Miracle-dz/UniFAR-FTUs huggingface dataset:
Surviving Ionizing Radiation: General Stress Response and Mechanisms for the Prevention and Repair of DNA Damage in Halobacterium sp. str. NRC-1

Title of Document: SURVIVING IONIZING RADIATION: GENERAL STRESS RESPONSE AND MECHANISMS FOR THE PREVENTION AND REPAIR OF DNA DAMAGE IN HALOBACTERIUM SP. STR. NRC-1 Adrienne Leah Kish, Doctor of Philosophy, 2007 Directed By: Assistant Professor Dr Jocelyne DiRuggiero, Department of Cell Biology and Molecular Genetics The effects of ionizing radiation on the extremely halophilic Archaeon Halobacterium sp. str. NRC-1 can be divided into three central themes: protection from oxidative damages, response to ionizing radiation, and repair of DNA double strand breaks (DSBs). Intracellular salts used to maintain osmotic balance in the hypersaline conditions Halobacterium cells require are shown in this study to provide in vivo protection from oxidative damages through the scavenging of hydroxyl radicals produced from the radiolysis of water by gamma radiation. These results highlight both the importance of the intracellular environment in determining radiation resistance and the multiplicity of pathways resulting in radiation resistance that can be utilized by various microbes resulting from their adaptations to common environmental stresses such as desiccation. The global stress response to gamma radiation was measured using both genomic and proteomic methods. The resulting systems view reveals cooperation amongst several cellular processes including DNA repair, increased protein turnover, apparent shifts in metabolism to favor nucleotide biosynthesis and an overall effort to repair oxidative damage. Further, we demonstrate the importance of time dimension while correlating mRNA and protein levels and suggest that steady state comparisons may be misleading while assessing dynamics of genetic information processing across transcription and translation. The repair of DNA DSBs incurred after exposure to gamma radiation was examined in greater detail. The in vivo role of the Mre11/Rad50 complex was determined in an archaeal model system to determine if these proteins performed the same role in homologous recombination repair as their eukaryotic homologs. Deletion of mre11 was found to reduce the rate of DSB repair, but not the overall survival of the cells. Taken together, the data presented here provide a halophilic model for radiation resistance that shares some common elements with other radiation resistant organisms such as Deinococcus radiodurans while presenting alternative mechanisms specific to extreme halophiles. SURVIVING IONIZING RADIATION: GENERAL STRESS RESPONSE AND MECHANISMS FOR THE PREVENTION AND REPAIR OF DNA DAMAGE IN HALOBACTERIUM SP. STR. NRC-1
Association entre les dérégulations des cellules dendritiques et les altérations des lymphocytes B présentes chez les patients infectés par le VIH

Dysregulations of the B cell compartment are an important consequence of human immunodeficiency (HIV) infection, which can lead to auto-immune manifestations and ultimately to B cell lymphomas. One of the first alterations is polyclonal activation, reflected by hyperglobulinemia (hyper-Ig) and elevated autoantibody titers. We can also observe alterations in population dynamics, namely an expansion of the pool of activated B cells. Furthermore, HIV infected patients evolve towards the incapacity to generate effective humoral responses, and experience a loss of immunological memory in the chronic phase, characterized by a decrease in the memory B cell pool and cell exhaustion. The mechanisms involved in this phenomenon are poorly understood and thus remain to be elucidated. Mucosal dendritic cells (DC) are among the first cell populations to encounter HIV during an infection and are directly and indirectly affected by the virus and viral components. Indeed, HIV infected individuals present decreased DC frequencies in their blood, mucosae and lymphoid organs, as well as a block in DC maturation process. However, whether these defects appear as soon as the acute phase and persist beyond ART, remains controversial. This is mainly due to the scarcity of longitudinal studies including patients’ visits from the earliest phases of infection and following ART. DC play an important role in T-dependent and T-independent B cell development, survival and activation, namely through the production of growth factors such as B Lymphocyte Stimulator (BLyS). Therefore, we hypothesize that B cell abnormalities in HIVinfected individuals may be modulated by altered DC populations. The main objective of this study is to evaluate DC involvement in the establishment of B cell alterations related to HIV infection. We have thus first characterized the DC status by longitudinally assessing the dynamics of peripheral blood DC populations of HIV infected individuals with different rates of disease progression. This allowed us to evaluate the potential correlation between DC population dynamics and rate of disease progression. We have then evaluated BLyS expression by mDC and their precursors, and measured plasma concentrations of BlyS and other cytokines with B cell growth factor properties. Finally, we have characterized the dynamics of blood B cell populations, with regard to the phase of HIV infection and the rate of clinical progression.
Practical atlas of ruminant and camelid reproductive ultrasonography

Preface. Acknowledgments. Introduction. Chapter 1 Principles and recommendations, essential concepts, and common artifacts in ultrasound imaging. Description and practical recommendations in the choice of ultrasound equipment with a view to image quality. General principles and essential concepts to improve image quality. Common artifacts. Chapter 2 Scanning techniques and common errors in bovine practice. Description of scanning technique. Manipulation of the probe. Common errors. Chapter 3 Anatomy of the reproductive tract of the cow. Genital tract. Descriptive terminology of the ovary and ovarian structures. Chapter 4 Bovine ovary. Endocrinology and ovarian structures in pubertal cows. Ovarian anomalies and differential diagnosis. Use of color Doppler to monitor blood flow. Ultrasound use in reproduction synchronization protocols for dairy cattle: Two perspectives. Chapter 5 Bovine uterus. Ultrasound of the uterus during the estrous cycle and normal postpartum period. Color Doppler sonography of the uterine blood flow. Ultrasound of the postpartum abnormal uterus and vagina. Chapter 6 Bovine pregnancy. Morphologic embryonic and fetal development up to day 55. Ultrasound landmarks of standard early pregnancy diagnosis. Early embryonic and fetal death. Twins. Chapter 7 Bovine fetal development after 55 days, fetal sexing, anomalies, and well-being. Fetal development after 55 days. Ultrasound fetal sexing. Fetal anomalies. Fetal well-being during late pregnancy (normal gestation, compromised pregnancy, and clone). Chapter 8 Bovine embryo transfer, in vitro fertilization, special procedures, and cloning. Embryo donors. Oocyte collection for in vitro fertilization. Recipients. Management of clone recipients. Chapter 9 Bull anatomy and ultrasonography of the reproductive tract. Ultrasound equipment and techniques. Anatomy of the reproductive system. Anomalies and ultrasonographic imaging of external and internal reproductive organs. Chapter 10 Buffalo and zebu cattle. Equipment and scanning techniques. Major differences between bovine and bubaline species. Pathology. Congenital and hereditary defects. Ultrasound services in buffalo and zebu. Chapter 11 Sheep and goats. Usefulness of ultrasonography in small ruminants. Equipment and scanning techniques. Ultrasound imaging of the female reproductive tract. Endocrine and ovarian processes that comprise the normal estrous cycle and pregnancy. Fetal count, age, and sex. Pathological conditions in the female. Ultrasonographic evaluation of the male genital system. Common abnormalities of the testis. Common abnormalities of the accessory glands. Chapter 12 Camelids. Usefulness of ultrasonography in camelids. Equipment and scanning techniques. Ultrasonographic anatomy. Ovarian function and endocrinology in South American camelids. Pregnancy diagnosis and evaluation of fetal growth. Uterine and ovarian abnormalities. Index.
The Biological Control Agent Trichoderma from Fundamentals to Applications

The practice of monoculture in modern agriculture enables us to continue to provide foodstuffs for the world’s ever increasing population. Monoculture is, however, an ecologically unnatural situation, that is inherently unstable and offers considerable opportunity for the development of diseases. Plant disease control has now therefore become heavily dependent on fungicides to combat the wide variety of fungal diseases that threaten agricultural crops. Even with intensive fungicide use, the destruction of crop plants by fungal pathogens is a serious problem worldwide that annually leads to losses of about 15% (Logemann and Schell 1993). The use of pesticides in general, has also resulted in significant costs to public health and the environment. Studies aimed at replacing pesticides with environmentally safer methods are currently being conducted at many research centers. In this context, control of plant pests by the application of biological agents holds great promise as an alternative to the use of chemicals. It is generally recognized that biological control agents are safer and sounder environmentally than is reliance on the use of high volumes of fungicides and other antimicrobial treatments. The heightened scientific interest in biological control of plant pathogens is a response, in part, to growing public concerns over chemical pesticides. However, there is an equally greater need for biological control of pathogens that presently go uncontrolled or only partially controlled by these “traditional” means (Cook 1993). Thus, biological control should and can be justified on its own merits, without giving it importance at the expense of chemical controls. Biocontrol must be effective, reliable, consistent, and economical before it becomes an important component of plant disease management. To meet these criteria, we must increase our understanding of the biology of the biocontrol agent in question, which in most cases is extremely limited. Furthermore, superior strains, together with delivery systems that enhance biocontrol activity, must be developed (Harman et al. 1989). In this context, many biological control agents can be modified genetically to enhance their attributes. In addition, we can now think of microorganisms with inhibitory activity against plant pathogens as potential sources of genes for disease resistance.
Lead Exposure, Homocysteine, DNA Methylation and Late-Onset Alzheimer's Disease.

1 Alzheimer’s disease 2 General Alzheimer’s disease epidemiology 2 Lead (Pb) exposure 5 Overview of Pb exposure as a risk factor 5 Pb exposure epidemiology 5 Biomarkers of Pb exposure 8 Pb as a neurotoxicant and risk factor for late-onset AD 8 Overview of epigenetics 10 Epigenetic epidemiology and Alzheimer’s disease 10 Epigenetics and heavy metals, with a focus on Pb 13 Data integrating Alzheimer’s disease, epigenetics and Pb exposure 14 Alzheimer’s disease and Pb exposure are associated with changes in one-carbon metabolism, the substrate for DNA methylation 14 Animal model studies linking Pb exposure, epigenetics, and amyloidogenesis 16 Challenges to LOAD epidemiologic research integrating epigenetics and Pb exposure 17 Potential approaches to study Pb exposure, epigenomics, and Alzheimer’s disease epidemiology 18 Figures 21 References 22 II. Research Chapter 1: Lead exposure, B-vitamins, and plasma homocysteine in the VA Normative Aging Study 39 Abstract 39 Introduction 41 Methods 45 Results 4939 Introduction 41 Methods 45 Results 49
The Dissolution State of a Triglyceride Molecule in Water and Its Orientation State at the Air-Water Interface

The relations between the surface tension and the concentration of the aqueous solutions of triacetin, tripropionin, tributyrin, tricaproin, and tricaprylin were determined at 37°. The solubilities and the adsorbed amounts of triglycerides were obtained from these results. Since the solubilities of tricaproin and tricaprylin were extremely low, the corrections for adsorption at the interfaces were necessary to obtain their solubilities. The linear relationship between the logarithm of solubility and the total surface area of hydrophobic groups in a triglyceride molecule which could contact maximally with the water, was found to hold. The smallness of the slope of this straight line in comparison with those of hydrocarbon and alcohol, was interpreted as showing that three hydrophobic chains in a triglyceride molecule may aggregate intramolecularly with one another in the water; threefifths of the total surface area of hydrophobic group are in contact with water and the two-fifths are in contact with hydrophobic group. Moreover, from the molecular area occupied at the air-water interface, it was suggested that the hydrophobic chains in adsorbed monolayer of triacetin might correspond to the "tune-forming" conformation like the β-form crystal of triglyceride; the chains in 1-and 3-position were directed toward the air and the chain in 2-position was directed toward the water.
Internet Addiction and Fear of Missing Out

Smartphones and the evolution of new ICTs have enabled people, especially the youth, to stay connected to their social and professional network. This has resulted in compulsive checking for status updates and messages, for fear of missing out (FOMO). FOMO, which is a form of internet addiction, has its downside among students. This chapter is an empirical study that seeks to examine the disruptive effect of FOMO on the academic performance of students. Four hundred twenty-two university students were surveyed on their use of internet (social media services) and its result on their academic activities. A Likert scale was used to measure their use of the internet (social media) and its relationship with their academic performance. Chi-square and factor analysis were conducted. The results showed that continuous use of internet had negative effect on students' academic performance and it affected the female students more than their male counterparts. Tertiary institutions should intensify guidance and counselling sessions for students in order to mitigate the negative effects of use of internet on students.
Cognitive Architecture to Generate Motivational Feelings: A Way to Improve Visual Learning in Robots

Expressions and voice pitch of an individual play an indispensable role in different cognitive processes. These factor help humans to learn a lot about different things present in their environment. This paper proposes a way to motivate robot learning through their environment and human around them. This mechanism is based on recognition of other agent’s facial expressions and voice pitch analysis by robot. A motivational level can be calculated through these feelings. Motivational level can impel the robots to improve their past learning. This mechanism can possibly help a robot to apprehend its environment and interact with other agents effectively. Keywords : cognition; motivation; facial expression; voice pitch; perception; memory.
The role of the BARD1 BRCT domains in the DNA damage response

The DNA within a cell is damaged on a continuous basis by both endogenous and exogenous agents. One of the most dangerous types of damage a cell can incur are DNA Double stranded breaks (DSBs) as failure to repair these types of lesions can lead to mutations, cell death and cancer. In order to maintain genome integrity, cells have several different mechanisms to repair various types of DNA damage. BRCA1 is a tumour suppressor gene commonly mutated in many inherited breast and ovarian cancers. BRCA1 is fundamental to the repair to DNA damage especially the faithful repair of DSB by homologous recombination (HR) as loss of BRCA1 results in aberrant HR, chromosomal translocation and cancer. BRCA1 is almost always found in the nucleus bound to BARD1. BARD1 retains BRCA1 in the nucleus and enhances the E3 ubiquitin ligase function of BRCA1. The importance of BRCA1 in the repair of DNA DSBs has been extensively researched, however the role of BARD1 in repair remains unknown. Similar to BRCA1, BARD1 contains tandem BRCT domains at its C-terminus which are important for binding phosphorylated proteins involved in DNA repair. Mutations in the BARD1 BRCT domains have been discovered in a few breast and ovarian cancers which suggested that BARD1 is important in the DNA damage response (DDR) independent of its function in stabilising BRCA1. Loss of the BARD1 BRCT domains also results in a decrease in the ability of cells to carry out HR. This thesis examines the contribution of the BARD1 BRCT domains to the repair of DNA DSBs. Using homologous recombination assays and colony survival assays, Bard1 DT40 cells reconstituted with BARD1ΔBRCT showed a significant decrease in their ability to carry out HR and were also extremely sensitive to PARP inhibitors suggesting that the BARD1 BRCT domains do indeed play an important role in HR. Work carried out in this thesis suggests that BARD1 contributes to the stabilisation of the BRCA1-C complex which is important in the repair of DSBs. The BARD1 BRCT domains also showed defects in localisation and delayed recruitment to sites of damage. The defects xviii in HR and localisation seen in the absence of the BARD1 BRCT domains potentially implicate a functional role for the BARD1 BRCT domains in DSB repair. Potential BARD1 BRCT domain interacting proteins were also identified my Mass spec, which may shed some light onto the functional role of BARD1 in DNA repair.
Determinisme et polymorphisme genetiques des sequences microsatellites de salmo trutta et d'autres salmonides. Comparaison avec le polymorphisme des locus enzymatiques

Ce travail cherche a verifier l'interet des microsatellites pour les etudes de macrodifferenciation genetique chez salmo trutta. Les microsatellites a motif (gt)n sont plus abondantes que ceux a motif (ct)n, tous segreguent mendeliennement et leurs taux de recombinaison suggerant leurs distributions genomiques uniformes. Sept locus sur dix etudies, sont tres polymorphes. Densite, hypervariabilite et repartition aleatoire sont des caracteristiques tres interessantes pour la cartographie genique. Le haut polymorphisme suggerant que ces marqueurs sont plus sensibles que les enzymes a des fluctuations d'effectifs efficaces entre generations. Les modeles de mutation a pas de un (79%) et a pas de deux (14%), expliquent de facon coherente les distributions alleliques. La variabilite des microsatellites confirme les rapports de variabilite entre populations, detectes avec les enzymes. La plus haute variabilite genetique a ete observe dans les populations atlantiques et les souches domestiques. La variabilite genetique est environ cinq fois plus elevee pour les microsatellites que pour les enzymes. Les relations phenetiques sont congruents avec la structuration geographique de cette espece. Elles indiquent une dichotomie genetique entre les regions atlantique et mediterraneenne-orientale. Dans la mediterranee on distingue: salmo carpio, salmo trutta fario et salmo marmoratus. Dans l'atlantique on observe une dichotomie sud-est de l'europe et atlantique du nord. Les hautes valeurs de bootstrap entre populations suggerent une grande utilite des microsatellites en systematique a l'echelle fine. La conservation des amorces de s. Trutta chez s. Salar (100%) et chez o. Mykiss (70%), est un avantage majeur pour les etudes d'hybridation interspecifique, de cartographie comparee et en systematique des salmonides
The Evolution Revolution

Partial table of contents: We are the Champions! : The Long-Playing Microbial Fossil Record. Rise of the Gutless Wonders: Early Animal Evolution. Head or Tails? : The Incredibly Lucky Rise of the First Vertebrates. Tracking Down the Bugs: The Evolution of Insects. Say it with Flowers: Evolution in Plants. Reign of Pterosaurs: The First Flying Vertebrates. Battle of the Bulge: Why Did Dinosaurs Grow so Big? Children of the Evolution: Human Evolution from the Inside. Final Thoughts. References. Index.
Why is that nucleotide there? Causes and consequences of kinetic and metabolic translational efficiency

A variety of sequence features at the levels of DNA, RNA, and protein affect the process of translation and may thus be under selection to increase the efficiency of that process. To ask whether they are and in what ways they might act, I first examine what the sequence-based mechanisms of elongation rate determination are. I show that positive charges in newly-translated peptides are the primary sequence-encoded elements modulating elongation rates, probably via their interaction with the negatively charged ribosomal exit tunnel. Contrary to common expectations, I do not find that codon usage has a significant effect on the velocity of ribosomes under normal in vivo conditions, while mRNA structure has only a marginal effect. That codons do not significantly slow ribosomes compared to the magnitude of the charge effect is seemingly at odds with a large body of literature which purports to show that they in fact do. Reviewing the literature, however, I suggest that these apparently at-odds findings can be reconciled by considering the supply (available tRNA) and demand (transcriptomic codon usage plus translation initiation rates). Taking supply and demand into account reveals that if codons do slow ribosomes, they are likely to do so significantly only under highly non-equilibrium, experimental conditions. That codons may not greatly differ in their translation speeds one to the next under normal in vivo conditions calls into question theories of selection on codon usage bias to modulate translational efficiency in a local, along-transcript fashion, for example the suggestion that codon usage is selected for at the 5’ end of transcripts as a kind of speed ramp to modulate ribosomal traffic just after translation initiation. That codons have similar translation speeds is still, however, consistent with a theory that codon usage is under general selection and even speed selection to increase the global translational efficiency of cells by limiting the number of bound ribosomes on mRNAs. Returning to the matter of positive charges, I ask whether they, instead of codons, might cause the suggested translational-ramping effect, as positive charges tend to be overloaded at the N-termini of proteins across various domains and taxa. I find however that their distribution at the starts of proteins is better explained by a biochemical, structural null rather than the gene regulatory hypothesis of the ramp: the use of positive charges at N-termini can be completely explained in terms of the needs of a subset of proteins to correctly orientate themselves in membranes. I end with an example of how selection for translational efficiency can act not just on the process of translation but on the finished protein product, showing that the need to manufacture metabolically cheap proteins contributes to the anomalous AT skews observed in the Firmicutes.