Miracle-dz/UniFAR-FTUs huggingface dataset:
Fonctions du facteur de transcription SCL dans les cellules souches et les progéniteurs hématopoïétiques

Studying the mecanisms goveming the hematopoietic system requires the understanding of interactions linking intrinsic regulators of hematopoiesis and cellular environment. Spatio-temporal expression of specifie transcription factors is central to cell differentiation and controls multiple biological functions. The environment is also a key pJayer in these processes as revealed by its ability to modulate gene expression and cclI fate. Here, we clearly demonstrate the essential role ofthe transcription factor seL in adult hematopoiesis by its capacity to control specifie biological functions at different lev el of hemopoietic hierarchy. The work presented in this thesis put into Iight the crucial role of Sel in the long term maintenance of hematopoietic stem cells. More precisely, Sel favors stem cell quiescence by directly controlling the expression of p21, a cell cycle inhibitor essential for hematopoietic stem cell maintenance over time. Furthermore, this work revealed the antiapoptotic function of SeL in hematopoietic progenitors. We also showed that these seL regulated functions are controlled by environmental eues. SeL indeed restrains the capacity of adult hematopoietic stem cells to transit from GO to G 1 in response to mitogenic signais, thereby preventing their excessive activation and early depletion. Finally, we also demonstrated that SeL controls progenitor survival downstream of c-Kit signaling. Together, our data unravel the central and multifunctional role of SeL in the adult hematopoietic system and in a more general manner, the instructive role of the environment on cell fate.
Ultrafast photodetector on the InP-membrane-on-silicon platform

We demonstrate the first electrically pumped laser in the “InP membrane on Si” platform. With pulsed current injection, the lasing occurs at threshold current of 200mA and peak optical power of 135μW in fiber. OCIS codes: (140.5960) Semiconductor lasers; (250.3140) Integrated optoelectronic circuits
Post‐Fire Population Dynamics of Two Tree Species in High‐Altitude Polylepis Forests of Central Ecuador

Fire is considered the main cause for the patchy distribution of high‐montane tropical forests growing below the upper limit of tree growth, but there are little quantitative data on the impacts of burning on the respective tree populations. This study compares adult tree survival as well as sapling (0.05–1.3 m) and seedling (<0.05 m) recruitment of Polylepis incana, and the coexisting Gynoxis acostae in burned and unburned forest stands in the Páramo de Guamaní, central Ecuador. In P. incana, adult survival after burning was low, whereas all G. acostae individuals survived through resprouting. Two years after fire, the density of P. incana seedlings and saplings was higher than that of G. acostae, but still not sufficient for forest recovery. A sowing experiment revealed a significantly lower seedling emergence of both species in the burned than in the unburned plots. Seedling emergence was comparable to laboratory studies performed under optimal conditions, suggesting there was no evidence for climate constraining emergence at the given altitude. Interactions between seedling survival and burning for P. incana indicate higher seedling survival after burning, which could not be shown for G. acostae. Our data imply that single fire events strongly decrease adult and seedling population sizes in P. incana and thus may be the main reason for the discontinuous forest distribution below the upper distribution limit of the species. In contrast, the high resprouting potential of G. acostae explains its relatively high percentage in the remaining Ecuadorian P. incana stands.
Subnuclear foci quantification using high-throughput 3D image cytometry

Ionising radiation causes various types of DNA damages including double strand breaks (DSBs). DSBs are often recognized by DNA repair protein ATM which forms gamma-H2AX foci at the site of the DSBs that can be visualized using immunohistochemistry. However most of such experiments are of low throughput in terms of imaging and image analysis techniques. Most of the studies still use manual counting or classification. Hence they are limited to counting a low number of foci per cell (5 foci per nucleus) as the quantification process is extremely labour intensive. Therefore we have developed a high throughput instrumentation and computational pipeline specialized for gamma-H2AX foci quantification. A population of cells with highly clustered foci inside nuclei were imaged, in 3D with submicron resolution, using an in-house developed high throughput image cytometer. Imaging speeds as high as 800 cells/second in 3D were achieved by using HiLo wide-field depth resolved imaging and a remote z-scanning technique. Then the number of foci per cell nucleus were quantified using a 3D extended maxima transform based algorithm. Our results suggests that while most of the other 2D imaging and manual quantification studies can count only up to about 5 foci per nucleus our method is capable of counting more than 100. Moreover we show that 3D analysis is significantly superior compared to the 2D techniques.
TAXONOMIC REVISION AND MITOCHONDRIAL SEQUENCE EVOLUTION OF THE CYPRINID GENUS SQUALIDUS (TELEOSTEI: CYPRINIDAE) IN TAIWAN WITH DESCRIPTION OF A NEW SPECIES

– Taxonomic studies of the cyprinid genus Squalidus was carried out in Taiwanese waters and three distinct species could be recognized. Among them, the endemic species, S. iijimae (Oshima, 1919) is only distributed around two river basins of Northwestern Taiwan. The slender species, S. argentatus (Sauvage & Dabry de Thiersant, 1874) is a newly-recorded species in Taiwanese waters and is only found in the Tanshuei River basin. A new species, S. banarescui has been discovered recently in the freshwater Wu River basin in Central Taiwan. The molecular phylogenetic studies also revealed that the three species are genetically distinct and there is a closer relationship between S. iijimae and S. banarescui than between S. iijimae and S. argentatus. The analysis of mitochondrial DNA (mtDNA) phylogeny shows the monophyletic group for the three Taiwanese species.
Identification of foraging behaviour and feeding areas of threeseabird species breeding sympatrically in a highly productive regime, the northern Gulf of Alaska

The Gulf of Alaska is a highly productive regime and supports several millions of seabirds. But populations fluctuate sharply and reasons for that are not completely understood. However, understanding of how seabirds react to their marine environment is essential in order to assess naturally or human induced changes of their abundances and distributions. This thesis focuses on the at-sea distribution, foraging ecology and diving behaviour of three seabird species breeding sympatrically on Middleton Island in the northern Gulf of Alaska. Pelagic Cormorants (Phalacrocorax pelagicus), Black-legged Kittiwakes (Rissa tridactyla) and Tufted Puffins (Fratercula cirrhata) were studied during three consecutive years using novel data logger technologies like GPS data loggers or time-depth-recorders (TDR’s). The present study provides several completely new aspects of the ecology of these species and indicates how these different seabird species use the marine environment successfully.
Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands, the Ryukyu Archipelago, Japan

Aim Phylogeographical patterns in the Ryukyu Archipelago have been explained primarily by landbridge formation and the opening of two straits in the Pliocene, namely the Tokara and Kerama gaps. These old straits have been considered to be the barriers most likely to determine genetic boundaries. To test this, we conducted a molecular analysis of the herb Ophiorrhiza japonica. We discuss the causes of and processes involved in its phylogeographical structure and explore aspects of island separation other than the duration of the straits to explain genetic boundaries at the gaps.
Histochemical studies of carbohydrates and proteins in the pulmonary bronchi of black Bengal goat (Capra hircus).

Histochemical studies were conducted on the pulmonary bronchi of ten adult healthy black Bengal goats of either sex. Goblet cells, glands, cartilage and perichondrium manifested intense positive reactions generally for carbohydrates whereas, connective tissue, muscle fibres and blood vessels showed generally weak to moderate positive reaction. The bronchial epithelium, glands, cartilage matrix and muscle layers manifested strong reactions for acid mucopolysaccharides. Reaction for proteins was strong to intense in the bronchial epithelium, glands, perichondrium of bronchial cartilages and muscle fibres.
Structural Studies on Immunogenic Proteins of Burkholderia pseudomallei

Burkholderia pseudomallei is a Gram negative bacterial pathogen and the causative agent of melioidosis, which is the third most frequent cause of death from infectious disease in Northeastern Thailand and also highly endemic in Southeast Asia and Northern Australia. Problems of melioidosis management include misdiagnosis and the increasing resistance of the bacteria to the current anti-infective treatment, resulting in high mortality and having a global impact as a potential bioweapon. Little is known about the ambiguous pathogenesis and virulence mechanisms of B. pseudomallei infection. One way to gain understanding is through the investigation of the structure/function relationships of potential target proteins, as a starting point for a rational drug discovery programme. Structural studies on the target proteins of B. pseudomallei can shed light on their biological functions at the molecular level. This thesis presents the structural studies on immunogenic proteins of B. pseudomallei as part of a targeted structural genomics programme on B. pseudomallei. Seven target genes were selected from lists of putative essential genes and also identified B. pseudomallei proteins that elicit an immuno cross reactivity to the sera of infected humans, which may be involved in virulence and/or pathogenicity of B. pseudomallei. Of those, BPSL0606, an uncharacterised protein, was cloned, over-expressed, purified, and crystallised. The first crystal structure of BPSL0606 was determined and revealed that it is structurally similar to the GCN5-related N-acetyltransferase (GNAT) superfamily. Dimer formation in the crystal packing agreed with gel filtration analysis and the interface of BPSL0606 was similar to many GNAT members. Structure-based alignment of BPSL0606 against known structures of GNATs showed that BPSL0606 has conserved residues that are involved in the binding of acetyl coenzyme A in members of GNATs, suggesting that BPSL0606 may bind the acetyl coenzyme A. Although co-crystallization of BPSL0606 and acetyl coenzyme A and ligand observation by nuclear magnetic resonance suggested that BPSL0606 did not bind to the acetyl coenzyme A. Analysis of the aminoglycoside binding site indicated that BPSL0606 could possibly bind to this substrate. The BPSL0606 structure with acetyl coenzyme A and kanamycin was modelled, proposing a possible clue related to the antibiotic resistance. The findings in this PhD thesis provide the molecular and structural information of B. pseudomallei proteins, which could contribute to further investigations.
Sequentielle Genotypisierung von Pseudomonas aeruginosa-Isolaten und Übereinstimmung von bakteriologischen Proben aus dem oberen und unteren Respirationstrakt von Patienten mit cystischer Fibrose

nachweisbar. -5-Abstract There is controversy about adequate specimen to detect and characterise colonisation of cystic fibrosis (CF) airways by Pseudomonas aeruginosa. Oropharyngeal, sputum and bronchoalveolar lavage (BAL) samples were evaluated sequentially from 38 stable CF patients for the detection of P. aeruginosa. Pseudomonas strains were typed by random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. The occurrence of genetically different isolates within the same host and longitudinal variations in the genotype during repeated examinations was assessed. Sensitivity, negative and positive predictive values and specificity to detect P. aeruginosa were 36%, 74%, 83% and 96% for oropharyngeal cultures in non-expectorating patients and 92%, 94%, 100% and 100% for sputum cultures from expectorating patients, respectively. RAPD analysis and PFGE were suitable to characterize P. aeruginosa CF isolates, although only DNA macrorestriction was able to distinguish between identical and closely related strains. Genotypes of Pseudomonas isolates recovered from oropharyngeal swabs and sputum differed to the strains recovered by bronchoscopy in 55% and 40%, respectively. In 62% longitudinal variations in the genotype occurred. Half of these alterations were only detectable from bronchoscopically obtained samples. In conclusion, sputum samples have the same value as specimens from BAL to detect P. aeruginosa colonisation, whereas cultures from the oropharynx are not suitable for characterising the bacterial conditions in the CF lungs in an early disease state. DNA macrorestriction is recommended as an excellent tool for epidemiological investigations. Different genotypes within the same host and longitudinal genetic alterations are common and may be detectable in the BAL fluid exclusively. -7
Floating Boards Improve Electricity Generation from Wastewater in Cassette-Electrode Microbial Fuel Cells

Microbial fuel cells (MFCs) are devices that are expected to be applied to the recovery of electric energy from wastewater. We have recently demonstrated that cassette-electrode MFCs (CE-MFCs) are useful for the treatment of wastewater. A concern about CE-MFCs is however relatively low columbic efficiency that may be caused by oxygen contamination from water surfaces. In the present study, floating boards were installed at the surface of water for minimizing oxygen diffusion from the air, and their effects on organics removal, electricity generation and microbial communities were analyzed. It was found that the installation of floating boards allowed an average of 10% increases in Columbic efficiency, while organic removal efficiency remained over 80%. The improved electricity generation was associated with changes in microbial communities as analyzed by denaturing gradient gel electrophoresis of 16S rRNA-gene amplicons. These results suggest the utility of floating boards for improving electricity generation in CE-MFCs used for wastewater treatment.
Mucosal T Cells Bearing TCRγδ Play a Protective Role in Intestinal Inflammation1

Intestinal intraepithelial lymphocytes (IEL) bearing TCRγδ represent a major T cell population in the murine intestine. However, the role of γδ IEL in inflammatory bowel diseases (IBD) remains controversial. In this study, we show that γδ IEL is an important protective T cell population against IBD. γδ T cell-deficient (Cδ−/−) mice developed spontaneous colitis with age and showed high susceptibility to Th1-type 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis at a young age. Transfer of γδ IEL to Cδ−/− mice ameliorated TNBS-induced colitis, which correlated with decrease of IFN-γ and TNF-α production and an increase of TGF-β production by IEL. Furthermore, a high level of IL-15, which inhibits activation-induced cell death to terminate inflammation, was expressed more in intestinal epithelial cells (EC) from TNBS-treated Cδ−/− mice than in those from wild-type mice. EC from wild-type mice significantly suppressed the IFN-γ production of IEL from TNBS-treated Cδ−/− mice, whereas EC from TNBS-treated Cδ−/− mice did not. These data indicate that γδ IEL play important roles in controlling IBD by regulating mucosal T cell activation cooperated with EC function. Our study suggests that enhancement of regulatory γδ T cell activity is a possible new cell therapy for colitis.
Dry reforming puts CO2 to work

It’s an industrial chemist’s dream to transform carbon dioxide into fuels and chemicals. A few processes do use the abundant waste gas as a starting point for polyols and specialty polymers. Other companies are looking to make chemicals by reacting CO with hydrogen acquired from water electrolysis. But multi-million-metric-ton use of CO2 as a chemical reagent is relegated mostly to old-school production of urea and sodium bicarbonate. The German industrial gas and engineering giant Linde is looking to change that. Company officials claim to have made a breakthrough in dry reforming, a process that reacts CO2, instead of steam or oxygen, with methane to yield the mixture of CO and H2 known as synthesis gas. Dry reforming may be the way to introduce CO2 into the manufacture of large-scale chemicals such as methanol, acetic acid, and the diesel substitute dimethyl ether (DME), according to Nicole Schoedel, head of chemical development
Étude des régions terminales de l'ADN génomique de bactériophages infectant lactococcus lactis

L'infection des bacteries lactiques par les bacteriophages est l'une des causes majeures d'accidents de fermentation en industrie laitiere. La comprehension des mecanismes regissant la multiplication de ces phages chez lactococcus lactis devrait faciliter la construction de souches plus resistantes. L'etude a ete realisee sur trois phages lytiques a petite tete isometrique, le phage de reference p008, le phage atcc 11955-b1 et le phage phivi, isole sur un site industriel francais. La determination des caracteristiques structurales de phivi a permis de montrer qu'il appartenait, comme les phages p008 et atcc 11955-b1, a l'espece 936. La cinetique de replication de l'ADN de phivi a ete etudiee et sa carte de restriction a ete etablie. Nous avons egalement montre que le genome de ces trois phages possedait des extremites simple brin complementaires (site cos) de 15 nucleotides protuberantes en 3 et de sequence identique. Une region de 2,8 kb contenant le site cos des phages phivi et p008 a ete sequencee. L'analyse des sequences revele la presence, dans les trois phages, d'un motif structural, proche du site cos et caracterise par un arrangement particulier de sequences repetees. Ce motif est sans doute implique dans les processus couples de maturation et d'encapsidation de l'ADN. Il est lui-meme suivi de deux phases ouvertes de lecture codant pour des proteines de 174 et 538 acides amines, qui pourraient, d'apres leur organisation et les caracteristiques des proteines codees, correspondre aux genes des deux sous-unites de la terminase. Une de ces proteines a pu etre exprimee chez e. Coli
The role of fatty acid quality in a maternal obesogenic diet for adipose tissue development in offspring mice

In NMRI outbred mice, exposure to a maternal adipogenic milieu appears to disturb adipose tissue expansion in the female offspring with activation of adipocyte de novo lipogenesis and development of adiposity during high fat diet feeding. Modification of the fat quality of a maternal obesogenic diet using medium-chain fatty acids and omega-3 polyunsaturated fatty acids might be a promising approach to ameliorate the maternal milieu with possible beneficial effects on the offspring metabolic phenotype.
A connectionist model of the Drosophila blastoderm

The authors present a phenomenological modeling framework for development, and apply it to the network of segmentation genes operating in the blastoderm of Drosophila. Their purpose is to provide a systematic method for discovering and expressing correlations in experimental data on gene expression and other developmental processes. The modeling framework is based on a connectionist or neural net dynamics for biochemical regulators, coupled to grammatical rules which describe certain features of the birth, growth, and death of cells, synapses and other biological entities. They present preliminary numerical results regarding regulatory interactions between the genes Kruppel and knirps that demonstrate the potential utility of the model. 14 refs., 5 figs.
Endocrine regulation of adipose tissue thermogenesis in the fetal and neonatal sheep

Leptin is produced primarily by white adipose tissue but also by brown adipose tissue (BAT) and the placenta. It has a major physiological role in the control of energy balance. BAT is critically important for the initiation of non-shivering thermogenesis in precocial newborns through the uncoupling protein, UCP1 unique to BAT. This is particularly important in neonatal lambs and infants in which levels of UCP1 peak at birth concomitant with a peak in plasma leptin and a surge in Cortisol. Other mitochondrial proteins may contribute to this effect e.g. VDAC which is located in the outer mitochondrial membrane. The aim of this thesis was to: 1. investigate the role of the late gestation Cortisol surge on BAT development 2. investigate the effect of route of delivery on subsequent neonatal plasma leptin concentrations 3. assess the effect of leptin administration to neonatal lambs on thermoregulation Late gestation fetuses were infused with Cortisol or saline or underwent adrenalectomy or sham operation. BAT was sampled at 129 and 144 days of gestation, respectively. UCPl abundance was significantly increased in the animals receiving Cortisol treatment compared to controls and was significantly reduced in adrenalectomised animals. Plasma leptin was analysed from lambs delivered vaginally or near term by caesarean section (CS). Cord plasma leptin decreased significantly after birth, an adaptation that was delayed by CS delivery. Acute and chronic administration of leptin to neonatal lambs improved thermoregulation by preventing a decline in body temperature. Chronic leptin treatment over 7 days (lOOp-g daily) promoted the loss of UCP1 mRNA and protein, but had no deleterious effects on body temperature. Polyclonal antibodies were developed against mitchondrial voltage-dependent anion channel (VDAC). The postnatal ontogeny of VDAC was found to be similar to that of UCP1 and cytochrome c, with abundance peaking around one day of age. VDAC was found in high abundance in organs with high metabolic requirements such as heart, muscle and BAT. These results suggest that VDAC is involved in ensuring BAT maintains a maximal rate of thermogenesis after birth. In conclusion, I have shown for the first time that leptin has an important role in thermogenesis during the transition from fetal to neonatal life. This is attenuated in CS animals, possibly linked to a reduced sympathetic nervous system activity. The rapid loss of UCP1 mRNA, which occurs within the first few days of life, appears to be modulated by leptin, possibly stimulating the development of white adipose tissue and generation of body heat through mechanisms other than nonshivering thermogenesis in BAT. VDAC may be important during this period in ensuring adequate substrate delivery to BAT. Intact adrenal glands are also necessary for the increase in UCP1 abundance during late gestation, an effect mediated in part by Cortisol. NB. This ethesis has been created by scanning the typescript original and may contain inaccuracies. In case of difficulty, please refer to the original text.