Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical studies on the pre-replication complex of Archaea.

Several proteins play a crucial role in the formation of the pre-replication complex (pre-RC) in eukaryotes: origin recognition complex (ORC), CDC6 and minichromosome maintenance proteins (MCM). In yeast, these proteins associate with DNA in a sequence-specific manner during the cell cycle. Archaea, the third kingdom of life, are believed to replicate DNA in a eukaryote-like fashion. Most archaeal species encode single MCM and two CDC6/ORC proteins. The reduced number of replication proteins suggests that archaea may provide a simplified model for assembly of the machinery required for initiation of eukaryotic DNA replication. This thesis describes a biochemical analysis of the proteins involved in the formation of pre-replication complex (pre-RC) in Archaea. The yeast two-hybrid system was employed to identify protein-protein interactions within the pre-replication complex of two archaeal species Archaeoglobus fulgidus and Aeropyrum pernix. A library of truncated MCM proteins was used to identify a region that appears to be responsible for hexamerisation of MCM. The pre-RC proteins of archaea belong to the AAA+ family of ATPases. AAA+ proteins function as ATP-driven conformational switches that can mediate the assembly, remodelling, or disassembly of protein complexes. Thus, the assembly of the replication initiation complex may involve an ordered sequence of ATP coupled conformational changes. A variety of biochemical techniques were used to investigate the relationship between ATP hydrolysis, DNA binding and protein interactions within the pre-RC of Archaea.
Développement d'approches protéomiques pour l'étude des interactions tique / Borrelia / peau

La maladie de Lyme, ou borreliose de Lyme, est une infection bacterienne causee par le spirochete Borrelia burgdorferi sensu lato et transmise a l’hote (homme, animal) par piqure de tique du genre Ixodes. Cette maladie, caracterisee par un polymorphisme clinique important, est la maladie a transmission vectorielle la plus repandue dans l’hemisphere nord. Un traitement par antibiotiques permet une guerison rapide, mais si la maladie est diagnostiquee tardivement, certains symptomes persistent. Actuellement, aucun vaccin n’est commercialise pour l’homme. Dans ce contexte, nous avons developpe des approches proteomiques afin d’apporter de nouveaux elements de comprehension du mecanisme d’interactions de la triade tique / bacterie / hote. Ces travaux, visant particulierement le developpement de nouvelles strategies vaccinales et diagnostiques, sont articules autour de trois parties : - L’identification, suite a de nombreuses optimisations, d’une methode d’analyse HPLC-UV et nanoLC-MS/MS, de proteines presentes dans des extraits de glandes salivaires de tiques et possedant une activite sur la reponse immunitaire innee cutanee. Ces developpements ont mis en evidence une liste restreinte de proteines potentiellement bioactives. - La mise au point, sur un modele murin, d’une methode de detection d’une proteine de Borrelia burgdorferi, OspC, dans des biopsies cutanees par spectrometrie de masse ciblee LC-SRM. Cette etude a ouvert des perspectives quant au developpement de nouveaux outils diagnostiques. - L’evaluation de la faisabilite de la detection de Borrelia burgdorferi directement a la surface de la peau par imagerie par spectrometrie de masse MALDI-MSI.
On the Production of Gastric Tumors, Bordering on Malignancy, in Javanese Monkeys through the Agency of Nochtia Nochti, a Parasitic Nematode

The discovery by Fibiger (1913) that development of a carcinoma in the forestomach of the rat could be initiated by the presence of a parasitic nematode, Gongylonema neoplasticum , was the first demonstration of the possibility of producing an autochthonous malignant tumor in a laboratory animal. This demonstration evoked considerable interest among cancer workers for, at least in part, it appeared to substantiate some of the old and largely discounted theories of the parasitic etiology of certain types of cancer. Subsequently the attention of many students of the problem has been directed to the carcinogenic potentialities of other parasitic worms. As a result, in the past quarter of a century numerous species of helminths, belonging to such diverse groups as the Trematoda, Cestoda and Nematoda, parasitic upon various organs and tissues of different animals, including man, have been found capable of playing a more or less direct role in inducing the formation of neoplasms, some of malignant character. The literature on parasites and tumor growth has been recently reviewed in a comprehensive manner by Hoeppli (1) who, in discussing the mechanism that may underlie the development of tumors of helminth origin, points out that there is not only a host and tissue specificity for the parasite, but that marked differences exist also in the disposition of various strains—and even individuals—of a species of host to react to the parasite9s presence by the production of malignant neoplasms.
Characteristics of flowering stems and raceme position in macadamia

Summary Macadamia (Macadamia integrifolia Maiden and Betche, M. integrifolia × tetraphylla Johnson) flowers are borne on racemes that usually originate from axillary buds in response to cool conditions. In this report, we examine the relationship between stem characteristics and the number of racemes produced, to improve our understanding of the control of floral initiation and axillary bud release. Two macadamia trees of each of the cultivars ‘A4’, ‘660’, ‘695’, and ‘A38’ were pruned annually for 3 years and the relationships between stem length, stem age, the number of vegetative flushes, stem orientation, and the number of racemes produced were quantified in year 4 (2006). In addition, trees of cultivar ‘849’ were pruned in Autumn and early Summer, and the flowering characteristics of the post-pruning vegetative flushes were monitored the following Spring (2006). There were significant differences in the extent and location of racemes between cultivars. Racemes were produced preferentially on short stems that consisted of few vegetative flushes. In cultivar ‘A4’, 1-year-old stems were more likely to flower than 2-year-old stems; whereas, in cultivar ‘A38’, 2-year-old stems were more likely to produce racemes than 1-year-old stems. As stem orientation changed from horizontal to vertical, the likelihood of raceme production increased in cultivar ‘660’ stems consisting of one flush and in ‘695’ stems consisting of two flushes. Stem characteristics, particularly stem age and vigour, indicate the likelihood of flowering, but position within the canopy may be another important consideration. Canopy management practices that promote the production of short stems may increase whole-tree raceme production and, given the variation in the location of raceme production with cultivar, canopy management practices specific to cultivar should be considered.
Characterisation of four Drosophila proteins involved in regulation of gene expression.

This thesis concerns the characterisation of four Drosophila proteins that are involved in different steps of gene expression. The first protein, dMCRS2, is a nuclear Forkhead associated (FHA) domain protein. dMCRS2 is an essential protein required for growth during development. Drosophila and human MCRS2/MSP58 was previously reported to form a complex with the MOF histone acetyl transferase. My data reveal that in addition to MOF, dMCRS2 can be purified in complex with multiple RNAP II-associated proteins including Cdkll/Pitslre. Moreover, dMCRS2 co-localises with RNAP II complexes on polytene chromosomes in vivo. Thus, dMCRS2 might provide a physical link between the chromatin remodelling MOF complex and RNAP II via its ability to associate with Pitslre. Interestingly, the interaction between dMCRS2 and Pitslre seems to be regulated in response to apoptotic stimuli. The second and third proteins characterised here correspond to the Drosophila homologues of Prp38p (dPrp38), a tri-snRNP splicing factor, and Microfibril-Associated Protein 1 (dMFAPl), a previously uncharacterised protein found in some human spliceosomal fractions. I show here that dMFAPl binds directly to dPrp38 and is required for pre-mRNA processing. dMFAPl, like dPrp38, is essential for growth during development, and my in vivo data show that cells with reduced levels of dMFAPl or dPrp38 proliferate more slowly than control cells and undergo apoptosis. Consistent with this, dsRNA-mediated depletion of dPrp38 or dMFAPl causes cells to arrest in G2/M, and this is paralleled by a reduction in mRNA levels of the mitotic phosphatase string/cdc25. Interestingly dsRNA-mediated depletion of a wide range of core splicing factors elicits a similar phenotype, suggesting that the observed G2/M arrest might be a general consequence of interfering with spliceosome function. The fourth protein, Pixie, can be isolated from cells in complex with eukaryotic initiation factor (elF) 3 and small ribosomal proteins and is required for the assembly of translation initiation competent ribosomes. Thus, depletion of Pixie results in the assembly of empty ribosomes lacking mRNAs and reduced levels of translation initiation. Moreover, Pixie associates with the 40S subunit in an ATP-dependent manner. These data are consistent with Pixie playing a catalytic role in the assembly of complexes required for translation initiation.
Coccolithophores : from molecular processes to global impact

1: Cell Biology and Biochemistry. - What is new in coccolithophore biology? - Calcification in coccolithophores: A cellular perspective. - Pigment diversity of coccolithophores in relation to taxonomy, phylogeny and ecological preferences. - 2: Physiology and bloom studies. - Emiliania huxleyi: bloom observations and the conditions that induce them. - Coccolithophore calcification and the biological pump: response to environmental changes. - Dimethyl sulfide production: what is the contribution of the coccolithophores? - Re-evaluation of the physiological ecology of coccolithophores. - Structure and morphogenesis of the coccoliths of the CODENET species. - The laboratory culture of coccolithophores. - 3: Molecular phytogeny and evolutionary biodiversity. - A review of the phylogeny of the Haptophyta. - Super-Species in the calcareous plankton. - Coccolithophorid biodiversity: evidence from the cosmopolitan species Calcidiscus leptoporus. - Species level variation in coccolithophores. - Coccolith contribution to South Atlantic carbonate sedimentation. - Biogeography of selected Holocene coccoliths in the Atlantic Ocean. - 4: Evolutionary development, fluxes and paleoproxies. - Why is the land green and the ocean red? - Plankton community behavior on ecological and evolutionary timescales: when models confront evidence. - Calcareous nannoplankton evolution and diversity through time. - Carbonate fluxes and calcareous nannoplankton. - Coccolithophorid-based geochemical paleoproxies. - 5: Index.
Putting the Pieces Together: Exons and piRNAs: A Dissertation

Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets.
EVALUATION OF SUGAR CANE BAGASSE SUBJECTED TO HAYING AND ENSILING 1 Avaliação do bagaço de cana-de-açúcar submetido à fenação e à ensilagem

ABSTRACTThis work aimed to evaluate sugar cane bagasse from cachaca production, subjected to hay-making and ensiling. Theexperiment was conduced at Universidade Federal de Lavras, MG, using the completely random delineation (CRD), with seventreatment and three repetitions. The treatments were constituted of in natura sugar cane bagasse (INB), manually hayed and baledsugar cane bagasse, mechanically hayed and baled, manually baled INB and mechanically baled INB, whole ensiled INB and choppedensiled INB. Bromatological composition, tampon capacity (TC), pH values and total sugar rate of the INB were evaluated. For theensilage, there were used cistern silos and for the baling, manual and mechanical balers. The bagasse was baled in natura, or afterreaching 89% rate of DM, according to the treatments. The evaluated characteristics were dry matter rate (DM), crude protein (CP),fiber in neutral detergent (FND), fiber in acid detergent (FAD). The results went through variance analyses and the averages werecompared by the Scott – Knott test (P<0.05). The INB presented rates of 51.70% of DM; 2% of CP; 79.43% of FND; 48.78% ofFAD and 16.4% of total sugar in the MS. The sugar cane bagasse presented low TC and the silage presented satisfactory pH for goodconservation. The dehydration followed by the manual baling provided a decrease in the cell wall components, revealing itself as thebest bagasse conservation method.Index terms: Hay, silage, sub-product.RESUMONeste trabalho, objetivou-se avaliar o bagacode cana-de-acucar proveniente da producao de cachaca, submetido a fenacao ea ensilagem. O experimento foi conduzido na Universidade Federal de Lavras, MG, utilizando-se o delineamento inteiramentecasualizado (DIC), com sete tratamentos e tres repeticoes. Os tratamentos foram constituidos por bagaco de cana in natura (BIN),bagaco de cana fenado e enfardado manualmente, bagaco de cana fenado e enfardado mecanicamente, BIN enfardado manualmente,BIN enfardado mecanicamente, BIN ensilado inteiro e BIN ensilado picado. Foram avaliadas a composicao bromatologica, capacidadetampao (CT), valores de pH e os teores de acucares totais do BIN. Para a ensilagem foram utilizados silos cisternas e para oenfardamento, enfardadoras manual e mecânica. O bagaco foi enfardado in natura, ou apos atingir teor de 89% de MS, conforme ostratamentos. As caracteristicas avaliadas foram os teores de materia seca (MS), proteina bruta (PB), fibra em detergente neutro (FDN)e fibra em detergente acido (FDA). Os resultados foram submetidos a analise de variância e as medias foram comparadas pelo testede Scott-Knott (P<0,05). O BIN apresentou teores de 51,70% de MS; 2% de PB; 79,43% de FDN; 48,78% de FDA e 16,4% deacucares totais na MS. O bagaco de cana apresentou baixa CT e as silagens apresentaram pH satisfatorio para boa conservacao. Adesidratacao seguida do enfardamento manual proporcionou diminuicao nos componentes da parede celular, revelando-se o melhormetodo de conservacao do bagaco.Termos para indexacao: Feno, silagem, sub-produto.
Lipid Analyses for Viable Microbial Biomass, Community Composition, Metabolic Status, and In Situ Metabolism

This chapter discusses how phospholipid fatty acids (PLFA) and other lipids can be used to estimate total viable microbial biomass, community composition, and metabolic status as well as the use of in situ 13C incorporation to determine metabolic pathways in environmental samples. The viable microbial biomass increases with the availability of metabolizable substrates and may decrease after their exhaustion. Gas chromatography-mass spectrometry (GC-MS) of PLFA as their methyl esters provides greater sensitivity and specificity than the LP method and additionally provides detailed information on the microbial community composition and metabolic status. Some PLFA are indicative of particular phylogenic groups, and considered together with the environment from which the sample was retrieved, can be helpful in interpreting results. Biomarkers for the metabolic status of microbial communities include those for starvation and toxicity, unbalanced growth, and aerobic versus anaerobic growth, among others. Ubiquinones (UQ) are biomarkers for oxic respiration that mediate electron transport to oxygen and nitrate, while menaquinones (MK) can carry electrons to any electron acceptor. Besides the major respiratory quinones UQ and MK, Bacteria and Archaea also contain desmethylmenaquinones, methionaquinones, plastoquinones, rhodoquinones, and caldariellaquinones, which can also vary in the length of the side chain and, in the case of MK, in the degree of hydrogenation of the side chain.
Comparative lethality of rice husk ash and a diatomaceous eartht adults of four storage beetles

Lethality of rice husk ash (RHA) and a diatomaceous earth (SilicoSec) (DE) to adults of Sitophilus zeamais, S. granarius, Lasioderma serricorne and Callosobruchus maculatus was investigated under controlled conditions of 25 ± 2° C and 60 ± 3% relative humidity. Each product was tested at 0.05 g to 0.5 g/20 g of grain respectively in glass Petri dishes against 20 adults of each beetle. Adult mortality was observed up to 10 days post treatment. RHA/DE mixtures (1:1, 3:1 and 1:3 ratios) were also tested at 2% of grain weight. Additionally, RHA and DE were tested at low dosages (0.01 g to 0.04 g/20 g) against adults of C. maculatus alone. The DE generally produced significantly higher mortality of all the adult storage beetles and at earlier observation times, than RHA at the lower dosages (< 0.2 g). Adult mortality produced by RHA and DE in S. zeamais and S. granarius increased with increase in dosage from 0.05 g to 0.5 g. The RHA/DE mixtures generally produced similar mortality of all the adult storage beetles irrespective of post-treatment exposure time. The S. zeamais and S. granarius were generally more tolerant to the DE and RHA treatments than L. serricorne and C. maculatus. Percentage mortality of C. maculatus adults when DE was applied at low dosages (0.01 g to 0.04 g) was generally higher than RHA applied at similar dosages, up to 3 days-post treatment. All treatments produced 100% mortality of C. maculatus adults 4 days-post treatment. The data further confirm the efficacy of DE and RHA as insecticidal dusts at the dosage rate of 0.5 g or more per kg of grain.
Effect of UV-C treatment on chlorophyll degradation, antioxidant enzyme activities and senescence in Chinese kale (Brassica oleracea var. alboglabra)

The changes in chlorophyll content, antioxidant enzyme activities and senescence in Chinese kale (Brassica oleracea var. alboglaba) irradiated with different UV-C dosages (1.8, 3.6, 5.4 and 7.2 kJ m -2 ) were determined during storage at 20°C. The irradiation dose of 3.6 and 5.4 kJ m -2 delayed leaf yellowing depicted as higher hue values and chlorophyll contents and lower activity of chlorophyllase, Mg-dechelatase and chlorophyll-degrading peroxidase as compared to the other treatments. Similarly, UV-C treatment delayed the decrease in activities of antioxidant enzymes, particularly peroxidase (POD) and superoxide dismutase (SOD). It also reduced ethylene production and respiration rates. The results indicate that UV-C irradiation could be a useful non-chemical treatment to delay senscence and improve shelf life of Chinese kale.
Methodological recommendations for cognition trials in bipolar disorder by the International Society for Bipolar Disorders Targeting Cognition Task Force

Abstract Objectives To aid the development of treatment for cognitive impairment in bipolar disorder, the International Society for Bipolar Disorders (ISBD) convened a task force to create a consensus‐based guidance paper for the methodology and design of cognition trials in bipolar disorder. Methods The task force was launched in September 2016, consisting of 18 international experts from nine countries. A series of methodological issues were identified based on literature review and expert opinion. The issues were discussed and expanded upon in an initial face‐to‐face meeting, telephone conference call and email exchanges. Based upon these exchanges, recommendations were achieved. Results Key methodological challenges are: lack of consensus on how to screen for entry into cognitive treatment trials, define cognitive impairment, track efficacy, assess functional implications, and manage mood symptoms and concomitant medication. Task force recommendations are to: (i) enrich trials with objectively measured cognitively impaired patients; (ii) generally select a broad cognitive composite score as the primary outcome and a functional measure as a key secondary outcome; and (iii) include remitted or partly remitted patients. It is strongly encouraged that trials exclude patients with current substance or alcohol use disorders, neurological disease or unstable medical illness, and keep non‐study medications stable. Additional methodological considerations include neuroimaging assessments, targeting of treatments to illness stage and using a multimodal approach. Conclusions This ISBD task force guidance paper provides the first consensus‐based recommendations for cognition trials in bipolar disorder. Adherence to these recommendations will likely improve the sensitivity in detecting treatment efficacy in future trials and increase comparability between studies.
The Impact of AGB Stars on Galaxies

Abstract At the end of their evolution, asymptotic giant branch (AGB) stars undergo strong pulsation, mass loss, and dust production. Their mass loss results in substantial chemical and dust enrichment of the interstellar medium. Dust evolution models and isotope abundances in presolar grains suggest that AGB stars play a key role in both dust evolution and the star formation process. They are also the brightest stars in galaxies, potentially dominating in the near-infrared. As a result, AGB stars have a significant influence on the evolution and appearance of their host galaxies and thus must be accounted for when interpreting a galaxy’s integrated light. I will highlight new results that describe the impact AGB stars have on galaxies, including how AGB stars are used to probe galaxy evolution.
Use of Telemorace Inhibition in Combination with Anti-Cancer Drugs to Induce Cell Death in Tumor Cells

Abstract : Telomerase is a ribonucleoprotein complex that maintains the stability of chromosome ends the telomeres and regulates cell replicative potential. The enzyme minimally contains a catalytic subunit with reverse transcriptase activity (hTERT) and a RNA subunit (hTR) with a region complementary to the telomeric repeats that is used as template. Telomerase is up-regulated in 05% of breast carcinoma but not in adjacent normal tissues and its activity increases with tumor aggressiveness. Therefore targeting telomerase may represent a promising approach for cancer therapy. Inhibition of telomerase would result in telomere shortening and cell death due to dysfunctional telomeres. The major limitation of this approach is the time necessary for the telomeres to shorten sufficiently to engage cell death. One possibility to overcome this lag phase is to target the telomeres by introducing hTRs with mutations in the template region which results in decreased cell viability and increased apoptosis. The aim of this study is to investigate the feasibility of a new anti-cancer approach based on the combination of telomere disturbances induced by mutant hTR and chemotherapeutic drugs. Our results show that interfering with telomere maintenance in breast cancer cells results in increased susceptibility to anti-cancer drugs independently of initial telomere length and mechanisms of telomere maintenance. These results suggest that this strategy could lead to the development of a general approach for the treatment of all human cancers.