discusses the importance of creating personal relationships and meeting people on their terms, as well as such topics as the identification of the research site, building rapport and trust with respondents, safeguarding anonymity and confidentiality, and working with local research assistants and partners.

Network Endpoint Assessment (NEA) is a set of protocols allowing an enterprise to automatically check a device's compliance with security policy when it attaches to the network. Compliance checks might specify, for example, that critical security patches and antivirus software are installed and up-to-date.

In this article, I argue that the political commitment of senior politicians to fight HIV/AIDS needs to be understood contextually by both analysts and practitioners. By this, I mean that progressive policy must be analysed with an appreciation of local power dynamics and household gender relations as well as within the broader socio-political climate in which HIV/AIDS services are delivered, something that donors and other international partners rarely do. Drawing on life history interviews conducted in 2006 with thirty-seven ordinary Rwandans, and using James Scott's concept of "state simplifications," I illuminate the politics behind who gets what kind of HIV/AIDS treatment in post-genocide Rwanda. Specifically, I focus on the politics of civil society membership and the nature of everyday interactions with local officials to illustrate the some of the ways in which the government's claims of universal access are a source of insecurity and vulnerability for HIV/AIDS affected individuals.

My [local official] doesn't understand that my people died because of the events [of 1994] and that I have even more problems that need solutions, since they say peace and unity have been restored....

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

A novel, commercially available reverse hybridization assay [GenoType Mycobacteria Direct (GTMD), version 2.0; Hain Lifescience] was evaluated for the direct detection of five clinically relevant mycobacterial species [Mycobacterium tuberculosis complex (MTBC), Mycobacterium avium, Mycobacterium malmoense, Mycobacterium kansasii and Mycobacterium intracellulare] from 54 smear-positive respiratory specimens and the findings were compared with culture results. Three approaches were used for specimen preparation using either whole or ‘split’ sample volumes and N-acetyl-l-cysteine/3 % NaOH or 4 % NaOH as decontamination chemicals. Forty-three out of 52 samples in which RNA amplification was successful gave GTMD results that concurred with the identification of the cultured isolate. All cases of MTBC were detected. Twenty-two samples contained M. tuberculosis complex, seven had M. kansasii, four had M. malmoense, seven contained atypical mycobacteria other than those detectable using the GTMD assay and three specimens contained no viable mycobacteria. The assay is easy to use and can be completed in one working day. Results interpretation is facilitated by the inclusion of an internal amplification control with each sample to allow identification of specimens containing amplification inhibitors. A positive GTMD result will quickly identify patients with MTBC infection or provide specific identification of four other atypical mycobacteria from the same specimen. This allows more rapid drug susceptibility testing, treatment, and public health and infection control decisions.

The Mental Health Commission of Canada’s (MHCC) strategy calls for promoting the health and wellbeing of all Canadians and to improve mental health outcomes. Each year, one in every five Canadians experiences one or more mental health problems, creating a significant cost to the health system. Mental health is pivotal to holistic health and wellbeing. This paper presents the key findings of a comprehensive literature review of Canadian research on the relationship between settlement experiences and the mental health and well-being of immigrants and refugees. A scoping review was conducted following a framework provided by Arskey and O’Malley (Int J Soc Res Methodol 8:19–32, 2005). Over two decades of relevant literature on immigrants’ health in Canada was searched. These included English language peer-reviewed publications from relevant online databases Medline, Embase, PsycInfo, Healthstar, ERIC and CINAHL between 1990 and 2015. The findings revealed three important ways in which settlement affects the mental health of immigrants and refugees: through acculturation related stressors, economic uncertainty and ethnic discrimination. The recommendations for public health practice and policy are discussed.

Background Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population ‘DMDD’ derived from the recently sequenced genome ‘DM’ represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation. Results Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male–female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as ‘compressed’, ‘round’, ‘oblong’, and ‘long-oblong’ mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as ‘obovoid’, ‘elliptic’, and ‘elongated’ were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified. Conclusions Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0213-0) contains supplementary material, which is available to authorized users.

Introduction: Current treatments for ischemia after stroke have not focused directly on the physiological effects of restoring or improving cerebral microvascular perfusion. Nanomolar concentrations of drag-reducing polymers (DRP) have been shown to improve hemodynamics and survival in animal models of the ischemic myocardium and peripheral circulation. We recently demonstrated that DRP improved microvascular perfusion in normal and traumatized rat brain. We hypothesized that DRP restores microvascular perfusion after focal ischemia and improves neurologic recovery in the rat. Methods: The suture permanent middle cerebral artery occlusion (MCAO) model in the rat was used. DRP was injected i.v. 90 minutes after MCAO. Controls were injected with an equal volume of saline. Using in vivo 2-photon laser scanning microscopy over the parietal cortex, we studied the acute effects of DRP on microvascular blood flow velocity, tissue oxygenation (NADH) and blood brain barrier (BBB) permeability for 5 hr after MCAO. Doppler cortical flow, rectal and cranial temperatures, arterial pressure, blood gases and electrolytes were monitored. Cerebral infarction was evaluated by triphenyltetrazolium chloride (TTC) staining 24 hr after MCAO and motor function by Rotarod at one week. Results: MCAO resulted in a progressive decrease in microvascular flow in the penumbra of the parietal cortex with hypoxia and increased BBB permeability during 5 hr monitored. DRP partially restored microvascular flow compared to control (21±6.7%, Mean ± SEM, p Conclusions: DRP restores cerebral microvascular flow after MCAO reducing tissue hypoxia and BBB damage. The improvement in flow is reflected by a reduction in infarct size 24 hours after MCAO and by improved motor neurological recovery at one week after MCAO. DRP can be a new effective therapy for ischemic stroke targeting microvascular perfusion.

During the initial stages of vertebrate retinogenesis, cells of the optic vesicle adopt one of two alternate cell fates. Cells in the distal-most part of the vesicle, immediately beneath the surface ectoderm, undergo neural differentiation; cells in the proximal part differentiate into retinal pigmented epithelial cells. The mechanisms that establish this pattern of differentiation are poorly understood. In the mouse embryo, Msx2, a homeobox-containing transcription factor, is expressed in cells of the optic vesicle that will form the neural retina, whilst the developing retinal pigmented epithelium (RPE) does not express this gene. Msx2 could therefore be involved in patterning the optic vesicle into neural and pigmented domains. To explore this possibility we ectopically expressed mouse Msx2 in cultures of chick RPE cells. Compared with cultures transfected with a control construct, Msx2-transfected cultures contained fewer cells expressing the RPE marker, Mitf, and more cells expressing class III β-tubulin, a neuronal marker. In addition a small proportion of Msx2-transfected cells acquired a neural-like morphology. These results show that Msx2 can suppress the differentiated state of RPE cells and promote their differentiation into neural cell types. We suggest that Msx2 may pattern the optic vesicle into neural and pigmented domains by affecting the balance between RPE and neural retina differentiation.

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new similar to 936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal pseudomolecules. Potato Genome Sequencing grant, UK; Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS); Department for Environment, Food and Rural Affairs (DEFRA)Department for Environment, Food & Rural Affairs (DEFRA); Agriculture and Horticulture Development Board (AHDB)-Potato Council; Biotechnology and Biological Sciences Research Council (BBSRC)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative; New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs); CBSG (Centre for BioSystems Genomics); STW (Netherlands Technology Foundation), The Netherlands [07796]; Teagasc Core Funding; DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYTComision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) [Fondap 1509007, PBCT-PSD-03]; CONICYT (Basal CMM); CIRIC INRIA; INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA [PE/09/02 MINCyT-CONCyTEC]; Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds); Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA [SEDI/AE-305 /09]; Proyecto Bilateral Argentina, Per; FINCyT [099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008)]; Prestamo BID [1663/OC-PE]; Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru; Peruvian Ministry of Agriculture, Technical Secretariat of coordination; CGIAR; Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC); Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru); Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640/1] We thank Andrzej Kilian (Diversity Arrays Technology, Australia) for DArT genotyping of the DMDD mapping population. We acknowledge Peter E. Hedley and Clare Booth (The James Hutton Institute, UK) for help with SNP genotyping. We thank S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) for technical assistance. We are also grateful to Luke Ramsay and Peter E. Hedley (The James Hutton Institute, UK) for comments on the manuscript. AFLP and WGP are (registered) trademarks owned by KeyGene N.V. We acknowledge the funding made available by the Potato Genome Sequencing grant, UK [Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board (AHDB)-Potato Council, Biotechnology and Biological Sciences Research Council (BBSRC, Grant BB/F012640)]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative and the New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation grant 07796), The Netherlands; Teagasc Core Funding, DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds) and Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA SEDI/AE-305 /09 (2008-2012), Proyecto Bilateral Argentina, Per; FINCyT (099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008), Prestamo BID no. 1663/OC-PE, Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru, Peruvian Ministry of Agriculture, Technical Secretariat of coordination with the CGIAR, Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC), Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru).

Onion and garlic are renowned for their roles as functional foods. The health benefits of garlic are attributed to di-2-propenyl thiosulfinate (allicin), a sulfur compound found in disrupted garlic but not found in disrupted onion. Recently, onions have been grown with repressed lachrymatory factor synthase (LFS) activity, which causes these onions to produce increased amounts of di-1-propenyl thiosulfinate, an isomer of allicin. This investigation into the key health attributes of LFS-silenced (tearless) onions demonstrates that they have some attributes more similar to garlic and that this is likely due to the production of novel thiosulfinate or metabolites. The key finding was that collagen-induced in vitro platelet aggregation was significantly reduced by tearless onion extract over normal onion extract. Thiosulfinate or derived compounds were shown not to be responsible for the observed changes in the inflammatory response of AGS (stomach adenocarcinoma) cells to tumor necrosis factor alpha (TNFα) when pretreated with model onion juices. A preliminary rat feeding trial indicated that the tearless onions may also play a key role in reducing weight gain.

Background GSL1 and GSL2, Gibberellin Stimulated-Like proteins (also known as Snakin-1 and Snakin-2), are cysteine-rich peptides from potato (Solanum tuberosum L.) with antimicrobial properties. Similar peptides in other species have been implicated in diverse biological processes and are hypothesised to play a role in several aspects of plant development, plant responses to biotic or abiotic stress through their participation in hormone crosstalk, and redox homeostasis. To help resolve the biological roles of GSL1 and GSL2 peptides we have undertaken an in depth analysis of the structure and expression of these genes in potato. Results We have characterised the full length genes for both GSL1 (chromosome 4) and GSL2 (chromosome 1) from diploid and tetraploid potato using the reference genome sequence of potato, coupled with further next generation sequencing of four highly heterozygous tetraploid cultivars. The frequency of SNPs in GSL1 and GSL2 were very low with only one SNP every 67 and 53 nucleotides in exon regions of GSL1 and GSL2, respectively. Analysis of comprehensive RNA-seq data substantiated the role of specific promoter motifs in transcriptional control of gene expression. Expression analysis based on the frequency of next generation sequence reads established that GSL2 was expressed at a higher level than GSL1 in 30 out of 32 tissue and treatment libraries. Furthermore, both the GSL1 and GSL2 genes exhibited constitutive expression that was not up regulated in response to biotic or abiotic stresses, hormone treatments or wounding. Potato transformation with antisense knock-down expression cassettes failed to recover viable plants. Conclusions The potato GSL1 and GSL2 genes are very highly conserved suggesting they contribute to an important biological function. The known antimicrobial activity of the GSL proteins, coupled with the FPKM analysis from RNA-seq data, implies that both genes contribute to the constitutive defence barriers in potatoes. The lethality of antisense knock-down expression of GSL1 and GSL2, coupled with the rare incidence of SNPs in these genes, suggests an essential role for this gene family. These features are consistent with the GSL protein family playing a role in several aspects of plant development in addition to plant defence against biotic stresses.

We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. ‘Bolting’, or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima’s D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large ‘Nasik Red × CUDH2150’ F2 family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F2 families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.

Academic literature rarely gives an account of the ‘story behind the findings’, meaning the ethical challenges and emotional pitfalls that you, the researcher, are confronted with before, during and after the field experience. These quagmires have a potentially profound impact upon both the research process and its findings. They deserve proper attention, not only to fathom the inevitable bias in researchers’ position in the field and to assess the quality of the research findings, but also to illustrate that the facade of ‘scientific validity and neutrality’ often hides a pragmatic approach that has shaped the empirical research process. As Wilkinson writes, ‘both as social scientists and as human beings, we have a responsibility to “tell it as it happened,” rather than how we would have liked it to be’ (2008, p. 60). Acknowledging this does not degrade the quality and value of empirical data; instead, it places the results of field research into broader socio-political context regardless of the academic discipline that produced the findings.

In September 2006, just six months into my planned year-long period of fieldwork in southern Rwanda (April 2006–2007), the government of Rwanda stopped my research. At the end of August 2006, following a long day of interviews at the prison in Butare town, the Director summoned me to his office, demanding that I share the names of the prisoners I spoke to in the course of my nearly three weeks visiting his prison on a daily basis. My initial agreement with the Director was that I would speak to the two prison Heads and as many prisoners as they could identify who might be willing to speak to me about their lives during and after the 1994 genocide. I spoke to 24 prisoners in total, with nine agreeing to multiple life interviews. I specifically asked for the Heads of Prisoners for both men and women to identify prisoners who might be willing to talk to, rather than submitting a generic request for prisoners to the Director to identify potential respondents. This put a layer of distance between the prisoners and the Director, particularly since I did not record the demographic information of any of the prisoners I spoke to as a safeguard to ensure confidentiality. When the Director of Butare prison asked me to give the names of those I spoke to, I only had a list of their initials, their alleged crimes and age during the genocide.

BackgroundAlthough modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers.ResultsWe report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepaL.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2progeny from a very large F2family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis.ConclusionsThe generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

The Glauconitic formation is a Cretaceous age sandstone reservoir located across a large area of central Alberta, Canada. Discovered in the late 1970’s, hydraulically fractured vertical wells could produce commercial volumes of natural gas from some of the higher permeability conventional sands. However, wide spread development of the majority of the tight gas sands was not economic with vertical wells. With the introduction of multiple fractured horizontal well (MFHW) technology in recent years, and much better definition of the geology, a large unconventional resource play has developed in the Glauconitic, which could contain in excess of 5 tcf of gas in place plus associated natural gas liquids (Scotia Capital, 2009). A pilot project was designed to test the completion effectiveness between a cased and cemented liner and an open hole packer system in this tight gas reservoir. Two vertical microseismic observation wells were located in close proximity to two proposed horizontal wellbores, giving ideal conditions to test how the hydraulic fractures would grow and the ultimate fracture geometry, from two different completion methods. In this paper we will present the microseismic results of the pilot project, as well as the early production history comparison between the two wells, and the hydraulic fracture effectiveness from a reservoir engineering aspect.