Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

Background: The amphiploid species Brassica napus (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types), 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results: Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions: The distribution of chloroplast haplotypes eliminates any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast haplotypes in B. napus and B. rapa accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within B. napus can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to B. napus occurred on more than one occasion, and involved different maternal genotypes

Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal

Standardized gene nomenclature for the Brassica genus

The genus Brassica (Brassicaceae, Brassiceae) is closely related to the model plant Arabidopsis, and includes several important crop plants. Against the background of ongoing genome sequencing, and in line with efforts to standardize and simplify description of genetic entities, we propose a standard systematic gene nomenclature system for the Brassica genus. This is based upon concatenating abbreviated categories, where these are listed in descending order of significance from left to right (i.e. genus – species – genome – gene name – locus – allele). Indicative examples are provided, and the considerations and recommendations for use are discussed, including outlining the relationship with functionally well-characterized Arabidopsis orthologues. A Brassica Gene Registry has been established under the auspices of the Multinational Brassica Genome Project that will enable management of gene names within the research community, and includes provisional allocation of standard names to genes previously described in the literature or in sequence repositories. The proposed standardization of Brassica gene nomenclature has been distributed to editors of plant and genetics journals and curators of sequence repositories, so that it can be adopted universally

Elevated ACKR2 expression is a common feature of inflammatory arthropathies

Objectives. Chemokines are essential contributors to leucocyte accumulation at sites of inflammatory pathology. Interfering with chemokine or chemokine receptor function therefore represents a plausible therapeutic option. However, our currently limited understanding of chemokine orchestration of inflammatory responses means that such therapies have not yet been fully developed. We have a particular interest in the family of atypical chemokine receptors that fine-tune, or resolve, chemokine-driven responses. In particular we are interested in atypical chemokine receptor 2 (ACKR2), which is a scavenging receptor for inflammatory CC-chemokines and that therefore helps to resolve in vivo inflammatory responses. The objective of the current study was to examine ACKR2 expression in common arthropathies. Methods. ACKR2 expression was measured by a combination of qPCR and immuno-histochemistry. In addition, circulating cytokine and chemokine levels in patient plasma were assessed using multiplexing approaches. Results. Expression of ACKR2 was elevated on peripheral blood cells as well as on leucocytes and stromal cells in synovial tissue. Expression on peripheral blood leucocytes correlated with, and could be regulated by, circulating cytokines with particularly strong associations being seen with IL-6 and hepatocyte growth factor. In addition, expression within the synovium was coincident with aggregates of lymphocytes, potentially atopic follicles and sites of high inflammatory chemokine expression. Similarly increased levels of ACKR2 have been reported in psoriasis and SSc. Conclusion. Our data clearly show increased ACKR2 in a variety of arthropathies and taking into account our, and others’, previous data we now propose that elevated ACKR2 expression is a common feature of inflammatory pathologies

A SQUAMOSA MADS-box gene involved in the regulation of anthocyanin accumulation in bilberry fruits

Anthocyanins are important health promoting phytochemicals that are abundant in many fleshy fruits. Bilberry (Vaccinium myrtillus L.) is one of the best sources of these compounds. Here we report on the expression pattern and functional analysis of a SQUAMOSA (SQUA) class MADS-box transcription factor, VmTDR4, associated with anthocyanin biosynthesis in bilberry. Levels of VmTDR4 expression were spatially and temporally linked with colour development and anthocyanin-related gene expression. Virus induced gene silencing (VIGS) was used to suppress VmTDR4 expression in bilberry resulting in substantial reduction in anthocyanin levels in fully ripe fruits. Chalcone synthase was used a positive control in the VIGS experiments. Additionally, in sectors of fruit tissue in which the expression of the VmTDR4 gene was silenced, the expression of R2R3 MYB family transcription factors related to the biosynthesis of flavonoids were also altered. We conclude that VmTDR4 plays an important role in the accumulation of anthocyanins during normal ripening in bilberry; probably through direct or indirect control of transcription factors belonging to the R2R3 MYB family

A serological investigation of caseous lymphadenitis in four flocks of sheep

A double antibody sandwich ELISA developed by ID-DLO, Lelystad to detect Corynebocterium pseudotuberculosis infection was used on 329 sheep from four pedigree Suffolk flocks in which clinical cases of caseous lymphadenitis (CLA) had occurred. At subsequent necropsy, typical CLA lesions were seen in 133 sheep, and the diagnosis was confirmed on culture. Lesions were most commonly seen in lungs (n = 46), parotid lymph nodes (n = 44), prescapular lymph nodes (n = 38) and mediastinal lymph nodes (n = 31). The sensitivity of the ELISA test for detecting culture-positive sheep was 0.88, while the specificity of the test was 0.55. The antibody ELISA detected 87.5 per cent of sheep that had CLA lesions restricted to internal organs only. It was concluded that the ELISA test has a valuable role in detecting sheep with both clinical and subclinical CLA

Multi-scale Structural Analysis of the A-site and Oxygen Deficient Perovskite Sr11Mo4O2

The long range average crystal structure, as well as the short and medium range structural features, of the A-site deficient and oxygen deficient perovskite Sr11Mo4O23 have been determined. Rietveld refinement of synchrotron X-ray and neutron powder diffraction data show that this compound is cubic with space group Fd-3m and a lattice parameter of a = 16.4108 Å. These findings contradict earlier reports of a tetragonal crystal structure. Sr11Mo4O23 appears to be isostructural with Ba11W4O23, except that the disordered coordination environment around one of the Mo sites seems to be a mixture of octahedral and square pyramidal instead of octahedral and tetrahedral. The short and medium range structural features have been inspected using the neutron pair distribution function (PDF). Short range correlations between the oxygen polyhedra surrounding the Mo(2) atom exist to avoid short O–O contacts. A model has been constructed which contains such correlations and is verified by reverse Monte Carlo (RMC) modeling of the PDF. The RMC refinements also give the distribution of inter-atomic distances in this compound which reveals how the various atomic positions are correlated and over what length scales. These results are important for understanding the ionic conduction pathways.Australian Research Counci

Assessing supply-side barriers to uptake of intermittent preventive treatment for malaria in pregnancy: A qualitative study and document and record review in two regions of Uganda

Background: Intermittent preventive treatment in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP), provided as part of routine antenatal care (ANC), is one of three malaria-in-pregnancy prevention and control mechanisms recommended by the World Health Organization (WHO). However, despite high ANC attendance and increased efforts to address known obstacles, IPTp uptake figures have remained low. This study aimed to identify and assess barriers that continue to impede IPTp uptake in Uganda, in particular for women who attend ANC. The paper focuses on supply-side barriers, i.e., challenges relating to the health service provider. Methods: In-depth interviews were conducted in two regions of Uganda in November 2013 and April/May 2014 with four different target audiences: seven district health officials, 15 health workers, 19 women who had attended ANC, and five opinion leaders. In addition, a document and record review was carried out at four health facilities. Results: Guidelines with regard to IPTp provision in Uganda have been shown to be inconsistent and, at the time of the research, did not reflect the most recent WHO policy recommendation. There is a lack of training and supervision opportunities for health workers, resulting in poor knowledge of IPTp guidelines and uncertainty about the safety and efficacy of SP. ANC is not consistently offered in health facilities, leading to some women being denied services. While strengthening of the supply chain appears to have reduced the occurrence of stock-outs of SP in public facilities, stock-outs reportedly continue to occur in the private sector. There are also sources of data inaccuracy along the data recording and reporting chain, limiting policy makers' ability to react adequately to trends and challenges. Conclusions: Given the high ANC attendance rates in Uganda, supply-side barriers are likely to account for many missed opportunities for the provision of IPTp in Uganda. Improvements will require consistent provision of ANC, implementation of current WHO IPTp policy recommendations, supply of SP to the private sector, availability of clear guidelines, as well as improved training and supervision for health workers. Improving facility and district-level recording and reporting will further strengthen the country's ability to address uptake of IPTp

Role of angiopoietin-like protein 3 in sugar-induced dyslipidemia in rhesus macaques: suppression by fish oil or RNAi.

Angiopoietin-like protein 3 (ANGPTL3) inhibits lipid clearance and is a promising target for managing cardiovascular disease. Here we investigated the effects of a high-sugar (high-fructose) diet on circulating ANGPTL3 concentrations in rhesus macaques. Plasma ANGPTL3 concentrations increased ∼30% to 40% after 1 and 3 months of a high-fructose diet (both P < 0.001 vs. baseline). During fructose-induced metabolic dysregulation, plasma ANGPTL3 concentrations were positively correlated with circulating indices of insulin resistance [assessed with fasting insulin and the homeostatic model assessment of insulin resistance (HOMA-IR)], hypertriglyceridemia, adiposity (assessed as leptin), and systemic inflammation [C-reactive peptide (CRP)] and negatively correlated with plasma levels of the insulin-sensitizing hormone adropin. Multiple regression analyses identified a strong association between circulating APOC3 and ANGPTL3 concentrations. Higher baseline plasma levels of both ANGPTL3 and APOC3 were associated with an increased risk for fructose-induced insulin resistance. Fish oil previously shown to prevent insulin resistance and hypertriglyceridemia in this model prevented increases of ANGPTL3 without affecting systemic inflammation (increased plasma CRP and interleukin-6 concentrations). ANGPTL3 RNAi lowered plasma concentrations of ANGPTL3, triglycerides (TGs), VLDL-C, APOC3, and APOE. These decreases were consistent with a reduced risk of atherosclerosis. In summary, dietary sugar-induced increases of circulating ANGPTL3 concentrations after metabolic dysregulation correlated positively with leptin levels, HOMA-IR, and dyslipidemia. Targeting ANGPTL3 expression with RNAi inhibited dyslipidemia by lowering plasma TGs, VLDL-C, APOC3, and APOE levels in rhesus macaques