Littérature scientifique sur le sujet « Techniques de knock-out de gènes »

SummaryThe study of coagulation factors has been rapidly advanced by studies performed in genetically engineered mouse strains. Investigation of factor IX (FIX) has benefited from excellent genedeleted mouse models that recapitulate many of the features of human haemophilia B. Moreover, advanced positional cloning techniques and availability of technology to allow not only knock-out mice, but also knock-in and knock-down mice, provide new opportunities to observe genotype-phenotype and structure-function correlations regarding FIX, as well as the interaction of FIX with inflammatory, immune, and tissue repair systems. In this paper, available FIX knock-out mice and additional haemophilia B mouse models are reviewed specifically in regards to observations these models have facilitated concerning: factor IX gene expression and factor IX protein pharmacokinetics; the role of FIX in haemostasis, thrombosis and wound healing; insights into coagulation FIX arising out of gene therapy applications in haemophilia mouse models; immunology of tolerance or loss of tolerance of FIX and inhibitor antibody formation.

Genetic manipulation is one of the indispensable techniques to examine gene functions both in vitro and in vivo. In particular, cardiovascular phenotypes such as blood pressure cannot be evaluated in vitro system, necessitating the creation of transgenic or gene-targeted knock-out and knock-in experimental animals to understand the pathophysiological roles of specific genes on the disease conditions. Although genome-wide association studies (GWAS) in various human populations have identified multiple genetic variations associated with increased risk for hypertension and/or its complications, the causal links remain unresolved. Genome-editing technologies can be applied to many different types of cells and organisms for creation of knock-out/knock-in models. In the post-GWAS era, it may be more worthwhile to validate pathophysiological implications of the risk variants and/or candidate genes by creating genome-edited organisms.

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.

South Sumatra has a lot of traditional houses across its region. Each house has its own characteristics. One notable design is houses built on stilts. In Ogan Ilir, especially Tanjung Batu, it is famous for the production of knock-down houses. Knock-down houses in Tanjung Batu are a stilt house with an architectural design that almost resembles a Limas house, only that these knock-down houses are specially designed to make it easy to disassemble and reassemble them elsewhere. This study aims to give a closer look at the design, structure and wood choices of knock-down houses that have become unique, cultural houses of Ogan Ilir people. This study will look at how the architectural design of the houses’ characteristics and wooden structures are adapted to the surrounding environment. This study was conducted qualitatively with an anthropological approach through ethnological techniques. To dig up information about knock-down houses, this was done through observation and data collection by conducting interviews and collecting written data such as journals and articles related to the topic. Observations and interviews were carried out in Tanjung Batu, which is the center for knock-down house craftsmen. The results obtained in this study are: (a) the daily activities of carpenters in the manufacture of knock-down houses, (b) tools and materials used in the construction of the knock-down houses, (c) sales of knock-down houses, (d) the development of wood tools and materials following the development of increasingly sophisticated technology, and (e) information about knock-down houses as a local, cultural building typical of Ogan Ilir.

The production of knock down houses is in a great demand especially in Tanjung BatuSeberang.The craft of knxok down houses was passed down from the era of Sriwijaya Kingdom untilnow. The demand of the craft is inscreasing from year to year this has turned out to be anopportunity so that many young people are engaged in this business. Kotler and Armstrong'sMarketing Strategy Theory (2004 in Varadarajan 2009). The research method uses qualitativeresearch. Collecting data through observation as the main source, interviews and documentation.While data analysis techniques, data presentation and data collection. The research refers to themain question: What is the knock down marketing strategy for the people of Tanjung Batu Seberang?. The subjects of this study were 4 knock down house entrepreneurs in Tanjung Batu District.Equipped with these 4 information so as to enrich the data, the results of this study do not know thatthe marketing strategy is used by all informants in marketing knock down house production

The paper presents a series of advanced lattice methods aimed at evaluating an EAKO European-American Knock-Out contract. The first part of the paper deals with the numerical methods implemented for pricing: Binomial and Trinomial Stochastic trees, Adaptive Mesh Model, Pentanomial and Heptanomial lattice. In the second part, specific tests are designed to validate the code written in Matlab language. The study concludes by applying the most performing model to a real market case.

In gasoline engines, the combustion process involves a flame’s propagation from the spark plug to the cylinder walls, resulting in the localized heating and pressurization of the cylinder content ahead of the flame, which can lead to the autoignition of the gasoline and air. The energy release from the autoignition event causes the engine cylinder to resonate, causing an unpleasant noise and eventual engine damage. This process is termed as knock. Avoiding knock has resulted in limiting the maximum engine pressures, and hence limiting the maximum efficiencies of the engine. Modern engines employ knock sensors to detect resonances, adjusting the spark plug timing to reduce pressures and temperatures, albeit at the expense of engine performance. This paper sets out to review the different signals that can be measured from an engine to detect the start of knock. These signals traditionally consist of the in-cylinder pressure, the vibrations of the engine block, and acoustic noise. This paper reviews each of these techniques, with a focus on recent advances. A number of novel methods are also presented, including identifying perturbations in the engine speed or exhaust temperature; measuring the ion charge across the spark plug leads; and using artificial intelligence to build models based on engine conditions. Each of these approaches is also reviewed and compared to the more traditional approaches. This review finds that in-cylinder pressure measurements remain as the most accurate for detecting knock in modern engines; however, their usage is limited to research settings. Meanwhile, new sensors and processing techniques for vibration measurements will more accurately detect knock in modern vehicles in the short term. Acoustic measurements and other novel approaches are showing promise in the long term.

Genome engineering makes the precise manipulation of DNA sequences possible in a cell. Therefore, it is essential for understanding gene function. Meganucleases were the start of genome engineering, and it continued with the discovery of Zinc finger nucleases (ZFNs), followed by Transcription activator-like effector nucleases (TALENs). They can generate double-strand breaks at a desired target site in the genome, and therefore can be used to knock in mutations or knock out genes in the same way. Years later, genome engineering was transformed by the discovery of clustered regularly interspaced short palindromic repeats (CRISPR). Implementation of CRISPR systems involves recognition guided by RNA and the precise cleaving of DNA molecules. This property proves its utility in epigenetics and genome engineering. CRISPR has been and is being continuously successfully used to model mutations in leukemic cell lines and control gene expression. Furthermore, it is used to identify targets and discover drugs for immune therapies. The descriptive and functional genomics of leukemias is discussed in this study, with an emphasis on genome engineering methods. The CRISPR/Cas9 system’s challenges, viewpoints, limits, and solutions are also explored.

CRISPR/Cas9 (hereafter Cas9)-mediated gene knockout is one of the most important tools for studying gene function. However, many genes in plants play distinct roles in different cell types. Engineering the currently used Cas9 system to achieve cell-type-specific knockout of functional genes is useful for addressing the cell-specific functions of genes. Here we employed the cell-specific promoters of the WUSCHEL RELATED HOMEOBOX 5 (WOX5), CYCLIND6;1 (CYCD6;1), and ENDODERMIS7 (EN7) genes to drive the Cas9 element, allowing tissue-specific targeting of the genes of interest. We designed the reporters to verify the tissue-specific gene knockout in vivo. Our observation of the developmental phenotypes provides strong evidence for the involvement of SCARECROW (SCR) and GIBBERELLIC ACID INSENSITIVE (GAI) in the development of quiescent center (QC) and endodermal cells. This system overcomes the limitations of traditional plant mutagenesis techniques, which often result in embryonic lethality or pleiotropic phenotypes. By allowing cell-type-specific manipulation, this system has great potential to help us better understand the spatiotemporal functions of genes during plant development.

Chez les vertébrés à mâchoires, les défenses antivirales innées sont principalement basées sur les interférons (IFN) de type I. Ces cytokines sont sécrétées en cas d'infection virale et induisent l'expression de gènes stimulés par l'IFN (ISGs). Les ISGs codent des protéines aux fonctions diverses dont l'expression conduit à l'établissement d'un état réfractaire à l'infection. Le système IFN de type I est globalement bien conservé entre les mammifères et les poissons, mais le répertoire des ISGs est plus diversifié chez ces derniers, en raison de leur histoire évolutive complexe et de leurs spécificités physiologiques. Par conséquent, la plupart des ISGs de mammifères ont un ou plusieurs orthologues chez les poissons. Il reste, cependant, à déterminer si les ISGs de poisson ont les mêmes fonctions et mécanismes d'action que leurs homologues mammaliens.Dans ce contexte, ma thèse avait pour but de caractériser fonctionnellement deux ISGs de poisson, pkr et viperin, en utilisant une approche in vitro d'invalidation génique. Chez les mammifères, la PKR est principalement impliquée dans l'inhibition de la traduction et l'apoptose, tandis que la Viperin agit en générant des ribonucléotides antiviraux et en modulant certaines voies métaboliques exploitées par les virus. Chez les poissons, ces fonctions restent à explorer en détail. Les objectifs de ma thèse s'articulaient autour de trois axes : (1) développer des lignées cellulaires de poisson pkr-/- et viperin-/- en utilisant la technologie CRISPR/Cas9 ; (2) caractériser fonctionnellement ces lignées, afin d'identifier les mécanismes d'action de la PKR et de la Viperin de poisson et leur rôle dans la régulation de la réponse IFN; (3) évaluer leur permissivité aux infections virales et leur capacité à produire des virus à plus hauts rendements que ceux obtenus en cellules sauvages.En utilisant des approches complémentaires de surexpression et d'invalidation génique, j'ai tout d'abord étudié les mécanismes d'action de la PKR en cellules de saumon Chinook (Oncorhynchus tshawytscha). Nos résultats montrent que la PKR de salmonidés a des fonctions moléculaires conservées : elle est impliquée dans l'activation de l'apoptose et l'inhibition de la synthèse des protéines de l'hôte. Cependant, la PKR n'a pas de rôle majeur lors de l'infection par le virus de la septicémie hémorragique virale (VSHV) : nos résultats suggèrent que le VSHV a développé des stratégies pour échapper aux effets antiviraux de la PKR, en limitant l'expression précoce de pkr, en évitant l'inhibition de la traduction et en tirant partie de l'apoptose médiée par la PKR à un stade d'infection tardif pour favoriser la propagation du virus.En parallèle, nous avons mené une analyse transcriptomique comparative des lignées cellulaires du poisson tête-de-boule (Pimephales promelas), sauvages ou viperin-/-, stimulées ou non par l'IFN de type I, dans le but d'avoir une vue d'ensemble du rôle régulateur de la Viperin chez les cyprinidés. Nos données montrent que la Viperin n'est pas impliquée dans la régulation de la réponse IFN de type I mais qu'elle régule négativement certaines voies inflammatoires. Notre analyse indique aussi que la Viperin a une fonction régulatrice dans d'autres processus métaboliques tels que l'organisation de la matrice extracellulaire, l'adhésion cellulaire et le métabolisme un-carbone.Au cours du processus de développement de lignées cellulaires pkr-/- initiales, deux lignées se sont révélées être infectées de façon persistante par le virus de la nécrose pancréatique infectieuse (IPNV). J'ai entrepris de caractériser ces lignées cellulaires infectées au cours de 40 passages. Nous avons ainsi observé la présence d'oscillations périodiques des titres viraux extracellulaires et des niveaux intracellulaires d'ARN viral au cours des passages. De plus, la réponse IFN de type I n'était pas déclenchée par l'infection, ce qui suggère que l'IPNV persistant est capable d'échapper à la réponse innée de l'hôte
In jawed vertebrates, innate antiviral defenses are primarily based on type I interferons (IFNs). These master cytokines are secreted following virus recognition and induce the expression of hundreds of IFN-stimulated genes (ISGs). ISGs encode proteins with diverse functions, including enhancers of the type I IFN pathway and antiviral effectors, which all work towards establishing an antiviral state refractory to viral infection. Overall, the type I IFN system is well-conserved between mammals and fish but the ISGs repertoire is more diverse in fish, largely due to their complex evolutionary history and physiological specificities. Consequently, most mammalian ISGs have one or more orthologs in fish. However, it is still unclear whether fish ISGs are true functional homologs and their mechanisms of action remain to be explored in detail.In this context, my thesis aimed to functionally characterize two key fish ISGs, namely dsRNA-dependent protein kinase (pkr) and virus inhibitory protein endoplasmic reticulum-associated, interferon-inducible (viperin), by using an in vitro knock-out approach. In mammals, both proteins are primarily regarded as antiviral effectors: PKR is involved in host translation inhibition and apoptosis, while Viperin operates by generating antiviral ribonucleotides and modulating metabolic pathways exploited during viral life cycles. However, the extent to which these functions are conserved in fish remains largely unknown. The objectives of my thesis were articulated along three axes: (1) to develop and validate pkr-/- and viperin-/- fish cell lines using the CRISPR/Cas9 technology; (2) to functionally characterize these cell lines, in order to identify the mechanisms of action of fish PKR and Viperin and their role in regulating the type I IFN response through feedback loops; (3) to assess their permissivity to viral infections and their ability to produce viral particles at higher yields than their wild-type counterparts.Using complementary overexpression and knockout approaches, I first studied the molecular mechanisms of action of PKR in Chinook salmon (Oncorhynchus tshawytscha) CHSE-EC cells. Our findings show that salmonid PKR has conserved molecular functions, including apoptosis activation and inhibition of host protein synthesis. However, endogenous PKR did not play a major antiviral role during viral hemorrhagic septicemia virus (VHSV) infection. In fact, our results suggest that VHSV has evolved strategies to subvert PKR antiviral action, by limiting early induction of pkr expression, evading PKR-mediated translational arrest and taking advantage of PKR-mediated apoptosis at a late infection stage to favor viral spread.In parallel, we conducted a comparative RNA-seq analysis of the viperin-/- and wild-type fathead minnow (Pimephales promelas) EPC-EC cell lines with or without stimulation with recombinant type I IFN to have a global overview of the regulatory role of fish Viperin. Our data show that cyprinid Viperin is not involved in the regulation of the canonical type I IFN but negatively regulates specific inflammatory pathways. Our analysis further indicates that it plays a regulatory role in other metabolic processes, even in non-induced conditions, including extracellular matrix organization, cell adhesion and one carbon metabolism.During the development process of initial pkr-/- cell lines, two CHSE-EC cell lines were found to be persistently infected with infectious pancreatic necrosis virus (IPNV), presumably due to inadvertent contamination. I set out to characterize these persistently IPNV-infected cell lines over the course of 40 passages. A striking feature in both cell lines was the periodic oscillatory pattern of extracellular titers and intracellular viral RNA levels over passages. We further showed that the type I IFN response was not triggered during persistent infection, suggesting that persistent IPNV is able to evade the host innate immune response

Dans le système nerveux central, la voie tryptophane/kynurénine (T/K) est considérée maintenant comme un acteur majeur de la physiopathologie des maladies neurodégénératives et psychiatriques associées à une inflammation chronique. Le diabète de type Ilest aussi associé à une activation chronique de l'immunité innée qui installe une inflammation chronique à bas bruit au niveau des îlots pancréatiques. Comme les cellules bêta pancréatiques partagent un grand nombre de similitudes avec les cellules neuronales, les îlots pancréatiques représententun nouveau tissu au sein duquel la voie T/K pourrait agir. Dans la première partie, nous avons évalué l'expression des gènes de la voie T/K dans des îlots de ratsnormauxet des cellules INS1 (qPCR, immunoblotting, immunocytochimie, tri cellulaire) et leur régulation par des facteurs de l'environnement insulaire. Nous rapportons, pour la première fois, que: 1) certains T/K gènes de la voie T/K sont exprimés de manière constitutive, à la fois dans des cellules(3 et non-a; 2) l'enzyme limitante indoleamine 2,3-dioxygénase (IDO1) n'est pas exprimée de façon constitutive ; 3) IDO1 et kynurénine 3- monooxygénase (KMO) sont respectivement activés par des cytokines pro-inflammatoires (IFNy, IL1 (3) et la glucolipotoxicité; 4) le rapport de production par les îlots de kynurénine/acide kynurénique est augmenté après IFNy et glucolipotoxicité. Dans une deuxième partie du travail, et en utilisant des îlots de rat GK spontanément diabétiques, nous avons trouvé pour la première fois que : 1/ certains gènes de la voie T/K (IDO1, TDO2, KMO, Kase et QPRT) sont fortement surexprimés dans les cellules (3; 2) la surexpression des gènes de la voie T/K est pas innée, mais elle représente une adaptation acquise. Dans la troisième partie du travail, nous avons étudié les conséquences fonctionnelles de la surexpression des gènes de la voie T/K dans les îlots GK en utilisant une stratégie basée sur l'emploi de morpholinoantisens ou d'inhibiteur pharmacologique in vitro. Nous fournissons les preuves expérimentales quele déficit de sécrétion de l'insulineinduitepar le glucose, caractéristique du diabète de type 2 des rats GK (et du diabète de type 2 humain), peut être corrigé par l'inhibition de la KMO ou l'exposition aiguë àcertainsmétabolites de la voie T/K tels que la kynurénine ou l'acide kynurénique. Nos résultats apportent la preuve de concept que la voie T/K des cellules insulaires représente une ciblé intéressante pour le développement de nouvelles molécules antidiabétiques
In the central nervous system,thetrytophane/kynurenine pathway (TKP) is now at the center of stage in virtually all major neurodegenerative and psychiatrie disorders which are associated with a mild but chronic pro-inflammatory state. Type 2 diabetesis also associatedwith a chronic activation of the innate immune system which drives the installation of an inflammatory phenotype at the level of the pancreatic islets. Since pancreatic beta cells share a large number of similarities with neuronal cells, we hypothesized that pancreatic islets may represent a new issue for the T/K pathway to operate in. In the first part, we have evaluated (qPCR, western blotting, immunocytochemistry, cell sorting) the pattern of T/K pathway gene expression in normal rat islets and INS-1 cells, and its regulation by factors from the local islet environment. We report for the first time that: 1) certain T/K pathway genes are constitutively expressed, both in (3-cells and non-(3-cells; 2) the rate-limiting enzyme indoleamine 2,3-dioxygenase (IDO1) is not constitutively expressed; 3) IDO1 and kynurenine 3-monoxygenase (KMO) expression are potently activated by proinflammatory cytokines (IFNy, ILI (3) and glucolipotoxicity respectively; 4) islet kynurenine/kynurenic acid production ratio is increased following IFNyandglucolipotoxicity. In the second part of this work, using islets from overtly diabetic GK rats, we report for the first timethat: 1/ certain T/K pathway genes (IDO1, TDO2, KMO, Kase and QPRT) are potently overexpressed; 2) overexpression of the T/K pathway genes is not innate, but it represents an acquired adaptation. In the third part of the work, we have investigated the functional consequences of overexpression of the T/K pathway genes in GK islets using morpholino antisense oligos or pharmacological inhibitor in vitro. We provide compelling evidences thatthe defective glucose-induced insulin secretion by the GK islets (anislet lesion also characteristic of human type 2 diabetes) can be reactivated by KMO inhibition or acute exposure to some T/K pathway metabolites such as kynurenine or kynurenic acid. Ours results suggest that the T/K pathway in the islet cells may be a new potential site to be targeted by drug discovery in diabetes

Même si les acteurs majeurs du développement musculaire ont été identifiés et les voies de transductions décrites, d’autres régulateurs restent encore à découvrir. Un crible ARNi pratiqué sur un modèle cellulaire couramment utilisé, la lignée myoblastique C2C12, a identifié 20 nouveaux gènes potentiellement impliqués dans la myogenèse in vitro. Au cours de ma thèse, deux de ces gènes ont été invalidés sur modèle souris en utilisant la technologie CRISPR/Cas9 pour valider in vivo leur implication. Pour l’un d’entre eux, seuls les animaux hétérozygotes ont pu être étudiés puisqu’une létalité précoce a été observée chez les homozygotes mutés. Aucune anomalie du développement musculaire n’a été mise en évidence. Une étude plus fine dans les premières phases du développement embryonnaire nous a permis de montrer le rôle indispensable de cette protéine précocement. L’étude du second gène – dont les analyses se poursuivent – semble confirmer in vivo le rôle de ce gène au cours de la myogenèse. Pour éviter la survenue de létalité embryonnaire et observer rapidement les effets de l’invalidation d’autres gènes, une technique de transgenèse somatique s’appuyant sur l’ARN interférence a été mis en place via l’injection de lentivirus contenant une cassette d’expression de shRNA directement dans le tibialis antérieur des souris. La validation de cette approche a été faite sur le gène de la myostatine, régulateur négatif du développement musculaire, et a montré une diminution de l’expression du gène associée à une augmentation de l’aire des fibres musculaires. La même approche appliquée à trois autres gènes renforce l’hypothèse de l’implication d’un des gènes dans le développement musculaire. Cette approche permet donc un crible rapide « in vivo » de gènes identifiés in vitro. Cependant, certaines améliorations doivent être apportées au protocole au regard des résultats obtenus
Even if the major actors and transduction pathways of muscle development have been identified, there are still unknown regulatory factors. An in vitro RNAi screening performed on C2C12 myoblastic cells has permitted to identify 20 novel genes potentially implicated in myogenesis. During my thesis, two of these genes were invalidated on mouse model using CRISPR/Cas9 technology in order to confirm their implication in vivo. For the first gene, due to an early lethality occurring in homozygous mutated animals, only heterozygous animals were studied and there was no muscular development anomaly detected. A refined study of earlier stages of embryonic development permitted to show the essential role of the protein in these phases. The study of the second gene, still in progress, seems to confirm in vivo the implication of the gene on the myogenesis. In order to avoid embryonic lethality due to germline invalidation and to observe more rapidly the effects of gene invalidation in muscle, we developed a technique of somatic transgenesis based on RNA interference. Lentivirus containing a shRNA expression cassette was injected directly into the tibialis anterior of mice. We validated this approach on Myostatin gene, a well-known negative regulator of muscle development, showing that the decrease of Myostatin gene expression was associated to an increase of muscle fibers area. The same approach was used with three genes and support the hypothesis of the implication of one of them in muscle development. Thus, this approach allows a rapid “in vivo” screening of in vitro identified genes. Nonetheless, some improvements should be brought on the protocol according to the first results

L'imagerie haute résolution des rongeurs de laboratoire s'est largement développée au cours des dernières années pour répondre aux besoins des chercheurs, demandeurs de techniques non invasives d'étude des centaines de modèles d'animaux transgéniques et knock-out actuellement disponibles. Les défis techniques étaient nombreux, mais les outils existent aujourd'hui. Dans cette thèse, l'auteur illustre les applications de l'échographie haute résolution à l'exploration non invasive des souris trangéniques dans différentes applications : en biologie moléculaire dans un modèle de souris déficiente en récepteur alpha à l'hormone thyroi͏̈dienne, et en oncologie, dans un modèle de souris bitransgénique développant spontanément des carcinomes hépatocellulaire. Il montre comment la résolution spatiale est une limitante aux anomalies détectables

Le gène néo(R) est couramment utilisé comme marqueur de sélection dans les expériences de recombinaison homologue. Mais il est également utilisé comme révélateur des mécanismes sous-jacents aux interactions de longue distance dans les loci complexes comme le locus IgH. Dans ce contexte, mon travail de thèse a porté sur les perturbations générées par le remplacement de séquences du locus IgH par le marqueur néoR. Le premier modèle correspond à des souris mutantes dans lesquelles la quasi-totalité de l'intron Iµ-Cµ (mais laissant intactes les séquences nécessaires à un épissage correct des pré-messagers µ) a été remplacé par néo(R). Nous avons trouvé que le compartiment B était profondément altéré avec un blocage dès les stades précoces du développement. En conséquence, une faible proportion de cellules B atteint les organes lymphoïdes secondaires. La transcription germinale initiée à partir du promoteur Iµ est bloquée. Dans le second modèle, nous avons généré des souris dans lesquelles le gène néoR a été inséré en aval de l'exon Iγ3 en laissant intacts tous les éléments nécessaires pour la transcription germinale et l'épissage normal des transcrits γ. L'expression du gène néoR interfère avec la transcription initiée à partir de Iγ3 et provoque une diminution de la commutation de classe vers IgG3. De plus, cette étude montre que le gène néoR apporte tous les éléments nécessaires à l'épissage des transcrits germinaux par l'activation de deux nouveaux sites cryptiques d'épissage, l'un dans la région codante du gène néoR et l'autre dans l'intron Iγ3-Cγ3. Une autre partie de mon travail a porté sur la mise en évidence d'une recombinaison interchromosomique au cours de la commutation de classe chez la souris. La première étude a été réalisée sur la lignée murine fr-Vκ pour laquelle un allèle de chaîne lourde a été rendu non fonctionnel par l'insertion d'un exon de chaîne légère entre JH4 et Eµ. Ce modèle nous a permis de montrer que le phénomène de trans-recombinaison participe activement à la commutation de classe vers IgA et IgG3. Dans une seconde étude, nous avons montré que le phénomène de trans-recombinaison participe à la commutation de classe vers tous les isotypes d'anticorps et permet la ré-expression d'un allèle exclu (au cours des réarrangements VDJ) lors du développement précoce B

Les pathologies valvulaires aortiques sont des pathologies plurifactorielles, comportant un déterminisme génétique indiscutable mais peu caractérisé. Ma thèse a pour but d’étudier le rôle du facteur de transcription Krox20 au cours du développement et de la maturation valvulaire à travers l’analyse de modèles murins. Nous avons montré que ce gène est nécessaire au développement et à la maturation de la valve aortique. L’invalidation de Krox20 chez la souris conduit à une hypertrophie des feuillets aortiques dès les stades fœtaux et à des insuffisances aortiques chez l’adulte. Ces anomalies sont associées à des défauts d’organisation de la matrice extracellulaire en partie liée à une régulation directe de l’expression des collagènes de type I et III. 25% des souris déficientes pour Krox20 présentent une bicuspidie de la valve aortique. Nous avons observé une diminution de l’expression de eNos chez ces mutants et pu mettre en évidence une interaction génétique entre Krox20 et eNos. De plus, nous avons identifié une sous population de cellules des crêtes neurales cardiaques impliquées dans l’apparition de la bicuspidie chez les mutants Krox20. Afin d’explorer le rôle de Krox20 dans la calcification de la valve aortique, nous avons étudié les conséquences de la surexpression de ce gène dans un modèle et montré que lcela induisait une activation de gènes pro-fibrotiques et pro-ostéogénique sans conduire à des dépôts calciques. Krox20 est donc un facteur de transcription important pour la valvulogenèse et à l’homéostasie valvulaire chez l’adulte. Mes travaux ont contribué à l’identification de Krox20 comme gène candidat potentiel aux valvulopathies rencontrées chez l’homme
Long seen as a consequence of aging and mechanical wear of aortic cusps, aortic valve diseases are currently considered multifactorial diseases, with an indisputable genetic determinism but not well characterized. My thesis aims to study the role of the transcription factor Krox20 during development and maturation of the valve through the analysis of mouse models. We have shown that this gene is necessary for the development and maturation of the aortic valve. Indeed, the deletion of Krox20 in the mouse leads to thickened aortic leaflets from the fetal stage and the onset of aortic valve disease in adults. These anomalies are associated with defects in the organization of the extracellular matrix and more particularly to direct regulsation of collagen type I and type III expression. Our analysis showed that 25% Krox20-/- mice have a bicuspid aortic valve. The analysis of this model has allowed us to identify a population of cardiac neural crest cells involved in the occurrence of this phenotype. In addition, we were able to observe a down regulation of eNos in Krox20-/- embryos and show a genetic interaction between Krox20 and eNos. To address the role of Krox20 in the process of calcification of the aortic valve, we have studied the effects of its overexpression. Our preliminary results indicate that this overexpression leads to activation of pro-fibrotic and pro-osteogenic genes, however, this is not sufficient to induce calcification of aortic valve leaflets.Therefore Krox20 is important for valvulogenesis but also for valvular homeostasis in the adult. My work has contributed to the identification of a potential candidate gene involved in human valve diseases

L'objectif de mon travail de doctorat était une caractérisation fonctionnelle des gènes TCTP et TSAP6. Ces gènes sont impliqués dans la réversion tumorale et forment un complexe protéique.
Tpt1, codant pour la protéine TCTP, est le gène le plus sous-exprimé lors de la réversion tumorale. L'analyse du cristal de TCTP humain montre une forte homologie entre ses hélices H2-H3 et les hélices H5-H6 de Bax. Grâce à ses hélices, TCTP inhibe l'apoptose induite par Bax au niveau des mitochondries. En effet, nous démontrons que TCTP, entre autres par le biais de ces hélices, empêche la dimérisation de Bax.
Nous avons aussi développé une lignée de souris TCTP knockout qui présentent une létalité embryonnaire précoce.
En parallèle, nous avons étudié TSAP6, qui encode pour une protéine à 6 domaines transmembranaires et qui est une cible transcriptionnelle directe de la p53. Nous avons établi une lignée murine TSAP6 knockout présentant une anémie microcytaire avec une splénomégalie. Les réticulocytes issus des souris knockout présentent un retard de maturation et une anomalie de sécrétion du Récepteur à la Transferrine par les exosomes. De manière plus générale, les résultats obtenus montrent, in vivo, que TSAP6 contrôle la sécrétion des exosomes induite par activation de la P53. Nous montrons aussi que la Sertraline et la Thioridazine empêchent la formation du complexe TSAP6-TCTP.

AbstractOverprocessing is a source of waste that occurs when unnecessary work is performed in a process. Overprocessing is often found in application-to-approval processes since a rejected application does not add value, and thus, work that leads to the rejection constitutes overprocessing. Analyzing how the knock-out checks are executed can help analysts to identify opportunities to reduce overprocessing waste and time. This paper proposes an interpretable process mining approach for discovering improvement opportunities in the knock-out checks and recommending redesigns to address them. Experiments on synthetic and real-life event logs show that the approach successfully identifies improvement opportunities while attaining a performance comparable to black-box approaches. Moreover, by leveraging interpretable machine learning techniques, our approach provides further insights on knock-out check executions, explaining to analysts the logic behind the suggested redesigns. The approach is implemented as a software tool and its applicability is demonstrated on a real-life process.

This chapter focuses on the history of cell signalling and provides an overview of some of the main techniques that could be used to study cell signalling. It presents a wide range of technologies which can be adopted for signalling studies: the use of antibodies, fluorescent probes and confocal microscopy, and traditional biochemical approaches. The chapter also looks at how the development of modern molecular biology techniques furthered our understanding of how many of these proteins function through the use of gene sequence analysis, overexpression, and knock-out and knock-down studies. It also discusses the post-genomics technologies, such as microarray analysis, RNA-seq and proteomics. The chapter also considers the ambition of ‘systems biology’.

Abstract The opinion addresses the genetic modification of animals brought about by DNA technology, including transfer of genes (transgenesis) and the deletion of genes (“knock-out”).Genetic modification of animals is a developing technology which will add to rather than replace existing techniques.

Abstract This article reviews technical and conceptual advances in unravelling the molecular bases of long-term potentiation (LTP), learning and memory using genetic approaches. We focus on studies aimed at testing a model suggesting that protein kinases and protein phosphatases balance each other to control synaptic strength and plasticity. We describe how gene ’knock-out’ technology was initially exploited to disrupt the Ca2+ /calmodulin-dependent protein kinase Ilc.t (CaMKifo) gene and how refined knock-in techniques later allowed an analysis of the role of distinct phosphorylation sites in CaMKII. Further to gene recombination, regulated gene expression using the tetracycline-controlled transactivator and reverse tetracycline-controlled transactivator systems, a powerful new means for modulating the activity of specific molecules, has been applied to CaMKlfo and the opposing protein phosphatase calcineurin.

Abstract For many years teratocarcinomas and their stem cells, embryonal carcinoma (EC) cells, have been well established tools for investigating cell differentiation as it relates to early embryogenesis, especially in the mouse (1, 2). More recently, lines of human EC cells have been characterized to extend this approach to human embryogenesis (3), while the isolation of embryonic stem (ES) cells (4, 5) has opened up important new approaches for the study of gene function during embryonic and fetal development. Many general aspects concerning the use of such cells were extensively covered in an earlier volume in this series (6), and the interested reader is encouraged to consult the relevant chapters of that volume for more comprehensive information. In the present chapter we shall repeat only the basic details necessary for working with these cells, and aim to supplement that earlier work with information more directly relevant to neurobiologists, and with newer techniques, such as homologous recombination and gene ‘knock-out’ experiments, which were not covered in detail previously.

Clustered Regularly Interspaced Short Palindromic Repeats, abbreviated as CRISPR, is a genome-editing technology that permits the creation of precise knock-out mutants by aiding the modification of gene sequences devoid of the steps involving the insertion of foreign DNA into pathogenic microorganisms. The microorganisms are ubiquitous in nature and harbor in the complex ecosystem of the human being. Cas (acronym for CRISPR-associated) genes are present in many microbial genomes. The variable nature of the microbial genome has been utilized as an integral typing tool in epidemiologic, diagnostic, and evolutionary analyses of the prokaryotic species. The past decade has seen an accumulating growth in the development of gene-editing tools utilizing the CRISPR-Cas system, which essentially is a part of the prokaryotic immune system. The development of these unique gene-editing techniques has empowered researchers to alter and investigate organisms with ease and efficiency as never before. This editing tool can efficiently be programmed and delivered into the bacterial populations to explicitly eliminate members of a targeted micro biome. Manipulation of the gene expression and regulation of the synthesis of metabolites and proteins can be achieved by utilizing an engineered CRISPR-Cas system. Put together, these tools present with the exhilarating opportunity to explore the complex interaction between the individual species of the microbiome and the host organism and thereby reveal novel avenues for the generation of drugs to selectively target the microbiome. CRISPR-Cas technology has been employed to cope with antibiotic resistance in intracellular and extracellular pathogens. The widespread use of antibiotics and the escalation of multidrug-resistant (MDR) bacteria boost the prospect of a post-antibiotic era, which emphasizes the need for novel strategies to target MDR pathogens. The development of permissive synthetic biology techniques offers favorable solutions to carry through safe and efficient antibacterial therapies.

A detailed analysis of knocking event can help improving engine performance and diagnosis strategies. The paper aim is a better understanding of the phenomena involved in knocking combustion through the combination of CFD and signals analysis tools. CFD simulations have been used in order to reproduce knock effect on the in-cylinder pressure trace. In fact, the in-cylinder pressure signal holds information about waves propagation and heat losses: for the sake of the diagnosis it is important to relate knock severity to knock indexes values. For this purpose, a CFD model has been implemented, able to predict the combustion evolution with respect to Spark Advance, from non-knocking up to heavy knocking condition. The CFD model validation phase is crucial for a correct representation of both regular and knocking combustions: the operation has been carried out by means of an accurate statistical analysis of experimental in-cylinder pressure data. The simulation results allow relating the combustion characteristics to their effect on the in-cylinder pressure signal. It is then possible to highlight critical issues regarding typical knock detection methodologies, while disclosing novel approaches. One of the main results is the validation of knock detection strategies based on the low-frequency content of the pressure signal. These strategies can be used together with standard high-frequency based techniques in order to improve the detection robustness.

Small animal models have been widely used in cardiovascular research when studying the development and treatment of different diseases. This kind of research has promoted the development of noninvasive techniques to assess cardiac tissue and blood vessels of small animals. Recently, we have developed a high-frequency ultrasound imaging system for small animals, in particular, mouse and rat models. In this work, we aim to elucidate the usefulness of using spectral analysis of the received radiofrequency (RF) ultrasound signals to extract quantitative parameters to assess mechanical properties of cardiac and vascular tissues. A custom system that employs high-frequency single-element ultrasound transducers (30–120 MHz) is used for scanning. Various signal and image processing techniques are applied on the received ultrasound signals to reconstruct high resolution B-mode and spectral images. In vitro imaging of isolated heart and vessels of APOE-KO “knock-out” mouse model with atherosclerosis was performed. Power spectral densities (PSD) of RF signals were evaluated within various regions of interests (ROI) including degassed water, normal cardiac tissue, and cardiac tissue with atheroma. Various parameters were extracted from the power spectrum such as the maximum power (Pmax), the frequency at maximum power (Fpeak), and the variance of power spectrum (Pvar). Results of the preliminary spectral analysis indicated larger values for the Pmax, Fpeak, and Pvar parameters for ROI contains atheroma than other regions. For example using the envelop data, the normalized maximum power (Pmax) value for cardiac tissue with atheroma was 0.0 ± 0.789 (dB), whereas for normal tissues it was about −13.71± 0.267 (dB). These results suggest the use spectral images as a quantitative method when assessing mouse hearts and blood vessels noninvasively.

<div class="section abstract"><div class="htmlview paragraph">With the increasing focus on reducing CO₂ emissions to combat global warming and climate change, the automotive industry is exploring near zero-emission alternative fuels to replace traditional fossil-based fuels like diesel, gasoline, and CNG. Methanol is a promising alternative fuel that is being evaluated in India due to its easy transportation and storage, as well as its production scalability and availability potential. This study focuses on the retro-fitment solution of M100 (pure methanol) SI port-fuel injection (PFI) mode of combustion. A heavy duty single-cylinder engine test setup was used to assess methanol SI combustion characteristic. Lean operation strategy has been investigated. At lean mixture conditions a significant drop in NO_X and CO emissions was achieved. The fuel injection techniques and the impact of exhaust gas recirculation (EGR) on the conventional stoichiometric combustion process is highlighted. Increase of the EGR ratio at stoichiometric operation led to 3% improvement in the thermal efficiency. The typical knock behaviour of the premixed combustion systems is analysed with different ignition sweep and EGR ratio. A higher EGR ratio is found to be beneficial in suppressing the knocking tendency. Moreover, NO_X emission well below 2 g/kWh were achieved, of adherence to the major emission legislations. The characteristics of engine aftertreatment are broadly discussed by analysing the engine out emission and operating condition. The article also focuses on development of the validated model using the Computational Fluid Dynamics (CFD) approach. The CFD investigation helps to understand and give insight of the evaporation challenges and wall-film formation at the critical engine components. Overall, the study provides an outlook into the combustion process and system layout of PFI methanol engines for retro fitment from base diesel engine, demonstrating their potential for improved engine performance and reduced emissions.</div></div>

Conventional combustion techniques struggle to meet the current emissions’ regulations while retaining high engine efficiency. Specifically in automotive diesel engines, oxides of nitrogen (NOx) and particulate matter (PM) emissions have limited the utilization of diesel fuel in compression ignition engines. By comparison, throttled, knock-limited conventional gasoline operated SI engines tend not to be fuel efficient. Advanced combustion systems that simultaneously address PM and NOx while retaining the high efficiency of modern diesel engines, are being developed around the globe [1]. One of the most difficult problems in the area of advanced combustion technology development is the control of combustion initiation [2] and retaining power density [3]. During the past several years, significant progress has been accomplished in reducing emissions of NOx and PM through strategies such as LTC/HCCI/PCCI/PPCI and other advanced combustion processes; however control of ignition and improving power density has suffered to some degree — advanced combustion engines tend to be limited to the 10 bar BMEP range and under [4]. Experimental investigations have been carried out on a light duty, DI, multi cylinder, diesel automotive engine. The engine is operated in low temperature combustion technology with 87 RON (Research Octane Number) fuel [7]. Using an Ignition Quality Test (IQT) device, the equivalent Cetane Number (CN) was measured to be 25. In the present work, various EGR rates are examined to determine the effect on the combustion, emissions and performance. Experiments were conducted at three different engine load/speed combinations that are part of General Motors’ reference points for vehicle operation. To reduce the complexity, boost pressure and injection pressure and timing were kept constant while EGR percentage and intake temperature were used as parameters in this study. The intake temperature was not truly independent, as it trended with EGR level, but based upon the boost level and the available EGR cooling, Intake Air Temperature (IAT) was kept in the range of 40–80 deg C. Additional cooling capacity will be added in future work in an effort to keep IAT more consistent. EGR rates have a detrimental effect on engine efficiencies at lower load while it appears to have little effect on efficiency at higher loads. A more significant effect at very low load appears to be higher intake temperatures (hot EGR) as opposed to the very slight decrease in oxygen concentration.