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Статті в журналах з теми "Executor genes"
1
Ji, Zhiyuan, Wei Guo, Xifeng Chen, Chunlian Wang, and Kaijun Zhao. "Plant Executor Genes." International Journal of Molecular Sciences 23, no. 3 (January 28, 2022): 1524. http://dx.doi.org/10.3390/ijms23031524.
Повний текст джерелаАнотація:
Executor (E) genes comprise a new type of plant resistance (R) genes, identified from host–Xanthomonas interactions. The Xanthomonas-secreted transcription activation-like effectors (TALEs) usually function as major virulence factors, which activate the expression of the so-called “susceptibility” (S) genes for disease development. This activation is achieved via the binding of the TALEs to the effector-binding element (EBE) in the S gene promoter. However, host plants have evolved EBEs in the promoters of some otherwise silent R genes, whose expression directly causes a host cell death that is characterized by a hypersensitive response (HR). Such R genes are called E genes because they trap the pathogen TALEs in order to activate expression, and the resulting HR prevents pathogen growth and disease development. Currently, deploying E gene resistance is becoming a major component in disease resistance breeding, especially for rice bacterial blight resistance. Currently, the biochemical mechanisms, or the working pathways of the E proteins, are still fuzzy. There is no significant nucleotide sequence homology among E genes, although E proteins share some structural motifs that are probably associated with the signal transduction in the effector-triggered immunity. Here, we summarize the current knowledge regarding TALE-type avirulence proteins, E gene activation, the E protein structural traits, and the classification of E genes, in order to sharpen our understanding of the plant E genes.
2
Wang, Jun, Dongsheng Tian, Keyu Gu, Xiaobei Yang, Lanlan Wang, Xuan Zeng, and Zhongchao Yin. "Induction of Xa10-like Genes in Rice Cultivar Nipponbare Confers Disease Resistance to Rice Bacterial Blight." Molecular Plant-Microbe Interactions® 30, no. 6 (June 2017): 466–77. http://dx.doi.org/10.1094/mpmi-11-16-0229-r.
Повний текст джерелаАнотація:
Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive bacterial diseases throughout the major rice-growing regions in the world. The rice disease resistance (R) gene Xa10 confers race-specific disease resistance to X. oryzae pv. oryzae strains that deliver the corresponding transcription activator-like (TAL) effector AvrXa10. Upon bacterial infection, AvrXa10 binds specifically to the effector binding element in the promoter of the R gene and activates its expression. Xa10 encodes an executor R protein that triggers hypersensitive response and activates disease resistance. ‘Nipponbare’ rice carries two Xa10-like genes in its genome, of which one is the susceptible allele of the Xa23 gene, a Xa10-like TAL effector-dependent executor R gene isolated recently from ‘CBB23’ rice. However, the function of the two Xa10-like genes in disease resistance to X. oryzae pv. oryzae strains has not been investigated. Here, we designated the two Xa10-like genes as Xa10-Ni and Xa23-Ni and characterized their function for disease resistance to rice bacterial blight. Both Xa10-Ni and Xa23-Ni provided disease resistance to X. oryzae pv. oryzae strains that deliver the matching artificially designed TAL effectors (dTALE). Transgenic rice plants containing Xa10-Ni and Xa23-Ni under the Xa10 promoter provided specific disease resistance to X. oryzae pv. oryzae strains that deliver AvrXa10. Xa10-Ni and Xa23-Ni knock-out mutants abolished dTALE-dependent disease resistance to X. oryzae pv. oryzae. Heterologous expression of Xa10-Ni and Xa23-Ni in Nicotiana benthamiana triggered cell death. The 19-amino-acid residues at the N-terminal regions of XA10 or XA10-Ni are dispensable for their function in inducing cell death in N. benthamiana and the C-terminal regions of XA10, XA10-Ni, and XA23-Ni are interchangeable among each other without affecting their function. Like XA10, both XA10-Ni and XA23-Ni locate to the endoplasmic reticulum (ER) membrane, show self-interaction, and induce ER Ca2+ depletion in leaf cells of N. benthamiana. The results indicate that Xa10-Ni and Xa23-Ni in Nipponbare encode functional executor R proteins, which induce cell death in both monocotyledonous and dicotyledonous plants and have the potential of being engineered to provide broad-spectrum disease resistance to plant-pathogenic Xanthomonas spp.
3
Liu, Zhiquan, Yujun Zhu, Huanbin Shi, Jiehua Qiu, Xinhua Ding, and Yanjun Kou. "Recent Progress in Rice Broad-Spectrum Disease Resistance." International Journal of Molecular Sciences 22, no. 21 (October 28, 2021): 11658. http://dx.doi.org/10.3390/ijms222111658.
Повний текст джерелаАнотація:
Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized.
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Ji, Zhiyuan, Hongda Sun, Yena Wei, Man Li, Hongjie Wang, Jiangmin Xu, Cailin Lei, Chunlian Wang, and Kaijun Zhao. "Ectopic Expression of Executor Gene Xa23 Enhances Resistance to Both Bacterial and Fungal Diseases in Rice." International Journal of Molecular Sciences 23, no. 12 (June 11, 2022): 6545. http://dx.doi.org/10.3390/ijms23126545.
Повний текст джерелаАнотація:
Bacterial blight (BB) and bacterial leaf streak (BLS), caused by phytopathogenic bacteria Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively, are the most serious bacterial diseases of rice, while blast, caused by Magnaporthe oryzae (M. oryzae), is the most devastating fungal disease in rice. Generating broad-spectrum resistance to these diseases is one of the key approaches for the sustainable production of rice. Executor (E) genes are a unique type of plant resistance (R) genes, which can specifically trap transcription activator-like effectors (TALEs) of pathogens and trigger an intense defense reaction characterized by a hypersensitive response in the host. This strong resistance is a result of programed cell death induced by the E gene expression that is only activated upon the binding of a TALE to the effector-binding element (EBE) located in the E gene promoter during the pathogen infection. Our previous studies revealed that the E gene Xa23 has the broadest and highest resistance to BB. To investigate whether the Xa23-mediated resistance is efficient against Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of BLS, we generated a new version of Xa23, designated as Xa23p1.0, to specifically trap the conserved TALEs from multiple Xoc strains. The results showed that the Xa23p1.0 confers broad resistance against both BB and BLS in rice. Moreover, our further experiment on the Xa23p1.0 transgenic plants firstly demonstrated that the E-gene-mediated defensive reaction is also effective against M. oryzae, the causal agent of the most devastating fungal disease in rice. Our current work provides a new strategy to exploit the full potential of the E-gene-mediated disease resistance in rice.
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Yang, Xu, Kai Chen, Yaohui Wang, Dehong Yang, and Yongping Huang. "The Sex Determination Cascade in the Silkworm." Genes 12, no. 2 (February 23, 2021): 315. http://dx.doi.org/10.3390/genes12020315.
Повний текст джерелаАнотація:
In insects, sex determination pathways involve three levels of master regulators: primary signals, which determine the sex; executors, which control sex-specific differentiation of tissues and organs; and transducers, which link the primary signals to the executors. The primary signals differ widely among insect species. In Diptera alone, several unrelated primary sex determiners have been identified. However, the doublesex (dsx) gene is highly conserved as the executor component across multiple insect orders. The transducer level shows an intermediate level of conservation. In many, but not all examined insects, a key transducer role is performed by transformer (tra), which controls sex-specific splicing of dsx. In Lepidoptera, studies of sex determination have focused on the lepidopteran model species Bombyx mori (the silkworm). In B. mori, the primary signal of sex determination cascade starts from Fem, a female-specific PIWI-interacting RNA, and its targeting gene Masc, which is apparently specific to and conserved among Lepidoptera. Tra has not been found in Lepidoptera. Instead, the B. mori PSI protein binds directly to dsx pre-mRNA and regulates its alternative splicing to produce male- and female-specific transcripts. Despite this basic understanding of the molecular mechanisms underlying sex determination, the links among the primary signals, transducers and executors remain largely unknown in Lepidoptera. In this review, we focus on the latest findings regarding the functions and working mechanisms of genes involved in feminization and masculinization in Lepidoptera and discuss directions for future research of sex determination in the silkworm.
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Kibriya, Muhammad G., Maruf Raza, Mohammed Kamal, Zahidul Haq, Rupash Paul, Andrew Mareczko, Brandon L. Pierce, Habibul Ahsan, and Farzana Jasmine. "Relative Telomere Length Change in Colorectal Carcinoma and Its Association with Tumor Characteristics, Gene Expression and Microsatellite Instability." Cancers 14, no. 9 (April 30, 2022): 2250. http://dx.doi.org/10.3390/cancers14092250.
Повний текст джерелаАнотація:
We compared tumor and adjacent normal tissue samples from 165 colorectal carcinoma (CRC) patients to study change in relative telomere length (RTL) and its association with different histological and molecular features. To measure RTL, we used a Luminex-based assay. We observed shorter RTL in the CRC tissue compared to paired normal tissue (RTL 0.722 ± SD 0.277 vs. 0.809 ± SD 0.242, p = 0.00012). This magnitude of RTL shortening (by ~0.08) in tumor tissue is equivalent to RTL shortening seen in human leukocytes over 10 years of aging measured by the same assay. RTL was shorter in cancer tissue, irrespective of age group, gender, tumor pathology, location and microsatellite instability (MSI) status. RTL shortening was more prominent in low-grade CRC and in the presence of microsatellite instability (MSI). In a subset of patients, we also examined differential gene expression of (a) telomere-related genes, (b) genes in selected cancer-related pathways and (c) genes at the genome-wide level in CRC tissues to determine the association between gene expression and RTL changes. RTL shortening in CRC was associated with (a) upregulation of DNA replication genes, cyclin dependent-kinase genes (anti-tumor suppressor) and (b) downregulation of “caspase executor”, reducing apoptosis.
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Read, Andrew C., Mathilde Hutin, Matthew J. Moscou, Fabio C. Rinaldi, and Adam J. Bogdanove. "Cloning of the Rice Xo1 Resistance Gene and Interaction of the Xo1 Protein with the Defense-Suppressing Xanthomonas Effector Tal2h." Molecular Plant-Microbe Interactions® 33, no. 10 (October 2020): 1189–95. http://dx.doi.org/10.1094/mpmi-05-20-0131-sc.
Повний текст джерелаАнотація:
The Xo1 locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused by Xanthomonas oryzae pv. oryzicola and X. oryzae pv. oryzae, respectively. Resistance is triggered by pathogen-delivered transcription activator-like effectors (TALEs) independent of their ability to activate transcription and is suppressed by truncated variants called truncTALEs, common among Asian strains. By transformation of the susceptible variety Nipponbare, we show that one of 14 nucleotide-binding, leucine-rich repeat (NLR) protein genes at the locus, with a zinc finger BED domain, is the Xo1 gene. Analyses of published transcriptomes revealed that the Xo1-mediated response is more similar to those mediated by two other NLR resistance genes than it is to the response associated with TALE-specific transcriptional activation of the executor resistance gene Xa23 and that a truncTALE dampens or abolishes activation of defense-associated genes by Xo1. In Nicotiana benthamiana leaves, fluorescently tagged Xo1 protein, like TALEs and truncTALEs, localized to the nucleus. And endogenous Xo1 specifically coimmunoprecipitated from rice leaves with a pathogen-delivered, epitope-tagged truncTALE. These observations suggest that suppression of Xo1-function by truncTALEs occurs through direct or indirect physical interaction. They further suggest that effector coimmunoprecipitation may be effective for identifying or characterizing other resistance genes.
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Xie, Zhen, Bingxiao Yan, Jianyao Shou, Jun Tang, Xin Wang, Keran Zhai, Jiyun Liu, et al. "A nucleotide-binding site-leucine-rich repeat receptor pair confers broad-spectrum disease resistance through physical association in rice." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1767 (January 14, 2019): 20180308. http://dx.doi.org/10.1098/rstb.2018.0308.
Повний текст джерелаАнотація:
Rice blast caused by Magnaporthe oryzae is the most destructive fungal disease in crops, greatly threatening rice production and food security worldwide. The identification and utilization of broad-spectrum resistance genes are considered to be the most economic and effective method to control the disease. In the past decade, many blast resistance ( R ) genes have been identified, which mainly encode nucleotide-binding leucine-rich repeat (NLR) receptor family and confer limited race-specific resistance to the fungal pathogen. Resistance genes conferring broad-spectrum blast resistance are still largely lacking. In this study, we carried out a map-based cloning of the new blast R locus Pizh in variety ZH11. A bacterial artificial chromosome (BAC) clone of 165 kb spanning the Pizh locus was sequenced and identified 9 NLR genes, among which only Pizh-1 and Pizh-2 were expressed. Genetic complementation experiments indicated that Pizh-1 but not Pizh-2 alone could confer blast resistance. Intriguingly, both mutations on Pizh-1 and Pizh-2 by CRISPR-Cas9 abolished the Pizh- mediated resistance. We also observed that Pizh-1 -mediated resistance was partially dependent on Pizh-2 . Pizh-1 and Pizh-2 form a complex of NLRs through direct interaction. This suggests that Pizh-1 may function as the executor NLR and Pizh-2 as a ‘helper’ NLR that shares functional redundancy with other NLRs. Our current study provides not only a good tool for rice disease resistance breeding but also deep insight into NLR association and function in plant immunity. This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.
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Mihailovic, Smiljana, Vesna Coric, Tanja Radic, Ana Savic Radojevic, Marija Matic, Dejan Dragicevic, Milica Djokic, et al. "The Association of Polymorphisms in Nrf2 and Genes Involved in Redox Homeostasis in the Development and Progression of Clear Cell Renal Cell Carcinoma." Oxidative Medicine and Cellular Longevity 2021 (April 17, 2021): 1–15. http://dx.doi.org/10.1155/2021/6617969.
Повний текст джерелаАнотація:
Deleterious effects of SNPs found in genes encoding transcriptional factors, as well as antioxidant and detoxification enzymes, are disputable; however, their functional significance seems to modify the risk for clear cell renal cell carcinoma (ccRCC) development and progression. We investigated the effect of specific Nrf2, SOD2, GPX1 gene variants and GSTP1ABCD haplotype on ccRCC risk and prognosis and evaluated the association between GSTP1 and regulatory (JNK1/2) and executor (caspase-3) apoptotic molecule expression in ccRCC tissue samples and the presence of GSTP1 : JNK1/2 protein : protein interactions. Genotyping was performed in 223 ccRCC patients and 336 matched controls by PCR-CTTP and qPCR. Protein expression was analyzed using immunoblot, while the existence of GSTP1 : JNK1 protein : protein interactions was investigated by immunoprecipitation experiments. An increased risk of ccRCC development was found among carriers of variant genotypes of both SOD2 rs4880 and GSTP1 rs1695 polymorphisms. Nrf2 rs6721961 genetic polymorphism in combination with both rs4880 and rs1695 showed higher ccRCC risk as well. Haplotype analysis revealed significant risk of ccRCC development in carriers of the GSTP1C haplotype. Furthermore, GSTP1 variant forms seem to affect the overall survival in ccRCC patients, and the proposed molecular mechanism underlying the GSTP1 prognostic role might be the presence of GSTP1 : JNK1/2 protein : protein interactions.
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Madaro, Luca, Valeria Marrocco, Piera Fiore, Paola Aulino, Piera Smeriglio, Sergio Adamo, Mario Molinaro та Marina Bouché. "PKCθ signaling is required for myoblast fusion by regulating the expression of caveolin-3 and β1D integrin upstream focal adhesion kinase". Molecular Biology of the Cell 22, № 8 (15 квітня 2011): 1409–19. http://dx.doi.org/10.1091/mbc.e10-10-0821.
Повний текст джерелаАнотація:
Fusion of mononucleated myoblasts to form multinucleated myofibers is an essential phase of skeletal myogenesis, which occurs during muscle development as well as during postnatal life for muscle growth, turnover, and regeneration. Many cell adhesion proteins, including integrins, have been shown to be important for myoblast fusion in vertebrates, and recently focal adhesion kinase (FAK), has been proposed as a key mediator of myoblast fusion. Here we focused on the possible role of PKCθ, the PKC isoform predominantly expressed in skeletal muscle, in myoblast fusion. We found that the expression of PKCθ is strongly up-regulated following freeze injury–induced muscle regeneration, as well as during in vitro differentiation of satellite cells (SCs; the muscle stem cells). Using both PKCθ knockout and muscle-specific PKCθ dominant-negative mutant mouse models, we observed delayed body and muscle fiber growth during the first weeks of postnatal life, when compared with wild-type (WT) mice. We also found that myofiber formation, during muscle regeneration after freeze injury, was markedly impaired in PKCθ mutant mice, as compared with WT. This phenotype was associated with reduced expression of the myogenic differentiation program executor, myogenin, but not with that of the SC marker Pax7. Indeed in vitro differentiation of primary muscle-derived SCs from PKCθ mutants resulted in the formation of thinner myotubes with reduced numbers of myonuclei and reduced fusion rate, when compared with WT cells. These effects were associated to reduced expression of the profusion genes caveolin-3 and β1D integrin and to reduced activation/phosphorylation of their up-stream regulator FAK. Indeed the exogenous expression of a constitutively active mutant form of PKCθ in muscle cells induced FAK phosphorylation. Moreover pharmacologically mediated full inhibition of FAK activity led to similar fusion defects in both WT and PKCθ-null myoblasts. We thus propose that PKCθ signaling regulates myoblast fusion by regulating, at least in part, FAK activity, essential for profusion gene expression.
Дисертації з теми "Executor genes"
1
Lachaux, Marlène. "Caractérisation de nouvelles sources de résistance aux souches africaines de Xanthomonas oryzae pv. oryzae, agent de la bactériose vasculaire du riz." Thesis, Montpellier, 2022. http://www.theses.fr/2022MONTG011.
Повний текст джерелаАнотація:
La bactériose vasculaire du riz, causée par la bactérie à Gram-négatif Xanthomonas oryzae pv. oryzae (Xoo), est une des maladies les plus dévastatrices des cultures de riz en Afrique de l'Ouest et en Asie. Grâce à son système de sécrétion de type III, Xoo injecte ses effecteurs de type TAL ("Transcription Activator-Like") au sein de la cellule végétale hôte. Grâce à leurs signaux de localisation nucléaire (NLS), les TALE sont ensuite importés au noyau où ils ont la capacité de se fixer, par le biais de leur région centrale composée de répétitions en tandem, au promoteur d'un gène hôte au niveau d’une séquence appelée EBE (pour "Effector Binding Element"), et d’initier la transcription via leur domaine d'activation (AD). Xoo est ainsi capable de moduler l'expression des gènes de la plante en détournant sa machinerie transcriptionnelle et d'induire des gènes dits de sensibilité (S) qui favorisent le développement de la bactérie et donc de la maladie. Dans certains cas, les TALE peuvent activer des gènes dits exécuteur (E) dont l'expression entraîne des réactions de défenses de la plante et provoque la résistance. Des analyses de diversité génétique ont montré que Xoo comprend deux lignées correspondant aux souches Africaines et Asiatiques. Elles se distinguent notamment par le nombre de gènes tal qu'elles possèdent, mais aussi par le type de résistance qu’elles élicitent. De fait, aucune des races identifiées en Afrique n’a été retrouvée en Asie.L'objectif de cette thèse était d'identifier des sources de résistance chez le riz afin d’apporter de nouvelles stratégies de contrôle de la bactériose vasculaire du riz en Afrique. Des analyses préliminaires avaient permis de mettre en évidence par une approche de gain de fonction, plusieurs TALE de la souche Malienne MAI1 ayant une activité potentielle d'avirulence sur les variétés de riz IR64, CT13432 et FKR47N. Afin de confirmer ces résultats, une approche par perte de fonction a été entreprise, consistant à cribler une banque de mutants BAI3Δtal générés dans la souche Burkinabè BAI3, dont le TALome (répertoire de gènes tal) est très proche de celui de MAI1, sur chacune des trois variétés résistantes. Ces travaux ont permis de valider le rôle d’avirulence de TalD et TalI sur les variétés IR64 et CT13432, respectivement. Il a également été démontré que la résistance de CT13432 aux souches MAI1 et BAI3 résultait de la combinaison de deux mécanismes de résistance, l'un reposant sur l'induction, médiée par TalI, d'un gène exécuteur encore inconnu, et l'autre sur un allèle du gène de résistance Xa1. Dans un second temps, afin d'approfondir nos connaissances sur la résistance conférée par IR64 aux souches Africaines de Xoo, le criblage d'une population de lignées recombinantes de génération F11, provenant du croisement entre la variété résistante IR64 et la variété sensible Azucena, a été mené. Cette étude a permis de confirmer deux QTL, qABB-7 et qABB-11, préalablement rapportés dans une autre étude, et d'identifier quatre nouveaux QTL de résistance aux souches Africaines de Xoo. Pour finir, des analyses de type RNAseq ont été réalisées sur la variété résistante IR64 et la variété sensible Nipponbare, dont les génomes séquencés sont disponibles, afin de caractériser leur transcriptome en réponse à des souches Africaines de Xoo. L'activité d'avirulence de TalD chez IR64 ayant été démontrée, une comparaison de l'expression différentielle des gènes indu its par MAI1 et BAI3 avec le mutant BAI3ΔtalD a été effectuée, permettant d'identifier de potentiels gènes E candidats expliquant la résistance TalD-dépendante de IR64. Ces travaux représentent une première étape dans le développement de nouvelles stratégies basées sur le déploiement de sources de résistance durables afin de lutter contre la bactériose vasculaire du riz en AfriqueBacterial Leaf Blight (BLB), caused by the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of rice in West Africa and Asia. Xoo injects through its type-III secretion system a full cocktail of TAL ("Transcription Activator-Like") effectors into the host plant cell. By means of their nuclear localization signals (NLS) TALEs are next imported into the host nucleus where they bind through central tandem repeats to host promoter targets at a sequence called EBE ("Effector Binding Element"), with the final aim of initiating gene transcription thanks to their activation domain (AD). Xoo is thus able to modulate the expression of plant genes by hijacking the plant transcriptional machinery and induce so-called susceptibility (S) genes that favor the development of the bacterium and disease consequently. In some cases, TALEs can activate so-called executor (E) genes whose expression leads to plant defense reactions and results in resistance. Genetic diversity analyses have shown that Xoo is comprised of two lineages that corresponding to strains from Africa for one and Asian strains for the other. African and Asian Xoo differ in their number of tal genes, but also in the type of resistance they elicit. Noteworthy, none of the races identified in Africa have been found in Asia.The objective of this thesis was to identify sources of resistance in rice in order to provide new strategies for the control of BLB in Africa. In a gain-of-function approach, preliminary analyses identified several TALEs of the Malian strain MAI1 with potential avirulence activity on the rice varieties IR64, CT13432 and FKR47N. To further confirm these results, a loss-of-function approach was undertaken, consisting in the inoculation of a library of BAI3Δtal mutants deriving from the Xoo Burkinabe strain BAI3, whose TALome (tal genes repertoire) is very similar to that of MAI1, on each of the three resistant varieties. This work validated the avirulence role of TalD and TalI on the matching rice varieties IR64 and CT13432, respectively. We also showed that the resistance exhibited by CT13432 against MAI1 and BAI3 results of the combination of two resistance mechanisms, one based on the TalI-mediated induction of an as yet unknown executor gene, and the other on an allele of the Xa1 resistance gene. In a second step, in order to deepen our knowledge on the resistance conferred by IR64 to African Xoo strains, the screening of a population of recombinant inbred lines of F11 generation, resulting from the cross between the resistant variety IR64 and the susceptible variety Azucena, was conducted. This study confirmed two QTL, qABB-7 and qABB-11, previously reported in another study, and also identified four new QTL of resistance against African Xoo strains. Finally, RNAseq analyses were performed on the resistant variety IR64 and the susceptible variety Nipponbare, which genomes are sequenced, to characterize their transcriptome in response to African Xoo. The avirulence activity of TalD in IR64 being demonstrated, a comparison of the differential expression of genes induced by MAI1 and BAI3 with the BAI3ΔtalD mutant was performed, allowing the identification of potential candidate E-genes induced by TalD in IR64. This work represents a first step in the development of new strategies based on the deployment of sustainable sources of resistance to control BLB in Africa
2
Lachaux, Marlène. "Caractérisation de nouvelles sources de résistance aux souches africaines de Xanthomonas oryzae pv. oryzae, agent de la bactériose vasculaire du riz." Thesis, Université de Montpellier (2022-….), 2022. http://www.theses.fr/2022UMONG011.
Повний текст джерелаАнотація:
La bactériose vasculaire du riz, causée par la bactérie à Gram-négatif Xanthomonas oryzae pv. oryzae (Xoo), est une des maladies les plus dévastatrices des cultures de riz en Afrique de l'Ouest et en Asie. Grâce à son système de sécrétion de type III, Xoo injecte ses effecteurs de type TAL ("Transcription Activator-Like") au sein de la cellule végétale hôte. Grâce à leurs signaux de localisation nucléaire (NLS), les TALE sont ensuite importés au noyau où ils ont la capacité de se fixer, par le biais de leur région centrale composée de répétitions en tandem, au promoteur d'un gène hôte au niveau d’une séquence appelée EBE (pour "Effector Binding Element"), et d’initier la transcription via leur domaine d'activation (AD). Xoo est ainsi capable de moduler l'expression des gènes de la plante en détournant sa machinerie transcriptionnelle et d'induire des gènes dits de sensibilité (S) qui favorisent le développement de la bactérie et donc de la maladie. Dans certains cas, les TALE peuvent activer des gènes dits exécuteur (E) dont l'expression entraîne des réactions de défenses de la plante et provoque la résistance. Des analyses de diversité génétique ont montré que Xoo comprend deux lignées correspondant aux souches Africaines et Asiatiques. Elles se distinguent notamment par le nombre de gènes tal qu'elles possèdent, mais aussi par le type de résistance qu’elles élicitent. De fait, aucune des races identifiées en Afrique n’a été retrouvée en Asie.L'objectif de cette thèse était d'identifier des sources de résistance chez le riz afin d’apporter de nouvelles stratégies de contrôle de la bactériose vasculaire du riz en Afrique. Des analyses préliminaires avaient permis de mettre en évidence par une approche de gain de fonction, plusieurs TALE de la souche Malienne MAI1 ayant une activité potentielle d'avirulence sur les variétés de riz IR64, CT13432 et FKR47N. Afin de confirmer ces résultats, une approche par perte de fonction a été entreprise, consistant à cribler une banque de mutants BAI3Δtal générés dans la souche Burkinabè BAI3, dont le TALome (répertoire de gènes tal) est très proche de celui de MAI1, sur chacune des trois variétés résistantes. Ces travaux ont permis de valider le rôle d’avirulence de TalD et TalI sur les variétés IR64 et CT13432, respectivement. Il a également été démontré que la résistance de CT13432 aux souches MAI1 et BAI3 résultait de la combinaison de deux mécanismes de résistance, l'un reposant sur l'induction, médiée par TalI, d'un gène exécuteur encore inconnu, et l'autre sur un allèle du gène de résistance Xa1. Dans un second temps, afin d'approfondir nos connaissances sur la résistance conférée par IR64 aux souches Africaines de Xoo, le criblage d'une population de lignées recombinantes de génération F11, provenant du croisement entre la variété résistante IR64 et la variété sensible Azucena, a été mené. Cette étude a permis de confirmer deux QTL, qABB-7 et qABB-11, préalablement rapportés dans une autre étude, et d'identifier quatre nouveaux QTL de résistance aux souches Africaines de Xoo. Pour finir, des analyses de type RNAseq ont été réalisées sur la variété résistante IR64 et la variété sensible Nipponbare, dont les génomes séquencés sont disponibles, afin de caractériser leur transcriptome en réponse à des souches Africaines de Xoo. L'activité d'avirulence de TalD chez IR64 ayant été démontrée, une comparaison de l'expression différentielle des gènes indu its par MAI1 et BAI3 avec le mutant BAI3ΔtalD a été effectuée, permettant d'identifier de potentiels gènes E candidats expliquant la résistance TalD-dépendante de IR64. Ces travaux représentent une première étape dans le développement de nouvelles stratégies basées sur le déploiement de sources de résistance durables afin de lutter contre la bactériose vasculaire du riz en AfriqueBacterial Leaf Blight (BLB), caused by the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of rice in West Africa and Asia. Xoo injects through its type-III secretion system a full cocktail of TAL ("Transcription Activator-Like") effectors into the host plant cell. By means of their nuclear localization signals (NLS) TALEs are next imported into the host nucleus where they bind through central tandem repeats to host promoter targets at a sequence called EBE ("Effector Binding Element"), with the final aim of initiating gene transcription thanks to their activation domain (AD). Xoo is thus able to modulate the expression of plant genes by hijacking the plant transcriptional machinery and induce so-called susceptibility (S) genes that favor the development of the bacterium and disease consequently. In some cases, TALEs can activate so-called executor (E) genes whose expression leads to plant defense reactions and results in resistance. Genetic diversity analyses have shown that Xoo is comprised of two lineages that corresponding to strains from Africa for one and Asian strains for the other. African and Asian Xoo differ in their number of tal genes, but also in the type of resistance they elicit. Noteworthy, none of the races identified in Africa have been found in Asia.The objective of this thesis was to identify sources of resistance in rice in order to provide new strategies for the control of BLB in Africa. In a gain-of-function approach, preliminary analyses identified several TALEs of the Malian strain MAI1 with potential avirulence activity on the rice varieties IR64, CT13432 and FKR47N. To further confirm these results, a loss-of-function approach was undertaken, consisting in the inoculation of a library of BAI3Δtal mutants deriving from the Xoo Burkinabe strain BAI3, whose TALome (tal genes repertoire) is very similar to that of MAI1, on each of the three resistant varieties. This work validated the avirulence role of TalD and TalI on the matching rice varieties IR64 and CT13432, respectively. We also showed that the resistance exhibited by CT13432 against MAI1 and BAI3 results of the combination of two resistance mechanisms, one based on the TalI-mediated induction of an as yet unknown executor gene, and the other on an allele of the Xa1 resistance gene. In a second step, in order to deepen our knowledge on the resistance conferred by IR64 to African Xoo strains, the screening of a population of recombinant inbred lines of F11 generation, resulting from the cross between the resistant variety IR64 and the susceptible variety Azucena, was conducted. This study confirmed two QTL, qABB-7 and qABB-11, previously reported in another study, and also identified four new QTL of resistance against African Xoo strains. Finally, RNAseq analyses were performed on the resistant variety IR64 and the susceptible variety Nipponbare, which genomes are sequenced, to characterize their transcriptome in response to African Xoo. The avirulence activity of TalD in IR64 being demonstrated, a comparison of the differential expression of genes induced by MAI1 and BAI3 with the BAI3ΔtalD mutant was performed, allowing the identification of potential candidate E-genes induced by TalD in IR64. This work represents a first step in the development of new strategies based on the deployment of sustainable sources of resistance to control BLB in Africa
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Dorer, Russell. "Saccharomyces cerevisiae cells execute a default pathway to select a mate in the absence of pheromone gradients /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/10285.
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Herrington, Robert Lloyd. "Transcriptional profiling of resting and actively cycling long-term and short-term hematopoietic stem cell populations identifies genes potentially involved in the specification, maintenance, and execution of self-renewal." 2007. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=789027&T=F.
Повний текст джерелаКниги з теми "Executor genes"
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Lee, Vincent. Vilcabamba. Edited by Sonia Alconini and Alan Covey. Oxford University Press, 2018. http://dx.doi.org/10.1093/oxfordhb/9780190219352.013.27.
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Peru’s Zona de Vilcabamba was the scene of the post-Conquest 35-year struggle by the Inca to remain free of Spanish domination, and the base from which they fought to regain their empire. This chapter discusses that conflict and the physical and historical setting in which it occurred, including Pachacuti’s 1440 conquest of the region, his royal estate at Vitcos, Manco Inca’s retreat there from Spanish pursuit in 1537, and his withdrawal to Vilcabamba, in the jungles of Espíritu Pampa in 1539. Also discussed are the burning of the sun temple at Ñusta Ispanan in 1570, the death of Titu Cusi and martyrdom of Padre Diego Ortiz in 1571, Viceroy Francisco de Toledo’s conquest of the province, and the capture and execution of Tupac Amaru Inca in 1572. Finally, the modern explorations of Hiram Bingham, Gene Savoy, and the Lees and the scholarly work of John Hemming are noted.
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Krasnow, Donna H., and M. Virginia Wilmerding. Motor Learning and Control for Dance. Human Kinetics, 2015. http://dx.doi.org/10.5040/9781718212749.
Повний текст джерелаАнотація:
As dance training evolves and becomes more complex, knowledge of motor behavior is foundational in helping dancers learn and master new skills and become more efficient in integrating the skills. Motor Learning and Control for Dance is the first resource to address motor learning theory from a dance perspective. Educators and students preparing to teach will learn practical ways to connect the science behind dance to pedagogy in order to prepare dancers for performance. Dancers interested in performance from the recreational to professional levels will learn ways to enhance their technical and artistic progress. In language accessible even to those with no science background, Motor Learning and Control for Dance showcases principles and practices for students, artists, and teachers. The text offers a perspective on movement education not found in traditional dance training while adding to a palette of tools and strategies for improving dance instruction and performance. Aspiring dancers and instructors will explore how to develop motor skills, how to control movement on all levels, and—most important—how motor skills are best taught and learned. The authors, noted experts on motor learning and motor control in the dance world, explore these features that appeal to students and instructors alike: • Dance-specific photos, examples, and figures illustrate how to solve common problems various dance genres. • The 16 chapters prepare dance educators to teach dancers of all ages and abilities and support the development of dance artists and students in training and performance. • An extensive bibliography of sports and dance science literature allows teachers and performers to do their own research. • A list of key terms is at the beginning of each chapter with an accompanying glossary at the back of the book. Part I presents an overview of motor behavior, covering motor development from birth to early adulthood. It provides the essential information for teaching posture control and balance, the locomotor skills underlying a range of complex dance skills, and the ballistic skills that are difficult to teach and learn, such as grand battement and movements in street dance. Part II explores motor control and how movement is planned, initiated, and executed. Readers will learn how the nervous system organizes the coordination of movement, the effects of anxiety and states of arousal on dance performance, how to integrate the senses into movement, and how speed and accuracy interact. Part III investigates methods of motor learning for dancers of all ages. Readers will explore how to implement a variety of instructional strategies, determine the best approaches for learning dance skills, and motivate and inspire dancers. This section also discusses how various methods of practice can help or hinder dancers, strategies for improving the recall of dance skills and sequences, and how to embrace somatic practice and its contribution to understanding imagery and motor learning. Motor Learning and Control for Dance addresses many related topics that are important to the discipline, such as imagery and improvisation. This book will help performers and teachers blend science with pedagogy to meet the challenge of artistry and technique in preparing for dance performaance.
Частини книг з теми "Executor genes"
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Batut, Bérénice, Marius van den Beek, Maria A. Doyle, and Nicola Soranzo. "RNA-Seq Data Analysis in Galaxy." In Methods in Molecular Biology, 367–92. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1307-8_20.
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AbstractA complete RNA-Seq analysis involves the use of several different tools, with substantial software and computational requirements. The Galaxy platform simplifies the execution of such bioinformatics analyses by embedding the needed tools in its web interface, while also providing reproducibility. Here, we describe how to perform a reference-based RNA-Seq analysis using Galaxy, from data upload to visualization and functional enrichment analysis of differentially expressed genes.
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Gallo, Diego S., Jose R. Brunheroto, and Kyung Dong Ryu. "Fast Full-System Execution-Driven Performance Simulator for Blue Gene/Q." In Euro-Par 2013 Parallel Processing, 16–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-40047-6_4.
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Jiang, Jie, Peter Philippen, Michael Knobloch, and Bernd Mohr. "Performance Measurement and Analysis of Transactional Memory and Speculative Execution on IBM Blue Gene/Q." In Lecture Notes in Computer Science, 26–37. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-09873-9_3.
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Harold, Franklin M. "From Egg to Organism." In On Life, 131–50. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780197604540.003.0010.
Повний текст джерелаАнотація:
How an egg turns into an organism continues to baffle the imagination. We can describe how it happens and many of the particulars, but still struggle to comprehend how events at the levels of genes and cells produce a fruit fly, a sea urchin, or a baby. The fertilized egg, at bottom a single cell, undergoes multiple cycles of division with concurrent differentiation and transformations of shape, resulting in a multicellular embryo whose several regions are committed to develop into distinct organs. Differentiation relies on elaborate networks of control on gene expression that promote certain genes and silence others. Spatial organization of the embryo commonly involves diffusible “morphogens,” hormone-like substances that instruct cells as to their developmental fate. Chemical gradients are supplemented by diverse processes that draw on active transport, mechanical forces, and cell migration. Genes do not hold a comprehensive blueprint for development. They operate in the context of cells that are directed by both genes and self-organization, and there is no plan separable from its execution. How an egg turns into an organism may no longer be mysterious or miraculous, but it remains as wondrous as ever that an assemblage of lifeless molecules can build a butterfly.
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Zeidman, Lawrence A. "Forced sterilization under the NazisPreventing people with neuropsychiatric disorders from polluting the German gene pool." In Brain Science under the Swastika, 319–70. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780198728634.003.0008.
Повний текст джерелаАнотація:
The first negative eugenic measure passed by the Hitler regime in July 1933 was the forced sterilization law, which primarily targeted neuropsychiatric patients with “feeblemindedness,” schizophrenia, and epilepsy. Also included were Huntington’s chorea, bipolar disorder, and alcoholism, along with other congenital defects. The law was based on a prior Weimar Germany draft that was never enacted. Although Germany was late to enact a sterilization law, it was more rapidly implemented and executed than in other countries. In 12 years of the Nazi regime, 400,000 people were forcibly sterilized. The hypocritical execution of the law, supposedly foolproof because of the use of “hereditary health courts” and appeals courts, resulted in people of lower socioeconomic background being preferentially affected, and also in non-hereditary forms of diseases (e.g., symptomatic epilepsy) being included. Most in German neuroscience also seemed unconcerned with the 0.5% mortality rate of sterilization procedures, resulting in at least 2000 deaths.
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Rasula, Jed. "Genre and Extravagance." In Genre and Extravagance in the Novel, 1–22. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780192897763.003.0001.
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This chapter outlines the theme running through the book as a whole: hybrid form and extravagant execution of narrative designs have accompanied the novel throughout its history. The canonical “great novels” have therefore been exceptions to any presumed rule that would define the parameters of the novel as genre. These exceptions equivocate between history and fiction, fantasy and reality, and by so doing establish the sui generis as a paradoxically normative venture within the literary domain of the novel. As a relatively late development in literary history, the novel lacks the defining parameters set out for other genres in antiquity. It has therefore thrived by assimilating material from any and all other genres, blending them into hybrid examples that become canonical by being unrepeatable.
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Pali, Erlina, and Mark Powell. "FACS-Based High-Throughput Functional Screening of Genetic Libraries for Drug Target Discovery." In Flow Cytometry for Biotechnology. Oxford University Press, 2005. http://dx.doi.org/10.1093/oso/9780195183146.003.0016.
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A primary aim of functional genomics in pharmaceutical applications is to identify genes whose function is critical to maintaining a disease state and to determining whether therapeutic modulation of this function results in a beneficial clinical response. However, although many genomic approaches can identify disease-associated genes, lengthy follow-up studies are usually required to determine which genes are functionally important and are causally linked to a given disease. In contrast, retrovirally mediated functional genetic screening approaches enable rapid identification of physiologically relevant targets. Genetic screens are designed to detect functional changes that result in changes in cellular function that correlate with disease amelioration. Retroviruses possess unique properties that allow delivery of complex libraries of potential genetic effectors to a variety of cell types. These effectors can perturb specific interactions required to achieve a complete functional response and establish a direct relationship with a cellular function. Functional screens are employed to select for cells endowed with a desired genetic effector–induced change in phenotype. Identification of a genetic effector that causes an altered cellular phenotype that correlates with clinical benefit can explicate critical signaling components suitable for therapeutic intervention. Flow cytometry represents a uniquely powerful methodology to monitor complex multiparametric changes of individual cells in large populations. In conjunction with recent advances in retroviral expression systems, the sensitivity and speed of flow cytometry enables a highly efficient functional screening of complex libraries in a wide range of cell-based assays. In this chapter, we discuss the process of functional genetic screening and show specific examples of its implementation. We focus particularly on the critical parameters involved in the design and execution of functional genetic screening approaches based on FACS (fluorescence activated cell sorter). Retroviruses provide a powerful method of introducing genes into mammalian cells in an efficient and stable manner. Recent advances in retroviral vector technology and packaging systems have extended their application to allow efficient and stable delivery of highly diverse libraries encoding various types of genetic effectors, including cDNAs, peptides, and ribozymes, into a broad range of cell types.
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Wills, David. "The Time of the Trap Door." In Killing Times, 54–86. Fordham University Press, 2019. http://dx.doi.org/10.5422/fordham/9780823283521.003.0003.
Повний текст джерелаАнотація:
This chapter offers an examination of the refining of the instant of execution that takes place with the introduction of trap door gallows in the seventeenth century and, more spectacularly and explicitly, in the late eighteenth century with the French Revolution and the guillotine. The death penalty is thereby distinguished from torture and a post-Enlightenment conception of punishment is introduced, lasting to the present. But the guillotine is bloody, and that underscores a complex visuality of the death penalty that also obtains during the same time period, playing out across diverse genres such as the execution sermon, political and scientific discourses relating to the guillotine, Supreme Court descriptions of crimes, and practices of an entity such as the Islamic State. What develops concurrent with the guillotine—yet remains constant through all those examples--is a form of realist photographic visuality.
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Cronin, Thomas W., Sönke Johnsen, N. Justin Marshall, and Eric J. Warrant. "Introduction." In Visual Ecology. Princeton University Press, 2014. http://dx.doi.org/10.23943/princeton/9780691151847.003.0001.
Повний текст джерелаАнотація:
This introductory chapter talks about how every creature is guided by its eyes as it carries out its accustomed behaviors. Each animal's eyes allows it to execute the behavior necessary for its survival. This study of how visual systems function to meet the ecological needs of animals is called visual ecology. Researchers who work at various levels of inquiry, from genes to behavior, call themselves visual ecologists, but all are primarily concerned with how animals use vision for natural tasks and behaviors. Although the outcomes of visual ecological research may well have implications for health or may be applicable for use in engineering or technology, the research itself centers on the animal of interest and on how it employs its visual system to meet its own ecological needs.
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Ravindran, Priya, S. Jayanthi, Arun Kumar Sivaraman, Dhanalakshmi R, A. Muralidhar, and Rajiv Vincent. "Proficient Mining of Informative Gene from Microarray Gene Expression Dataset Using Machine Intelligence." In Advances in Parallel Computing. IOS Press, 2021. http://dx.doi.org/10.3233/apc210076.
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The quick improvement of DNA microarray innovation empowers analysts to quantify the expression levels of thousands of genomic data and permits scientists effortlessly pick up and understanding the mind-boggling prediction in tumors based on genomic expression levels. The application in malignancy has been demonstrated and extraordinary achievement has been performed in both conclusion and clarification using the neurotic methodologies. In many cases, DNA microarray information about gene contains a large number of qualities and the majority of them are turned out to be uninformative and excess. In the interim, little size of tests of microarray information undermines the determination precision of factual models. In this way, choosing profoundly discriminative qualities from crude quality genetic expression can enhance the execution of genetic prediction and chopped down the cost of medicinal analysis. Pearson Correlation based Feature Selection strategy with machine learning methodologies is effective to locate a conspicuous arrangement of components which can be utilized to anticipate and idealize the blend of quality to analyze the disease. As conflicting to the customary cross approval, filter one cross approval technique is connected for the analyses. As needs be, the proposed blend between the PCBFS and Machine Learning methodology is an effective apparatus for disease grouping and can be actualized as a genuine clinical supportive system.
Тези доповідей конференцій з теми "Executor genes"
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Johar, Alreem, Najlaa Al-Thani, Sara Al-Hadidi, Elyes Dlissi, Mahmoud Mahoud, and Nahla Eltai. "Antibiotic Resistance and Virulence Gene Patterns Associated with Avian Pathogenic Escherichia coli from Broiler Chickens in Qatar." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2021. http://dx.doi.org/10.29117/quarfe.2021.0102.
Повний текст джерелаАнотація:
Introduction: Avian Pathogenic Escherichia coli (APEC) is the contributing agent behind the avian infectious disease colibacillosis, which causes substantial fatalities in poultry industries that significantly impact the economy and food safety. Several virulence genes have been shown to be concomitant with the extra-intestinal survival of APEC. This study investigates the antibiotic resistance patterns and APEC‐associated virulence genes content in Escherichia coli (E. coli) isolated from non‐healthy and healthy broiler chickens from a commercial poultry farm in Qatar. Material and Methods: 158 E. coli strains were isolated from 47 chickens from five different organs (air sac, cloacal, kidney, liver, and trachea). Genomic DNA was extracted from E. coli using the QIAamp Pathogen Mini Kit. Multiplex PCR was executed to detect tsh, iucD, ompT, hlyF, iroN, iss, vat, cvi/cva genes associated with PPEC. Antibiotic susceptibility testing was performed using the standard Kirby-Bauer disk and E-test. Amplified virulence genes detected were sequenced and analyzed. Graph Pad version 8 and PAST software version 4.03 were used for statistical and clustering analysis. The chi-square test was performed on all data to compare the antibiotic resistance and virulence gene patterns between non-healthy and healthy chicken samples Results: 65% of the isolated bacteria were APEC strains containing five or more virulence genes, and 34% were non‐pathogenic E. coli (NPEC) strains. The genes ompT, hlyF, iroN, tsh, vat, iss, cvi/cva, and iucD were significantly prevalent in all APEC strains. E. coli isolates showed 96% resistance to at least one of the 18 antibiotics, with high resistance to ampicillin, cephalothin, ciprofloxacin, tetracycline, and fosfomycin. Conclusions: Our findings indicate high antibiotic resistance prevalence in non-healthy and healthy chicken carcasses. Such resistant E. coli can spread to humans. Hence, special programs are required to monitor the use of antibiotics in chicken production in Qatar.
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Kimura, Shuhei, Masato Tokuhisa, and Mariko Okada-Hatakeyama. "Simultaneous execution method of gene clustering and network inference." In 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2016. http://dx.doi.org/10.1109/cibcb.2016.7758123.
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Lin, Yun-Jeng, and Sherif T. Noah. "Using Genetic Algorithms for the Optimal Design of Fluid Journal Bearing." In ASME 1999 Design Engineering Technical Conferences. American Society of Mechanical Engineers, 1999. http://dx.doi.org/10.1115/detc99/vib-8171.
Повний текст джерелаАнотація:
Abstract The current methods of designing journal bearings are achieved by trial and error and mathematical programming. A new method is used here to design the journal bearings, i.e., Genetic Algorithms (GA). GA is a very efficient method, providing relatively an easy way to find the optimum solution. For that purpose we need to construct the proper objective function for the design of the journal bearing. Then the rest exhaustive and repeated task could be left to the computer. GA can solve the linear or nonlinear, single parameter or multiparameter system. Genetic Algorithms are very different from the traditional optimization techniques. It is a new generation of artificial intelligence and its principles mimic the behavior of the biologic genes in the natural world. It will search the best set of parameters of the objective function, reproduce them, eliminate unsuitable sets of parameters, cross-couple the survival sets of parameters, execute mutations and then return to plug the values of the new variables into objective function to repeat these procedures. Its execution is simple and could reach the solution in a very short time. According to these characteristics, it is a very powerful method for finding the minimum dissipation of energy in the journal bearing. This approach opens new paradigm for optimization. The GA’s procedure is robust and works even if the functions involve are not continuous and have no derivatives. The resulting set of optimal parameters was compared with the results of a recent paper addressing the same problem.
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Hou, Yuemin, and Ji Linhong. "Gene Transcription and Translation in Design." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-46128.
Повний текст джерелаАнотація:
An organism grows from very small to the whole body, while an engineering product is assembled from elements. An organism is formed autonomously and adaptable to his/her/its environment, while an engineering product can only execute very limited actions. The formation of a product determines its functionality. Nature is the best teacher for learning how structures are formed for specific functionality. This paper compares the design process with the developmental process of embryo and proposes a qualitative development framework that simulates the gene transcription and translation in biology. The key step in design is transforming behaviors to structures. This is a process from information to the form and it bears some similarity with the process from DNA to the protein in embryogenesis. Three basic steps are required from DNA to the protein: gene transcription, transport and protein synthesis, which is named as gene expression. Key mechanisms contributing to this transformation process are investigated and a qualitative development framework are constructed for a growth design process. Simple examples are presented for illustration of proposed methods.
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Somavarapu, Dhathri H., and Kamran Turkoglu. "A Parallel Processing and Diversified-Hidden-Gene-Based Genetic Algorithm Framework for Fuel-Optimal Trajectory Design for Interplanetary Spacecraft Missions." In ASME 2017 Dynamic Systems and Control Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/dscc2017-5148.
Повний текст джерелаАнотація:
This paper proposes a new parallel computing genetic algorithm framework for designing fuel-optimal trajectories for interplanetary spacecraft missions. The framework can capture the deep search-space of the problem with the use of a fixed chromosome structure and hidden-genes concept, can explore the diverse set of candidate solutions with the use of the Adaptive and Twin-Space Crowding techniques, can execute on any High-Performance Computing (HPC) platform with the adoption of the portable Message Passing Interface (MPI) standard. New procedures are developed for determining trajectories in legs of the flight from the launch planet, and deep-space maneuver legs of the flight from the launch and non-launch planets. The chromosome structure maintains the time of flight as a free parameter within certain boundaries. The fitness or the cost function of the algorithm uses only the mission ΔV, and does not include the time of flight. The proposed algorithm is proven superior to the classical genetic algorithm both in terms of convergence characteristics for the cost function and the depth of the search space explored.
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Perumalla, Kalyan S. "Scaling time warp-based discrete event execution to 104 processors on a Blue Gene supercomputer." In the 4th international conference. New York, New York, USA: ACM Press, 2007. http://dx.doi.org/10.1145/1242531.1242543.
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De Carvalho Ribeiro Júnior, Egidio, Omar Andres Carmona Cortes, and Osvaldo Ronald Saavedra. "A Parallel Mix Self-Adaptive Genetic Algorithm for Solving the Dynamic Economic Dispatch Problem." In Simpósio Brasileiro de Sistemas Elétricos - SBSE2020. sbabra, 2020. http://dx.doi.org/10.48011/sbse.v1i1.2499.
Повний текст джерелаАнотація:
The purpose of this paper is to propose a parallel genetic algorithm that has adaptive and self-adaptive characteristics at the same time for solving the Dynamic Economic Dispatch (DED) problem that is a challenging problem to solve. The algorithm selects the proper operators (using adaptive features) and probabilities (using the self-adaptive code) that produce the most fittable individuals. Regarding operations, the choice is made between four different types of crossover: simple, arithmetical, non-uniform arithmetical, and linear. Concerning mutation, we used four types of mutations (uniform, non-uniform, creep, and enhanced apso). The choice is made scholastically, which is uniform at the beginning of the algorithm, being adapted as the AG executes. The crossover and mutation probabilities are coded into the genes, transforming this part of the algorithm into self-adaptive. The multicore version was coded using OpenMP. An ANOVA test, along with a Tukey test, proved that the mixed self-adaptive algorithm works better than both: a random algorithm, which chooses operators randomly, and a combination of operators set previously in the DED optimization. Regarding the performance of the parallel approach, results have shown that a speedup of up to 3.19 can be reached with no loss in the quality of solutions.
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Hanganu, Dumitru, and Svetlana Badrajan. "Aspects of the treatment of the technical-expressive and interpretative means of the trumpet in the Concert Study by Alexandr Sochireanschii and Oleandra by Vladimir Slivinskii." In Patrimoniul cultural: cercetare, valorificare, promovare. Institute of Cultural Heritage, Republic of Moldova, 2021. http://dx.doi.org/10.52603/9789975351379.05.
Повний текст джерелаАнотація:
The instrumental chamber music works by composers from the Republic of Moldova are rich and diverse, both in terms of the musical genres addressed and the instruments required, either for the ensemble or solo parts. The trumpet, an instrument with wide technicalinterpretative and expressive possibilities, offers composers an ample opportunity for harnessing its potential. The two works, which we will analyze from an interpretive point of view – “The Concert Study” for trumpet and piano (in B) by Alexandr Sokireanski (1977) and “Oleandra” for trumpet and piano (in B) by Vladimir Slivinski (1979), are part of the active repertoire of trumpeters and are of interest to researchers. They require certain execution skills and a certain level of handling the instrument, as they contain elements with a high degree of difficulty; we refer here to the rhythmic structure, the complexity of dynamic nuances, technical elements, the change of tempo during the proceeding of the musical discourse, the exploitation of the acute register of the trumpet.
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Pinzetta, Giulia, Allan Alcará, Isadora Ghilardi, Vitoria Pimentel, Nicole Becker, Laura Provenzi, Gabriel Leal, Giovani Zocche, et al. "Modulation of the expression of the SLC12A2 gene that encodes the cationic co- transporter NKCC1 in epileptic animals treated with mesenchymal stem cells." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.689.
Повний текст джерелаАнотація:
Introduction: Temporal Lobe Epilepsy (TLE) can be identified by synchronized and rhythmic firing of neuronal populations that results in spontaneous and recurrent seizures in individuals affected by it1 . This type of epilepsy is clinically relevant because of its high incidence and refractoriness rate2,3. Thus, the search for therapeutic alternatives becomes important. Due to its benefits and less invasive administration, the mesenchymal stem cells (MSCs)4 appears as a possible therapeutic alternative, because can stimulate and provide a favorable niche for recovery based on their paracrine activities5 . Objectives: The present work aim to highlight the effect promoted by MSCs on the transcription of mRNA of the NKCC1 gene in the TLE induced by pilocarpine model in rats. NKCC1 plays a role in controlling the potential reversal of current and voltage signals executed by Gamma-aminobutyric acid receptors, contributing to inhibitory GABAergic efficacy6 . Design and setting: Experimental design was held at the Pontifical Catholic University of Rio Grande do Sul. Methods: Bone marrow cells were extracted from donor rats, then cultured and transplanted intranasally in animals induced to status epilepticus by pilocarpine7,11. Results: It was observed the ability of the MSCs to alter the amount of transcripts in the brain of the animals. When analyzing the stratified areas of the brain, an increase in NKCC1 expression12 was observed directly to the amygdalas and hippocampi, which are limbic lobe structures affected in epilepsy. Conclusion: MSCs had a modulatory function in the levels of gene expression of cation- chloride co-transporter NKCC1 during acute phase of epilepsy.
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Paz, Cândida Verônica de Andrade, EDUARDA MARTINS DOS SANTOS, TÁSSIA AIMÊ TEIXEIRA NASCIMENTO, RAFAEL PEREIRA CAMARGO, and LAURI PAULO MALACARNE JUNIOR. "CONFORMAÇÕES GENÉTICAS E IMUNOLÓGICAS DA DOENÇA DE ALZHEIMER." In II Congresso Brasileiro de Imunologia On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/ii-conbrai/6783.
Повний текст джерелаАнотація:
Introdução: A doença de Alzheimer (DA) é uma patologia neurodegenerativa irreversível e a principal causa de demência na senescência. Essa doença é caracterizada por lesões cerebrais responsáveis pelo controle da memória e funções cognitivas. Estudos apontam uma relação aparente em alterações gênicas, fatores ambientais, bem como nos processos imunológicos interconectados a principais interleucinas. Objetivo: Analisar aspectos imunogenéticos envolvidos na DA. Material e métodos: Revisão narrativa de literatura nas plataformas científicas PUBMED, SCIELO e MEDLINE. Como critério de busca para seleção dos estudos elegíveis foram aplicadas os unitermos: “alzheimer” AND “mutação” AND “imunologia” AND “genética”. Foram identificados 153 artigos publicados entre 2016 a 2022, nos idiomas português e inglês e após a leitura avaliativa dos resumos dos estudos, 11 trabalhos científicos foram elencados para a produção do presente trabalho. Foram desconsiderados estudos repetidos ou que não atendiam a temática. Resultados: Verificou-se que a DA é destacada pela complexidade de fatores genéticos associados, sendo a neurodegeneração relacionada a alterações no processo de splicing alternativo, onde íntrons passam a executar função codificadora no mRNA. Estudos em animais apontam que mutações nos genes que codificam a DNA polimerase, proteína chave no reparo do DNA, podem acarretar em doenças com o fenótipo de envelhecimento acelerado, resultando em uma disfunção e perda neuronal por meio da privação de energia, a qual é oriunda tanto do descarrilamento metabólico quanto do acúmulo de mitocôndrias danificadas. Biomarcadores inflamatórios, como a interleucina-10 (IL-10), mostram-se com níveis séricos baixos relacionados com a DA. Observaram-se, também, alterações significativas ao nível das células B, as quais nos doentes apresentavam uma expressão aumentada dos marcadores CD69 e CD40, moléculas co-estimuladoras essenciais para troca de classe de imunoglobulina. Conclusão: Sendo assim, fica evidente o papel dos fatores de riscos genéticos e relacionados à imunidade que se convergem para o surgimento e agravamento da neurodegeneração, bem como da neuroinflamação, processos estes que podem ser desacelerados com tratamentos, terapias e mudanças no estilo de vida. Todavia, mais estudos moleculares são necessários para o manejo da solução e prevenção desta patologia.
Звіти організацій з теми "Executor genes"
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Meir, Shimon, Michael Reid, Cai-Zhong Jiang, Amnon Lers, and Sonia Philosoph-Hadas. Molecular Studies of Postharvest Leaf and Flower Abscission. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696523.bard.
Повний текст джерелаАнотація:
Original objectives: Understanding the regulation of abscission competence by exploring the nature and function of auxin-related gene expression changes in the leaf and pedicelAZs of tomato (as a model system), was the main goal of the previously submitted proposal. We proposed to achieve this goal by using microarray GeneChip analysis, to identify potential target genes for functional analysis by virus-induced gene silencing (VIGS). To increase the potential of accomplishing the objectives of the previously submitted proposal, we were asked by BARD to show feasibility for the use of these two modern techniques in our abscission system. Thus, the following new objectives were outlined for the one-year feasibility study: 1.to demonstrate the feasibility of the VIGS system in tomato to perform functional analysis of known abscission-related genes; 2. to demonstrate that by using microarray analysis we can identify target genes for further VIGS functional analysis. Background to the topic: It is a generally accepted model that auxin flux through the abscission zone (AZ) prevents organ abscission by rendering the AZ insensitive to ethylene. However, the molecular mechanisms responsible for acquisition of abscission competence and the way in which the auxin gradient modulates it are still unknown. Understanding this basic stage of the abscission process may provide us with future tools to control abscission for agricultural applications. Based on our previous study, performed to investigate the molecular changes occurring in leaf and stem AZs of MirabillisJalapaL., we have expanded our research to tomato, using genomic approaches that include modern techniques for gene discovery and functional gene characterization. In our one-year feasibility study, the US team has established a useful system for VIGS in tomato, using vectors based on the tobacco rattle virus (TRV), a Lcreporter gene for silencing (involved in regulation of anthocyanin biosynthesis), and the gene of interest. In parallel, the Israeli team has used the newly released Affymetrix Tomato GeneChip to measure gene expression in AZ and non-AZ tissues at various time points after flower removal, when increased sensitivity to ethylene is acquired prior to abscission (at 0-8 h), and during pedicelabscission (at 14 h). In addition, gene expression was measured in the pedicel AZ pretreated with the ethylene action inhibitor, 1-methylcyclopropene (1-MCP) before flower removal, to block any direct effects of ethylene. Major conclusions, solutions and achievements: 1) The feasibility study unequivocally established that VIGS is an ideal tool for testing the function of genes with putative roles in abscission; 2) The newly released Affymetrix Tomato GeneChip was found to be an excellent tool to identify AZ genes possibly involved in regulation and execution of abscission. The VIGS-based study allowed us to show that TAPG, a polygalacturonase specifically associated with the tomato AZ, is a key enzyme in the abscission process. Using the newly released Affymetrix Tomato GeneChip we have identified potential abscission regulatory genes as well as new AZ-specific genes, the expression of which was modified after flower removal. These include: members of the Aux/IAAgene family, ethylene signal transduction-related genes, early and late expressed transcription factors, genes which encode post-translational regulators whose expression was modified specifically in the AZ, and many additional novel AZ-specific genes which were previously not associated with abscission. This microarray analysis allowed us to select an initial set of target genes for further functional analysis by VIGS. Implications: Our success in achieving the two objectives of this feasibility study provides us with a solid basis for further research outlined in the original proposal. This will significantly increase the probability of success of a full 3-year project. Additionally, our feasibility study yielded highly innovative results, as they represent the first direct demonstration of the functional involvement of a TAPG in abscission, and the first microarray analysis of the abscission process. Using these approaches we could identify a large number of genes involved in abscission regulation, initiation and execution, and in auxin-ethylene cross-talk, which are of great importance, and could enable their potential functional analysis by VIGS.
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Meir, Shimon, Michael S. Reid, Cai-Zhong Jiang, Amnon Lers, and Sonia Philosoph-Hadas. Molecular Studies of Postharvest Leaf and Flower Senescence. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7592657.bard.
Повний текст джерелаАнотація:
Original objectives: To understand the regulation of abscission by exploring the nature of changes of auxin-related gene expression in tomato (Lycopersicon esculatumMill) abscission zones (AZs) following organ removal, and by analyzing the function of these genes. Our specific goals were: 1) To complete the microarray analyses in tomato flower and leaf AZs, for identifying genes whose expression changes early in response to auxin depletion; 2) To examine, using virus-induced gene silencing (VIGS), the effect of silencing target genes on ethylene sensitivity and abscission competence of the leaf and flower AZs; 3) To isolate and characterize promoters from AZ-specific genes to be used in functional analysis; 4) To generate stable transgenic tomato plants with selected genes silenced with RNAi, under the control of an AZ-specific promoter, for further characterization of their abscission phenotypes. Background: Abscission, the separation of organs from the parent plant, results in postharvest quality loss in many ornamentals and other fresh produce. The process is initiated by changes in the auxin gradient across the AZ, and is triggered by ethylene. Although changes in gene expression have been correlated with the ethylene-mediated execution of abscission, there is almost no information on the initiation of the abscission process, as the AZ becomes sensitized to ethylene. The present project was focused on elucidating these early molecular regulatory events, in order to gain a better control of the abscission process for agricultural manipulations. Major conclusions, solutions, achievements: Microarray analyses, using the Affymetrix Tomato GeneChip®, revealed changes in expression, occurring early in abscission, of many genes with possible regulatory functions. These included a range of auxin- and ethylene-related transcription factors (TFs), other TFs that are transiently induced just after flower removal, and a set of novel AZ-specific genes. We also identified four different defense-related genes, including: Cysteine-type endopeptidase, α- DOX1, WIN2, and SDF2, that are newly-associated with the late stage of the abscission process. This supports the activation of different defense responses and strategies at the late abscission stages, which may enable efficient protection of the exposed tissue toward different environmental stresses. To facilitate functional studies we implemented an efficient VIGS system in tomato, and isolated two abscission-specific promoters (pTAPG1 and pTAPG4) for gene silencing in stable transformation. Using the VIGS system we could demonstrate the importance of TAPGs in abscission of tomato leaf petioles, and evaluated the importance of more than 45 genes in abscission. Among them we identified few critical genes involved in leaf and flower abscission. These included: PTRP-F1, PRP, TKN4, KNOTTED-like homeobox TF, KD1, and KNOX-like homeodomain protein genes, the silencing of which caused a striking retardation of pedicel abscission, and ERF1, ERF4, Clavata-like3 protein, Sucrose transporter protein, and IAA10 genes, the silencing of which delayed petiole abscission. The importance of PRPand KD1 genes in abscission was confirmed also by antisense–silencing using pTAPG4. Experiments testing the effects of RNAi silencing of few other genes are still in progress, The analysis of the microarray results of flower and leaf AZs allowed us to establish a clear sequence of events occurring during acquisition of tissue sensitivity to ethylene, and to confirm our hypothesis that acquisition of ethylene sensitivity in the AZ is associated with altered expression of auxin-regulated genes in both AZs. Implication, both scientific and agricultural: Our studies had provided new insights into the regulation of the abscission process, and shaded light on the molecular mechanisms that drive the acquisition of abscission competence in the AZ. We pointed out some critical genes involved in regulation of abscission, and further expanded our knowledge of auxin-ethylene cross talk during the abscission process. This permits the development of novel techniques for manipulating abscission, and thereby improving the postharvest performance of ornamentals and other crops.
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Friedman, Haya, Julia Vrebalov, James Giovannoni, and Edna Pesis. Unravelling the Mode of Action of Ripening-Specific MADS-box Genes for Development of Tools to Improve Banana Fruit Shelf-life and Quality. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592116.bard.
Повний текст джерелаАнотація:
Fruit deterioration is a consequence of a genetically-determined fruit ripening and senescence programs, in which developmental factors lead to a climacteric rise of ethylene production in ethylene-sensitive fruits such as tomato and banana. Breeding of tomato with extended fruit shelf life involves the incorporation of a mutation in RIN, a MADS-box transcription factor participating in developmental control signalling of ripening. The RIN mode of action is not fully understood, and it may be predicted to interact with other MADS-box genes to execute its effects. The overall goal of this study was to demonstrate conservation of ripening control functions between banana and tomato and thus, the potential to genetically extend shelf-life in banana based on tools developed in tomato. The specific objectives were: 1. To increase the collection of potential RIN-like genes from banana; 2. To verify their action as developmental regulators; 3. To elucidate MADS-box gene mode of action in ripening control; 4. To create transgenic banana plants that express low levels of endogenous Le-RIN- like, MaMADS- gene(s). We have conducted experiments in banana as well as in tomato. In tomato we have carried out the transformation of the tomato rin mutant with the MaMADS1 and MaMADS2 banana genes. We have also developed a number of domain swap constructs to functionally examine the ripening-specific aspects of the RIN gene. Our results show the RIN-C terminal region is essential for the gene to function in the ripening signalling pathway. We have further explored the tomato genome databases and recovered an additional MADS-box gene necessary for fruit ripening. This gene has been previously termed TAGL1 but has not been functionally characterized in transgenic plants. TAGL1 is induced during ripening and we have shown via RNAi repression that it is necessary for both fleshy fruit expansion and subsequent ripening. In banana we have cloned the full length of six MaMADS box genes from banana and determined their spatial and temporal expression patterns. We have created antibodies to MaMADS2 and initiated ChI assay. We have created four types of transgenic banana plants designed to reduce the levels of two of the MaMADS box genes. Our results show that the MaMADS-box genes expression in banana is dynamically changing after harvest and most of them are induced at the onset of the climacteric peak. Most likely, different MaMADS box genes are active in the pulp and peel and they are differently affected by ethylene. Only the MaMADS2 box gene expression is not affected by ethylene indicating that this gene might act upstream to the ethylene response pathway. The complementation analysis in tomato revealed that neither MaMADS1 nor MaMADS2 complement the rin mutation suggesting that they have functionally diverged sufficiently to not be able to interact in the context of the tomato ripening regulatory machinery. The developmental signalling pathways controlling ripening in banana and tomato are not identical and/or have diverged through evolution. Nevertheless, at least the genes MaMADS1 and MaMADS2 constitute part of the developmental control of ripening in banana, since transgenic banana plants with reduced levels of these genes are delayed in ripening. The detailed effect on peel and pulp, of these transgenic plants is underway. So far, these transgenic bananas can respond to exogenous ethylene, and they seem to ripen normally. The response to ethylene suggest that in banana the developmental pathway of ripening is different than that in tomato, because rin tomatoes do not ripen in response to exogenous ethylene, although they harbor the ethylene response capability This study has a major contribution both in scientific and agricultural aspects. Scientifically, it establishes the role of MaMADS box genes in a different crop-the banana. The developmental ripening pathway in banana is similar, but yet different from that of the model plant tomato and one of the major differences is related to ethylene effect on this pathway in banana. In addition, we have shown that different components of the MaMADS-box genes are employed in peel and pulp. The transgenic banana plants created can help to further study the ripening control in banana. An important and practical outcome of this project is that we have created several banana transgenic plants with fruit of extended shelf life. These bananas clearly demonstrate the potential of MaMADS gene control for extending shelf-life, enhancing fruit quality, increasing yield in export systems and for improving food security in areas where Musaspecies are staple food crops.
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Elizur, Abigail, Amir Sagi, Gideon Hulata, Clive Jones, and Wayne Knibb. Improving Crustacean Aquaculture Production Efficiencies through Development of Monosex Populations Using Endocrine and Molecular Manipulations. United States Department of Agriculture, June 2010. http://dx.doi.org/10.32747/2010.7613890.bard.
Повний текст джерелаАнотація:
Background Most of Australian prawn aquaculture production is based on P. monodon. However, the Australian industry is under intense competition from lower priced overseas imports. The availability of all-female monosex populations, by virtue of their large size and associated premium prize, will offer competitive advantage to the industry which desperately needs to counteract competitors within this market. As for the redclaw production in Israel, although it is at its infancy, the growers realized that the production of males is extremely advantageous and that such management strategy will change the economic assumptions and performances of this aquaculture to attract many more growers. Original objectives (as in original proposal) Investigating the sex inheritance mechanism in the tiger prawn. Identification of genes expressed uniquely in the androgenic gland (AG) of prawns and crayfish. The above genes and/or their products will be used to localize the AG in the prawn and manipulate the AG activity in both species. Production of monosex populations through AG manipulation. In the prawn, production of all-female populations and in the crayfish, all-male populations. Achievements In the crayfish, the AG cDNA library was further screened and a third AG specific transcript, designated Cq-AG3, had been identified. Simultaneously the two AG specific genes, which were previously identified, were further characterized. Tissue specificity of one of those genes, termed Cq-AG2, was demonstrated by northern blot hybridization and RNA in-situ hybridization. Bioinformatics prediction, which suggested a 42 amino acid long signal anchor at the N-terminus of the deduced Cq-AG2, was confirmed by immunolocalization of a recombinant protein. Cq-IAG's functionality was demonstrated by dsRNA in-vivo injections to intersex crayfish. Cq-IAGsilencing induced dramatic sex-related alterations, including male feature feminization, reduced sperm production, extensive testicular apoptosis, induction of the vitellogeningene expression and accumulation of yolk proteins in the ovaries. In the prawn, the AG was identified and a cDNA library was created. The putative P. monodonAG hormone encoding gene (Pm-IAG) was identified, isolated and characterized for time of expression and histological localization. Implantation of the AG into prawn post larvae (PL) and juveniles resulted in phenotypic transformation which included the appearance of appendix masculina and enlarged petasma. The transformation however did not result in sex change or the creation of neo males thus the population genetics stage to be executed with Prof. Hulata did not materialized. Repeated AG implantation is currently being trialed. Major conclusions and Implications, both scientific and agricultural Cq-IAG's involvement in male sexual differentiation had been demonstrated and it is strongly suggested that this gene encodes an AG hormone in this crayfish. A thorough screening of the AG cDNA library shows Cq-IAG is the prominent transcript within the library. However, the identification of two additional transcripts hints that Cq-IAG is not the only gene mediating the AG effects. The successful gene silencing of Cq-IAG, if performed at earlier developmental stages, might accomplish full and functional sex reversal which will enable the production of all-male crayfish populations. Pm-IAG is likely to play a similar role in prawns. It is possible that repeated administration of the AG into prawn will lead to the desired full sex reversal, so that WZ neo males, crossed with WZ females can result in WW females, which will form the basis for monosex all-female population.
5
Sessa, Guido, and Gregory Martin. A functional genomics approach to dissect resistance of tomato to bacterial spot disease. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7695876.bard.
Повний текст джерелаАнотація:
The research problem. Bacterial spot disease in tomato is of great economic importance worldwide and it is particularly severe in warm and moist areas affecting yield and quality of tomato fruits. Causal agent of spot disease is the Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv), which can be a contaminant on tomato seeds, or survive in plant debris and in association with certain weeds. Despite the economic significance of spot disease, plant protection against Xcvby cultural practices and chemical control have so far proven unsuccessful. In addition, breeding for resistance to bacterial spot in tomato has been undermined by the genetic complexity of the available sources of resistance and by the multiple races of the pathogen. Genetic resistance to specific Xcvraces have been identified in tomato lines that develop a hypersensitive response and additional defense responses upon bacterial challenge. Central goals of this research were: 1. To identify plant genes involved in signaling and defense responses that result in the onset of resistance. 2. To characterize molecular properties and mode of action of bacterial proteins, which function as avirulence or virulence factors during the interaction between Xcvand resistant or susceptible tomato plants, respectively. Our main achievements during this research program are in three major areas: 1. Identification of differentially expressed genes during the resistance response of tomato to Xcvrace T3. A combination of suppression subtractive hybridization and microarray analysis identified a large set of tomato genes that are induced or repressed during the response of resistant plants to avirulent XcvT3 bacteria. These genes were grouped in clusters based on coordinate expression kinetics, and classified into over 20 functional classes. Among them we identified genes that are directly modulated by expression of the type III effector protein AvrXv3 and genes that are induced also during the tomato resistance response to Pseudomonas syringae pv. tomato. 2. Characterization of molecular and biochemical properties of the tomato LeMPK3MAP kinase. A detailed molecular and biochemical analysis was performed for LeMPK3 MAP kinase, which was among the genes induced by XcvT3 in resistant tomato plants. LeMPK3 was induced at the mRNA level by different pathogens, elicitors, and wounding, but not by defense-related plant hormones. Moreover, an induction of LeMPK3 kinase activity was observed in resistant tomato plants upon Xcvinfection. LeMPK3 was biochemically defined as a dual-specificity MAP kinase, and extensively characterized in vitro in terms of kinase activity, sites and mechanism of autophosphorylation, divalent cation preference, Kₘand Vₘₐₓ values for ATP. 3. Characteriztion of molecular properties of the Xcveffector protein AvrRxv. The avirulence gene avrRxvis involved in the genetic interaction that determines tomato resistance to Xcvrace T1. We found that AvrRxv functions inside the plant cell, localizes to the cytoplasm, and is sufficient to confer avirulence to virulent Xcvstrains. In addition, we showed that the AvrRxv cysteine protease catalytic core is essential for host recognition. Finally, insights into cellular processes activated by AvrRxv expression in resistant plants were obtained by microarray analysis of 8,600 tomato genes. Scientific and agricultural significance: The findings of these activities depict a comprehensive and detailed picture of cellular processes taking place during the onset of tomato resistance to Xcv. In this research, a large pool of genes, which may be involved in the control and execution of plant defense responses, was identified and the stage is set for the dissection of signaling pathways specifically triggered by Xcv.
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Or, Etti, David Galbraith, and Anne Fennell. Exploring mechanisms involved in grape bud dormancy: Large-scale analysis of expression reprogramming following controlled dormancy induction and dormancy release. United States Department of Agriculture, December 2002. http://dx.doi.org/10.32747/2002.7587232.bard.
Повний текст джерелаАнотація:
The timing of dormancy induction and release is very important to the economic production of table grape. Advances in manipulation of dormancy induction and dormancy release are dependent on the establishment of a comprehensive understanding of biological mechanisms involved in bud dormancy. To gain insight into these mechanisms we initiated the research that had two main objectives: A. Analyzing the expression profiles of large subsets of genes, following controlled dormancy induction and dormancy release, and assessing the role of known metabolic pathways, known regulatory genes and novel sequences involved in these processes B. Comparing expression profiles following the perception of various artificial as well as natural signals known to induce dormancy release, and searching for gene showing similar expression patterns, as candidates for further study of pathways having potential to play a central role in dormancy release. We first created targeted EST collections from V. vinifera and V. riparia mature buds. Clones were randomly selected from cDNA libraries prepared following controlled dormancy release and controlled dormancy induction and from respective controls. The entire collection (7920 vinifera and 1194 riparia clones) was sequenced and subjected to bioinformatics analysis, including clustering, annotations and GO classifications. PCR products from the entire collection were used for printing of cDNA microarrays. Bud tissue in general, and the dormant bud in particular, are under-represented within the grape EST database. Accordingly, 59% of the our vinifera EST collection, composed of 5516 unigenes, are not included within the current Vitis TIGR collection and about 22% of these transcripts bear no resemblance to any known plant transcript, corroborating the current need for our targeted EST collection and the bud specific cDNA array. Analysis of the V. riparia sequences yielded 814 unigenes, of which 140 are unique (keilin et al., manuscript, Appendix B). Results from computational expression profiling of the vinifera collection suggest that oxidative stress, calcium signaling, intracellular vesicle trafficking and anaerobic mode of carbohydrate metabolism play a role in the regulation and execution of grape-bud dormancy release. A comprehensive analysis confirmed the induction of transcription from several calcium–signaling related genes following HC treatment, and detected an inhibiting effect of calcium channel blocker and calcium chelator on HC-induced and chilling-induced bud break. It also detected the existence of HC-induced and calcium dependent protein phosphorylation activity. These data suggest, for the first time, that calcium signaling is involved in the mechanism of dormancy release (Pang et al., in preparation). We compared the effects of heat shock (HS) to those detected in buds following HC application and found that HS lead to earlier and higher bud break. We also demonstrated similar temporary reduction in catalase expression and temporary induction of ascorbate peroxidase, glutathione reductase, thioredoxin and glutathione S transferase expression following both treatments. These findings further support the assumption that temporary oxidative stress is part of the mechanism leading to bud break. The temporary induction of sucrose syntase, pyruvate decarboxylase and alcohol dehydrogenase indicate that temporary respiratory stress is developed and suggest that mitochondrial function may be of central importance for that mechanism. These finding, suggesting triggering of identical mechanisms by HS and HC, justified the comparison of expression profiles of HC and HS treated buds, as a tool for the identification of pathways with a central role in dormancy release (Halaly et al., in preparation). RNA samples from buds treated with HS, HC and water were hybridized with the cDNA arrays in an interconnected loop design. Differentially expressed genes from the were selected using R-language package from Bioconductor project called LIMMA and clones showing a significant change following both HS and HC treatments, compared to control, were selected for further analysis. A total of 1541 clones show significant induction, of which 37% have no hit or unknown function and the rest represent 661 genes with identified function. Similarly, out of 1452 clones showing significant reduction, only 53% of the clones have identified function and they represent 573 genes. The 661 induced genes are involved in 445 different molecular functions. About 90% of those functions were classified to 20 categories based on careful survey of the literature. Among other things, it appears that carbohydrate metabolism and mitochondrial function may be of central importance in the mechanism of dormancy release and studies in this direction are ongoing. Analysis of the reduced function is ongoing (Appendix A). A second set of hybridizations was carried out with RNA samples from buds exposed to short photoperiod, leading to induction of bud dormancy, and long photoperiod treatment, as control. Analysis indicated that 42 genes were significant difference between LD and SD and 11 of these were unique.
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Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.
Повний текст джерелаАнотація:
Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.
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Chalutz, Edo, Charles Wilson, Samir Droby, Victor Gaba, Clauzell Stevens, Robert Fluhr, and Y. Lu. Induction of Resistance to Postharvest Diseases and Extension of Shelf-Life of Fruits and Vegetables by Ultra-Violet Light. United States Department of Agriculture, February 1994. http://dx.doi.org/10.32747/1994.7568093.bard.
Повний текст джерелаАнотація:
Following preliminary observations by one of the collaborating scientists on this project and the completion of a 1-year, BARD-supported feasibility study (IS-1908-90F), this 3-year BARD project has been executed. The main objectives of the research were to elucidate biochemical and pathological aspects of UV-induced resistance in fruits and vegetables, to characterize physical and biological variables of induced resistance and delay of ripening, and to explore the application of the treatment as a control practice of postharvest diseases and shelf-life extension of fruits and vegetables. Our findings, which are detailed in numerous joint publications, have shown that the effect of UV-C light on induction of resistance and delay of ripening is a general one and of wide oddurrence. Apart from surface sterilization of the commodity, the reduction of decay of different fungi has been associated with and induced resistance phenomenon which gradually builds up within 24 to 48 hours after the UV treatment and can be reversed by visible light. In citrus, induced resistance has been associated with increased activity of the enzymes phenylalanine ammonia-lyase and peroxidase, and with the levels of endglucanase and chitinase. In tomato, resistance was correlated with the production of high levels of tomatine. Our study of some molecular aspects of the induced resistance in grapefruit has revealed the induction of a cDNA which represents a gene encoding for an isoflavone reductase-like protein that, in legumes, has been associated with phytoalexin biosynthesis. This gene was cloned and sequenced. Delay of ripening was associated in tomato with inhibition of ethylene production, carotenoid synthesis, and chlorophyll degradation and with the presence of high levels of polyamines. In peach fruit epiphytic populations of a yeast increased following the UV treatment. Pilot-size treatment and packing lines were constructed in the US and Israel to test the application of the UV treatment on a semi-commercial scale. Although effective in reduction of decay and delay of ripening, a number of problems will have to be addressed before practical application of this methodology can be realized. The main issues are associated with the temporal and variable response to the treatment, and its relationship to the maturity and date of harvest of the commodity.
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Citovsky, Vitaly, and Yedidya Gafni. Suppression of RNA Silencing by TYLCV During Viral Infection. United States Department of Agriculture, December 2009. http://dx.doi.org/10.32747/2009.7592126.bard.
Повний текст джерелаАнотація:
The Israeli isolate of Tomato yellow leaf curl geminivirus (TYLCV-Is) is a major tomato pathogen, causing extensive (up to 100%) crop losses in Israel and in the south-eastern U.S. (e.g., Georgia, Florida). Surprisingly, however, little is known about the molecular mechanisms of TYLCV-Is interactions with tomato cells. In the current BARD project, we have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing, and showed that V2 interacts with the tomato (L. esculentum) member of the SGS3 (LeSGS3) protein family known to be involved in RNA silencing. This proposal will use our data as a foundation to study one of the most intriguing, yet poorly understood, aspects of TYLCV-Is interactions with its host plants – possible involvement of the host innate immune system, i.e., RNA silencing, in plant defense against TYLCV-Is and the molecular pathway(s) by which TYLCV-Is may counter this defense. Our project sought two objectives: I. Study of the roles of RNA silencing and its suppression by V2 in TYLCV-Is infection of tomato plants. II. Study of the mechanism by which V2 suppresses RNA silencing. Our research towards these goals has produced the following main achievements: • Identification and characterization of TYLCV V2 protein as a suppressor of RNA silencing. (#1 in the list of publications). • Characterization of the V2 protein as a cytoplasmic protein interacting with the plant protein SlSGS3 and localized mainly in specific, not yet identified, bodies. (#2 in the list of publications). • Development of new tools to study subcellular localization of interacting proteins (#3 in the list of publications). • Characterization of TYLCV V2 as a F-BOX protein and its possible role in target protein(s) degradation. • Characterization of TYLCV V2 interaction with a tomato cystein protease that acts as an anti-viral agent. These research findings provided significant insights into (I) the suppression of RNA silencing executed by the TYLCV V2 protein and (II) characterization some parts of the mechanism(s) involved in this suppression. The obtained knowledge will help to develop specific strategies to attenuate TYLCV infection, for example, by blocking the activity of the viral suppressor of gene silencing thus enabling the host cell silencing machinery combat the virus.