Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis

Background: Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. Results: A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. Conclusion: This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development

A mathematical model that simulates control options for African swine fever virus (ASFV)

A stochastic model designed to simulate transmission dynamics of African swine fever virus (ASFV) in a free-ranging pig population under various intervention scenarios is presented. The model was used to assess the relative impact of the timing of the implementation of different control strategies on disease-related mortality. The implementation of biosecurity measures was simulated through incorporation of a decay function on the transmission rate. The model predicts that biosecurity measures implemented within 14 days of the onset of an epidemic can avert up to 74% of pig deaths due to ASF while hypothetical vaccines that confer 70% immunity when deployed prior to day 14 of the epidemic could avert 65% of pig deaths. When the two control measures are combined, the model predicts that 91% of the pigs that would have otherwise succumbed to the disease if no intervention was implemented would be saved. However, if the combined interventions are delayed (defined as implementation from > 60 days) only 30% of ASF-related deaths would be averted. In the absence of vaccines against ASF, we recommend early implementation of enhanced biosecurity measures. Active surveillance and use of pen-side diagnostic assays, preferably linked to rapid dissemination of this data to veterinary authorities through mobile phone technology platforms are essential for rapid detection and confirmation of ASF outbreaks. This prediction, although it may seem intuitive, rationally confirms the importance of early intervention in managing ASF epidemics. The modelling approach is particularly valuable in that it determines an optimal timing for implementation of interventions in controlling ASF outbreaks.S1 Data. File containing simulation data that was used in this manuscript.CISA-INIA (TF069018), Commonwealth Scientific and Industrial Research Organisation, University of Pretoria, Wellcome Trust (085308), and CGIAR research program on 'Livestock and Fish.' Remove selectedhttp://www.plosone.orgam2016Veterinary Tropical Disease

Estimating the basic reproductive number (R0) for African swine fever virus (ASFV) transmission between pig herds in Uganda

African swine fever (ASF) is a highly contagious, lethal and economically devastating haemorrhagic disease of domestic pigs. Insights into the dynamics and scale of virus transmission can be obtained from estimates of the basic reproduction number (R0). We estimate R0 for ASF virus in small holder, free-range pig production system in Gulu, Uganda. The estimation was based on data collected from outbreaks that affected 43 villages (out of the 289 villages with an overall pig population of 26,570) between April 2010 and November 2011. A total of 211 outbreaks met the criteria for inclusion in the study. Three methods were used, specifically; (i) GIS- based identification of the nearest infectious neighbour based on the Euclidean distance between outbreaks, (ii) epidemic doubling time, and (iii) a compartmental susceptible-infectious (SI) model. For implementation of the SI model, three approaches were used namely; curve fitting (CF), a linear regression model (LRM) and the SI/ N proportion. The R0 estimates from the nearest infectious neighbour and epidemic doubling time methods were 3.24 and 1.63 respectively. Estimates from the SI-based method were 1.58 for the CF approach, 1.90 for the LRM, and 1.77 for the SI/N proportion. Since all these values were above one, they predict the observed persistence of the virus in the population. We hypothesize that the observed variation in the estimates is a consequence of the data used. Higher resolution and temporally better defined data would likely reduce this variation. This is the first estimate of R0 for ASFV in a free range smallholder pig keeping system in sub-Saharan Africa and highlights the requirement for more efficient application of available disease control measures.S1 Data. The data that was used in all the computations and Figures.S1 Fig. Generation tree following the nearest infectious neighbour route. Nearest infectious neighbour generation tree also known as a transmission network. Epidemic is suspected to have been introduced at herd/ node 1 coloured red (bottom extreme left). The critical node at which the disease could have been stopped from further spread as highlighted in green in the generation tree. (Designed in network analysis tool ORA)S2 Fig. The SIR model used to simulate outbreak data of African swine fever, Gulu District, Uganda, April 2010—November 2011.S3 Fig. Distribution of bootstrapped monthly transmission rate coefficient β estimates.S4 Fig. Sensitivity of basic reproduction number R0 to variation in initial number of herds.S5 Fig. Spatial distribution of ASF infected herds (April 2010—November 2011).S1 Text. Philosophical underpinning of R0.The Commonwealth Scientific and Industrial Research Organisation (CSIRO)- Australian Agency for International Development (AusAID) Africa-Australia Food Security Initiative (MBB, EAO,RPB); Consortium of International Agricultural Research Centers (CGIAR) Research Program for Agriculture for Nutrition and Health, led by IFPRI (BB, AS); Wellcome Trust (grant 085308) (EMF); the Swedish research council FORMAS (Grant No. 221-2009-1984) (KS, CM, TA); and CISA-INIA Grant no. TF069018 (MBB, RPB).http://www.plosone.orgam201

Proton Therapy for Breast Cancer:A Consensus Statement From the Particle Therapy Cooperative Group Breast Cancer Subcommittee

Radiation therapy plays an important role in the multidisciplinary management of breast cancer. Recent years have seen improvements in breast cancer survival and a greater appreciation of potential long-term morbidity associated with the dose and volume of irradiated organs. Proton therapy reduces the dose to nontarget structures while optimizing target coverage. However, there remain additional financial costs associated with proton therapy, despite reductions over time, and studies have yet to demonstrate that protons improve upon the treatment outcomes achieved with photon radiation therapy. There remains considerable heterogeneity in proton patient selection and techniques, and the rapid technological advances in the field have the potential to affect evidence evaluation, given the long latency period for breast cancer radiation therapy recurrence and late effects. In this consensus statement, we assess the data available to the radiation oncology community of proton therapy for breast cancer, provide expert consensus recommendations on indications and technique, and highlight ongoing trials' cost-effectiveness analyses and key areas for future research. (c) 2021 Elsevier Inc. All rights reserved

Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study

Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully revealed common variants associated with disease risk, the role of common variation in partial epilepsies has not yet been explored in a well-powered study. We undertook a genome-wide association-study to identify common variants which influence risk for epilepsy shared amongst partial epilepsy syndromes, in 3445 patients and 6935 controls of European ancestry. We did not identify any genome-wide significant association. A few single nucleotide polymorphisms may warrant further investigation. We exclude common genetic variants with effect sizes above a modest 1.3 odds ratio for a single variant as contributors to genetic susceptibility shared across the partial epilepsies. We show that, at best, common genetic variation can only have a modest role in predisposition to the partial epilepsies when considered across syndromes in Europeans. The genetic architecture of the partial epilepsies is likely to be very complex, reflecting genotypic and phenotypic heterogeneity. Larger meta-analyses are required to identify variants of smaller effect sizes (odds ratio <1.3) or syndrome-specific variants. Further, our results suggest research efforts should also be directed towards identifying the multiple rare variants likely to account for at least part of the heritability of the partial epilepsies. Data emerging from genome-wide association-studies will be valuable during the next serious challenge of interpreting all the genetic variation emerging from whole-genome sequencing studie

A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus.

Esophageal adenocarcinoma is a cancer with rising incidence and poor survival. Most such cancers arise in a specialized intestinal metaplastic epithelium, which is diagnostic of Barrett's esophagus. In a genome-wide association study, we compared esophageal adenocarcinoma cases (n = 2,390) and individuals with precancerous Barrett's esophagus (n = 3,175) with 10,120 controls in 2 phases. For the combined case group, we identified three new associations. The first is at 19p13 (rs10419226: P = 3.6 × 10(-10)) in CRTC1 (encoding CREB-regulated transcription coactivator), whose aberrant activation has been associated with oncogenic activity. A second is at 9q22 (rs11789015: P = 1.0 × 10(-9)) in BARX1, which encodes a transcription factor important in esophageal specification. A third is at 3p14 (rs2687201: P = 5.5 × 10(-9)) near the transcription factor FOXP1, which regulates esophageal development. We also refine a previously reported association with Barrett's esophagus near the putative tumor suppressor gene FOXF1 at 16q24 and extend our findings to now include esophageal adenocarcinoma