Miracle-dz/UniFAR-FTUs huggingface dataset:
Efecto del pH y temperatura sobre el crecimiento y actividad antagónica de Bacillus subtilis sobre Rhizoctonia solani

En este estudio, se evaluaron los efectos de las condiciones ambientales (pH y temperatura) sobre la tasa de crecimiento y el efecto inhibitorio de diferentes cepas de Bacillus subtilis sobre Rhizoctonia solani . Las cepas de B. subtilis se cultivaron en caldo de infusion de papa. Se analizaron el comportamiento fisiologico y la tasa de crecimiento (dN / dt) de las cepas bajo diferentes condiciones de pH y temperatura. Las cepas mostraron un comportamiento diferente, lo que permitio establecer las condiciones optimas y suboptimas de crecimiento para cada cepa. Los sobrenadantes exentos de celulas obtenidos en diferentes condiciones de crecimiento se usaron en una prueba cuantitativa de actividad antagonista in vitro frente a R. solani . Se demostro que el efecto inhibitorio de las cepas se presenta principalmente en la fase estacionaria.
CHAPTER 5:Pharmacogenomics and Epigenomics of Age-Related Neurodegenerative Disorders: Strategies for Drug Development

Age-related neurodegenerative disorders (NDDs) are polygenic/complex disorders in which genomic, epigenomic, cerebrovascular, metabolic and environmental factors converge to define a progressive neurodegenerative phenotype. Age-related pheno-genotypes in the general population are highly influenced by the individual genomic background and substantially differ from those of specific NDDs such as Alzheimer’s disease (AD) or Parkinson’s disease (PD), as prevalent prototypes of NDDs. Major determinants of therapeutic outcome in NDDs include age- and sex-related factors, pathogenic phenotype, concomitant disorders, treatment modality and polypharmacy, and pharmaco(epi)genetics. Different categories of genes are potentially involved in the pharmacogenetic network responsible for drug efficacy and safety. Pathogenic, mechanistic, metabolic, transporter, and pleiotropic genes represent the major genetic determinants of response to treatment in NDDs. Epigenetic changes (DNA methylation, histone modifications, miRNA dysregulation) are present in pathogenic genes associated with NDDs, and epigenetic aberrations in genes configuring the pharmacoepigenetic cascade influence the response/resistance to drugs. New pharmacological categories of anti-aging products obtained from different sources are promising candidates with potential neuroprotective effects to halt disease progression in age-related NDDs. Novel strategies in drug development, either preventive or therapeutic, for NDDs should take into consideration pharmaco(epi)genetic determinants for treatment optimization.
Exploration of the Use of the “Bialaphos Genes” for Improving Bioherbicide Efficacy

We are studying the possibility of altering the virulence and host range of a phytopathogen by transferring and expressing certain genes from the soil-dwelling saprophyte, Streptomyces hygroscopicus, in a plant pathogen model, Xanthomonas campestris pv. campestris (XCC). The genes, referred to herein as the “bialaphos genes,” encode the production of bialaphos, a potent glutamine-synthetase-inhibiting herbicide. This cluster of genes was originally isolated from several biosynthetically blocked mutants of S. hygroscopicus and constructed into a plasmid vector, pBG9. We have transferred a fragment of the gene cluster into pLAFR3, a plasmid that functions in both Escherichia coli and XCC and contains a tetracycline resistance marker. The resulting plasmid, named pIL-1, was used to transform E. coli and was incorporated into XCC by conjugation. The transfer of the fragment was confirmed by Southern analysis. The genes were maintained in XCC for about 47 generations in the absence of selection for tetracycline, and no changes in cultural phenotypes were seen in the transformed XCC (XCC/pIL-1). The XCC/pIL-1 cells were pathogenic to their natural hosts cabbage and broccoli, but induced an altered hypersensitive response in the nonhosts bean, pepper, sunflower, and tobacco. The pathogenic host-reaction, induced by the parent XCC, XCC/pLAFR3, and XCC/pIL-1, was a typical black rot disease in inoculated leaves of the two hosts. The nonhost reaction on the nonhost leaves was necrotic hypersensitivity, induced by XCC and XCC/pLAFR3, or the inhibition of hypersensitivity accompanied by only chlorosis at sites inoculated with XCC/pIL-1. We hypothesize that the altered hypersensitivity phenotype may be due to the transformed XCC becoming more compatible with the nonhosts, a step toward acquiring nonhost-virulence, or due to disruption of the normal expression of the hypersensitivity and pathogenicity genes in the transformed XCC. More work is needed to confirm that the introduced genes are being expressed in XCC. With further understanding, this approach may provide a useful model to study host range, virulence, and strain improvement of plant pathogens for biological control of weeds.
Quantifying Elements in Arctic Grayling and Bull Trout in the South Nahanni River Watershed, Northwest Territories, Using Nonlethal Tissue Samples

AbstractMonitoring of contaminants in fish generally involves lethal sampling, but public scrutiny and increased pressure on fisheries have driven the need to develop nonlethal sampling methods. We examined the ability of adipose, anal, and caudal fin tissues to serve as nonlethal surrogates for lethal muscle tissue samples in the analysis of metals (elements). First, we evaluated the use of biopsies by examining relationships between concentrations of 39 elements in low-volume dorsal muscle biopsies and high-volume muscle samples from Arctic Grayling Thymallus arcticus and Bull Trout Salvelinus confluentus collected in the South Nahanni River watershed, Northwest Territories, Canada. Low-volume dorsal biopsy samples in this study served to most closely model the concentrations of elements found in high-volume dorsal samples; caudal and anal fins were more representative of high-volume dorsal samples than were adipose fins. Regressions between high- and low-volume dorsal muscle samples were significant fo.
Application of Dermal Fibroblast Cells in Cell Therapy of Wound

ContextandEvidenceAcquisition: Celltherapy,withautologousdermalﬁbroblasts,showsremarkablepotentialandiscurrently achieved by diﬀerent methods, such as spraying, grafting, and injecting to treat various types of ulcers, wrinkles, acne scars, and surgical wounds. Results: Toprepareﬁbroblastsforclinicaluse,somecriticalpointsmustbetakenintoconsideration: isolationandcultureof these cells to produce a homogeneous population of non-contaminated cells, a method for rapid growth, and development of a propor-tional number of ﬁbroblast cells with proper strength and viability. In addition, an appropriate site for a biopsy should be selected based on indications of treatment and maintenance. Conclusions: Ultimately, the clinical use of ﬁbroblasts in wound healing obviates the need for ready to use reservoir of these cells. In this regard, dermal allografts can be used in both fresh and frozen forms. The fresh type is more desirable due to its high chance of survival. Developing the appropriate preservation methods for allogeneic ﬁbroblasts is the emerging research ﬁeld of interest. Furthermore, applying biomaterials will increase the eﬃcacy of ﬁbroblasts in wound healing.
Development of hybrid haemagglutinin pseudotyped lentiviruses to assess heterosubtypic immunity to influenza

The influenza virus still causes hundreds of thousands of deaths globally, on top of morbidity and associated economic burden. We are currently at the height of efforts surrounding the development and employment of 'universal' vaccines against this virus, with clinical trials commencing on the most promising candidates. Despite this, the influenza virus poses more of a threat to human life than it ever has previously, with multiple subtypes of pandemic potential circulating around the globe. The key to current efforts lies in the priming of the immune system towards generating long lasting defences against conserved epitopes and conferring heterosubtypic immunity against the surface glycoprotein haemagglutinin. While vaccine strategies have expanded rapidly over recent years with the advent of 'headless' constructs as well as those derived from consensus, mosaic or chimeric sequences, the serological techniques to test how effective these vaccines are, have advanced less rapidly. Classical serological assays have been shown to be ineffective at detecting the antibodies which modern 'universal' vaccines strife to elicit, replaced by ELISA based approaches combined with mouse models measuring in vivo protection. In this thesis, an alternative method for the detection of heterosubtypic antibodies is used in depth across multiple platforms. Influenza pseudotypes have been employed using chimeric haemagglutinin constructs in a comprehensive project aimed at dissecting head and stalk directed antibodies present in human serum. Characterised broadly neutralising monoclonal antibodies have been tested on panels of influenza pseudotypes including divergent bat influenza viruses which hitherto have not been encountered in humans. A further aspect of influenza immunity has been covered in the detection of anti neuraminidase antibodies which have an important role to play in influenza heterosubtypic immunity. Finally, influenza pseudotypes bearing the glycoproteins from the less studied influenza B virus have been assayed in a large scale project aimed at correlating pseudotype assays with classical approaches.
Lactarius splendens, a second species with white latex in Lactarius section Deliciosi

An uncommon, small, orange-capped Lactarius Pers. with white latex was confirmed, using molecular studies of the type specimens, to be Lactarius splendens Hesler & A.H. Sm. Phylogenetic analysis revealed that the species falls within Lactarius section Deliciosi (Fr.) Redeuilh, Verbeken & Walleyn. , very closely related to L. rubrilacteus Hesler & A.H. Sm. and L. porninsis Rolland. Hitherto L. porninsis was the only white-latex species known in the otherwise orange-latex section Deliciosi; both are associated with Larix Mill.
Tracking transition in calorie-intake among Indian households: Insights and policy implications

The long-run trend in calorie-intake among rural and urban households in India has shown a decline till the year 2009–10 which got reversed during 2011–12. The reversal in the trend in calorie-intake has several important implications for dietary transition and nutritional interventions. The improvement in nourishment during 2011–12 is accompanied by a decline in inequality in calorie-intake. Among the economic forces, squeezed food budget has been the major factor responsible for the decline in dietary energy intake during 1993–94 to 2004–05, while the sufficiently large increase in income along with improved PDS after 2004–05 has triggered the upward trend in energy intake during the recent years. The paper has indicated that effect of subsidies spent on in-kind PDS transfer on calorie-intake is 3.5–3.9 times the effect of direct cash transfer of food subsidy. Therefore, the study has underlined the strengthening of PDS functioning or conditional cash transfers for improved nutritional status of Indian households.
Screening and statistical optimization of media ingredients for production of microbial transglutaminase

Transglutaminase is a calcium dependent enzyme that catalyses acyl transfer reactions between primary amino groups and protein bound glutamine residues. Eighteen bacterial and twenty eight actinomycetes were screened for the presence of transglutaminase. Among the microbial cultures screened Streptomyces sp. D1, showed maximum transglutaminase activity. In this study characterization of transglutaminase and its application to modifying the properties of panner (Indian cottage cheese) in the form of cross linking was investigated. Optimum temperature and pH for enzyme was found to be at 50°C and 6.0, respectively. Optimization of media ingredients for maximizing the transglutaminase activity using Streptomyces sp. D1 was carried out using central composite design. Response surface methodology was employed to standardize the optimum media composition for maximum enzyme activity. Three factors such as carbon source, nitrogen source and pH were tested for the maximum enzyme activity as response. The optimized medium with sugarcane molasses as carbon source 6.0% (w/v), peptone as nitrogen source 1.75% (w/v) were found to be optimal at initial pH 6.5 and incubation temperature 30.0°C with agitation at 100 rpm for 96h. The enzyme activity of transglutaminase obtained from the optimized medium was found to be 4.1 (AU/ml). Low cost substrate such as sugarcane molasses in the form of a renewable substrate is proposed to be suitable even for scale-up production of enzyme and for industrial applications. The ethanol fractionated transglutaminse treated milk was found to produce more paneer with increased moisture content while reduction in cooking loss of the paneer prepared using enzyme treated milk is also reported.
Identification of Conserved miRNAs and Their Target Genes in Faba Bean by EST Based Homology Analysis

MicroRNAs (miRNAs) are a class of endogenous, non-coding short RNAs, around 21 nucleotides (nt) in length found in eukaryotic cells and some viruses. To date, miRNAs are identified in several plant species through experimental and computational approaches where they play important roles in growth and development, metabolism, stress responses by guiding mRNA cleavage or repressing translation. Although the faba bean ( Vicia faba ) is an important source of protein widely used for human and animal nutrition, not a single miRNA has been identified in it up till now. Evolutionary conserved characteristics of plant miRNAs allow the identification of conserved plant miRNAs by homology analysis. The aim of this study is the identification and characterization of miRNAs in faba bean using the EST based homology analysis approach. For computational identification of novel miRNAs in faba bean, 8496 known and unique plant miRNAs from 73 plant species were searched for homology against 20697 expressed sequence tags (EST) and 577 genome survey sequences (GSS). Candidate miRNAs including protein coding sequences were recognized following the miRNA criteria of secondary structure and biogenesis. In this study, 262 candidate miRNAs belonging to 143 miRNA families have been identified for the first time in faba bean. Moreover, psRNATarget server predicted 712 potential target genes of these candidate miRNAs from faba bean. Predicted target genes seem to be involved in the regulation of several important biological processes. The results of this study will contribute to further research on miRNAs, leading to an improved understanding of the role miRNAs play in biological processes and the underlying environmental stress related molecular mechanisms of faba bean.
Regulation of the tumor suppressor LKB1 by the acetyltransferase GCN5

The tumor suppressor gene LKB1 encodes a serine/threonine kinase which regulates the cellular metabolism and polarity. Its biological activity is partly exerted through the phosphorylation and activation of 14 kinases which belong to the AMP-activated protein kinases (AMPK). The eponym member of this family acts as an essential nutritional sensor in the cell. The research that I conducted during my PhD focused on the regulation of LKB1. The LKB1 holoenzyme is a constitutively active heterotrimer comprising two other proteins called STRAD and MO25. My PhD project shows that LKB1 is acetylated on the lysine 48 residue by the acetyltransferase GCN5. Using biochemical approaches and cell imaging, I have shown that the acetylation of LKB1 by GCN5 favors its nuclear localization, while the non-acetylated fraction is localized in both the nucleus and the cytoplasm. GCN5 also promotes the cytoplasmic export of LKB1 in an HAT-independent manner and regulates its expression levels. In order to investigate the contribution of this acetylation to the functions of LKB1 in vivo, I have used the experimental model of the neural crest (NC) in chick embryos. Indeed, during my PhD, I have contributed to a study, initiated by my host laboratory, in which we show that LKB1 is required for the delamination, polarized migration and survival of neural crest cells (NCCs) which contribute to the formation of most craniofacial structures in vertebrates. LKB1 signaling is mediated by AMPK and the ROCK kinase and converges towards the actin-dependent molecular motor, Myosin II. Using the same experimental model, I have shown that GCN5 is expressed in NCCs during embryogenesis and that the functional interaction between GCN5 and LKB1 is essential for the activity of LKB1 in the cephalic NCCs ontogenesis and head formation.
Identification and characterization of MicroRNAs modulating cardiac hypertrophy

The adult heart is capable of remodelling in response to different pathological stimuli; in most cases, a phase of compensated hypertrophy evolves into frank dysfunction and heart failure. To identify microRNAs able to prevent cardiac hypertrophy and preserve cardiac function, we performed a high-content microscopy, high-throughput functional screening for human microRNAs able to reduce neonatal cardiomyocyte (CM) cell size using a whole-genome microRNA library. The most effective anti-hypertrophic microRNA was hsa-miR-665. In a model of transverse abdominal aortic constriction (TAC) in 8 weeks old CD1 mice (n=14 per group), AAV9-mediated delivery of miR-665 showed remarkable capacity to protect against pathological cardiac hypertrophy and preserve function over time. This effect was observed when the vectors were delivered either before (LVEF at 60 day after TAC: 51.3% ±5.8% in treated vs 34.82% ±0.77% in controls; P<0.005) or after hypertrophy onset (LVEF at 60 days after TAC: 57.5%±5.60% in treated vs 28.4%±15% in controls; P<0.001). Global mRNA changes in hearts treated with miR-665 were evaluated by mRNA deep sequencing. All the 43 genes, for which siRNA were available, out of the 67 genes that were found to be significantly expressed ≤2 fold over control were individually down-regulated by specific siRNAs and tested for being direct miR-665 targets. This approach identified three sarcomeric proteins as direct mediators of miR-665 activity, namely Enah, Fhl1 and Xirp2, which are known to be involved in sarcomeric mechanotransduction and myofibrillar remodelling. In conclusion, miR-665 represents an important tool to decipher the molecular mechanisms of hypertrophy and offers a potential lead for the development of new biotherapeutics.
Human Gut Microbiota and Obesity:
How Is Gut Microbiota Associated with Obesity Improvement Induced by Bariatric Surgeries or Low-Calorie Diet Treatment?

vii CHAPTER ONE: INTRODUCTION . 1 1.1 Obesity . 1 1.1.1 History of Obesity . 1 1.1.2 Causes of Obesity . 2 1.1.3 Harmful Effects of Obesity . 4 1.1.4 Treatment of Obesity . 5 1.2 Gut Microbiota . 6 1.2.1 Microbiota . 6 1.2.2 Human Microbiota . 6 1.2.3 Human Intestinal Microbiota . 6 1.2.4 The Microbiota in Human Gut May Play an Important Role in Regulating Adiposity . 7 1.3 Bariatric Surgeries (BRS). 8 1.3. 1 Bariatric Surgical Treatments Show Extremely Promising Results in Severe Obesity . 8 1.3. 2 A Comparison between Gastric Bypass, Sleeve Gastrectomy, and Gastric Banding . 8 1.3. 3 Bariatric Surgeries Help Weight Loss . 10 1.4 Low-Calorie Diet Treatment (LCD) . 12 1.5 The ‘BARIA’ Project . 13 1.6 Hypotheses and Experimental Design . 13 CHAPTER TWO: MATERIALS AND METHODS . 17 2.1 Stool Sample Collection . 17 2.2 DNA Extraction. 17 2.3 Illumina Sequencing . 17 2.4 HumiChip Analysis . 19 2.5 Quantitative Polymerase Chain Reaction (qPCR) . 22 2.6 Gas Chromatography. 24 2.6. 1 Instrumentation . 26 2.6. 2 GC condition. 26
Numerical Analysis of the Burger Equation using Finite Differences

119 Numerical Analysis of the Burger Equation using Finite Differences Saad A. Manna Badran J. Salem College of Computer Science and Mathematics College of Basic Education University of Mosul, Iraq Received on: 23/07/2006 Accepted on: 04/10/2006 ABSTRACT The Burger equation had been solved numerically by using two finite differences methods. The first is explicit scheme method and the second is Crank–Nicholson method. A comparison had been made between the two and we find that the Crank–Nicholson method is the best and most accurate than the explicit scheme method, as it is shown in (Table 1). Also the numerical stability for both methods has been made, the explicit scheme method is conditionally stable and the condition is   2 1  , while Crank–
Postbreeding Movements in Marbled Newts (Caudata, Salamandridae): A Comparative Radiotracking Study in Two Habitat Types

Abstract: The maintenance of gene flow and colonization of new areas are influenced by an organism's movements in the landscape. Movement favors genetic mixing and limits inbreeding risk, hence decreasing the risk of extinction. Movement is a multifactorial process, however, and might be influenced by both individual traits and environmental factors. Studying the influence of individual characteristics and landscape features on movement is becoming an important challenge in evolutionary ecology and conservation biology, especially among threatened species such as amphibians. In a low-disperser species (Triturus marmoratus), we expected differences in movement ability to vary with individual traits, such as body length, as well as features of the landscape. On the basis of radiotracking surveys in both forests and agricultural lands, we revealed that landscape features and climatic conditions influenced the distances traveled by newts. Moreover, the individual traits, and particularly the body length and the hind-limb length, were also important factors explaining movement patterns in Marbled Newts. Highlighting such movement-related traits in a salamander species could improve estimates of movement potential based on morphological traits. Our results can assist in recommendations for conservation plans of the Marbled Newts, and more generally of amphibians.
Integrated RNA-seq and sRNA-seq revealed differences in transcriptome between susceptible and resistant tomato responding to Fusarium oxysporum

Tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a worldwide destructive disease of tomato. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed RNA-seq and sRNA-seq analysis to unravel regulated genes and miRNAs in tomato infected by FOL. Differentially expressed (DE) protein coding gene and miRNA gene profiles upon inoculation with FOL were presented at twenty-four hours post-inoculation including four treatments. Total of more than 182.6 million and 132.2 million high quality clean reads were obtained by RNA-seq and sRNA-seq, respectively. A large overlap was found in DE mRNAs between susceptible cultivar Moneymaker and resistant cultivar Motelle. All Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. Combining with qRT-PCR, five disease resistance genes, Solyc01g095630, Solyc03g059080, Solyc00g174340, Solyc11g071750 and Solyc05g050350, were verified to involved in the disease resistance in the resistant cultivar Motelle treated with FOL. Northern blot analysis further confirmed the results from sRNA-Seq and demonstrated that several miRNAs including Sly-miR477-5p, sly-miR167a, novel_mir_675, novel_mir_504 and novel_mir_762 conferred FOL infection. Our data resulted that pathogen resistant genes/miRNAs may play a critical role with the benefit of a coordinated machinery in prompting the response in prompting FOL response in tomato, which offered us with a future direction and surely help in generating models of mediated resistance responses with assessment of genomic gene expression patterns.