Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Regulation by the SACCHAROMYCES CEREVISIAE Centromere-Binding Protein CP1: a Dissertation

CP1 (encoded by the gene CEPl) is a sequence-specific DNA-binding protei of Saccharomyces cerevisiae that recognizes a sequence element (CDEI) found in both yeast centromeres and gene promoters. Strains lacking CP1 are viable but exhibit defects in growth, chromosome segregatio , and methionine biosynthesis. To investigate the basis of the methionine requirement, a YEp24-based yeast genomic DNA library was screened for plasmids which suppressed the methionine auxotrophy of a cepl null mutant. The suppressing plasmids contained either CEPI or DNA derived from the PH04 locus. PH04 encodes a factor which positively regulates transcription of genes involved in phosphate metabolism via an interaction with CDEIlike elements within the promoters of these genes. Sub cloning experiments confirmed that suppression correlated with increased dosage of PH04. PH04 pho80, and pho84 mutations, all of which lead to constitutive activation of the PH04 transcription factor, also suppressed cepl methionine auxotrophy. The suppression appeared to be a direct effect of PH04, not a secondary effect of PHO regulon derepression, and was dependent on a second transcriptional regulatory protein encoded by PH02. Spontaneously arising extragenic suppressors of the cepl methionine auxotrophy were also isolated; approximately one-third of the them were alleles of pho80. While PH04 overexpressio suppressed the methionine auxotrophy of a cepl mutant CEPI overexpressian failed to suppress the phenotype of a pho4 mutant; however, a cepl null mutation suppressed the lOWgrowth deficiency of a pho84 mutant. The results suggest that CP1 functions as a transcriptional regulator of MET genes,
Multiplexing With MicroRNAs: Mismatch Probes and Temperature Compensation for Increased Specificity and Reduced Variability in Hybridization Assays

MicroRNAs constitute a very interesting class of circulating biomarkers. They are present in many body fluids, and appear to avoid degradation by enzymes or the immune system. Organs shed microRNAs into the blood stream, offering the exciting possibility of detecting solid tumors or other hidden pathologies without invasive tissue biopsy. Multiplex microRNA assays offer superior specificity and differential diagnosis relative to quantitation of single analytes. A variety of multiplex assay technologies exists, including RNA sequencing, quantitative polymerase chain reaction, and hybridization, with different tradeoffs of cost, coverage, throughput and sample volume. The focus of this work is on improving reproducibility and specificity of a hybridization-based multiplex microRNA assay. The assay binds microRNA targets in solution to complementary DNA probes conjugated in a hydrogel particle matrix. The hydrogel environment differs from a classic surface-bound or bead-bound hybridization assay and has advantages for binding nucleic assay from complex biological samples, for instance tissue lysates and serum. Non-specific binding combined with variable well temperature across a plate is shown here to be a major source of assay variability. We describe the development of novel probes to reduce non-specific binding is described, and the development of a methodology to correct for temperature. An over 10-fold reduction in non-specific binding is achieved, and well-to-well variability is reduced from ~30% in raw data to single-digit percentages in most cases.
Novel Repression Mechanisms for Metal Transport Genes in Saccharomyces cerevisiae

Author(s): Nery, Camille Reyes | Advisor(s): Chanfreau, Guillaume F | Abstract: The transition metals iron and zinc are essential requirements for all living organisms. They participate in a variety of critical metabolic pathways, enzymatic activity, and provide structural support for countless proteins. Metal ion imbalance can be detrimental to organisms, as metal deficiency can alter many biological processes while metal excess can lead to toxicity. To alleviate these detrimental situations, the yeast Saccharomyces cerevisiae has developed tightly controlled regulatory mechanisms for the proper expression of proteins that control import, export, and storage of these essential metals. This regulation is required to ensure the efficient uptake, transport, and storage of specific metal ions during periods of metal concentration fluctuations. The work presented in the first chapter of this dissertation identifies the use of cryptic transcription as a means for regulatory control of the subtelomeric metal genes ZRT1 and FIT3. These transcripts arise from promoter units upstream of the ZRT1/FIT3 transcription unit and extend into the open reading frame (ORF). We show that these transcripts are degraded by the cytoplasmic Non-Sense Mediated Decay (NMD) Pathway and are only stabilized in the absence of the NMD Pathway; hence termed Cytoplasmically Degraded Cryptic Unstable Transcripts (CD-CUTs). We further show that these CD-CUTs act to prevent expression of ZRT1 by interfering with RNA polymerase II binding and activator binding (Zap1p) to the ZRT1 promoter unit. As we identified the use of CD-CUTs to mediate the repression of ZRT1/FIT3 during normal zinc/iron conditions, the mechanistic mode of action of these transcripts remained elusive. In an attempt to identify how a cytoplasmically degraded transcript can mediate transcription in the nucleus, we chose to study the cytoplasmic trafficking of these species. In chapter two, we show that the export of the ZRT1/FIT3 CD-CUTs is likely mediated by the SR-type mRNA export factor Hrb1p and dependent on the essential mRNA export factor Mex67p. Lastly, we identify an additional mode of regulation for the iron transport gene FIT3 by the glucose repressor Mig1p. Mig1p has been extensively characterized as a repressor of glucose responsive genes and in chapter three, we show that this regulation can be applied to iron regulation. We believe that Mig1p regulates the repression of FIT3 during conditions of normal iron and/or after switch back to normal iron conditions following iron starvation to prevent the deleterious expression of FIT3, thereby preventing the potentially harmful effects of iron toxicity.
Surface Adsorption Model Calculation Database and Its Application to Activity Prediction of Heterogeneous Catalysts

recent advances in the data-science methods have drawn attention to high-throughput quantum chemical calculations. in this study, we will report the surface model calculation database, which we are constructing by systematically carrying out the calculations of various chemical species adsorbed on metal surface models and storing their results, for heterogeneous catalytic reaction analyses. as an application example of this database, we attempted to evaluate the catalytic activity (namely, conversion rate) obtained from experiments for the following methane steam reforming (Msr) reaction, Ch4 + h2O → CO + 3H2, by analyzing the information from the database and to specify its activation factor. our script program realized semi-automatic and systematic quantum chemical calculations with siesTa program [1]. The current database collects the results for the three-layer 3×3 fcc (111), (100), and (211) surface slab models (with 15 Å vacuum layer) and these surfaces with adsorbates at gga-Pbe/dZP level of calculations. doping effect can be considered by substituting the central atom in the first layer with dopant. For each surface-adsorbate pair, various adsorption structures were considered by randomly generating 100 initial structures except for single-atom adsorption cases. up to now, 32,454 calculation results are collected in this database. For the analysis of Msr reaction, we recollected 1,028 calculation results, namely, those for clear surface and adsorption structures of h, C, o, h2, Ch, oh, C2, and Co, for each metal surface from the database. as the statistical analysis, we utilized sparse modeling methods, where the following equation (1) for the least square estimation with the regularization term p is minimized to perform the descriptor selection and regression simultaneously:
The Early Development of Xenopus Laevis: An Atlas of the Histology

Xenopus laevis is the key model for developmental, differential and embryological studies in vertebrates. Using molecular biological techniques it has become possible within the last few years to analyze developmental processes up to the level of genes. On obtaining results it is necessary to correlate them with morphological and histological stages. This excellent work documents and describes such developmental stages in finite detail. After an informative introduction to The Early Development of Xenopus laevis follows the highlight of the book, namely the 42 plates, each consisting of at least four high resolution micrographs. The reader is thus provided with a histological presentation of immaculate quality. Each plate is complemented by a schematic diagram describing the details shown on the plate, an additional scheme indicating the section and an explanatory short text, making this a potentially highly sought after work.
Bioluminescent mouse models of prostate cancer progression and therapy

Prostate cancer is the most common visceral neoplasm and second leading cause of cancer death in US men. It is a complex heterogeneous and multi-factorial disease whose mechanistic basis is poorly understood. Furthermore, treatment options for advanced metastatic prostate cancer are limited and do not impart significant survival benefits, highlighting the need for novel and more effective therapeutic strategies. To this end we examined the use of RNAi therapy based on the systemic delivery of optimized small interfering RNAs (siRNAs) targeting the androgen receptor (AR). siRNA treatment induced massive cell death in vitro but was unable to induce tumor regression or improve survival in an animal model of advanced human prostate cancer due to inefficient cellular delivery and uptake of siRNAs at metastatic sites. To explore further, we developed a bioluminescent animal model that enables the high throughput screening of siRNA pharmacodynamic and biodistribution properties. Systemically delivered siRNAs, although potent, were only effective at inhibiting gene expression in the liver. Reliable and tractable animal models of prostate cancer are needed in order to help better understand the molecular mechanisms of disease progression. Here we describe an improvement on the previously characterized Pten mutant model of prostate cancer by incorporation of a luciferase reporter allele. Specifically, the cancer initiating event is coupled to activation of firefly luciferase from the endogenous ROSA26 promoter in the same prostate epithelial cells. Additionally, we have extensively backcrossed our model onto the albino C57BL6TYRC2J and BALB/c backgrounds which enhances bioluminescence imaging (BLI) sensitivity. Consistent with previous studies, we show that progression of prostate cancer from 3-12 weeks is rapid and correlates with an increase in bioluminescence. However, longitudinal BLI from 12-40 weeks reveals a plateau in bioluminescence signal that is correlated with a halt in cellular proliferation as evidenced by Ki67 staining at necropsy. In contrast to other studies, prostate cancer never
Optimization Techniques For Next-Generation Sequencing Data Analysis

High-throughput RNA sequencing (RNA-Seq) is a popular cost-efficient technology with many medical and biological applications. This technology, however, presents a number of computational challenges in reconstructing full-length transcripts and accurately estimate their abundances across all cell types. Our contributions include (1) transcript and gene expression level estimation methods, (2) methods for genome-guided and annotation-guided transcriptome reconstruction, and (3) de novo assembly and annotation of real data sets. Transcript expression level estimation, also referred to as transcriptome quantification, tackle the problem of estimating the expression level of each transcript. Transcriptome quantification analysis is crucial to determine similar transcripts or unraveling gene functions and transcription regulation mechanisms. We propose a novel simulated regression based method for transcriptome frequency estimation from RNA-Seq reads. Transcriptome reconstruction refers to the problem of reconstructing the transcript sequences from the RNA-Seq data. We present genome-guided and annotation-guided transcriptome reconstruction methods. Empirical results on both synthetic and real RNA-seq datasets show that the proposed methods improve transcriptome quantification and reconstruction accuracy compared to currently state of the art methods. We further present the assembly and annotation of Bugula neritina transcriptome (a marine colonial animal), and Tallapoosa darter genome (a species-rich radiation freshwater fish). INDEX WORDS: Transcriptome quantification, Regression, Transcriptome reconstruction, Alternative splicing, RNA-Seq, Assembly and annotation. OPTIMIZATION TECHNIQUES FOR NEXT-GENERATION SEQUENCING DATA ANALYSIS
Phylogeny and subgeneric classification of Bouteloua with a new species, B. herrera‐arrietae (Poaceae: Chloridoideae: Cynodonteae: Boutelouinae)

Bouteloua (Poaceae: Chloridoideae: Cynodonteae; Boutelouiane) is an important genus of forage grasses containing 60 species found primarily in the Americas with a center of diversity in northern Mexico. A modern subgeneric classification is lacking. The goals of our study were to reconstruct the evolutionary history among the species of Bouteloua using molecular data with increased species sampling compared to previous studies. A phylogenetic analysis was conducted on 209 samples, of which 59 species (206 individuals) were in Bouteloua, using two plastid (rpl32‐trnL spacer and rps16‐trnK spacer) and nuclear ITS 1&2 (ribosomal internal transcribed spacer) sequences to infer evolutionary relationships and produce a subgeneric classification. Overall, ITS and plastid phylogenies rendered similar patterns. However, the ITS phylogeny lacked backbone structure, recovering only four internal clades out of nine found in the plastid phylogeny. The ITS network shows a radiative evolutionary pattern and indicates a number of incompatible splits, suggesting past hybridization between species of different sections. The maximum‐likelihood tree from the combined plastid and ITS regions is well resolved and depicts a strongly supported monophyletic Bouteloua that includes ten strongly supported clades and one moderately supported clade. The molecular results support the recognition of 10 sections and two subsections within Bouteloua s.l. ; three sections are new: Barbata, Hirsuta, and Trifida; four sections are new combinations: Buchloe, Cyclostachya, Opizia, and Triplathera; and two subsections are new: Eriopoda and Hirsuta. Based on our molecular results and the possession of unique morphological characters we describe a new species from Nuevo León, Bouteloua herrera‐arrietae.
Genetic and physiological characterization of seed dormancy regulation in common waterhemp [Amaranthus tuberculatus (Moq) Sauer]

vi CHAPTER 1. GENERAL INTRODUCTION 1 Seed dormancy and seed bank dynamics 2 Primary and secondary dormancy 3 Hormones, dormancy and germination 3 Environmental factors can induce or repress germination 5 Genetic factors involved in seed dormancy and germinability 7 Common waterhemp and seed dormancy 11 References 13 CHAPTER 2. SEPARATING SEED DORMANCY FROM GERMINATION IN AMARANTHUS TUBERCULATUS SEEDS. TEMEPERATURE AND HORMONE REGULATION, TWO DIFFERENT STORIES 24 Abstract 24 Introduction 25 Materials and methods 29 Plant materials 29 Stratification conditions 29 Germination bioassays 30 ABA and GA extraction and quantification 30 Experimental design and data analysis 31
Nucleic acid techniques in bacterial systematics

Isolation and purification of nucleic acids DNA reassociation experiments DNA-rRNA hybridization and methods DNA sequencing in bacterial systematics direct sequence analysis of small RNAs 16S/23S rRNA sequencing the polymerase chain reaction development and application of nucleic acid probes DNA fingerprinting from macromolecules to trees.
Favorable Condition for Mycelial Growth of Tricholoma matsutake

The main objectives of this research were to study the cultural and nutritional characteristics of Tricholoma matsutake and to establish its liquid culture system. The optimum growth of T. matsutake was observed in HA and TMM agar media. Similarly highest growth was observed in PDB and TMM liquid media. The optimal temperature for the mycelial growth was . The most suitable carbon source was dextrin among 12 different carbon sources tested. Yeast extract and peptone were best nitrogen sources among 17 different sources tested. The optimum mineral salts were and KCl among 9 different sources tested. Shaking culture gave higher mycelial growth compared to stationary culture. Similarly, optimum medium amount for shaking culture was 100 ml per 250 ml flask. The highest mycelial growth was obtained when mycelial discs were inoculated in 100 ml of medium and incubated for weeks, respectively. The highest proportion of mycelial growth was observed at 40 : 1 ratio of medium to inoculum volume in 8 l air-lift fermenter.
COMPARATIVE TRANSMISSION EFFICIENCY OF TWO BROAD BEAN WILT VIRUS 1 ISOLATES BY MYZUS PERSICAE AND APHIS GOSSYPII

We tested the transmission efficiency of two genetically divergent isolates of Broad bean wilt virus 1 (BBWV- 1), PV-132 from the USA, and Ben from Spain, by two aphid species, Myzus persicae (Sulzer) and Aphis gossypii (Glover) collected in Spain. Efficiency was estimated as the number of infected plants divided by the number of single-aphid-inoculated plants. The two aphid species transmitted the virus isolates with equivalent efficiency, but the transmission rate was significantly higher for isolate Ben than for PV-132. It is hypothesized that the specificity determinants for vector-virus interaction might be similar for M. persicae and A. gossypii, whereas transmission rate could be affected by amino acid differences in the coat proteins of the two isolates.
Molecular and Biochemical Characterisation of Armillaria

Armillaria root and butt rot disease is a common problem in peach orchards, tea and pine plantations in the Eastern Highlands of Zimbabwe. The species of Armillaria causing this disease have not been accurately identified but it is believed that at least three species are involved. These included A. fuscipes (previously referred to as RFLP Group I) and two unnamed species known as RFLP Group II and RFLP Group III. The aim of the study was to use PCR-RFLP, sequences of the IGS-1 region of the rDNA operon and AFLP fingerprinting to characterise 27 Zimbabwean Armillaria isolates. PCR-RFLP tests showed that the isolates resided in five groups. Analysis of sequence data elucidated four groups, which were also supported by AFLP data. Eleven isolates belonged to RFLP Group I which is considered to represent A. fuscipes, four isolates were most similar to those previously referred to as Zimbabwean RFLP Group II and two isolates clustered most closely with RFLP Group III. The remainder of the isolates appear to represent Armillaria taxa not previously found in Zimbabwe. University of Pretoria etd – Maphosa, L (2005)
Scholarly Communication Cycle: SWOT Analysis

Communication (formal/informal) is the key for making society attentive and advance scholarly communication (SC) worldwide openly. Components of SC (accumulation, creation, evaluation, publication, dissemination and preservation) are cycling towards elevation of education, research and innovation. Stakeholders have critical role in managing the SC cycle. In this study, SWOT analysis is used to evaluate strengths, weaknesses,opportunities and threats of SC and its components emphasizing the internal and external ecosystem. Based the SWOT analysis, the stakeholders potentials, resources, drawbacks, advantages, risks etc. are drawn in order to make strategic decisions to manage system effectively. Results revealed that accumulation of resource infrastructure facilitations brings an idea into creativity, reviewed it for quality, originality and publication (stamp of validity) that was disseminated through various media & modes and preserved for longevity. Imperatively, the SC carries authenticity and recognition globally. It also shown that an inactive infrastructure, mentorship and policies often indulge scientific creativity through misconduct and biased decisions of reviewing make futile or fake publication that will always spoiling the system. Taking opportunities to create and access resource repositories, helping to publish research to innovation monetize into products marketing globally with cloud safe and security. Finally, handicap of intellectual infrastructure vacuum (brain-drain) pressures the academia to leap into predatory journals crediting no transparency and accountability.
Intérêts de l’ovocyte de Xenopus laevis en écotoxicologie ? : Caractérisation des effets de contaminants environnementaux sur ce modèle alternatif

Les amphibiens constituent le groupe le plus menace d’extinction parmi les vertebres. Neanmoins, peu de travaux en toxicologie des amphibiens tiennent compte des stades precoces de leur cycle de vie. Pourtant, un individu est expose directement aux substances presentes dans le milieu aquatique des l’emission des gametes. Cette these de doctorat a pour objectifs d’apporter de nouvelles donnees sur les effets d’expositions a des xenobiotiques d’ovocytes de Xenopus laevis, de rechercher des cibles au sein de ce gamete et de participer au developpement d’un nouveau modele en ecotoxicologie pour evaluer la qualite de milieux aquatiques.Les avantages, que presentent ces ovocytes, nous ont permis de developper des protocoles efficaces pour apprehender la toxicite de substances. Des endpoints ont pu etre definis autour de la maturation ovocytaire, de la fecondation, du developpement embryonnaire et de la formation de jeunes tetards. Les effets d’expositions au cadmium, au plomb, au cuivre, a la bouillie bordelaise, au glyphosate, au RoundUp® GT Max et a la deltamethrine ont ete determines. Des essais ont ete egalement conduits pour des echantillons de milieux soumis a differentes pressions anthropiques.Il est apparu que l’ovocyte de xenope est sensible aux expositions, notamment au cadmium et au glyphosate et differentes signatures d’expositions sont apparues, comme la formation de doubles structures cytologiques induites par le glyphosate.Les reponses mises en evidence prouvent que l’ovocyte de X. laevis est un modele pertinent et permettent de recommander l’etude des premieres etapes du cycle de vie de l’amphibien en toxicologie aquatique.
Immune responses in broiler chickens supplemented with prebiotic, probiotic, their combination and G-probiotic Spl.

The immune responses in terms of relative spleen, bursa of Fabricius and thymus weights, absolute lymphocyte count (ALC) and hemagglutination inhibition titers (HIT) against New Castle disease were studied upon supplementation of lactose (2.5% in drinking water) as prebiotic, Lactobacillus acidophilus (0.1% in drinking water) as probiotic, their combination and G –Probiotic Spl® (0.5% in diet), a commercial probiotic preparation in broiler chickens on day 21 and 42 of age. The relative organ weights were numerically increased in supplemented groups indicating the improvement of immune response in broiler chickens. The ALC values (8481.1 ± 265.2 to 1088.3 ± 141.4) on both day 21 and 42 were significantly increased (P 0.05) between the supplemented groups and control groups. It was concluded that the prebiotics, probiotics, their combination and G-Probiotic Spl® could improve the immune response in broiler chickens and maintain good health status.