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Tabibnâme, 18. yüzyılda Fakîr Ahmed Şeyhzâde tarafından yazılmış olan alternatif tıp, eczacılık ve bitki bilimi konularını içeren Türkçe el yazması bir metindir. Metin ayrıca dönemin siyasi, dinî ahlaki, tıbbi, felsefi vb. hususlarında da bilgiler taşımaktadır. Tabibnâme, barındırdığı söz varlığı ve dil özellikleri nedeniyle tıp ve eczacılık terminolojisi bakımından olduğu kadar Türk dili ve Türk kültürü tarihi bakımından da oldukça önemlidir. Tabibnâme metninde 101 adet bitki adı kullanılmıştır. Bu makalede, metinde kullanılan bitki adları art zamanlı ses değişiklikleri bakımından ve bugün Türkiye Türkçesinde kullanılıp kullanılmadıklarına göre değerlendirildi. 35 bitki adı bugün Türkiye Türkçesinde çeşitli ses değişikliklerine uğramış biçimleriyle ve 46 bitki adı ise aynı biçimleriyle kullanılmaktadır. Buna karşılık 20 bitki adı bugün Türkiye Türkçesinde kullanılmamaktadır. Bitki adlarının 27’si Türkçe, 25’i Arapça, 22’si Farsça, 18’i Yunanca ve 1 tanesi de Endonezya dilindendir. 8 bitki adı birden çok dillidir. 101 bitki adı, Tabibnâme metninde 152 kere kullanılmıştır. Ayrıca 7 bitki adı, alt tür adlarıyla birlikte 14 kere kullanılmıştır. Tabibnâme was written by Fakîr Ahmed Şeyhzâde in the 18th century. The manuscript is in Turkish and includes the subjects of alternative medicine, pharmacy and plant science. The text also consists of political, religious, moral, medical and philosophical information. Therefore, Tabibnâme is very important both in terms of the information it contains about Turkish language and Turkish cultural history and medicine and pharmacy terminology due to its vocabulary use and linguistic features. 101 plant names were used in Tabibnâme. In this article, we examined these plant names in terms of diachronic phonetic changes. In addition, we examined whether or not these names are used in Turkish. Today, 35 plant names are used with various phonetic changes and 46 plant names are used in the same forms and 20 plant names are no longer used in Turkish. 27 plant names are Turkish, 25 are Arabic, 22 are Persian, 18 are Greek and 1 is Indonesian. 8 plant names are observed crosslinguistically. 101 plant names were used for 152 times in Tabibnâme. In addition, 7 plant names were used 14 times with the subtype names.

La présentation de M. Vinatier rassemble quinze années de recherche en écologie du paysage appliquée aux agrosystèmes, de l'étude des propriétés des paysages agricoles en terme de structure, composition et configuration jusqu'à celle des flux biotiques (bioagresseurs des cultures et insectes auxiliaires, végétation spontanée) et abiotiques (eau principalement) qui y circulent. Sa stratégie de recherche repose sur une manipulation des hétérogénéités du paysage pour mieux gérer deux services d'intérêt: la régulation de la ressource en eau et le maintien de la biodiversité fonctionnelle. Il procède selon un continuum observation-expérimentation-simulation pour mener à bien cette stratégie, en considérant l'agriculteur comme principal pilote de la restauration des fonctions des agrosystèmes. Ces perspectives de recherche, axées sur la poursuite de l'étude des relations duales eau-végétation, traiteront également de l'impact du changement climatique, de plus en plus prégnant dans les agrosystèmes méditerranéens et susceptible de déstabiliser durablement leur fonctionnement.

Background With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. Results We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. Conclusions With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1479-z) contains supplementary material, which is available to authorized users.

This article was published in the Weekly of the Association for the Promotion of Horticulture in the Royal States of Prussia for Gardening and Botany (Wochenschrift des Vereines zur Beförderung des Gartenbaues in den Königlich Preussischen Staaten für Gärtnerei und Pflanzenkunde), Berlin, Germany, on August 9, 1862. The author was the botanist Eduard Sell, german based then in San Ramón de Alajuela, Costa Rica. El presente artículo fue publicado en el Wochenschrift des Vereines zur Beförderung des Gartenbaues in den Königlich Preussischen Staaten für Gärtnerei und Pflanzenkunde (Semanario de la Asociación para la Promoción de la Horticultura en los Estados Reales de Prusia para la Jardinería y la Botánica), Berlín, Alemania, el 9 de agosto de 1862, bajo el título “Die Kautschukgewinnung in Costa-Rica”. El autor fue el botánico Eduard Sell, alemán radicado entonces en San Ramón de Alajuela, Costa Rica.

The formation of the haustorium in holoparasitic plants as demonstrated in Phelipanche ramosa is initiated through perception of a host-exudated cytokinin and a cytokinin signaling response., The heterotrophic lifestyle of parasitic plants relies on the development of the haustorium, a specific infectious organ required for attachment to host roots. While haustorium development is initiated upon chemodetection of host-derived molecules in hemiparasitic plants, the induction of haustorium formation remains largely unknown in holoparasitic species such as Phelipanche ramosa. This work demonstrates that the root exudates of the host plant Brassica napus contain allelochemicals displaying haustorium-inducing activity on P. ramosa germinating seeds, which increases the parasite aggressiveness. A de novo assembled transcriptome and microarray approach with P. ramosa during early haustorium formation upon treatment with B. napus root exudates allowed the identification of differentially expressed genes involved in hormone signaling. Bioassays using exogenous cytokinins and the specific cytokinin receptor inhibitor PI-55 showed that cytokinins induced haustorium formation and increased parasite aggressiveness. Root exudates triggered the expression of cytokinin-responsive genes during early haustorium development in germinated seeds, and bio-guided UPLC-ESI(+)-/MS/MS analysis showed that these exudates contain a cytokinin with dihydrozeatin characteristics. These results suggest that cytokinins constitutively exudated from host roots play a major role in haustorium formation and aggressiveness in P. ramosa.

International audience; The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis ‘Old Blush’ genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70–80 million years ago during the Cretaceous period.

Le mycologue et botaniste René Maire (1878-1949) était considéré prodigieux par ses pairs. De souche lorraine, il a découvert les plantes et les champignons dans la propriété familiale du Fréhaut avec son père Ernest qui était dans les « Eaux et Forêts ». Il publie sa première note scientifique à l’âge de 15 ans et soutient sa thèse de doctorat es sciences à 24 ans sur la cytologie et la taxonomie des champignons supérieurs. En 1908, il devient maître de conférences à la faculté des sciences de Caen, puis il obtient la chaire de botanique à l’Université d’Alger en 1911. Suite à des problèmes occulaires, il abandonne les études microscopiques et se lance dans l’étude de la flore de l’Afrique du Nord pendant presque 40 ans. Il décrit 2 500 espèces nouvelles. Ce travail monumental, en 16 volumes sera publié après sa mort grâce au concours de ses collègues M. Guinochet, L. Faurel et P. Quézel. L’originalité de René Maire est d’avoir été à la fois un homme de laboratoire et de terrain à une époque où la spécialisation se développait à grand pas. Il a eu deux passions entremêlées, celle du mycologue et du botaniste phytogéographe. Dans le contexte colonial de l’époque, René Maire a été en contact avec des nombreuses personnalités devenues célèbres comme Conrad Kilan, inventeur du pétrole saharien et le naturaliste Théodore Monod. A travers une vie consacrée uniquement à la science désintéressée, on a l’opportunité de comparer les conditions et le pourquoi de la recherche scientifique à un siècle de distance. Pour René Maire, le but était depuis son adolescence de déchiffrer les « arcanes de la nature » selon sa propre expression, donc d’explorer, de découvrir et de faire connaître la richesse végétale et mycologique du monde méditerranéen et saharien. The mycologist and botanist René Maire (1878-1949) was considered prodigious by his peers. Of Lorraine origin, he discovered the plants and mushrooms in the family property of Fréhaut with his father Ernest who worked in the «Waters and Forests». He published his first scientific note at 15 yers old and supported his doctoral thesis at 24 years on the cytology and taxonomy of superior fungi. In 1908, he became lecturer at the Faculty of Science of Caen, then he obtained the chair of botany at the University of Algiers in 1911. Because of eye problems, he abandoned the microscopic studies and devots his life into the study of the flora of North Africa for almost 40 years. It describes 2 500 new species. This monumental work in 16 volumes will be published after his death thanks to the collaboration of his colleagues M. Guinochet, L. Faurel and P. Quézel. The originality of René Maire is to have been both a man of laboratory and field at a time when specialization was developing rapidly. He had two intertwined passions, that of the mycologist and the phytogeographer botanist. In the colonial context of this time, René Maire was in contact with many famous personalities like the geologist Conrad Kilan, inventor of the Saharan oil and the naturalist Théodore Monod. Through a life devoted solely to selfless science, this is the opportunity to compare the conditions and the why of scientific research to a century away. For René Maire, the goal was since his adolescence to decipher the «mysteries of nature» according to his own expression, so to explore, to discover and to make known the plant and mycological wealth of the Mediterranean and Saharan world.

The shoot branching pattern is a determining phenotypic trait throughout plant development. During shoot branching, BRANCHED1 (BRC1) plays a master regulator role in bud outgrowth, and its transcript levels are regulated by various exogenous and endogenous factors. RhBRC1 (the homologous gene of BRC1 in Rosa hybrida) is a main branching regulator whose posttranscriptional regulation in response to sugar was investigated through its 3&prime, UTR. Transformed Rosa calluses containing a construction composed of the CaMV35S promoter, the green fluorescent protein (GFP) reporter gene, and the 3&prime, UTR of RhBRC1 (P35S:GFP::3&prime, UTRRhBRC1) were obtained and treated with various combinations of sugars and with sugar metabolism effectors. The results showed a major role of the 3&prime, UTR of RhBRC1 in response to sugars, involving glycolysis/the tricarboxylic acid cycle (TCA) and the oxidative pentose phosphate pathway (OPPP). In Rosa vegetative buds, sequence analysis of the RhBRC1 3&prime, UTR identified six binding motifs specific to the Pumilio/FBF RNA-binding protein family (PUF) and probably involved in posttranscriptional regulation. RhPUF4 was highly expressed in the buds of decapitated plants and in response to sugar availability in in-vitro-cultured buds. RhPUF4 was found to be close to AtPUM2, which encodes an Arabidopsis PUF protein. In addition, sugar-dependent upregulation of RhPUF4 was also found in Rosa calluses. RhPUF4 expression was especially dependent on the OPPP, supporting its role in OPPP-dependent posttranscriptional regulation of RhBRC1. These findings indicate that the 3&prime, UTR sequence could be an important target in the molecular regulatory network of RhBRC1 and pave the way for investigating new aspects of RhBRC1 regulation.

International audience; Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with similar to 100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.

International audience; Genetic and epigenetic variations are commonly known to underlie phenotypic plastic responses to environmental cues. however, the role of epigenetic variation in plastic responses harboring ecological significance in nature remains to be assessed. The shade avoidance response (SAR) of plants is one of the most prevalent examples of phenotypic plasticity. It is a phenotypic syndrome including stem elongation and multiple other traits. Its ecological significance is widely acknowledged, and it can be adaptive in the presence of competition for light. Underlying genes and pathways were identified, but evidence for its epigenetic basis remains scarce. We used a proven and accessible approach at the population level and compared global DNA methylation between plants exposed to regular light and three different magnitudes of shade in seven highlyinbred lines of snapdragon plants (Antirrhinum majus) grown in a greenhouse. Our results brought evidence of a strong SAR syndrome for which magnitude did not vary between lines. They also brought evidence that its magnitude was not associated with the global DNA methylation percentage for five of the six traits under study. The magnitude of stem elongation was significantly associated with global DNA demethylation. We discuss the limits of this approach and why caution must be taken with such results. In-depth approaches at the DNA sequence level will be necessary to better understand the molecular basis of the SAR syndrome

Texture plays a major role in the determination of fruit quality in apple. Due to its physiological and economic relevance, this trait has been largely investigated, leading to the fixation of the major gene PG1 controlling firmness in elite cultivars. To further improve fruit texture, the targeting of an undisclosed reservoir of loci with minor effects is compelling. In this work, we aimed to unlock this potential with a genomic selection approach by predicting fruit acoustic and mechanical features as obtained with a TA.XTplus texture analyzer in 537 individuals genotyped with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set (TRS) of 259 individuals were obtained for the acoustic linear distance (0.64). Prediction accuracy was further improved through the optimization of TRS size and composition according to the test set. With this strategy, a maximal accuracy of 0.81 was obtained when predicting the synthetic trait PC1 in the family ‘Gala × Pink Lady’. We discuss the impact of genetic relatedness and clustering on trait variability and predictability. Moreover, we demonstrated the need for a comprehensive dissection of the complex texture phenotype and the potentiality of using genomic selection to improve fruit quality in apple.HighlightA genomic selection study, together with the optimization of the training set, demonstrated the possibility to accurately predict texture sub-traits valuable for the amelioration of fruit quality in apple.

International audience; The extraction of desirable heritable traits for crop improvement from high-throughput phenotyping (HTP) observations remains challenging. We developed a modeling workflow named Digital Plant Phenotyping Platform, D3P, to access crop architectural traits from HTP observations. D3P couples the ADEL (architectural model of development based on L-systems) wheat (Triticum aestivum) model, that describes the time course of the three-dimensional architecture of wheat crops, with simulators of images acquired with HTP sensors. We demonstrated that a sequential assimilation of the green fraction derived from RGB (Red Green Blue) images of the crop into D3P provides accurate estimates of five key parameters (phyllochron, lamina length of the first leaf, rate of elongation of leaf lamina, number of green leaves at the start of leaf senescence and minimum number of green leaves) of the ADEL-Wheat model that drive the time course of green area index and the number of axes with more than three leaves at the end of the tillering period. However, leaf and tiller orientation and inclination characteristics were poorly estimated. D3P was also used to optimize the observational configuration. The results, obtained from in silico experiments conducted on wheat crops at several vegetative stages, showed that the accessible traits could be estimated accurately with observations made at 0{degree sign} and 60{degree sign} zenith view inclination with a temporal frequency of 100 {degree sign}Cd. This illustrates the potential of the proposed holistic approach that integrates all the available information into a consistent system for interpretation. The potential benefits and limitations of the approach are further discussed.

L’étude de la diversité de la flore arvale et rudérale du centre INRA Antilles-Guyane avait pour objectif d’inventorier l’ensemble des espèces végétales présentes sur nos parcelles expérimentales. Cet inventaire, basé sur les travaux du botaniste Jacques Fournet, nous a permis d’identifier et caractériser cette flore, de classer les espèces en fonction de leurs caractéristiques agronomiques, écologiques, et médicinales et ainsi d’en prévoir l’évolution. En nous appuyant sur la méthode phytosociologique, nous avons découpé notre zone d’études en plusieurs parties à partir d’une cartographie des parcelles du centre. A l’aide de quadrats et de transects, nous avons procédé par comptage des espèces trouvées selon leur fréquence. 205 espèces, dont sept nouvelles pour la Guadeloupe, ont ainsi été inventoriées pour l’ensemble de la dition que nous avons ensuite classées en fonction de services ou de nuisibilités par rapport à l’environnement et aux agrosystèmes. Il nous reste maintenant à comprendre l’organisation des communautés végétales, les dynamiques d’association, et les éventuels liens (traits fonctionnels, allélopathie) entre les plantes cultivées sur place et les herbes de nos champs., The study of the weed flora of the French Antilles and Guyana agronomic research center, aimed at making an inventory of all the plant species that occur in our fields. With the help of the book of the botanist Jacques Fournet, we could identify, characterize, and classify this flora according to its agronomic, ecological and medicinal characteristics, and thus, to predict its ecological dynamics. Based on phytosociological methodology, using a field map of our research center, we divided our main study area in smaller sets. With quadrats and line transects, we assessed species frequency. We found 205 species, including 7 new ones for Guadeloupe, in the entire prospected zone. Afterwards, we classified them in terms of services or harmfulness, for environment and agrosystems. We now need to understand the organization of plant communities, weeds association dynamics, and others interactions (functional traits, allelopathy) between crops and weeds.

National audience; Trees are able to grow high and to live old thanks to the remarkable properties of their wood. As a matter of a fact, wood delivers three major functions: (1) water conduction from roots to crown, (2) support of the ever-increasing mass of the growing tree and (3) storage of temporary reserves, important for tree growth over the years. In angiosperm trees, different wood cell types are affected to each of these functions. Fibers are involved in tree mechanical support, vessels in water conduction and parenchyma rays in starch and/or lipid storage during the resting period. In addition, these cell types have distinct developmental programs. While fibers and vessels are early-dying cells, parenchyma rays stay alive longer. Therefore wood is a complex patchwork of cells and its structure results from the three-dimensional assembly of the cell walls of dead fibers and vessels, interconnected with still living parenchyma rays. This great complexity stands as an obstacle when studying wood formation and the construction of wood properties. However, this can be circumvented thanks to the development of cell-specific approaches. We developed a non-destructive method based on ATR-FTIR imaging on poplar wood sections. This technology enables to collect IR-absorbance spectra from small areas of cross-sections, which makes possible to differentiate between wood cell-types or even between the different cell wall layers from a single fiber. We first demonstrated that spectra taken from fiber cell walls on cross-sections differed from spectra obtained from wood powder. We also showed that ATR-FTIR imaging is able to discriminate the cell walls of fibers, vessels and rays. These findings are in accordance with other studies [1], but with an improved spatial resolution. ATR-FTIR microspectroscopy is thus a promising tool to finely characterize the cell wall of different wood cell types. This work has been partly supported by the OPeNSPeNU project (funded by the Centre Val de Loire Region)

International audience; The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.

Dormancy and germination vigor are complex traits of primary importance for adaptation and agriculture. Intraspecific variation in cytoplasmic genomes and cytonuclear interactions were previously reported to affect germination in Arabidopsis using novel cytonuclear combinations that disrupt co-adaptation between natural variants of nuclear and cytoplasmic genomes. However, specific aspects of dormancy and germination vigor were not thoroughly explored, nor the parental contributions to the genetic effects. Here, we specifically assessed dormancy, germination performance and longevity of seeds from Arabidopsis plants with natural and new genomic compositions. All three traits were modified by cytonuclear reshuffling. Both depth and release rate of dormancy could be modified by a changing of cytoplasm. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, consistent with the idea that a single physiological consequence of the new genetic combination affected both traits oppositely. However, this was not always the case. Interestingly, the ability of parental accessions to contribute to significant cytonuclear interactions modifying the germination phenotype was different depending on whether they provided the nuclear or cytoplasmic genetic compartment. The observed deleterious effects of novel cytonuclear combinations (in comparison with the nuclear parent) were consistent with a contribution of cytonuclear interactions to germination adaptive phenotypes. More surprisingly, we also observed favorable effects of novel cytonuclear combinations, suggesting suboptimal genetic combinations exist in natural populations for these traits. Reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Taken together, our results strongly support that cytoplasmic genomes represent an additional resource of natural variation for breeding seed vigor traits.

International audience; Understanding the spatiotemporal dynamics of human-wildlife interfaces is important for the sustainable management of protected areas and wildlife conservation. We investigated the drivers of domestic and wild herbivore habitat selection at the edge of an unfenced protected area adjacent to Hwange National Park, Zimbabwe. We used GPS data to quantify the movement patterns of elephant bulls, buffalo and cattle at multiple scales and according to seasonal changes of surface water availability. Cattle, elephant and buffalo prefer open grassland habitats found close to water but elephant and buffalo avoid cattle differently. During the rainy season, cattle enter the protected area daily; buffalo avoid cattle completely at the home range scale, whereas elephant bulls avoid cattle at finer scales by favoring temporal niche shift. Elephant bulls avoid direct encounters with cattle (or people) during the day but come closer to the boundary and to water at night when cattle are kept in enclosures close to the homesteads. During the dry season, when cattle range further into the protected area in search of forage, buffalo and cattle spatial overlap increases as water dependence takes precedence over avoidance. Elephant bulls range closer to the boundary at night and increase the number of excursions into the Communal Area. Cattle herding creates a buffer zone between wildlife areas and human settlements because wild herbivores strongly avoid livestock and people. However, avoidance only lasts as long as resources are abundant. Our study suggests that long-term planning of both artificial water provisioning and traditional cattle herding practices could help maintaining spatial segregation and thus mitigate conservation conflicts such as pathogen transmission, crop raiding or livestock depredation.

Theory predicts that environmental challenges can shape the composition of populations, which is manifest at the molecular level. Previously, we demonstrated that oil pollution affected gene expression patterns and altered genetic variation in natural populations of the foundation salt marsh grass, Spartina alterniflora. Here, we used a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), to examine relationships among DNA sequence, DNA methylation, gene expression, and exposure to oil pollution. We documented genetic and methylation differentiation between oil-exposed and unexposed populations, suggesting that the Deepwater Horizon oil spill may have selected on genetic variation, and either selected on epigenetic variation or induced particular epigenotypes and expression patterns in exposed compared to unexposed populations. In support of the potential for differential response to the Deepwater Horizon oil spill, we demonstrate genotypic differences in response to oil under controlled conditions. Overall, these findings demonstrate genetic variation, epigenetic variation and gene expression are correlated to exposure to oil pollution, which may all contribute to the response to environmental stress.

International audience; Post-transcriptional regulation of gene expression plays a crucial role in many processes. In cells, it is mediated by diverse RNA-binding proteins. These proteins can influence mRNA stability, translation, and localization. The PUF protein family (Pumilio and FBF) is composed of RNA-binding proteins highly conserved among most eukaryotic organisms. Previous investigations indicated that they could be involved in many processes by binding corresponding motifs in the 3UTR or by interacting with other proteins. To date, most of the investigations on PUF proteins have been focused on Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae, while only a few have been conducted on Arabidopsis thaliana. The present article provides an overview of the PUF protein family. It addresses their RNA-binding motifs, biological functions, and post-transcriptional control mechanisms in Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, and Arabidopsis thaliana. These items of knowledge open onto new investigations into the relevance of PUF proteins in specific plant developmental processes.

As indoor horticulture gathers momentum, electric (also termed artificial) lighting systems with the ability to generate specific and tunable wavelengths have been developed and applied. While the effects of light quality on plant growth and development have been studied, authoritative and reliable sets of light formulae tailored for the cultivation of economically important plants and plant traits are lacking as light qualities employed across laboratories are inconsistent. This is due, at least in part, to the lack of molecular data for plants examined under electric lights in indoor environments. It has hampered progress in the field of indoor horticulture, in particular, the transition from small-scale indoor farming to commercial plant factories. Here, we review the effects of light quality on model and crop plants studied from a physiological, physical and biochemical perspective, and explain how functional genomics can be employed in tandem to generate a wealth of molecular data specific for plants cultivated under indoor lighting. We also review the current state of lighting technologies in indoor horticulture specifically discussing how recent narrow-bandwidth lighting technologies can be tailored to cultivate economically valuable plant species and traits. Knowledge gained from a complementary phenotypic and functional genomics approach can be harvested not only for economical gains but also for sustainable food production. We believe that this review serves as a platform that guides future light-related plant research., Indoor horticulture: Lighting the way to sustainability Tailored multidisciplinary approaches to hone sustainable indoor horticulture could significantly improve plant yields and crop quality. Advances in artificial lighting systems could transform commercial-scale indoor horticulture, but the current technology is limited by a lack of molecular data for plants grown under such lighting schemes. Aloysius Wong at Wenzhou-Kean University in Wenzhou, China, and co-workers reviewed research into the effects of light quality and differing wavelengths on plant growth. The team advocate the use of plant type-specific and functional genomics studies to examine light-determined molecular traits and associated gene expression. These could be used to build an extensive catalog of light qualities that enhance indoor crop yields and quality. Combining LED lights of different colors and wavelengths shows promise, and the researchers highlight the potential of tunable narrow wavelength lights, such as lasers.

International audience; Background and Aims: Several studies have found seasonal and temporal variability in leaf photosynthesis parameters in different crops. This variability depends upon the environment, the developmental stage of the plant and the presence or absence of sinks. Girdling involves the removal of the bark and phloem down to the youngest xylem all around the stem and prevents export of photoassimilates out of the stem. The load of developing fruits has often been reported to influence the individual net leaf photosynthesis rate (Pn) in tree crops. In this study, we chose (1) to model the key parameters of photosynthesis models of leaves (Pgmax, Rd, α and θ) as a function of time and using these two means (girdling and low fruit load) to alter the source-sink balance and (2) to compare three models: the rectangular and non-rectangular hyperbola model by Thornley, as well as the non-rectangular hyperbola model by Marshall and Biscoe.Methods: Six-year-old fruit-bearing branches of 10-year-old apple trees were used to study and model the seasonal variation of photosynthetic parameters in leaves of vegetative shoots, as a function of global fruit load (at the branch level), with or without girdling, during the growing season of 2015. Three treatments were applied: control, low load (LL) or low load + girdling (LLG). For each fruit-bearing branch, light-response curves of Pn for two leaves of vegetative shoots were measured at two different positions, proximal and distal.Key Results: The model of Marshall and Biscoe was the most accurate for the simulation of Pn in fruit-bearing branches of apple trees with time (season) and the three treatments applied.Conclusion: The present study proposed a way to model the photosynthesis rate by temporal and environmental variables only. A proper validation of this model will be necessary to extend its utilization and appreciate its predictive capacity fully.

Context Current production from natural forests will not satisfy future world demand for timber and fuel wood, and new land management options are required. Aims We explore an innovative production system that combines the production of short rotation coppice in wide alleys with the production of high-value trees on narrow strips of land; it is an alternative form of alley cropping which we propose to call ‘alley coppice’. The aim is to describe this alley coppice system and to illustrate its potential for producing two diverse products, namely high-value timber and energy wood on the same land unit. Methods Based on a comprehensive literature review, we compare the advantages and disadvantages of the alley coppice system and contrast the features with well-known existing or past systems of biomass and wood production. Results We describe and discuss the basic aspects of alley coppice, its design and dynamics, the processes of competition and facilitation, issues of ecology, and areas that are open for future research. Conclusion Based on existing knowledge, a solid foundation for the implementation of alley coppice on suitable land is presented, and the high potential of this system could be shown.

In mountain areas, hays are the main forage in winter diets for livestock. Barn-dried hays can be an alternative to traditional hays, which are generally characterized by a low feed value. The aim of this study was to compare the feed value of barn-dried hays with that of the fresh forage from a permanent meadow. The study was carried out over three periods during the first growth cycle of the meadow&rsquo, s vegetation (from 30 May to 3 June, from 13 to 17 June, and from 27 June to 1 July). Fresh forage and barn-dried hays of the same fresh forages were tested for dry matter digestibility (DMD), organic matter digestibility (OMD), and voluntary intake (VI). Both types of forage obtained each period were tested with an interval of 15 days. Chemical composition and OMD of forages did not change (p &gt, 0.05) according to the feeding method. However, the DMD values for barn-dried hays were higher (p &lt, 0.05) than for fresh forages at the end of the cycle. VI and digestible organic matter intake of barn-dried hays were higher (p &lt, 0.05) than that of fresh forages. In conclusion, barn-dried hays obtained from permanent grasslands presented a higher feed value than fresh forages.

Necrológica., No és la nostra intenció glossar aquí amb detall l’extensa i prolífica obra del professor Montserrat, don Pedro, com l’anomenaven a l’Instituto Pirenaico de Ecología (IPE-CSIC) de Jaca, i «el teu amic pirinenc, Pere», com signava algunes notes que ens enviava, sinó més aviat de retre un discret, però emocionat, homenatge a un eminent botànic i ecòleg que, de prop o de lluny, ha estat present a les nostres carreres científiques.

The effect of plant diversity on aboveground organisms and processes was largely studied but there is still a lack of knowledge regarding the link between plant diversity and soil characteristics. Here, we analyzed the effect of plant identity and diversity on the diversity of extractible soil organic compounds (ESOC) using 87 experimental grassland plots with different levels of plant diversity and based on a pool of over 50 plant species. Two pools of low molecular weight organic compounds, LMW1 and LMW2, were characterized by GC-MS and HPLC-DAD, respectively. These pools include specific organic acids, fatty acids and phenolics, with more organic acids in LMW1 and more phenolics in LMW2. Plant effect on the diversity of LMW1 and LMW2 compounds was strong and weak, respectively. LMW1 richness observed for bare soil was lower than that observed for all planted soils; and the richness of these soil compounds increased twofold when dominant plant species richness increased from 1 to 6. Comparing the richness of LMW1 compounds observed for a range of plant mixtures and for plant monocultures of species present in these mixtures, we showed that plant species richness increases the richness of these ESOC mainly through complementarity effects among plant species associated with contrasted spectra of soil compounds. This could explain previously reported effects of plant diversity on the diversity of soil heterotrophic microorganisms.

Tabîbnâme, 18. yüzyılda Nevşehirli Damat İbrahim Paşa'nın isteği üzerine Fakîr Ahmed Şeyhzâde tarafından yazılmıştır. Metin; alternatif tıp, eczacılık ve bitki bilim konularını içermektedir. Bu eser, birçok kaynağın günümüze ulaşmasını sağlayan Sultan I. Mahmud Han tarafından vakfedilmiştir.Eski tıp bilimindeki yaygın görüşte olduğu gibi bu eserde de birçok hastalığın sebebi olarak vücutta bulunan birtakım maddeler arasındaki dengenin bozulması gösterilmiştir. Bozulan dengeyi yerine getirebilmek için hekimler öncelikle dengesizliği oluşturması muhtemel maddenin eksikliğinin ya da fazlalığının teşhisini koyarlar. Sonrasında hangi maddenin hastaya şifa vereceğinin tahlilini yapar ve bu muayenenin ardından hastaya gerekli tedaviyi uygularlar. Bu içerikte yazılmış tıp kitapları bir dönem sonraki hekimlere kaynak niteliği taşımış ve günümüzdeki tıp biliminin temellerinin oluşmasında rol oynamışlardır. Çalışmamız dört kısımdan oluşmaktadır: Giriş, Dil İncelemesi, Çeviri Yazı Metin ve Dilbilgisel Dizin. Giriş Bölümünde Tabîbnâme adlı eserin yazarı, konusu ve yazıldığı dönem hakkında bilgi verilmiştir. Metnin ilk dört varağında yer alan giriş mahiyetindeki Arapça kısmın görselleri ve Türkçeye çevirileri bu bölümde yer almaktadır. İnceleme kısmında Tabîbnâme metninin biçim bilgisi, özellikleri ve söz varlığı ile ilgili bilgiler bulunmaktadır. Çeviri Yazılı Metin kısmında 70 varak 1456 satırdan oluşan metnin çeviri yazısı verilmiştir. Dizin kısmında Tabîbnâme metninde yer alan bütün biçim birimler dilbilgisi özelliklerine göre sıralanmıştır ve geçtikleri cümle ve satır numaralarıyla birlikte verilmiştir. Dizinde sözlük başı olarak kaydedilen tüm sözcüklerin hangi dile ait oldukları, Türkiye Türkçesindeki anlamları ve metinde geçen cümledeki anlamları verilmiştir. Anahtar Sözcükler: Tabîbnâme, Fakîr Ahmed Şeyhzâde, Alternatif Tıp, Botanik, Ezcacılık. Tabîbnâme was written by Fakîr Ahmed Şeyhzâde on the request of Nevşehirli Damat İbrahim Paşa in 18th century. This manuscript contains related topics as alternative medicine, pharmaceutics and botanics. Manuscript has endowed by Sultan Mahmud Han the First, who is provided access many important knowledge sources as this one to last till today.As the common opinion in old medicinal science, the main reason of many diseases is imbalancement among some matters in human body. This opinion stays same in this manuscript. To balance this imbalancement, physicians firstly diagnose the deficiency or excess of probable matter then they analyse the which matter can cure the patient and after this medical examination process, they apply the treatment to the patient. The books have written about similar contents as this one have played a great role of founding today's medicinal sciences and being sources of knowledge for physicians. Our dissertation consists of four main sections: Introduction, Grammar Analysis, Transcripted Text and Grammatical Index. In Introduction section, information has given about Tabîbnâme's author, main subject and era that it was written in. First eight pages of this manuscript are written in Arabic language and their translations to Turkish are placed in the Introduction section. In Grammar Analysis section, there are information about morphological contents and vocabulary of Tabîbnâme. Transcripted Text section consists 140 pages (1456 lines) of transcripted text of manuscript. Index section contains all of the morphemes in Tabîbnâme and they are put in order according to their grammatical features with their line numbers. All index entries have been given with their lingual origins, meanings in Turkish and where they were mentioned in manuscript with their contextual meanings. Keywords: Tabîbnâme, Fakîr Ahmed Şeyhzâde, Alternative Medicine, Botanics, Pharmaceutics. 365

This paper presents a 3D phenotyping method applied to sunflower, allowing to compute the leaf area of an isolated plant. This is a preliminary step towards the automated monitoring of leaf area and plant growth through the plant life cycle. First, a model-based segmentation method is applied to 3D data derived from RGB images acquired on sunflower plants grown in pots. The RGB image acquisitions are made al l around the isolated plant with a single hand-held standard camera (Sony A5100) and a 3D point cloud is computed using Structure from Motion and Multiple-view Stereo techniques [1, 2]. To do that, we used Bundler [3] and PMVS [4], Open Source libraries which can produce an accurate point cloud for plant phenotyping [5]. Then a model-based segmentation method is applied in order to segment and label the plant leaves, i.e. to split up the point cloud in regions, one for the stem, the other ones for the leaves [6, 7, 8]. The leaf label is determined using the elevation of its petiole insertion point on the stem, and the relative orientation with respect to the previous leaf. In sunflower, it is observed that the leaves labeled 5 and 6 have opposite orientations while insertion points of the remaining leaves have relative orientations around 137° with the previous ones [9]. Every leaf is then reconstructed with NURBS, as made in [5] and its area is computed from the triangular mesh. The segmentation method is validated comparing these areas with the ones measured manually using a planimeter. Results from segmentation and 3D reconstruction are presented on Figure 1; it is shown on Figure 2 that differences between automatic and manual measurements are less than 10%; Figure 3 shows how the extracted sunflower model is consistent with the known phyllotaxic model. The present results open interesting perspectives in direction of high-throughput sunflower phenotyping.

International audience; Phyllody is a flower abnormality in which leaf-like structures replace flower organs in all whorls. Here, we investigated the origin and the molecular mechanism of phyllody phenotype in Rosa chinensis cv. Viridiflora, an ancient naturally occurring Chinese mutant cultivar. Reciprocal grafting experiments and microscopy analyses, demonstrated that the phyllody phenotype in Viridiflora is not associated with phytoplasmas infection. Transcriptome comparisons by the mean of RNA-Seq identified 672 up regulated and 666 down-regulated genes in Viridiflora compared to its closely related genotype R. chinensis cv. Old Blush. A fraction of these genes are putative homologs of genes known to be involved in flower initiation and development. We show that in flower whorl 2 of Viridiflora, a down-regulation of the floral organ identity genes RcPISTILLATA (RcPI), RcAPETALA3 (RcAP3) and RcSEPALLATA3 (RcSEP3), together with an up -regulation of the putative homolog of the gene SUPPRESSOR of OVEREXPRESSION of CONSTANS1 (RcSOC1) are likely at the origin of the loss of petal identity and leaf -like structures formation. In whorl 3 of Viridiflora, ectopic expression of RcAPETALA2 (RcAP2) along with the down regulation of RcPI, RcAP3, and RcSEP3 is associated with loss of stamens identity and leaf -like structures formation. In whorl 4, the ectopic expression of RcAP2 associated with a down -regulation of RcSEP3 and of the C-class gene RcAGAMOUS correlate with loss of pistil identity. The latter also suggested the antagonist effect between the A and C class genes in the rose. Together, these data suggest that modified expression of the ABCE flower organ identity genes is associated with the phyllody phenotype in the rose Viridiflora and that these genes are important for normal flower organs development.

En 1997, le manque de données disponibles sur les Orchidaceae Juss. d'Afrique centrale atlantique et l'importance des menaces pesant sur la forêt africaine, comme sur les épiphytes qu'elles abritent, nous ont amenés à entreprendre une vaste campagne d'échantillonnage sur l'ensemble de cette région. L'examen du matériel récolté et des collections historiques a permis des avancées taxonomiques sur un grand nombre d'espèces endémiques de la région, ou jusqu'à présent considérées comme telles, et a abouti à la mise à jour de leurs aires de distribution. Des mises en synonymie sont proposées : Ancistrorhynchus constrictus Szlach. & Olszewski est inclus dans Ancistrorhynchus capitatus (Lindl.) Summerh. ; Bulbophyllum mayombeense Garay est mis en synonymie de Bulbophyllum schinzianum Kraenzl. var. schinzianum ; et Bulbophyllum kupense P.J.Cribb & B.J.Pollard devient synonyme de Bulbophyllum teretifolium Schltr. Une néotypification est faite pour cette dernière espèce, de même que pour Liparis goodyeroides Schltr. La distribution géographique de plusieurs taxons est modifiée : Aerangis megaphylla Summerh. est bien endémique de l'île d'Annobon, Polystachya superposita Rchb.f. est de nouveau considéré comme endémique du Cameroun et Liparis suborbicularis Summerh. n'est plus signalé qu_au Nigeria et au Cameroun. Trois nouvelles signalisations sont mentionnées : Aerangis bouarensis Chiron pour le Cameroun, Bulbophyllum schinzianum Kraenzl. var. schinzianum pour la République du Congo et Liparis goodyeroides Schltr. pour le Liberia. Les statuts de conservation selon les catégories et critères de l'IUCN sont donnés pour chaque taxon.

International audience; Accurate localization of phytoalexins is a key for better understanding their role. This work aims to localize stilbenes, the main phytoalexins of grapevine. The cellular localization of stilbene fluorescence induced by Plasmopara viticola, the agent of downy mildew, was determined in grapevine leaves of very susceptible, susceptible, and partially resistant genotypes during infection. Laser scanning confocal microscopy and microspectrofluorimetry were used to acquire UV-excited autofluorescence three-dimensional images and spectra of grapevine leaves 5-6 days after inoculation. This noninvasive technique of investigation in vivo was completed with in vitro spectrofluorimetric studies on pure stilbenes as their fluorescence is largely affected by the physicochemical environment in various leaf compartments. Viscosity was the major physicochemical factor influencing stilbene fluorescence intensity, modifying fluorescence yield by more than two orders of magnitude. Striking differences in the localization of stilbene fluorescence induced by P. viticola were observed between the different genotypes. All inoculated genotypes displayed stilbene fluorescence in cell walls of guard cells and periclinal cell walls of epidermal cells. Higher fluorescence intensity was observed in guard-cell walls than in any other compartment due to increased local viscosity. In addition stilbene fluorescence was found in epidermal cell vacuoles of the susceptible genotype and in the infected spongy parenchyma of the partially resistant genotype. The very susceptible genotype was devoid of fluorescence both in the epidermal vacuoles and the mesophyll. This strongly suggests that the resistance of grapevine leaves to P. viticola is correlated with the pattern of localization of induced stilbenes in host tissues.