Philosophiae Doctor - PhD / Retinoblastoma-binding protein 6 (RBBP6) is a multi-domain human protein known to play a role in mRNA splicing, cell cycle control and apoptosis. The protein interacts with tumour suppressor proteins p53 and pRb and recent studies have shown that it plays a role in the ubiquitination of p53 by interacting with Hdm2, the human homologue of mouse double minute protein 2 (Mdm2), in which the RING finger domain plays an essential role. Recently, RBBP6 has been shown to ubiquitinate the mRNA-associated proteinYB-1 through its RING finger domain, causing it to be degraded in the proteasome.RING (Really Interesting New Gene) fingers are small commonly-occurring domains of approximately 70 amino acids in length which coordinate two zinc ions in a cross-brace fashion.They are characterized by a conserved pattern of eight Cysteine or Histidine residues which are involved in coordinating the zinc ions. In terms of this conserved consensus, the RING finger from RBBP6 is expected to coordinate the zinc ions through eight Cysteine residues, making it a “C4C4” RING finger similar to those identified in transcription-associated proteins CNOT4(CCR4-NOT transcription complex, subunit 4) and p44 (interferon-induced protein 44). The amino acid sequence of the domain also shares many similarities with the U-box family of domains, which have an identical three-dimensional structure despite not requiring zinc ions in order to fold. This thesis reports the bacterial expression of a fragment containing the RING finger domain from human RBBP6, and determination of its structure using heteronuclear Nuclear Magnetic Resonance (NMR) spectroscopy. Preliminary NMR analysis of the fragment revealed that the domain was folded, but that it was preceded by an unstructured region at the N-terminus. A shortened fragment was therefore expressed and used for structural studies. Isotope-enriched protein samples were generated by growing bacteria in minimal media supplemented with 15NNH4Cl and 13C-glucose and purified using a combination of glutathione agarose affinity chromatography, anion exchange and size exclusion chromatography. A complete set of heteronuclear NMR data was collected at 600 MHz from which almost complete assignment of the backbone, side-chain and aromatic resonances was achieved. By exchange of Zn2+ with 113Cd2+ we managed to confirm that the domain binds two Zn2+ ions, and confirm that they are coordinated in the expected cross-brace manner. Structural data in the form of 2-Dimensional Nuclear Overhauser Enhancement Spectroscopy (2D-NOESY), 15N-separated NOESY and 13Cseparated NOESY spectra were recorded and used to determine the structure using restrained molecular dynamics on the Combined Assignment and Dynamics Algorithm for NMR Applications (CYANA) platform.As expected, the structure contains a triple-stranded β-sheet packing against an α-helix and two zinc-stabilized loops as found in all RING fingers. However, it also contains a C-terminal helix which packs against an N-terminal loop which is similar to that found in many U-box domains.A search using the DALI server revealed that the structure is most similar to the U-box from CHIP (C-terminus of Hsp70-interacting protein), an E3 ligase that cooperates with Hsp70 to degrade unfolded proteins that cannot be refolded. Using NMR we showed that the domain dimerizes with a KD of approximately 200 Μm, which means that it is dimeric at the concentrations used for NMR structure determination. Chemical shift analysis showed the dimerization interface to be very similar to that identified in U-box domains found in C-terminus of Hsp70 interacting proteins (CHIP).The structural similarities reported here between the RING finger from RBBP6 and the U-box family lead us to conclude that RBBP6 may, like CHIP, play a role in protein quality control.

Pour faciliter l’initiation de la transcription par l’ARN Polymérase II, le complexe co-activateur de la transcription SAGA possède une activité d’acétylation des histones H3 et une activité de déubiquitination des histones H2B, catalysée chez l’homme par l’enzyme USP22. Mon travail de thèse a porté sur l’étude de la régulation de cette activité de déubiquitination.Au sein de SAGA, USP22 interagit fortement avec trois protéines pour former un module structural appelé module de déubiquitination (DUBm). Nous avons montré que la formation d’un tel module était requise pour activer USP22. D’autre part, deux sous-unités du DUBm humain, ATXN7 et ATXN7L3, contiennent un domaine SCA7. Nos résultats montrent que le repliement structural adopté par ces deux doigts de zinc n’avait pas encore été décrit. Nous avons démontré que le domaine SCA7 de ATXN7 peut interagir avec un nucléosome in vitro et que cette interaction participe à la régulation fine de l’activité de déubiquitination de SAGA. Nous proposons qu’en interagissant avec le nucléosome, le domaine SCA7 de Sgf73 ou de ATXN7 pourrait positionner le DUBm de façon optimale par rapport à son substrat. / The SAGA complex is one of the most studied transcriptional co-activator complexes. To facilitate transcription by RNA Polymerase II, SAGA presents a modular organization and harbours two enzymatic activities. In human cells, these two enzymes are called GCN5 and USP22 and they can respectivelly acetylate histones H3 and deubiquitinate histones H2B. During my PhD thesis, I have worked on the regulation of SAGA deubiquitination activity. In the SAGA complex, USP22 interacts strongly with three other subunits to form a structural and functionnal module, named deubiquitination module (DUBm). We have shown that the free recombinant USP22 enzyme is not active, but that the formation of a stable DUBm triggers a strong stimulation of USP22 catalytic activity. Secondly, in human cells, two subunits of the DUBm, ATXN7 and ATXN7L3, contain a domain, called SCA7, that is not found in any other protein. Our results show that the new structural fold adopted by these two domains is specific to these zinc-fingers. These two SCA7 domains share a common structural heart, but their atomic structures reveal also differences, especially in the spatial organization of secondary structure elements. Indeed, we have shown that ATXN7 SCA7 domain can interact in vitro with a nucleosome which is not the case of ATXN7L3 SCA7 domain. Finally, I could show that in vivo the SCA7 domain of Sgf73, the ortholog of ATXN7 has a role in fine tunning SAGA deubiquitination activity. We hypothesize that the interaction between a nucleosome and the SCA7 domain of ATXN7 or Sgf73 would regulate SAGA deubiquitination activity by an optimal positionning of the module to its substrate.

Climbing is a rapidly growing sport, and the inclusion in the 2021 Olympics will further push the popularity.  The numerous originalities of Sport climbing (SC) is the intense use of finger, hands and forearms to displace the body on vertical to fully overhangning wall profiles. Therefore, climbers are prone to specific injuries different from many other sports, mainly located in the fingers and hand. The main objective of this study was to evaluate the relationship between finger flexion (FF) and wrist extension (WE) for force max (F-max) and force average (F-avg). Another aim of the study was to analyse the ratio between FF and WE in regards of injuries. A total of 26 climbers were tested on two separate occasions for underarm capacities in FF in a half crimped position and WE.  Isometric contraction was measured for F-max during a three sec interval and anaerobic power, F-avg, during a 30 sec interval. Correlation between variables were analysed by linear regression and one way ANOVA was used to analyse previously injured vs non injured groups. Statistical significance was set at P = 0.05. This study found that climbers showed a significant relationship between FF and WE for both the F-max and 30s F-average tests R² > 0.30, P < 0.004. This can be valuable information for climbers and coaches for training. Furthermore an increased ratio was seen in more experienced climbers, and the same group also showed a higher prevalence of injuries than moderate climbers.

付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラム / 京都大学 / 新制・課程博士 / 博士(人間健康科学) / 甲第23127号 / 人健博第89号 / 新制||人健||6(附属図書館) / 京都大学大学院医学研究科人間健康科学系専攻 / (主査)教授 杉本 直三, 教授 黒木 裕士, 教授 松田 秀一 / 学位規則第4条第1項該当 / Doctor of Human Health Sciences / Kyoto University / DFAM

In eubacteria, stalled ribosomes are rescued by a conserved quality-control mechanism involving transfer-messenger RNA (tmRNA) and its protein partner SmpB. Mimicking a tRNA, tmRNA enters stalled ribosomes, adds Ala to the nascent polypeptide, and serves as a template to encode a short peptide that tags the nascent protein for destruction. To further characterize the tagging process, we developed two genetic selections that link tmRNA activity to cell death. These negative selections can be used to identify inhibitors of tagging or to identify mutations in key residues essential for ribosome rescue. Little is known about which ribosomal elements are specifically required for tmRNA activity. Using these selections, we isolated ribosomal RNA mutations that block the rescue of ribosomes stalled at rare Arg codons or at the inefficient termination signal Pro-opal. We find that deletion of A1150 in the 16S rRNA blocks tagging regardless of the stalling sequence, suggesting that it inhibits tmRNA activity directly. The C889U mutation in 23S rRNA, however, lowers tagging levels at Pro-opal and rare Arg codons but not at the 3'-end of an mRNA lacking a stop codon. We conclude that the C889U mutation does not inhibit tmRNA activity per se but interferes with an upstream step intermediate between stalling and tagging.

The goal of the master thesis is the design and construction of a device for capturing video sequences of the cardiovascular system of the finger of a human hand and the subsequently design and implementation of a method of data extraction for its reconstruction into a 3D model.

Thesis (M.Sc. Agriculture (Pasture Science)) -- University of Limpopo, 2021 / Finger millet (Eleusine coracana) is believed to be adapted to the arid and semi-arid regions, highly tolerant to pests, diseases and drought. It has the potential to produce a high forage biomass with fewer inputs under good production practices. The aim of the study was to evaluate the potential of finger millet as a fodder crop on the Pietersburg Plateau under rainfed and irrigation conditions, planted in rows and broadcast. The study was conducted for two consecutive seasons (2017 and 2018) at the Syferkuil Experimental Farm (SEF), University of Limpopo. Treatments consisted of two watering treatments (irrigation and rainfed) and two planting methods (broadcast and row planting). Seeding rate was 10 kg ha-1 with the inter row spacing of 25 cm. Irrigation had a significant effect on the dry matter production of finger millet (P ≤ 0.05). During 2017 growing season, under rainfed condition, the crop experienced zero production due to low rainfall. The total dry matter production of finger millet under rainfed conditions in 2018 was 3371 kg ha-1 for row planting and 3770 kg ha-1 for broadcasting. The dry matter production of finger millet under irrigation and row planting was 5318 kg ha-1 compared to 3371 kg ha-1 produced under row planting in the rainfed conditions. Broadcasting under irrigation produced 4890 kg ha-1 whereas broadcasting under rainfed conditions yielded 3770 kg ha-1. Planting method had no significant effect on the dry matter production of finger millet (P ≤ 0.05). The total dry matter production in 2017 was 5668 kg ha-1 and 5122 kg ha 1 under row planting and broadcast respectively, 2018 season produced the total dry matter production of 5122 kg ha-1 under row planting and 4892 kg ha-1 under broadcast. Finger millet planted under rainfed in rows had the CP% of 14.76 and 16.87% when broadcasted. In all the treatments CP% was higher than 10%. The ADF% was 33.02% under rainfed conditions and it ranged between 30.99% and 31.53% in 2017 and 2018 for row planting under irrigation. Finger millet can be considered an alternative fodder crop for livestock farmers in the Pietersburg Plateau

No description available.

Les transposases sont des enzymes qui reconnaissent des séquences spécifiques sur l'ADN aux bornes des transposons (éléments à transposer) et catalysent des réactions de coupure et de transfert de brins. La mobilité des transposons entraîne la plasticité des génomes, et dans certains cas, l'exaptation de gènes de transposons contribue à l'émergence de nouvelles fonctions cellulaires. La paramécie est un modèle eucaryote unicellulaire extraordinaire pour étudier le rôle des transposases domestiquées de PiggyBac (nommées PiggyMac et PiggyMac-like) dans le réarrangement programmé de son génome. Ces dernières contribuent à l'assemblage de son génome somatique au cours du cycle sexuel. Les principaux axes de ce projet se sont centrés sur l’étude structurale de la transposase PiggyBac (issue de Trichoplusia ni) et une étude d’interaction avec des séquences particulières de son transposon. Ainsi qu’une étude structurale de la transposase domestiquée PiggyMac chez la paramécie.La première structure obtenue (domaine riche en cystéine de la transposase PiggyBac) montre une structuration en doigt de zinc de type PHD-RING. Il a été démontré in vivo et in vitro l’importance du domaine riche en cystéines (CRD) de PiggyBac pour une activité d’excision et d’intégration du transposon PiggyBac. Nous avons pu mettre en évidence que le CRD de PiggyBac cible des séquences spécifiques d’ADN qui sont localisées dans les séquences TIR (Terminal Inverted Repeat) gauche et droite du transposon. Grâce aux résultats issus de la RMN, des modèles de complexes protéine-ADN ont pu être établis.Concernant PiggyMac (transposase PiggyBac domestiquée), son domaine riche en cystéines et histidines a pu être produit doublement marqué (15N et 13C) dans E.coli. Des études structurales en RMN et l'utilisation d'un programme de modélisation moléculaire CYANA ont permis d’accéder à la structure tridimensionnelle de ce domaine.Nous montrons que celui-ci se replie en doigt de zinc entrelacé qui lie deux ions zinc avec un total de huit histidines et cystéines (résultat en cours de publication). La configuration de ce doigt de zinc est différente de celui de PiggyBac et même nouveau dans la littérature concernant ce peptide. Cette étude a permis de mettre en évidence un nouveau type de doigt de zinc. / Transposases are enzymes that recognize specific DNA sequences across transposons (elements to transpose) and catalyze cleavage and transfer reactions strands. The mobility of transposons causes the genome plasticity, and in some cases, the transposon gene exaptation contributes to the emergence of new cellular functions. Paramecium is an extraordinary unicellular eukaryotic model to study the role of transposases domesticated PiggyBac (named PiggyMac and PiggyMac-like) in the programmed rearrangement of its genome. These contribute to the assembly of the somatic genome during sexual cycle. The main axes of this project have focused on the structural study of the transposase PiggyBac (derived from Trichoplusia ni) and an interaction study with particular sequences of the transposon. And a structural study of the transposase domesticated PiggyMac in Paramecium.The first structure obtained (cysteine-rich domain of the transposase PiggyBac) shows a structure in PHD-RING-type zinc finger. It has been demonstrated in vivo and in vitro the importance of the cysteine-rich domain (CRD) of PiggyBac for excision activity and integration of the transposon PiggyBac. We were able to show that the CRD PiggyBac target specific DNA sequences that are located in the TIR sequences (Inverted Terminal Repeat) left and right of the transposon. Thanks to the NMR results, protein-DNA complexes models were established.Regarding PiggyMac (PiggyBac domesticated transposase), its cysteine ​​and histidine rich domain has been doubly labeled product (15N and 13C) in E. coli. NMR structural studies and the use of a CYANA molecular modeling program allowed to access the three-dimensional structure of this domain.We show that it folds into interlaced zinc finger that binds two zinc ions with a total of eight histidine and cysteine ​​(results being published). The configuration of this zinc finger is different from that of PiggyBac and even new in the literature concerning this peptide. The study highlighted a new type of zinc finger.

Studiens syfte är att beskriva hur elever i de lägre åldrarna använder handgester när de löser aritmetikuppgifter. Den teoretiska utgångspunkten i studien är embodied cognition, där det centrala i teorin är att vi lär oss genom kroppen. Tio elever i sjuårsåldern i Sydafrika har observerats med fokus på deras användning av handgester. Resultatet visade att flera av eleverna använder handgester när de löser additions- och subtraktionsuppgifter och att det finns ett antal olika handgester de använder sig av. De olika handgesterna delades in i taktila och icke-taktila gester, som i sin tur kopplades till konkreta och abstrakta gester. Slutsatsen av studien är att elever använder sig av olika handgester i olika kombinationer när de löser aritmetikuppgifter. Deras gester med händer och fingrar kan vara ett uttryckssätt för deras utvecklingsprocess och kan fungera som en bro mellan konkret och abstrakt tänkande. / The aim of the study is to describe how students of the lower ages use hand gestures when solving arithmetic tasks. The theoretical basis of the study is embodied cognition. The viewpoint of embodied cognition holds that the body is a tool for learning. Ten students in South Africa, aged seven, have been observed based on their use of hand gestures. The result showed that several students use hand gestures when solving addition and subtraction tasks and there were a number of different hand gestures being used. The various hand gestures were divided into tactile and non-tactile gestures. These could in turn be linked to concrete and abstract gestures. The conclusion of the study is that students use different types of hand gestures and also in various combinations when solving arithmetic tasks. Their hand gestures can be a way of expressing their development process and to function as a bridge between concrete and abstract thinking.