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Copyright of Nouveau Praticien Vétérinaire - Équine is the property of EDP Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This article summarizes recent advances in our knowledge of plankton biogeography obtained by genomic approaches and the impacts of global warming on it. Large-scale comparison of the genomic content of samples of different plankton size fractions revealed a partitioning of the oceans into genomic provinces and the impact of major oceanic currents on them. By defining ecological niches, these provinces are extrapolated to all oceans, with the exception of the Arctic Ocean. By the end of the 21st century, a major restructuring of these provinces is projected in response to a high emission greenhouse gas scenario over 50% of the surface of the studied oceans. Such a restructuring could lead to a decrease in export production by 4%. Finally, obtaining assembled sequences of a large number of plankton genomes defining this biogeography has allowed to better characterize the genomic content of the provinces and to identify the species structuring them. These genomes similarly enabled a better description of potential future changes of plankton communities under climate change. [ABSTRACT FROM AUTHOR]

Comment les outils de la génomique peuvent-ils concrètement contribuer à la transition agroécologique de la production agricole ? Cette question est traitée au travers de l’analyse d’un corpus des 1 200 projets de recherche dans les différents domaines de la génomique, financés par l’Agence nationale de la recherche (ANR) entre 2005 et 2019. L’analyse débouche sur une proposition de quatre pistes prioritaires pour les recherches futures en génomique pour l’agroécologie.

Copyright of Psycho-Oncologie is the property of Tech Science Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Domestication is the process of organism evolution under selection by humans, and as such has been a model for studying adaptation since Charles Darwin. Here we review recent studies on the genomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicillium roqueforti used for maturing blue cheeses, and the Penicillium camemberti species complex used for making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontal gene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiated populations with contrasted traits, several populations having independently been domesticated for cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial for cheese making in comparison to non-cheese populations, regarding color, spore production, growth rates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/or competitive ability. The cheese populations also show degeneration for some unused functions such as decreased ability of sexual reproduction or of growth under harsh conditions. These recent findings have fundamental importance for our understanding of adaptation and have applied interest for strain improvement.

Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The advent of high throughput sequencing approaches and ancient DNA techniques have enabled reconstructing the history of human populations at an unprecedented level of resolution. The symposium from the French Academy of Sciences "50,000 ans d'épopée humaine dans notre ADN" has reviewed some of the latest contributions from the fields of genomics, archaeology, and linguistics to our understanding of >300,000 years of human history. DNA has revealed the richness of the human journey, from the deep divergences between human populations in Africa, to the first encounters of Homo Sapiens with other hominins on their way to Eurasia and the peopling of Remote Oceania. The symposium has also emphasized how migrations, cultural practices, and environmental pathogens have contributed to shape the genetic diversity of modern humans, through admixture, genetic drift or genetic adaptation. Finally, special attention was also given to how human behaviours have shaped the genome of other species, through the spreading of microbes and pathogens, as in the case of Yersinia Pestis, or through domestication, as elegantly demonstrated for dogs, horses, and apples. Altogether, this conference illustrated how the complex history of human populations is tightly linked with their contemporary genetic diversity that, in turn, has direct effects on their identity and health. [ABSTRACT FROM AUTHOR]

Clubroot, a soil-borne disease caused by the obligate parasite Plasmodiophora brassicae Woronin, is a threat to canola (Brassica napus L.) production in western Canada. Genetic resistance represents the most effective tool to manage this disease. However, given the rapid spread of clubroot and the emergence of new virulent pathotypes of P. brassicae, it is important to accelerate the resistance breeding effort. The advent of genome-sequencing technologies has created a new toolbox that can aid in breeding strategies. Many genomic approaches, such as genotyping-by-sequencing, high-density single nucleotide polymorphism (SNP) arrays, genome-wide association studies, and transcriptomic approaches such as bulked segregant RNA-seq analysis and microarray/RNA-seq differential expression analysis have been applied to studies of clubroot resistance or susceptibility. Here, we review the impact of traditional marker-assisted selection-based breeding for clubroot resistance, and then discuss how omics approaches have contributed to the (1) detection and genotyping of genome-wide SNP markers linked with clubroot resistance genes or quantitative trait loci, (2) understanding of host resistance mechanisms upon P. brassicae infection, and (3) acceleration of resistance breeding by identifying and characterizing candidate genes, especially those with differential efficacy against new pathotypes of P. brassicae. We suggest that the use of different omics approaches together could improve the efficiency of clubroot-resistance breeding. Finally, we propose that the CRISPR/Cas9 system for genome editing is a promising tool to facilitate the validation and use of candidate genes for clubroot-resistance breeding. [ABSTRACT FROM AUTHOR]

Le palmier dattier possède certaines caractéristiques qui en font des organismes difficiles à étudier pour la localisation et l’identification des gènes. L’amélioration de la productivité, la qualité du fruit et la résistance aux stress biotiques et abiotiques est le principal objectif des analyses moléculaires chez le palmier dattier. Dans ce papier, nous examinons les progrès considérables dans ce domaine et leur état. On a passé en revue les progrès des études de la génomique chez le palmier dattier afin de fournir une référence utile aux chercheurs travaillant dans ce domaine. Le progrès des techniques moléculaires facilitera les programmes d'amélioration au moyen de la sélection moléculaire

Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

New genomic techniques are revolutionizing the prenatal screening and diagnosis, by allowing access to diagnoses of fetal and/or parental conditions whose penetrance is not always complete. These techniques raise many questions, in a sensitive context, ethically different from postnatal follow-up. The creation of multidisciplinary national and international think tanks is fundamental to consider about the important diagnoses or susceptibility factors to relate to the couple during pregnancy. [ABSTRACT FROM AUTHOR]

The questions of when and how humans reached Sahul, the Pleistocene continent of Australia and New Guinea, has remained a central issue of Australian archaeology since its development as an academic discipline in the mid‐twentieth century. Modelling this event has persistently appealed to minimal assumptions – the simplest watercraft, the shortest routes, the smallest viable colonising groups. This paper argues that Australian archaeology can no longer ignore the way our understanding of this initial colonisation is being reshaped by current genomic research. It reviews this evidence and concludes that a colonising wave of hundreds or perhaps low thousands of people was involved. If correct, it suggests that we need to rethink our models, modify or discard the minimalist assumptions that have so far driven them and consider how this different paradigm affects our understanding of early settlement in Sahul. [ABSTRACT FROM AUTHOR]

This article describes how RNA expression data of 173 genes were produced on 384 sunflower hybrids grown in field conditions. Sunflower hybrids were selected to represent genetic diversity within cultivated sunflower. The RNA was extracted from mature leaves at one time seven days after anthesis. These data allow to differentiate the different genotype behaviours and constitute a valuable resource to the community to study the adaptation of crops to field conditions and the molecular basis of heterosis. It is available on data.inra.fr repository. [ABSTRACT FROM AUTHOR]

Species of Phytophthora pose one of the most serious biosecurity threats to forest ecosystems worldwide. Despite management efforts and increased awareness of forest pathogens, there is continued introduction and spread of Phytophthora species. Uncertainty about the center of origin for many of the invasive species hampers disease control efforts. Additionally, the management efforts are often made impossible either by the vast host range or the extreme susceptibility of naïve hosts. In this review, we discuss how genomics has shed light on the extent of spread and destruction caused by invasive Phytophthora species, and how approaches leveraged by genomics can be applied to enhance the management of these invasive forest pathogens. Four case studies, Phytophthora ramorum, Phytophthora lateralis, Phytophthora cinnamomi, and Phytophthora pluvialis are used to illustrate how genomics can be applied to forest management. We urge researchers, governmental research institutes, private companies, and citizens to collaborate in order to stop the spread of invasive Phytophthora species. To accomplish this, we see the following themes as critical parts of resolving this forest health crisis: i) integration of DNA-based pathogen detection into forest inventory programs; ii) development of practical and affordable DNA-based diagnostic methods; iii) sequence hosts as models for resistance gene identification; iv) prediction of pathogen impact based on genomic data; and v) increase collaborative projects and outreach to raise awareness of forest diseases. [ABSTRACT FROM AUTHOR]

Parasite population structure can be used to infer fine-scale movement in host species. Many penguin species form large social colonies, and are highly philopatric, returning to the same nest or burrow, along the same route, after each trip to sea. Within a colony, however, the local abundance, physical similarity, and nocturnal habits of penguins hinder the observation of fine-scale movements. To determine the extent of movement and interaction of penguins within colonies, a genotyping by sequencing (GBS) approach was used to study the fine-scale structure of ticks--which depend on host movements for dispersal--exploiting the largest Little Penguin (Eudyptula novaehollandiae) colony in Australia (Phillip Island, Victoria). No barriers to tick gene flow were identified, and we infer that extensive penguin movement occurs throughout the colony. Our findings support the hypothesis that some penguin species are highly gregarious, socializing widely within colonies despite strong nest-site philopatry. [ABSTRACT FROM AUTHOR]

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum ( Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger. [ABSTRACT FROM AUTHOR]

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems. [ABSTRACT FROM AUTHOR]

Résumé Les nombreuses avancées dans les systèmes informatiques (collection de données, bases de données, stockage), les possibilités diagnostiques et thérapeutiques sont responsables d’une augmentation et d’une diversification des données disponibles. Les big data offrent les capacités, dans le domaine de la santé, d’accélérer les découvertes et d’optimiser la prise en charge des patients en combinant un nombre de données presque infini par la création de modèles thérapeutiques. En radiothérapie, le développement des big data est attrayant car les données à traiter sont très nombreuses et hétérogènes (démographiques, radiomiques, génomiques, radiogénomiques, etc.). La prédiction de l’efficacité et de la tolérance du traitement par irradiation serait alors optimisée. Avec ces nouveaux concepts, encore au stade préliminaire, il apparaît possible de développer une médecine de haute précision et personnalisée, toujours plus sécurisée et fiable. The many advances in data collection computing systems (data collection, database, storage), diagnostic and therapeutic possibilities are responsible for an increase and a diversification of available data. Big data offers the capacities, in the field of health, to accelerate the discoveries and to optimize the management of patients by combining a large volume of data and the creation of therapeutic models. In radiotherapy, the development of big data is attractive because data are very numerous et heterogeneous (demographics, radiomics, genomics, radiogenomics, etc.). The expectation would be to predict the effectiveness and tolerance of radiation therapy. With these new concepts, still at the preliminary stage, it is possible to create a personalized medicine which is always more secure and reliable. [ABSTRACT FROM AUTHOR]

Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale. [ABSTRACT FROM AUTHOR]

Copyright of VertigO is the property of La Revue Electronique en Sciences de l'Environnement VertigO and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Canadian Journal of Animal Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Canadian Journal of Animal Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Globalization has allowed for rapid movement of plant pathogens that threaten food security. Successful disease management largely depends on timely and accurate detection of plant pathogens causing epidemics. Thus, biosurveillance of epidemic plant pathogens such asPseudoperonospora cubensis, the causal agent of cucurbit downy mildew, is becoming a priority to prevent disease outbreaks and deploy successful control efforts. Next Generation Sequencing (NGS) facilitates rapid development of genomics resources needed to generate molecular diagnostics assays forP. cubensis. Having information regarding the presence or absence of the pathogen, amount of inoculum, crop risk, time to initiate fungicide applications, and effective fungicides to apply would significantly contribute to reducing losses to cucurbit downy mildew. In this article, we discuss approaches to identify unique loci for rapid molecular diagnostics using genomic data, to develop molecular diagnostic tools that discriminate economically important pathogen alleles (i.e. mating type and fungicide resistance), and how to use molecular diagnostics with current and future spore trap strategies for biosurveillance purposes of important downy mildew pathogens. The combined use of these technologies within the already existent disease management framework has the potential to improve disease control. [ABSTRACT FROM PUBLISHER]

Phylodynamics is a recent field that aims at using genetic sequence data to estimate epidemiological parameters such as the viral population growth rate, the number of infections in the population or even their duration. Its main underlying assumption is that the way viruses spread leaves marks in their genome. In this review, we first introduce the originality of phylodynamics inferences compared to 'classical' phylogenetic approaches. Then, we present the novelty of using phylogenies of infections compared to species trees, while giving some directions to infer of such objects. We discuss the birth of phylodynamics and its first successes, in order to present some of the questions the approach can address. Finally, we highlight some future challenges for the field. [ABSTRACT FROM AUTHOR]

Breeding the oil palm (Elaeis guineensis Jacq.) for climate change requires multidisciplinary and collaborative research by nature: indeed - besides genetics and structural and functional genomics - almost all disciplines related to life sciences are involved. Research work also relies on the identification of genetic variation in the strategies of response to stress developed by the plant: this implies the exploration of resources provided by natural variation, germplasm collections, selected genitors from breeding programs together with material of interest collected from smallholders. The phenotyping of selected plant material under biotic/abiotic stress will involve new methods for high-throughput phenotyping and genomic approaches will be followed for the identification of genes underlying the variation of traits which will be used as selection targets. Also, improvements in understandinghow climate change may influence chemical and physical processes in soils, how this may affect nutrient availability, and how the plant responds to changed availability of nutrients will also influence oil palm breeding programs. Molecular approaches and tools have great potential to optimize patterns of plant breeding, especially for perennial species. In recent years, there has been an exponential increase in molecular resources and methods aimed at identifying polymorphisms which control the traits of interest and exploring the mechanisms linking these polymorphisms to phenotypes. With genomic resources becoming increasingly available for the oil palm (sequencing, resequencing and chips development) the exploration of the genetic basis of complex traits such as oil yield or resistance to disease is now possible. Consequently the availability and sharing of such a large amount of data is currently reshapingmost of oil palm breeding strategies. [ABSTRACT FROM AUTHOR]

Management of high grade, serous and/or endometrioid, advanced (stages III-IV) ovarian carcinomas and HRD-BRCA testing in 2023: update according to data published/presented in 2022 Molecular analysis of ovarian carcinomas must be now systematically performed to determine BRCA1 and BRCA2 status as well as genomic instability score. Several types of tests are available. From a clinical perspective, new data from phase III clinical trials presented in 2022 confirm the key role of PARP inhibitors in first-line medical treatment of high-grade serous ovarian cancers. A new algorithm that includes all new evidence is proposed for selection of first-line therapy., (Copyright © 2023 Elsevier Masson SAS. Tous droits réservés. All rights reserved.)

Copyright of Biotechnologie, Agronomie, Societe et Environnement is the property of Les Presses Agronomiques de Gembloux and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This year, the theme of the American Association for Cancer Research (AACR) conference that held from the 16th to the 20th of April 2016 was “Delivering Cures through Cancer Science”. Its objective was to reinforce the link existing between research and advances in patient’s care. As usual, the multidisciplinary program covered all the areas of cancer science. Beyond the plenary sessions and symposiums, the program of the meeting included didactic educational workshops on specific areas of research offering a good opportunity to learn or to extend knowledge on particular issues. The meeting also permitted active discussion and exchanges with colleagues through the poster sessions. In this issue of Oncologie, and for the third year in a row, mentoring medical doctors of the French association, AERIO (Association d’enseignement et de recherche des internes d’oncologie) focus on presentations that, to our opinion, warranted a particular attention. The aim of this exciting and informative project is not only to provide details to researchers and physicians but also to the general public who could not attend the conference. This year, genetic and epigenetic cancer heterogeneity as well as tumor immunology received a particular and still increasing attention by the AACR steering committee. However, we also report here the most recent advances on tumor metabolism and its signaling pathways, a rapidly growing research field that should allow, in the near future, to identify potential drug targets and to develop compounds capable of starving and inhibiting tumor progression. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are the major components of eukaryotic genomes. Their propensity to densely populate and in some cases invade the genomes of plants and animals is in contradiction with the fact that transposition is strictly controlled by several molecular pathways acting at either transcriptional or post-transcriptional levels. Horizontal transfers, defined as the transmission of genetic material between sexually isolated species, have long been considered as rare phenomena. Here, we show that the horizontal transfers of transposable elements (HTTs) are very frequent in ecosystems. The exact mechanisms of such transfers are not well understood, but species involved in close biotic interactions, like parasitism, show a propensity to exchange genetic material horizontally. We propose that HTTs allow TEs to escape the silencing machinery of their host genome and may therefore be an important mechanism for their survival and their dissemination in eukaryotes. [ABSTRACT FROM AUTHOR]

This article discusses changes in sunflower breeding objectives since the introduction of hybrid varieties 50 years ago. After a reminder of the importance of some early programmes, Canadian in particular, the present situation for each breeding objective is compared with those encountered earlier. Breeding for yield has changed from maximum possible yield under intensive agriculture to yield with resistance to abiotic stresses, moderate droughts and shallow soils in particular, helped by collaboration with agronomists to produce crop models. Breeding for oil has changed from quantity to quality and the value of seed meal is again becoming economically important. Necessary disease resistances vary with agronomic practises and selection pressure on pathogens according to varietal genetics. The possibilities of new types of sunflower are also discussed. Advances in genomics will change breeding procedures, but with rapidly changing molecular techniques, international collaboration is particularly important. [ABSTRACT FROM AUTHOR]

Q fever is a zoonosis of worldwide distribution with the exception of New Zealand. It is caused by an intracellular bacterium, Coxiella burnetii. The disease often goes underdiagnosed because the main manifestation of its acute form is a general self-limiting flu-like syndrome. The Dutch epidemics renewed attention to this disease, which was less considered before. This review summarizes the description of C. burnetii (taxonomy, intracellular cycle, and genome) and Q fever disease (description, diagnosis, epidemiology, and pathogenesis). Finally, vaccination in humans and animals is also considered. [ABSTRACT FROM AUTHOR]

The genetic basis for the interaction(s) between plants and pathogens has been classically illustrated as a gene-for-gene relationship, through which a single gene product from the pathogen interacts within a single gene product found within the plant. In the simplest terms, it is the outcome of these interactions that underpin resistance and/or susceptibility signalling processes. While this basic concept shapes our understanding of many of the molecular-genetic mechanisms controlling immune signalling in plants, current research has revealed that the timing and ultimate outcome of these interactions are far more complex, and are typically regulated in a genome-by-genome manner. As a central theme for this review, we will focus on recent discoveries in the field of plant-oomycete interactions, primarily on the downy mildews, an important group of obligate oomycete pathogens of plants. Recent transcriptome-based studies have shown that survival, adaptation and virulence rely on complex, bi-directional interactions between the host and pathogen genomes. Taking advantage of the obligate nature of the downy mildews, insight into the transcriptional plasticity of these genomes has revealed a remarkable ability to adapt to host and environmental stressors. Herein, we will highlight a recent body of research using thePseudoperonospora cubensis – Cucumis sativusinteraction, which has identified a suite of alternative splicing and sRNA-based regulatory signals that are induced in a temporal and host-specific manner. In combination with recent studies in other plant-oomycete pathosystems, a comprehensive transcriptional profile of resistance and susceptibility within the host and pathogen illustrates the remarkable ability of this group of pathogens to adapt to host and environment to infect and cause disease in a diverse array of agriculturally important crops. [ABSTRACT FROM AUTHOR]

DNA barcoding-the sequencing of short, standardized DNA regions for specimen identification and species discovery-has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources. [ABSTRACT FROM AUTHOR]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Il existe dans les bases de données publiques une énorme quantité de séquences d’ADN dérivées de plantes, et notamment la séquence complète du génome d’Arabidopsis thaliana, une plante modèle pour les oléagineux, proche parente du colza. Ces données constituent une ressource importante non seulement pour la compréhension de métabolisme lipidique et de sa régulation, mais aussi pour la sélection et le développement de variétés nouvelles d’oléagineux produisant davantage d’huiles ou des huiles de composition nouvelle. Cette abondance de séquences peut être exploitée, en utilisant les recherches d’homologies, pour identifier les gènes, pour obtenir des informations sur leur fonction, comme pour repérer des gènes candidats codant des fonctions nouvelles. L’analyse de ces bases de données a révélé que la majeure partie des gènes codant des enzymes impliquées dans le métabolisme lipidique appartient à des petites familles multigéniques, reflétant la diversification des fonctions des isoformes. Une analyse du catalogue des ADNc séquencés en aveugle reflète les niveaux d’expression des différents gènes et fournit un aperçu des régulations des flux au travers des voies métaboliques conduisant à la biosynthèse des lipides de réserve. La disponibilité de mutants et de lignées transgéniques d’Arabidopsis et le développement de puces à ADN qui permettent l’analyse simultanée de plusieurs milliers de gènes conduiront à une meilleure compréhension des facteurs qui régulent le métabolisme des huiles dans les graines. Une telle connaissance facilitera la manipulation de la composition des huiles et des quantités produites dans les graines.

Today, a range of biotechnological approaches, from somatic embryogenesis to biomolecular research, play an increasingly important role in breeding strategies for oil palm (Elaeis guineensis Jacq.). Clonal micropropagation. Methods of cloning by in vitro culture led to the development of a micropropagation technique for oil palm based on somatic embryogenesis which was tested at the pilot stage on elite genotypes, thus enabling the production of high oil yielding clones. This phase allowed the identification of limiting factors associated with scaling-up, with respect in particular to the scale of mass production required to meet the needs of planters and to the problem of ensuring genetic fidelity in the regenerated plant material. These two concerns led researchers to look further into the underlying physiological and/or molecular mechanisms involved in somatic embryogenesis and the somaclonal variation events induced by the in vitro cloning procedure. Structural and functional genomics. Marker-assisted breeding in oil palm is a long-term multi-stage project including: molecular analysis of genetic diversity in both E. guineensis and E. oleifera germplasms; large scale development of PCR-based microsatellite markers; and parallel development of three genome mapping and QTL detection projects studying key agronomic characters. Post-genomics. In order to tackle the problem of the mantled flowering abnormality, which is induced during the micropropagation process, studies of gene expression have been carried out in tissue cultures as a means of establishing an early clonal conformity testing procedure. It is important to assess what kind of methodology is the most appropriate for clonal conformity testing by comparing RNA, protein and DNA (PCR) based approaches. Parallel studies on genomic DNA methylation changes induced by tissue culture suggest that the latter may play an important role in the determination of the mantled abnormality.

The challenge of the basic and translational research on pancreatic adenocarcinoma is not only to obtain a better understanding in the biology of the pancreatic cancer cells and in the microenvironment but also in the different faces of the disease: resectable versus unresectable, metastatic versus locally advanced, and short versus long survivors. The recent studies summarized in the present review aimed to investigate at a large scale genome, exome, and transcriptome. These works attempted to isolate different molecular profiles depending on the prognosis, the activation of oncogene/tumor suppressor genes, and on the response to chemotherapy. The second set of studies is focused on the microenvironment of the pancreatic cancer. This microenvironment plays a key role in the invasive and metastatic process of pancreatic carcinoma with a strong relationship between cancerous cells and pancreatic stellate cells, as well as extracellular matrix. All these works are based on the transgenic mice KRAS-G12D models after crossing or not with other transgenic models bearing a knock out of various tumor suppressor genes. All these studies concluded that targeting the microenvironment significantly influences the prognosis and the response to chemotherapy. This targeting aims to modify the modeling of tumoral stroma (matrix, vascularization) and to inhibit secretion of pancreatic stellate cells. All these new molecular profiles and biomarkers should be validated on prospective clinicobiological cohorts and with early therapeutic phases. [ABSTRACT FROM AUTHOR]

Résumé L’objectif initial en radiothérapie oncologique est de proposer une personnalisation thérapeutique en ayant une analyse fine de la tumeur notamment à l’échelle moléculaire en prenant en compte la susceptibilité individuelle notamment de réactivité des tissus sains à plus ou moins long terme. Radiomics permet une analyse qualitative et quantitative ultraperformante, consistant en l’extraction à haut débit de données numériques d’imagerie médicale afin d’obtenir des informations prédictives et/ou pronostiques concernant les patients pris en charge pour une pathologie cancéreuse. Une approche différente permet de définir la radiomics comme une information biologique somatique ou constitutionnelle qui modifiera la prise en charge par radiothérapie. Elle inclut la susceptibilité individuelle des tissus sains mais également la réponse potentielle de la tumeur à une radiothérapie. Ces « omics » sont des techniques biologiques à haut débit, permettant d’identifier et d’explorer simultanément un ensemble de gènes, lipides, protéines ou autres sujets d’étude de façon compartimentée. The ultimate goal in radiation oncology is to offer a personalized treatment to all patients indicated for radiotherapy. Radiomics is a tool that reinforces a deep analysis of tumors at the molecular aspect taking into account intrinsic susceptibility in a long-term follow-up. Radiomics allow qualitative and quantitative performance analyses with high throughput extraction of numeric radiologic data to obtain predictive or prognostic information from patients treated for cancer. A second approach is to define biological or constitutional that could change the practice. This technique included normal tissue individual susceptibility but also potential response of tumors under ionizing radiation treatment. These “omics” are biological and technical techniques leading to simultaneous novel identification and exploration a set of genes, lipids, proteins. [ABSTRACT FROM AUTHOR]

The 6th International Barcode of Life Conference (Guelph, Canada, 18-21 August 2015), themed Barcodes to Biomes, showcases the latest developments in DNA barcoding research and its diverse applications. The meeting also provides a venue for a global research community to share ideas and to initiate collaborations. All plenary and contributed abstracts are being published as an open-access special issue of Genome. Here, I use a comparison with the 3rd Conference (Mexico City, 2009) to highlight 10 recent and emerging trends that are apparent among the contributed abstracts. One of the outstanding trends is the rising proportion of abstracts that focus upon multiple socio-economically important applications of DNA barcoding, including studies of agricultural pests, quarantine and invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and marketplace surveys evaluating the authenticity of seafood products and medicinal plants. Other key movements include the use of barcoding and metabarcoding approaches for dietary analyses--and for studies of food webs spanning three or more trophic levels--as well as the spread of next-generation sequencing methods in multiple contexts. In combination with the rising taxonomic and geographic scope of many barcoding iniatives, these developments suggest that several important questions in biology are becoming tractable. "What is this specimen on an agricultural shipment?", "Who eats whom in this whole food web?", and even "How many species are there?" are questions that may be answered in time periods ranging from a few years to one or a few decades. The next phases of DNA barcoding may expand yet further into prediction of community shifts with climate change and improved management of biological resources. [ABSTRACT FROM AUTHOR]

Genes and environment make the organism. Darwin stood firm in his denial of any direct role of environment in the modification of heredity. His theory of evolution heralded two debates: one about the importance and adequacy of natural selection as the main mechanism of evolution, and the other about the role of genes versus environment in the modification of phenotype and evolution. Here, I provide an overview of the second debate and show that the reasons for the gene versus environment battle were twofold: first, there was confusion about the role of environment in modifying the inheritance of a trait versus the evolution of that trait, and second, there was misunderstanding about the meaning of environment and its interaction with genes in the production of phenotypes. It took nearly a century to see that environment does not directly affect the inheritance of a phenotype (i.e., its heredity), but it is nevertheless the primary mover of phenotypic evolution. Effects of genes and environment are not separate but interdependent. One cannot separate the effect of genes from that of environment, or nature from nurture. To answer the question posed in the title, it is partly because the 20th century has been a century of unending progress in genetics. But also because unlike physics, biology is not colorblind; progress in biology has often been delayed beyond the Kuhnian paradigm change due to built-in interest in negating the influence of environment. Those who are against evolution, of course, cannot be expected to understand the role of environment in evolution. Those for it, many biologists included, believing in the supremacy of genes empowers them by giving adaptation a solely gene-directed (self-driven) 'teleological' interpretation. [ABSTRACT FROM AUTHOR]

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Genomic big data is an emerging information technology, which presents new opportunities for medical innovation, as well as new challenges to our current ethical social, and legal infrastructure. Rapid, affordable whole genomic sequencing translates patients' most sensitive personal information into petabytes of digital health data. While a biomedical approach traditionally focuses on risks and benefits to the human body, the fields of Communication and Science and Technology Studies (STS) can provide some of the critical and theoretical tools necessary to navigate the newly emerging terrain of the human body as digital code. Core areas of expertise from these fields, including the Internet, the network society and the social constructions of technology, ground our discussion of the social implications of open access genomic databases, privacy, and informational risk. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Microsporidia are a group of obligate intracellular eukaryotic parasites that infect a wide variety of species, including humans. Phylogenetic analysis indicates a relationship between the Microsporidia and the Fungi. However, most results are based on the analysis of relatively few genes. DarkHorse analysis involves the transformation of BLAST results into a lineage probability index (LPI) value and allows for the comparison of genes for an entire genome with those of other genomes. Thus, we can see which genes from the microsporidia score most closely based on the LPI with other eukaryotic organisms. In this analysis, we calculated the LPI for each gene from the genomes of 7 Microsporidia, Antonospora locustae, Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis, Nosema bombycis, Nosema ceranae, and Nematocida parisii, to analyze the genetic relationships between Microsporidia and other species. It was found that many (91%) genes were most closely correlated with genes from other microsporidial genomes and had the highest mean LPI (0.985), indicating a monophyletic origin of the Microsporidia. In a subsequent analysis, we excluded the other Microsporidia from the analysis to look for relationships before the divergence of Microsporidia, and found that 43% of the microsporidial genes scored highest with fungal genes, and a higher mean LPI was found with Fungi than with other kingdoms, suggesting that Microsporidia is closely related to Fungi at the genomic level. Microsporidial genes were functionally clustered based on the KOG (Eukaryotic COG) database, and the possible lineages for each gene family were discussed in concert with the DarkHorse results. [ABSTRACT FROM AUTHOR]

Copyright of Forestry Chronicle is the property of Canadian Institute of Forestry and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Major innovations about targeted anticancer therapies were discussed during the TAT 2014 congress, in Washington, March 5-7, 2014. Dr Patricia M. LoRusso (Detroit), one of the most productive oncology phase 1 investigators, introduced the congress with her speech about 'The Changing Landscape of Early Phase Trials.' Then, various presentations on a broad range of new promising targeted cancer therapeutics and their development issues confirmed this idea. As a major topic, immunotherapy began the congress, wondering about the role of Programmed Death Ligand 1 (PDL1) as efficacy biomarker and possibilities of immunologic agents association. Among the promising molecules, the congress presented inhibitors of cdk4/6 as cell cycle targets and FGFR inhibitors with their major challenge of identifying accessible response biomarker. Special sessions were devoted to methodological evolutions such as preclinical models development, circulating tumoral DNA, or the role of genomics in early-phase drug development. The French basket trial SHIVA was presented to illustrate the place of genomics in newly conceived trials. SHIVA is a phase II trial evaluating efficacy and feasibility of a targeted treatment according to the molecular profile versus standard treatment. Finally, methodological issues in early drug development were discussed with biomarker's challenge, correlating signaling inhibition and drug resistance to targeted agents. [ABSTRACT FROM AUTHOR]

Genomic medicine is often presented as a new paradigm for personalized healthcare. Encompassing both a translational approach in research and a vision of future medical practice, genomic medicine may have important impact on the way healthcare professionals diagnostics, treat and prevent diseases. We discuss some ethical and social issues raised by the prospect of genome-based medical practice, namely: changing definitions of disease and identity, assessment of clinical validity and utility of genome screening, mastery of genomic information by healthcare professionals and its communication to patients, and questions related to the costs of genomic medicine for future healthcare. [ABSTRACT FROM AUTHOR]