Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

Abstract Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection

Selection of coatings for tribological applications

Les revêtements sont souvent utilisés pour réduire le frottement et protéger les surfaces contre l usure. Cependant, choisir le revêtement approprié pour une application tribologique donnée est toujours compliqué pare que la réponse tribologique d un système revêtu dépend de beaucoup trop de facteurs. Les objectifs de cette thèse sont de développer un outil de pré-sélection de revêtements, et de proposer quelques approches permettant d évaluer et de comparer des revêtements. Basé sur l étude de la littérature et sur trois études de cas tribologiques, un outil de pré-sélection est développé, en considérant tous les aspects des exigences requises et des limites d application et caractéristiques des revêtements. Deux études expérimentales sont ensuite effectuées. Un revêtement de MoS2 pulvérisé sous pression est examiné dans trois différentes configurations d essai pour identifier l effet des conditions d essai sur sa performance tribologique. La durée de vie de ce revêtement peut être prévue par les courbes maîtresses basées sur l énergie dissipée. Cinq revêtements de type vernis de glissement sont également étudiés par des techniques simples d évaluation et par des essais de fretting. Les performances tribologiques de revêtements dépendent de leur propriétés, et les techniques simples dévaluation peuvent être utilisées pour éliminer de mauvais revêtements, lors du processus de choix. Les performances tribologiques des revêtements sont évaluées en comparant les courbes maîtresses reliant durée de vie et énergie dissipée. Le meilleur revêtement peut alors être choisi, en comparant synthétiquement les revêtements selon divers aspects dans un diagramme polaire.Coatings are often used to reduce friction and protect the substrate surface from wear. However, selecting the appropriate coating from numerous ones for a given tribological application is still complicated because the tribological response of a coating system depends on many factors. The objectives of the thesis are to develop a coating pre-selection tool, and to propose some approaches to evaluate and compare coatings, sequentially to help the coating selection. Based on the study of literature and three different tribological cases, a pre-selection tool is developed by comprehensively considering the requirements and limits of applications and the characteristics of coatings. Two kinds of experiments are carried out to understand the relationships between tribological behaviors and running conditions and coating properties. Pressure sprayed MoS2 coating is investigated under three contact configurations to identify the effect of test conditions on its tribological performance. The coating lifetime can be predicted by relevant dissipated energy master curves. 5 bonded solid lubricant coatings are studied by simple evaluation techniques and fretting tests. The tribological performances of the coatings are closely related to their properties, and the simple evaluation techniques can be used to screen out the poor coatings. The tribological performances of the coatings are evaluated by comparing their dissipated energy coating lifetime master curves. The best coating can be selected by synthetically comparing the coatings from various aspects in a polar diagram.LYON-Ecole Centrale (690812301) / SudocSudocFranceF

The first complete chloroplast genome of Fagopyrum leptopodum (Diels) Hedberg (Caryophyllales: Polygonaceae) with phylogenetic implications

In the present study, we sequenced and assembled the complete chloroplast genome of Fagopyrum leptopodum (Diels) Hedberg. The chloroplast genome of F. leptopodum was composed of 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The F. leptopodum chloroplast genome is 159,375 bp in length, with a GC content of 37.81%. Phylogenetic analysis based on the combined chloroplast gene dataset indicated that the F. leptopodum exhibited a close relationship with Fagopyrum luojishanense

An energy harvesting shock absorber for powering on-board electrical equipment in freight trains

Summary: To realize smart detection and safe operation of freight trains, a continuous and stable energy source is required for electrical equipment on the train. It is a feasible scheme to harvest the vibration energy of train suspension to supply power for on-board electrical equipment. This paper presents an energy-harvesting shock absorber (EHSA) based on the slider-crank mechanism and ratchet-pawl mechanism, which provide a vibration reduction effect and renewable electricity. To determine the damping performance and the power generation performance of EHSA, a dynamic model is established based on MATLAB. According to the tests on the mechanical testing and sensing (MTS) bench, the maximum power generation mechanical efficiency of the EHSA is 67.75%, and the maximum output power of the EHSA is 1.65W. In addition, the charging tests on the MTS bench show that the proposed device is applicable to power on-board electrical equipment on freight trains

Carbon Starved Anther Encodes a MYB Domain Protein That Regulates Sugar Partitioning Required for Rice Pollen Development[W][OA]

The authors identified a rice R2R3 MYB transcription factor, Carbon Starved Anther (CSA), that regulates sugar partitioning from leaves to anthers and is required for the production of functional pollen. CSA directly regulates the expression of the monosaccharide transporter gene MST8, which encodes a key component of the anther sugar unloading pathway

TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

Abstract Background Although ductal carcinoma in situ (DCIS) is a non-invasive breast cancer, many DCIS lesions may progress to invasive cancer and the genes and pathways responsible for its progression are largely unknown. FGFR1 plays an important role in cell proliferation, differentiation and carcinogenesis. The purpose of this study is to examine the roles of FGFR1 signaling in gene expression, cell proliferation, tumor growth and progression in a non-invasive DCIS model. Methods DCIS.COM cells were transfected with an empty vector to generate DCIS-Ctrl cells. DCIS-iFGFR1 cells were transfected with an AP20187-inducible iFGFR1 vector to generate DCIS-iFGFR1 cells. iFGFR1 consists of the v-Src myristoylation membrane-targeting sequence, FGFR1 cytoplasmic domain and the AP20187-inducible FKBP12 dimerization domain, which simulates FGFR1 signaling. The CRISPR/Cas9 system was employed to knockout ERK1, ERK2 or TNFAIP3 in DCIS-iFGFR1 cells. Established cell lines were treated with/without AP20187 and with/without FGFR1, MEK, or ERK1/2 inhibitor. The effects of these treatments were determined by Western blot, RNA-Seq, real-time RT-PCR, cell proliferation, mammosphere growth, xenograft tumor growth, and tumor histopathological assays. Results Activation of iFGFR1 signaling in DCIS-iFGFR1 cells enhanced ERK1/2 activities, induced partial epithelial-to-mesenchymal transition (EMT) and increased cell proliferation. Activation of iFGFR1 signaling promoted DCIS growth and progression to invasive cancer derived from DCIS-iFGFR1 cells in mice. Activation of iFGFR1 signaling also altered expression levels of 946 genes involved in cell proliferation, migration, cancer pathways, and other molecular and cellular functions. TNFAIP3, a ubiquitin-editing enzyme, is upregulated by iFGFR1 signaling in a FGFR1 kinase activity and in an ERK2-dependent manner. Importantly, TNFAIP3 knockout not only inhibited the AP20187-induced proliferation and tumor growth of DCIS-iFGFR1 cells, but also further reduced baseline proliferation and tumor growth of DCIS-iFGFR1 cells without AP20187 treatment. Conclusions Activation of iFGFR1 promotes ERK1/2 activity, EMT, cell proliferation, tumor growth, DCIS progression to invasive cancer, and altered the gene expression profile of DCIS-iFGFR1 cells. Activation of iFGFR1 upregulated TNFAIP3 in an ERK2-dependent manner and TNFAIP3 is required for iFGFR1 activation-promoted DCIS.COM cell proliferation, mammosphere growth, tumor growth and progression. These results suggest that TNFAIP3 may be a potential target for inhibiting DCIS growth and progression promoted by FGFR1 signaling

Effects of <i>Eurotium cristatum</i> Fermentation on Tartary Buckwheat Leaf Tea: Sensory Analysis, Volatile Compounds, Non-Volatile Profile and Antioxidant Activity

Background: Eurotium cristatum (E. cristatum) is the probiotic fungus in Fu-brick tea, with which fermentation brings a unique flavor and taste and health-promoting effects. Tartary buckwheat leaves are rich in functional active substances such as flavonoids and phenolic compounds, yet are not effectively utilized. Methods: Tartary buckwheat leaves were processed into raw green tea first and subsequently fermented with E. cristatum to develop a novel fermented leaf tea. The tea quality was evaluated by the aspects of the sensory scores by E-tongue, the volatile compounds by HS-SPME-GC-MS, the non-volatile profile by biochemical and UPLC-MS/MS methods and the antioxidant activity by the colorimetric assay. Results: Fermented leaf tea displayed a golden yellow color, a unique “flower” aroma and a dark-tea taste, with an improved sensory acceptability. Fermentation raised the content of volatile heterocyclic and aromatic compounds, alkenes and other aromatic components, which produced a unique floral flavor. The proportion of sour, bitter and astringency accounting non-volatile compounds such as phenolic acids and amino acids decreased, while the proportion of umami and sweet accounting substances such as responsible amino acids increased. Fermented leaf tea displayed a relative stronger total antioxidant activity against ABTS. Conclusion: E. cristatum fermentation exerted positive effects on Tartary buckwheat leaf tea quality

The FLORAL ORGAN NUMBER4 Gene Encoding a Putative Ortholog of Arabidopsis CLAVATA3 Regulates Apical Meristem Size in Rice

To understand the molecular mechanism regulating meristem development in the monocot rice (Oryza sativa), we describe here the isolation and characterization of three floral organ number4 (fon4) alleles and the cloning of the FON4 gene. The fon4 mutants showed abnormal enlargement of the embryonic and vegetative shoot apical meristems (SAMs) and the inflorescence and floral meristems. Likely due to enlarged SAMs, fon4 mutants produced thick culms (stems) and increased numbers of both primary rachis branches and floral organs. We identified FON4 using a map-based cloning approach and found it encodes a small putatively secreted protein, which is the putative ortholog of the Arabidopsis (Arabidopsis thaliana) CLAVATA3 (CLV3) gene. FON4 transcripts mainly accumulated in the small group of cells at the apex of the SAMs, whereas the rice ortholog of CLV1 (FON1) is expressed throughout the SAMs, suggesting that the putative FON4 ligand might be sequestered as a possible mechanism for rice meristem regulation. Exogenous application of the peptides FON4p and CLV3p corresponding to the CLV3/ESR-related (CLE) motifs of FON4 and CLV3, respectively, resulted in termination of SAMs in rice, and treatment with CLV3p caused consumption of both rice and Arabidopsis root meristems, suggesting that the CLV pathway in limiting meristem size is conserved in both rice and Arabidopsis. However, exogenous FON4p did not have an obvious effect on limiting both rice and Arabidopsis root meristems, suggesting that the CLE motifs of Arabidopsis CLV3 and FON4 are potentially functionally divergent

In-silico prediction of digested fragments of the rice genome.

<p>(A) In-silico digestion with TaqαI of rice genome, showing 130,940 digested fragments between 400–600 bp in size. The X axis indicates the length of digested fragments; The Y axis indicates the number of digested fragments. (B) Density distribution of TaqαI recognition sites in the rice genome. The X axis indicates twelve chromosomes; The Y axis indicates the number of restriction enzyme sites. The result showed the restriction digestion sites for TaqαI were evenly distributed in the rice genome.</p