A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome

Based on next-generation sequencing data, we assembled the mitochondrial (mt) genome of date palm (Phoenix dactylifera L.) into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp) over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast)-derived (10.3% with respect to the whole genome length) and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower) showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry), and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters–18S-5S rRNA, rps3-rpl16 and nad3-rps12–in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms

Atelier ORIXAS: Projeto Tripartite África/Brasil/França: luta contra a desertificação: promoção da segurança alimentar e redução da pobreza.

No âmbito do Programa de Cooperação Científica Tripartite entre a Agence Inter-établissements de Recherche pourle Développement (AIRD), Agence Panafricaine de la Grande Muraille Verte (APGMV) e o Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), o projeto ORIXAS "Observatórios Regionais Integrados de Regiões Árida, Semiáridas e Sub-úmidas secas" concebido em uma visão transversal, foca principalmente em metodologias e ferramentas para apoiar dispositivos de monitoramento ambiental para ser aplicado nos países inseridos na iniciativa africana Grande Muralha Verde - GMV (Burkina-Faso, Djibouti, Érythrée, Éthiopie, Mali, Mauritanie, Niger, Nigeria, Sénégal, Soudan, Tchad) e tem como objetivo desenvolver abordagens metodológicas e produtos compartilhados para melhorar a avaliação e monitoramento da desertificação e os impactos diretos ou indiretos de iniciativas para lutar contra o desmatamento e desertificação no âmbito da GMV. Esta publicação contempla aspectos metodológicos utilizados pelo projeto "ORIXAS" durante a primeira oficina de trabalho coletivo África-Brasil-França - Atelier (MAISON DE LA TÉLÉDÉTECTION), realizada de 10 a 19 de junho de 2014, em Montpellier França, objetivando informar a forma de execução dos estudos que vêm sendo realizados no escopo do projeto, visando principalmente a luta contra a desertificação, promoção da segurança alimentar e redução da pobreza nos países inseridos na iniciativa africana Grande Muralha Verde - GMV.bitstream/item/123193/1/DOC-174-Atelier-Orixas.pd

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite

Sunlight-Exposed Biofilm Microbial Communities Are Naturally Resistant to Chernobyl Ionizing-Radiation Levels

BACKGROUND: The Chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. Though studies of these effects on plants and animals are abundant, the study of how Chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. Environments enduring extreme desiccation and UV radiation, such as sunlight exposed biofilms could in principle select for organisms highly resistant to ionizing radiation as well. METHODOLOGY/PRINCIPAL FINDINGS: To test this hypothesis, we explored the diversity of microorganisms belonging to the three domains of life by cultivation-independent approaches in biofilms developing on concrete walls or pillars in the Chernobyl area exposed to different levels of radiation, and we compared them with a similar biofilm from a non-irradiated site in Northern Ireland. Actinobacteria, Alphaproteobacteria, Bacteroidetes, Acidobacteria and Deinococcales were the most consistently detected bacterial groups, whereas green algae (Chlorophyta) and ascomycete fungi (Ascomycota) dominated within the eukaryotes. Close relatives to the most radio-resistant organisms known, including Rubrobacter species, Deinococcales and melanized ascomycete fungi were always detected. The diversity of bacteria and eukaryotes found in the most highly irradiated samples was comparable to that of less irradiated Chernobyl sites and Northern Ireland. However, the study of mutation frequencies in non-coding ITS regions versus SSU rRNA genes in members of a same actinobacterial operational taxonomic unit (OTU) present in Chernobyl samples and Northern Ireland showed a positive correlation between increased radiation and mutation rates. CONCLUSIONS/SIGNIFICANCE: Our results show that biofilm microbial communities in the most irradiated samples are comparable to non-irradiated samples in terms of general diversity patterns, despite increased mutation levels at the single-OTU level. Therefore, biofilm communities growing in sunlight exposed substrates are capable of coping with increased mutation rates and appear pre-adapted to levels of ionizing radiation in Chernobyl due to their natural adaptation to periodical desiccation and ambient UV radiation

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes

Conséquences de la nuisibilité des mauvaises herbes sur la production du blé d'hiver en Tunisie : les seuils d'intervention et la rentabilité du désherbage

Consequence of negative effects of weeds on winter wheat crop in Tunisia : economic tresholds and weed control rentability. The evolution of diclofopmethyl + mecoprop weed control on winter wheat has been followed up during 8 years in 13 experimental sites through the north of Tunisia. In the trials, the level of pluriannual yield of the untreated control, the yield increase due to weed control, the relative losses, the economic thresholds and the weed control rentability have been successively studied. The results show that the winter weath weed control by diclofopmethyl + mecoprop must be set into a technical route as a necessary cultural operation to increase the productivity of the farming estates

Computational Study of a Possible Improvement of Cancer Detection by Diffuse Optical Tomography

Abstract In general, malignant tumors manifest an increase of the refractive index compared to the normal tissue which encircles them. So, medical imaging by diffuse optical tomography should take advantage from the emergence of the refractive index as a supplementary contrast parameter. The present paper gives a new computational framework within which theoretical aspect of cancer detection by diffuse optical tomography can be studied. We use radiative transfer theory in a varying refractive index biological tissue. In our previous works, Legendre transform was used as an innovative view to handle the angular derivative terms in the case of uniform refractive index spherical medium. In this paper, we try to extend this technique to modelling near infrared radiation interaction with biological tissue in a rectangular geometry. In biomedical optics, our analysis can be considered as a forward problem solution in a diffuse optical tomography imaging scheme. We consider a rectangular biological tissue-like domain with spatially varying refractive index submitted to a near infrared continuous light source. Interaction of radiation with the biological material into the medium is handled by a radiative transfer model. In the studied situation, the model displays two angular redistribution terms that are treated with Legendre integral transform. Transmitted radiance on the boundary is computed. The model is used to study a possible detection of abnormalities in a general biological tissue. The effect of the embedded non-homogenous objects on the transmitted signal is studied. Particularly, detection of targets of localized heterogeneous inclusions within the tissue is discussed. Results show that models accounting for variation of refractive index can yield useful predictions about the target and the location of abnormal inclusions within the tissue