Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the mechanism of geminin inactivation

xvii Chapter 1 – Introduction 1 1.1 The Cell Cycle 1 1.2 The Replicon Model 3 1.2.1 DNA Replication Initiation in Bacteria 4 1.2.2 DNA Replication Initiation of the SV40 Virus 5 1.3 Eukaryotic Origins of Replication 5 1.3.1 Requirement for multiple origins 5 1.3.2 Origins of Replication in Yeast 7 1.3.3 Origins of Replication in Higher Eukaryotes 8 1.4 DNA Replication Occurs Once per Cell Cycle 10 1.4.1 Dealing with thousands of origins 10 1.4.2 Cell Fusion Experiments 10 1.4. 3 Xenopus laevis Cell Free System 11 1.4. 4 Licensing Factor Model 12 1.4. 5 Evidence Supporting the Licensing Factor Model 13 1.5 DNA Replication Licensing 15 1.5. 1 The MCM2-7 Complex is The Licensing Factor 15 1.5. 2 Reconstitution of Licensing: the essential factors 19 ii 1.5. 2.1. The Origin Recognition Complex 19 1.5. 2.2 Cdc6 21 1.5. 2.3 Cdt1 22 1.5. 3 Molecular Mechanism of Licensing 22 1.5. 4 Additional Factors that Effect Licensing 27 1.5. 4.1 Hbo1 28 1.5. 4.2 ORCA 29 1.5. 5 MCM Stability on Chromatin 29 1.6 DNA Replication 30 1.6. 1 Reconstitution of Initiation in S. cerevisiae 30 1.6. 2 Metazoan pre-IC 33 1.6. 3 Replication Elongation 34 1.6. 4 Termination of Replication Forks 35 1.7 Cell Cycle Regulation of Replication Licensing 35 1.7. 1 Importance of Once Per Cycle DNA Replication 35 1.7. 1.1 Consequences of Under-replication 35 1.7. 1.2 Consequences of Rereplication 37 1.7. 2 Regulation of Licensing Factors in S. cerevisiae 38 1.7. 2.1 ORC 38 1.7. 2.2. Cdc6 39 1.7. 2.3. Cdt1/MCM2-7 40 1.7. 2.4 Redundancy and Rereplication 40 1.7. 3 Regulation of Licensing Factors in Metazoans 40 1.7. 3.1 Inhibition of Cdt1 by Geminin 41 1.7. 3.2 Inhibition of Cdt1 by Destruction 42 1.7. 3.3 CDKs, ORC and Cdc6 43
Inferring reciprocal evolutionary histories in associated species of plants and insects in two european pollination systems

Dr. Nadir Alvarez, co-directeur de thèse Prof. Martine Rahier, co-directeur de thèse Prof. Bryan C. Carstens (Louisiana State University, USA), rapporteur Dr. Laurence Després (Université de Grenoble, France), rapporteur Dr. Marc Gibernau (CNRS Toulouse, France), rapporteur Dr. Felix Gugerli (WSL, Birmensdorf, Zürich, Suisse), rapporteur Prof. Philippe Küpfer (Université de Neuchâtel, Suisse), rapporteur
Genes, chromosomes & cancer

Specific areas covered include: -Chromosomal abnormalities in all benign and malignant disorders, including changes that occur during neoplastic progression -Changes in gene structure and regulation as a consequence of genomic rearrangements -Chromosomal alterations involving genes related to the regulation of cell proliferation and differentiation -The correlation between genomic abnormalities and cellular phenotypic alterations -The predictive value of alterations at the chromosomal and DNA levels in disease prognosis, and in designing and monitoring cancer therapies -Cytogenetic, molecular, and epidemiologic analyses of inherited disorders predisposing to cancer -Chromosomal and/or genetic damage caused by external factors -Descriptions of novel molecular biological and cytogenetic methods for genomic analysis
Melatonin

Melatonin is a ubiquitous molecule and widely distributed in nature, with functional activity occurring in unicellular organisms, plants, fungi and animals. In most vertebrates, including humans, melatonin is synthesized primarily in the pineal gland and is regulated by the environmental light/dark cycle via the suprachiasmatic nucleus. Pinealocytes function as ‘neuroendocrine transducers’ to secrete melatonin during the dark phase of the light/dark cycle and, consequently, melatonin is often called the ‘hormone of darkness’. Melatonin is principally secreted at night and is centrally involved in sleep regulation, as well as in a number of other cyclical bodily activities. Melatonin is exclusively involved in signaling the ‘time of day’ and ‘time of year’ (hence considered to help both clock and calendar functions) to all tissues and is thus considered to be the body's chronological pacemaker or ‘Zeitgeber’. Synthesis of melatonin also occurs in other areas of the body, including the retina, the gastrointestinal tract, skin, bone marrow and in lymphocytes, from which it may influence other physiological functions through paracrine signaling. Melatonin has also been extracted from the seeds and leaves of a number of plants and its concentration in some of this material is several orders of magnitude higher than its night‐time plasma value in humans. Melatonin participates in diverse physiological functions. In addition to its timekeeping functions, melatonin is an effective antioxidant which scavenges free radicals and up‐regulates several antioxidant enzymes. It also has a strong antiapoptotic signaling function, an effect which it exerts even during ischemia. Melatonin's cytoprotective properties have practical implications in the treatment of neurodegenerative diseases. Melatonin also has immune‐enhancing and oncostatic properties. Its ‘chronobiotic’ properties have been shown to have value in treating various circadian rhythm sleep disorders, such as jet lag or shift‐work sleep disorder. Melatonin acting as an ‘internal sleep facilitator’ promotes sleep, and melatonin's sleep‐facilitating properties have been found to be useful for treating insomnia symptoms in elderly and depressive patients. A recently introduced melatonin analog, agomelatine, is also efficient for the treatment of major depressive disorder and bipolar affective disorder. Melatonin's role as a ‘photoperiodic molecule’ in seasonal reproduction has been established in photoperiodic species, although its regulatory influence in humans remains under investigation. Taken together, this evidence implicates melatonin in a broad range of effects with a significant regulatory influence over many of the body's physiological functions.
New records of pigmentation disorders in molossid and phyllostomid (Chiroptera) bats from Peru

Abstract Pigmentation disorders, either from the complete absence (albinism), partial (leucism), or excess (melanism) of melanin, are rare in vertebrates. Worldwide, only a few records of these disorders had been reported for bats. Thanks to recent fieldwork and examination of museum specimens of the collections of the AMNH and MUSM, we report five species with those conditions in Peru. In this study, we report the first cases of leucism in Artibeus anderseni, Chiroderma trinitatum, and Desmodus rotundus and partial melanism in Carollia perspicillata. Additionally, we report the first record of an albino bat (Molossus molossus) for Peru.
TNF‐α impairs regulation of muscle oxidative phenotype: implications for cachexia?

Chronic obstructive pulmonary disease (COPD) is characterized by weight loss, muscle wasting (in advanced disease ultimately resulting in cachexia), and loss of muscle oxidative phenotype (oxphen). This study investigates the effect of inflammation (as a determinant of muscle wasting) on muscle oxphen by using cell studies combined with analyses of muscle biopsies of patients with COPD and control participants. We analyzed markers (citrate synthase, fi‐hydroxya‐cyl‐CoA dehydrogenase, and cytochrome c oxidase IV) and regulators (PGC‐1α, PPAR‐α, and Tfam) of oxphen in vastus lateralis muscle biopsies of patients with advanced COPD and healthy smoking control participants. Here 17 of 73 patients exhibited elevated muscle TNF‐α mRNA levels. In these patients, significantly lower mRNA levels of all oxidative markers/regulators were found. Interestingly, these patients also had a significantly lower body mass index and tended to have less muscle mass. In cultured muscle cells, mitochon‐drial protein content and myosin heavy chain isoform I (but not II) protein and mRNA levels were reduced on chronic TNF‐α stimulation. TNF‐α also reduced mito‐chondrial respiration in a nuclear factor kappaB (NF‐κB) ‐dependent manner. Importantly, TNF‐α‐induced NF‐κB activation decreased promoter transactivation and transcriptional activity of regulators of mitochon‐drial biogenesis and muscle oxphen. In conclusion, these results demonstrate that TNF‐α impairs muscle oxphen in a NF‐κB‐dependent manner. —Remels, A. H. V. , Gosker, H. R. , Schrauwen, P., Hommelberg, P. P. H. , Sliwinski, P., Polkey, M. , Galdiz, J., Wouters, E. F. M. , Langen, R. C. J., Schols, A. M. W. J. TNF‐α impairs regulation of muscle oxidative phenotype: implications for cachexia? FASEBJ. 24, 5052–5062 (2010). www.fasebj. org
Genetically determined angiotensin converting enzyme level and myocardial tolerance to ischemia

Angiotensin I‐converting enzyme (ACE; kininase II) levels in humans are genetically determined. ACE levels have been linked to risk of myocardial infarction, but the association has been inconsistent, and the causality underlying it remains undocumented. We tested the hypothesis that genetic variation in ACE levels influences myocardial tolerance to ischemia. We studied ischemia‐reperfusion injury in mice bearing 1 (ACElc), 2 (ACE2c, wild type), or 3 (ACE3c) functional copies of the ACE gene and displaying an ACE level range similar to humans. Infarct size in ACElc was 29% lower than in ACE2c (P<0.05). Pretreatment with a kinin B2 receptor antagonist suppressed this reduction. In ACE3c, in‐farct size was the same as in ACE2c. But ischemic preconditioning, which reduced infarct size in ACE2c (‐63%, P<0.001) and ACElc (‐52%, P<0.05), was not efficient in ACE3c (‐2%,NS, P<0.01 vs. ACE2c). In ACE3c, ischemic preconditioning did not decrease myocardial inflammation or cardiomyocyte apopto‐sis. Pretreatment with a renin inhibitor had no car‐dioprotective effect in ACE2c, but in ACE3c partially restored (38%) the cardioprotection of ischemic preconditioning. Thus, a modest genetic increase in ACE impairs myocardial tolerance to ischemia. ACE level plays a critical role in cardiac ischemia, through both kinin and angiotensin mediated mechanisms. — Messadi, E. , Vincent, M. ‐P., Griol‐Charhbili, V. , Man‐det, C. , Colucci, J., Krege, J. H. , Bruneval, P., Bouby, N. , Smithies, O. , Alhenc‐Gelas, F. , Richer, C. Genetically determined angiotensin converting enzyme level and myocardial tolerance to ischemia. FASEB J. 24, 4691–4700 (2010). www.fasebj. org
Organization of Membrane Rafts in Chicken Sperm

Being transcriptionally and translationally inactive, sperm must utilize preassembled pathways into specific compartments in which they function to fertilize ovum. Membrane rafts are specific membrane regions enriched in sterols and glycosphingolipids such as ganglioside GM1 (GM1) and play an important role in a variety of cellular functions. Recent findings have demonstrated that membrane rafts are present in mammalian sperm and are involved in regulating the induction of acrosome exocytosis. However, no information is available on whether avian sperm possess membrane rafts. Thus, we investigated the organization of membrane rafts in chicken sperm. Our localization experiments for GM1 and sterols showed that the plasma membrane overlaying the sperm head possesses specific membrane domains enriched in both aforementioned lipids. Caveolin-1, which localizes into membrane rafts in other systems, was localized only to the sperm tail. Based on the biochemical definition that membrane rafts are insoluble membranes when subjected to a Triton X-100 treatment, we isolated detergent-insoluble membranes from chicken sperm and quantified the GM1 content, which showed an enrichment of GM1 in the membrane fraction relative to the detergent-soluble fraction. Together with the results of localization and biochemical experiments, we demonstrate for the first time that membrane rafts exist in chicken sperm. Thus, our results provide a foundation for investigating a novel cellular pathway inherent in avian sperm membranes that might be involved in functions necessary to achieve fertilization.
Erratum

A plant-derived edible vaccine against hepatitis B virus. J. Kapusta, A. Modelska, M. Figlerowicz, T. Pniewski, M. Letellier, O. Lisowa, V. Yusibov, H. Koprowski, A. Plucienniczak, and A.B. Legocki (1999) FASEB J., 1796–1799. The legends for figures 1–4 of this article were published under the wrong figures of the original article. The two pages are reproduced correctly here. The editors apologize for the error.
Regulation of Endothelial Phenotype in Rat Soleus Muscle Feed Arteries: Influence of Aging and Exercise Training

Regulation of Endothelial Phenotype in Rat Soleus Muscle Feed Arteries: Influence of Aging and Exercise Training. (December 2010) Daniel Wayne Trott, B.S. University of New Mexico Chair of Advisory Committee: Dr. Christopher Woodman Aging is associated impaired endothelial function in the skeletal muscle vasculature which contributes to decreased ability to increase muscle blow during exercise. This endothelial dysfunction is mediated, primarily, by impairments in the nitric oxide (NO) pathway in the skeletal muscle vasculature. The major purpose of this dissertation is to determine the mechanisms that mediate age-related endothelial dysfunction in rat soleus feed artery (SFA) and determine whether exercise training ameliorates this impairment in endothelial function. Therefore in these series of studies we sought to test three major hypotheses: 1) That exercise training reverses age-related decrements in endothelium-dependent dilation in SFA and that this improved endotheliumdependent dilation is the result of increased NO bioavailability due to increased content and phosphorylation of eNOS and/or increased antioxidant enzyme content; 2) That age-related endothelial dysfunction in rat SFA is mediated in part, by NAD(P)H oxidase-derived reactive oxygen species (ROS); 3) and, that impaired endothelium-dependent dilation in senescent SFA is due to an impaired potential for p-eNOSser1177. To test these hypotheses, SFA from young (4
β‐Adrenergic receptors (ßAR) regulate cardiomyocyte proliferation during early postnatal life

Cardiomyocyte development switches from hyperplasmic to hypertrophic growth between postnatal days 3 and 4 in rats. The mechanisms responsible for this transition have been controversial. β‐Adrenergic receptor (βAR) activation of mitogenic responses in vitro has been reported. We hypothesized that tonic activation of the βAR signaling regulates cell division in neonatal cardiomyocytes via effects on signaling ki‐nases known to be important in cell cycle regulation. The purpose of the current study was to elucidate the roles of βAR in rat cardiomyocyte growth in vivo. We demonstrated that βAR blockade induced a significant reduction in cardiomyocyte proliferation as measured by the BrdU labeling index. Blockade of βAR did not affect p38 or p44/42 MAPK activities. We further demonstrated that βAR blockade induced a prompt deactivation of the p70 ribosomal protein S6 kinase (p70 S6K). To confirm these results, we measured p70 S6K activity directly. Basal activity of p70 S6K in neonatal cardiomyocytes was fourfold higher than that of insulin‐treated adult rat liver. The activity of p70 S6K was reduced by 60% within 1 min after βAR blockade. We conclude that the βAR are involved in regulation of neonatal cardiomyocyte proliferation and that this mi‐togenic control may be mediated via the p70 S6K pathway.
Cigarette smoking reduces histone deacetylase 2 expression, enhances cytokine expression, and inhibits glucocorticoid actions in alveolar macrophages

Cigarette smoke is the major cause of chronic obstructive pulmonary disease (COPD), a chronic inflammatory disease of the airway. The increased expression of inflammatory proteins results from enhanced gene transcription, as these mediators are induced in a cell‐specific manner. Changes in transcription depend on chromatin remodeling and the relative activities of histone acetyl‐transferases (HATs) and histone deacetylases (HDACs). We have shown that cigarette smoke reduces the expression of HDAC2 expression and HDAC activity in biopsies and alveolar macrophages. Cigarette smoke also enhanced IL‐1β–induced expression of tumor necrosis factor α (TNF‐α) by alveolar macrophages. TNF‐α release was enhanced by the HDAC inhibitor Trichostatin A and correlated significantly with HDAC activity. In addition, we show that glucocorticoid‐responsiveness is reduced in these cells and correlates with HDAC activity. Using a macrophage cell line, we show that hydrogen peroxide mimics cigarette smoke effects on HDAC activity and markedly attenuates dexamethasone inhibition of cytokine release. These results offer the first evidence for a suppressive effect of cigarette smoke on histone acetylation status. Reduced HDAC expression may account for the enhanced expression of inflammatory mediators such as GM‐CSF, IL‐8 and TNF‐α by cigarette smoke seen in lavage samples of smokers and patients with COPD. In addition, this mechanism may account for the reduced effectiveness of glucocorticoids in COPD.
Oltipraz regenerates cirrhotic liver through CCAAT/enhancer binding protein‐mediated stellate cell inactivation

Liver cirrhosis (LC) is a chronic disease with high mortality rate. In the United States and Western world as well as Asian countries, LC is the major leading cause of death by disease. Yet, no effective therapeutic agent is available for LC treatment. Laboratory cirrhotic rats produced by dimethylnitrosamine administrations simulate the clinical features of human LC such as mortality, ascites, hepatic parenchymal cell destruction, and formation of connective tissue and nodular regeneration, providing a preclinical model to evaluate therapeutic efficacy of drugs and the underlying mechanisms. Oltipraz [5‐(2‐pyrazinyl)‐4‐methyl‐1,2‐dithiol‐3‐thione] has been used clinically and is of little toxicity. Comprehensive mechanistic and phase IIa clinical studies supported the notion that oltipraz exerts chemopreventive effects against chemical carcinogenesis. We report here that oltipraz within the clinical dose range regenerates cirrhotic liver in the established LC rats as a result of reduction of the intensities of cirrhotic nodules, elimination of accumulated extracellular matrix, and inactivation of stellate cells, thereby improving survival rate. We also reveal that activation of CCAAT/enhancer binding protein by oltipraz inhibits transforming growth factor β1 gene expression in stellate cells, which provides a molecular target for pharmacological treatment of LC. Oltipraz is the first therapeutic agent that regenerates cirrhotic liver.
Cellular Responses to Chondroitin-6-Sulphate Releasing Brushite Bone Cements

As the field of implant dentistry continually develops, clinicians and patients alike strive for optimal treatment outcomes. Prosthodontically driven implant placement has become the established and accepted method to obtain the most advantageous functional as well as aesthetic results. Prior to, or simultaneously with, implant placement it may be necessary to use bone augmentation procedures to rebuild or replace missing bone. The alloplastic calcium phosphate based bone substitute materials are available in various formulations and methods of delivery. Hydroxyapatite is considered to show minimal resorption with time, however when the natural glycosaminoglycan, chondroitin sulphate, is incorporated into this material it has demonstrated increased bone regenerative capacity in vivo. Brushite bone cement is a more recent calcium phosphate material that appears to be superior for the purpose of bone grafting relative to hydroxyapatite because it allows new bone to be laid down more quickly. To investigate the clinical potential of combining chondroitin-6-sulphate with brushite bone cements this material has been previously characterised. It was established that the incorporation of up to ten per cent chondroitin-6-sulphate into brushite does not affect its setting reaction or cause any chemical change in the set cement. In the present study, it has been shown using scanning electron microscopy imaging to study cellular attachment, as well as the Alamar Blue® assay to study cellular proliferation, that cells can grow on brushite bone cements. The MG-63 osteosarcoma cell line was used for these in vitro experiments. The use of these osteoblast-like cells is an established model for investigating osteoblast function. Furthermore these experiments indicate that the concentration of chondroitin-6-sulphate present in the brushite cement does have an adverse effect upon the cellular response observed, in terms of both cellular attachment and proliferation.
Pattern of ovulation in the East African root rat (Tachyoryctes splendens) from Tanzania: induced or spontaneous ovulator?

The East African root rat (Tachyoryctes splendens (Ruppell, 1835)) is a solitary subterranean rodent that exhibits a marked seasonal reproduction linked to the bimodal rainfall pattern of East Africa. The current study sets out to determine whether the East African root rat is an induced or spontaneous ovulator. Five wild caught adult females were monitored noninvasively for ovarian cyclicity by measuring urinary progesterone every 2 days over a period of 120 days. Females were subjected to three different experimental treatments, namely, initially singly housed or control (C), nonphysical contact with a male (NPC), and physical contact with a vasectomised male (PC), respectively. The concentration of urinary progesterone was higher during PC than during either NPC or C. The act of coitus appears to be necessary for ovulation to occur in the females. The male East African root rats were found to possess epidermal spines on the penis that can be used to bring about cervical stimulation during coitus. The s.
Functional role of gangliotetraosylceramide in epithelial‐to‐mesenchymal transition process induced by hypoxia and by TGF‐β

The epithelial‐to‐mesenchymal transition (EMT) is a basic cellular process that plays a key role in normal embryonic development and in cancer progression/metastasis. Our previous study indicated that EMT processes of mouse and human epithelial cells induced by TGF‐β display clear reduction of gangliotetraosylceramide (Gg4) and ganglioside GM2, suggesting a close association of glycosphingolipids (GSLs) with EMT. In the present study, using normal murine mammary gland (NMuMG) cells, we found that levels of Gg4 and of mRNA for the UDP‐Gal:β1–3galactosyltransferase‐4 (β3GalT4) gene, responsible for reduction of Gg4, were reduced in EMT induced by hypoxia O2) or CoCl2 (hypoxia mimic), similarly to that for TGF‐β‐induced EMT. An increase in the Gg4 level by its exogenous addition or by transfection of the β3GalT4 gene inhibited the hypoxia‐induced or TGF‐β ‐induced EMT process, including changes in epithelial cell morphology, enhanced motility, and associated changes in epithelial vs. mesenchymal molecules. We also found that Gg4 is closely associated with E‐cad‐herin and β‐catenin. These results suggest that the β 3GalT4 gene, responsible for Gg4 expression, is down‐regulated in EMT;and Gg4 has a regulatory function in the EMT process in NMuMG cells, possibly through interaction with epithelial molecules important to maintain epithelial cell membrane organization. — Guan, F. , Schaffer, L. , Handa, K. , and Hakomori, S. Functional role of gangliotetraosylceramide in epithelial‐to‐mesenchymal transition process induced by hyp‐oxia and by TGF‐β. FASEB J. 24, 4889–4903 (2010). www.fasebj. org