Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Markers and Mixed Stock Fisheries

Abstract This paper reviews and discusses the uses of genetic markers in analyzing the composition of population mixtures of fishes. Such analyses require (1) the existence of genetic differences identified in base-line data from contributing populations, and (2) an adequate sampling of individuals from the mixture to characterize its composition. Genetic analyses of complex population mixtures of salmonids began around 1980 and subsequently have been increasing; applications have included estimates of geographic origins in marine and freshwater fisheries, and of ancestral origins in populations reestablished from multiple sources. The potential for applications of genetic analyses of population mixtures is more limited in most marine species because such species are typically less genetically subdivided than salmonid species. However, genetic analyses are feasible in any species in areas of intermingling of genetically distinguishable populations. In addition, genetic marking by preferential breeding of .
Plastic Microbial Acclimation and Optimisation of Composting and Anaerobic Digestion Processes may Improve Degradation Times

Plastic Microbial Acclimation and Optimisation of Composting and Anaerobic Digestion Processes may Improve Degradation Times Conference or Workshop Item How to cite: Boardman, C. P.; Summers, S. S. ; Olsson-Francis, K. and Gladding, T. (2017). Plastic Microbial Acclimation and Optimisation of Composting and Anaerobic Digestion Processes may Improve Degradation Times. In: 16th International Waste Management and Landfill Symposium (Sardinia 2017), 2-6 Oct 2017, S. Margherita di Pula, Sardinia, Italy,.
Examining biological function and recombination using nucleotide sequences

The ratio of the synonymous substitution rate (K s ) to the nonsynonymous sub­ stitu tion rate ( K a ) is a measure of biological functionality that is commonly used by molecular biologists. In this dissertation, a simple m ethod is proposed to estim ate Ks-, Ka, the ratio K s ! K a , and the variances of these estim ators. The estimators have been developed based on both Jukes and C antor’s one-param eter model, and K im ura’s two-param eter model. Recombination is a m ajor source of genetic diver­ sity. One way to detect recombination is in the context of phylogenetic analysis. A likelihood-based m ethod is developed to detect any differences between two under­ lining phylogenetic trees by using nucleotide sequences. To ensure the independence between the inferred tree and the nucleotide site being evaluated, a leave-one-out technique is employed when computing the m axim um likelihood value of each poly­ morphic site. Both of these two méthodologie developments are applied to problems in HIV disease.
Endocrine disruption in the marine environment

The term endocrine disruption came into common use following the observation that fish showed intersex conditions in UK rivers. Male fish were found to have egg-like structures in their testes and egg yolk protein (vitellogenin) at high levels in their bloodstreams. Work at CEFAS and Brunel University in the UK demonstrated that if fish (trout) were held in the diluted effluent of sewage treatment works they quickly developed high levels of vitellogenin (VTG) in their blood (e.g. Purdom et al., 1994, Routledge et al., 1998). Further from sewage inputs the levels of VTG were lower and it seemed that the effect was caused by chemical(s) in sewage. The chemicals causing the effect were isolated and identified by CEFAS. They were found to be a number of different human derived steroids such as estradiol and the active ingredient of the contraceptive pill; ethinyl estradiol (Desbrow et al.,1998; Routledge et al., 1998).
Engineering and Production of Glucooligosaccharide Oxidases for Site-specific Activation of Cellulose and Hemicellulose Substrates

Canada has an extensive supply of residual biomass, which comprises plant polysaccharides that represent a renewable resource for the production of biochemicals, polymers and fuels. Enzymatic oxidation of plant oligoand poly-saccharides can alter the characteristics of these compounds, enhancing their application in food products; enzymatic oxidation could also facilitate site-specific chemical derivatizations of carbohydrates, leading to new bio-based polymers. A glucooligosaccharide oxidase from Sarocladium strictum (GOOX) with reported activity on oligosaccharides comprising up to seven glucose units, was engineered in this study using a genetic engineering approach to extend the activity of this enzyme on a wider range of plant polysaccharides and oligosaccharides. For the first time, in addition to the previously reported celloand malto-oligosaccharides, activity of wild type GOOX on xylooligosaccharides was reported. The catalytic efficiency of two mutant enzymes (GOOX-Y300A, GOOX-Y300N) on cellooligosaccharides and xylooligosaccharides was 2-fold higher than the wild-type enzyme. Notably, the binding affinity of these mutants
Determination and Characterization of Microbial Community Structure of Activated Sludge

Abstract All data suggest that microbial community structures or samples of sludge with a content of phosphate between 8 and 12.3% were very similar but distinct from those containing phosphate at 1.8%. In all samples analyzed, ubiquinones, menaquinone and fatty acids were the main components. Dominance and E5 suggested that a large number of organisms belonging to the b and subclasses Proteobacteria and Actinobacteria from higher GMC Grampositive bacteria, respectively, were present. Denaturing gradient gel electrophoresis analysis revealed at least 6-10 predominant DNA bands and numerous other fragments in each sample. Five major denaturing gradient gel electrophoresis fragments from each of 1.8% and 11.8% phosphate containing sludge samples, respectively, were successfully isolated and sequenced. Phylogenetic analysis of the sequences revealed that both 3% and 15% phosphate -containing sludge samples shared three common phylotypes which are separately associated with new bacterial groups of subclass C Proteobacteria, two E5 containing Actinobacteria, and Caulobacter spp. The subclass Proteobacteria. Phylogenetic analysis revealed useful phylotypes unique for both samples sludge. Therefore, changes in the phosphate content did not affect the composition and quantity prevailing microbial population, although specific phylotypes could not be unambiguously associated with EBPR.
DNA Barcoding and Genome Size: an assessment of utility for Biomonitoring Mosquito Vectors of Malaria in Western Kenya

NSERC Travel Grant to Dr. T. Ryan Gregory, University of Guelph College of Biological Science Student Bursary for International Collaborative Research, support for sequencing generously provided by the Biodiversity Institute of Ontario and Dr. Tara Gariepy, Queen Elizabeth II Grad Scholarship in Science and Technology, Kenya Entomological Medical Research Institute
Muscle-bone interactions and the development of skeletal phenotype

The association between the musculature and the skeleton is both physiological and physical. Cell origins for the two tissues are not identical. For example, the cranial neural crest forms much of the skull but contributes only connective tissue to the muscles (Noden and Trainor, 2005). Nevertheless, muscular and skeletal cells go through a common mesenchymal stage of differentiation. Muscles and bones are also linked by genes and hormones which affect both tissues. Muscles and bones are attached to each other and jointly share the responsibility for support and movement of body parts. The most fundamental aspect of the interaction between muscles and bones is mechanical. Muscles load bones—indeed, are the major source of bone loading—probably even before birth or hatching and certainly after, especially in flying and aquatic vertebrates, whose skeletons are partially relieved of weight bearing. As
Integration von Connexonen in Lipidmembranen auf porösen Oberflächen

Connexin26 (Cx26) is a member of the connexin family, the building blocks for gap junction intercellular channels. These dodecameric assemblies are involved in gap junction-mediated cell-cell communication allowing the passage of ions and small molecules between two neighboring cells. As central nervous system diseases like Alzheimer, Parkinson or depressions are today one of the most important medical challenges and are accompanied by significant economical impact in our society we want to use this biological elementary communication pathway in a joint research project. The goal is to develop a biochip to assay target receptors or ion channels of neurons expressed in a cellular system. These cells are supposed to be investigated without the need to apply a technically elaborate electrical contact of the cellular interior via patch clamp electrodes. This cellular access shall be achieved via the electrical coupling of the cells on a connexon-doped pore suspending membrane and the formation of gap junctions between the cells and the artificial membrane system. This setup would lead to a high throughput detection system, which is essential in the quest to find new pharmacological active substances. Towards achieving this goal, the integration of connexons in lipid bilayers on porous substrates is a basic milestone to be achieved and therefor aim of this PhD thesis. Using a cytochrome c based vesicle assay we first prove, that the hexameric connexon hemichannels of Cx26 can be reconstituted in a simple artificial membrane system. We also demonstrate that its activity can be inhibited using Cx specific blockers like carbenoxolone, calcium ions and α-cyclodextrin. In a next step, two different substrates and reconstitution methods are used to prove the functional integration of Cx26 connexons in artificial pore suspending membranes. One the one hand, we are able to show that Cx26 wild-type forms active hemichannels when reconstituted with a detergent based method in nano-BLMs. Besides the wild-type, this technique was used to characterize the Cx26 mutants M34A and V84L on a single channel level, revealing a similar behavior of M34A and different properties of V84L compared to the wild-type. On the other hand, Cx26 is reconstituted in micro-BLMs via spreading of connexon-doped giant unilamellar vesicles on a microporous substrate. Using a fluorescently labeled antibody we provide evidence that Cx26 is immobile on the functionalized substrate, whereas fluorescently labeled lipids stay laterally mobile. With a giant unilamellar vesicle based dye transfer assay we finally succeed in obtaining the first evidence of a functional gap junction formation. Together with the work of our cooperation partners, the goal to provide a biochip based application for pharmacological high throughput screening will be within reach in the near future.
Terrestrial–aquatic linkages in spring-fed and snowmelt-dominated streams

ABSTRACT The importance of trophic linkages between aquatic and terrestrial ecosystems is predicted to vary as a function of subsidy quantity and quality relative to in situ resources. To test this prediction, I used multi-year diet data from Bonneville cutthroat trout Oncorhynchus clarki Utah in spring-fed and snowmelt-driven streams in the high desert of western North America. I documented that trout in spring-fed streams consumed more (number and weight) aquatic than terrestrial invertebrates, while trout in snowmelt-driven streams consumed a similar number of both prey types but consumed more terrestrial than aquatic invertebrates by weight. Trout in spring-fed streams consumed more aquatic invertebrates than trout in snowmelt streams and trout consumed more terrestrial invertebrates in snowmelt than in spring-fed streams. Up to 93% of trout production in spring-fed streams and 60% in snowmelt streams was fueled by aquatic invertebrates, while the remainder of trout production in each stream type was from terrestrial production. I found that the biomass and occurrence of consumed terrestrial invertebrates were not related to our measures of in situ resource quality or quantity in either stream type. These empirical data highlight the importance of autotrophic-derived production to trout in xeric regions.
Epigenetic modification of gene expression in colorectal carcinogenesis

często występującym zarówno u kobiet, jak i u mężczyzn. Obecne sposoby leczenia tej choroby obejmują zabieg chirurgiczny, chemioterapię i radioterapię guzów odbytnicy. Jednak nowotwory w tym samym stadium zaawansowania, leczone w identyczny sposób, w różnym stopniu poddają się terapii. Różnice te przypisuje się pewnym cechom molekularnym, za pomocą których można zróżnicować nowotwory o podobnym obrazie histologicznym. W procesie kancerogenezy w jelicie grubym, poza zmianami genetycznymi, brane są pod uwagę inne zaburzenia wpływające na ekspresję genów, określane mianem regulacji epigenetycznej. Efektem epigenetycznym nazywa się zmiany w ekspresji genu, wynikające z modyfikacji struktury chromatyny bez zmian w sekwencji DNA. Podstawowym procesem epigenetycznym u człowieka jest metylacja DNA oraz kowalencyjna modyfikacja histonów, obejmująca przede wszystkim ich acetylację i metylację. Wykazano, iż część raków jelita grubego powstaje na podłożu tego właśnie zaburzenia epigenetycznego. Hipermetylację wykryto m.in. w regionach promotorowych następujących genów – p16, p14, APC, MGMT oraz MLH1.
DIMENSIONS OF DISSENT: THE URBAN LANDSCAPES OF THE 2017 WOMEN’S MARCH IN THE UNITED STATES

How do the landscapes of the 2017 Women’s March in the United States embrace the potential for socio-political dialogue within the urban context of 21st century cities? This research examines the routes and destinations taken by march participants in six American cities, looking at the design of the route, mode of procession, space of gathering, edge of dissension, and focus of the occupation. This analysis will provide perspectives on how people use and occupy urban spaces for democratic peaceful protest. The analysis of the spatial framework for these planned protests will suggest ways for landscape architects to understand and advocate for the relationship between designed public space and the ideals of public democracy. “We are experiencing a global shift toward a ‘social movement society’ in which protest is a routine part of political bargaining. ” -Jenkins et all
Identification of candidate proteins interacted with ovalbumin during the early phase of embryonic development

ABSTRACT In the present study, protein complexes emerged in high molecular weight (MW) region (95–170 kDa) were observed in fertilised chicken egg white after 7 days of incubation. Investigations were performed to reveal the possible proteins involved in these complexes. The emerged 10 protein bands from SDS-PAGE gel were confirmed to be ovalbumin through matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS) followed by Western blot analysis. To reveal the possible interactions among ovalbumin and other egg white proteins, LC connected to LTQ-Orbitrap mass spectrometer was used. Besides ovalbumin, 11 egg white proteins were identified including ovotransferrin, lysozyme, ovalbumin-related protein X, ovalbumin-related protein Y, hep21, alpha-enolase, ovoinhibitor, and a protein similar to ryanodine receptor 1. These results indicated widespread thermal-induced protein interactions among ovalbumin and other egg white proteins.
RELAÇÕES FISIOECOLÓGICAS NO DIPLÓPODO Oxidus gracilis (POLYDESMIDA, STRONGYLOSOMIDADE): O CONSUMO DE OXIGÊNIO EM RELAÇÃO AO TAMANHO, SEXO E CONDIÇÃO ALIMENTAR

The oxygen consumption of the millipede Oxidus gracilis was determined in an Warburg respirometer at 25oC, using males and females in order to detect the physioecologic and metabolic responses related to size, sex and alimentary conditions. Expressing metabolism (M) in function to body mass (P), and employing logarithmic data in the allometrical relationships, result of the M = a. Pb equations, were: M = 2,589.P0,89 for males (21 individuals), M = 2,715.P0,78 for females (24 individuals), and M = 2,6814.P0,86 for males and females, conjointly. The regression coefficients (b indexes) showed that respiratory metabolism of Oxidus gracilis would stay in an intermediary level of dependence between body mass, and body surface. The effects of alimentary condition were studied right before feeding, and after 24, 48, 72 and 96 hours of fasting. At the end of the 5th day (96 h), animals had a reduction of 21,46% in body mass, and 52,37% in oxygen uptake. In both cases, reductions were significant (P<0,05). Despite of no deaths have occurred, results indicate that stress due to abstinence from food, produce more changes in metabolism than in body mass of Oxidus gracilis.
Characterization of different native american physalis species and evaluation of their processing potential as jelly in combination with brie-type cheese

Physalis (Physalis L) is an exotic fruit which presents various compounds of nutritional and pharmacological interest (Bravo et al., 2015; Bravo & Osorio, 2016; Moura et al., 2016a). Among the physalis species whose fruits are rich in compounds beneficial to human health and have potential as a food stand out Physalis peruviana L. , Physalis pubescens L. , Physalis angulata L. , Physalis mínimos L. and Physalis ixocarpa Brot.
Biochemical Characterization of Peptidoglycan O-Acetyltransferases

Biochemical Characterization of Peptidoglycan O-Acetyltransferases Patrick J. Moynihan Advisor: : University of Guelph, 2013 Anthony J. Clarke The O-acetylation of the essential cell wall polymer peptidoglycan is a major virulence factor identified in many bacteria, both Gram positive and Gram negative, including Staphylococcus aureus, Bacillus anthracis, Neisseria gonorrhoeae and N. meningitidis. With Gram-negative bacteria, the translocation of acetate from the cytoplasm is thought to be performed by an integral membrane protein, PatA. The acetate is then transferred to peptidoglycan by a peripheral membrane O-acetyltransferase PatB, whereas a single bimodal membrane protein, OatA, appears to catalyze both reactions of the process in Gram-positive bacteria. Only phenotypic evidence existed in support of these pathways because no in vitro biochemical assay was available for their analysis, which reflected the complexities of investigating integral membrane proteins that act on a totally insoluble and heterogeneous substrate such as peptidoglycan. In this thesis, I present the first kinetic and biochemical analysis of a PG O-acetyltransferase using PatB from N. gonorrhoeae as the model system. The enzyme has specificity for muropeptides that possess tetrapeptide stems on muramoyl residues and with simple chitooligosaccharides as substrates, rates of reaction increase with increasing degrees of polymerization to 5/6. The data provided here strongly supports a mechanism whereby catalysis occurs by a double-displacement nucleophilic pathway involving a ping-pong bi-bi mechanism that proceeds through a covalent acetyl-serine intermediate. In addition to the catalytic serine, the aspartic acid and histidine residues that complete the catalytic triad were identified. I then applied the tools developed for the analysis of PatB to the Gram-positive Oacetyltransferase, OatA. The preliminary characterization of the catalytic domain of that enzyme detailed in this thesis will form the basis for future high-throughput screening with the goal of identifying OatA inhibitors. This information will be valuable for the identification and development of peptidoglycan O-acetyltransferase inhibitors, which could represent potential leads to novel classes of antibiotics. Together, these data solidify our understanding of the mechanism by which an important bacterial virulence factor is produced and pave the way for future development of novel antimicrobials.
Characterization of in vitro lytic activity of bacteriophagepreparation STAFAL against Staphylococcus aureus

Staphylococcus aureus is one of the most common gram-positive opportunistic pathogens in humans causing from minor skin to severe systemic infections. The newly acquired genes responsible for virulence and resistance to antibiotics are rapidly disseminated in the staphylococcal population and multiple-resistant S. aureus strains represent a significant medical problem. Bacteriophages with a broad host range are suitable for fighting these pathogenic bacteria as an alternative to antibiotic therapy. In this work we summarize the results of susceptibility testing of S. aureus strains to bacteriophage preparation STAFAL in a routine clinical microbiology laboratory. STAFAL is an antistaphylococcal phage lysate for topical application produced under GMP by IMUNA s.r. o. in the Czech Republic, containing highly effective virulent phage particles with a strong and rapid lytic and polyvalent effect. A set of 400 S. aureus strains collected from 10 health-care facilities in Brno (Czech Republic) during 2011 -2013 , including isolates from outpatients' and inpatients' departments was tested in this work.
Variant discovery in the sheepmeat odour and flavour in javanese fat tailed sheep using RNA sequencing

High-throughput RNA sequencing (RNA-Seq) reveals new challenges for the detection of transcriptome variants (SNPs) in different tissues and species. The aims of this study was to characterize a SNP discovery analysis in the sheep meat odour and flavour transcriptome using RNA-Seq. Six liver samples from divergent sheep meat odour and flavour were analyzed using the Illumina Genome Hiseq 2500 Analyzer. The SNP detection analysis revealed 142 SNPs in sheep meat samples, and a large number of those corresponded to differences between high and low sheep meat odour and flavour ovis genome assembly OAR v4.0. Among them, about 90.4% of genes had multiple polymorphisms within 12 genes (JAML, ANGPTL8, LOC101103463, SEPW1, SCN5A, LOC101113036, DOCK6, GTSE1, KIF12, KCTD17, KANK2, CYP2A6). Several of the SNPs (JAML, CYP2A6, SEPW1, and KIF12) found in this study could be included as suitable markers in genotyping platforms to perform association analyses in commercial populations and apply genomic selection protocols in the sheep meat production.
Exploring the Potential of Endophytes in Agriculture: A Minireview

Very little is known about the endophyte directed mechanisms of plant growth promotion.6 Endophytes mediate plant growth promotion through direct or indirect mechanisms. Since endophytes start their journey as rhizosphere bacteria, it is assumable that they may retain their attributes inside plant. Their mechanisms of benefit seem related to rhizosphere bacteria because most of endophytes can be cultured and can survive outside host in rhizosphere.
A replication legacy

Fanconi anemia (FA) is a chromosome instability syndrome characterized by progressive bone marrow failure and cancer proneness. The proteins mutated in FA constitute the so-called FANC/ BRCA pathway, involved in DNA replication and damage response. However, it is not completely understood how the FANC proteins perform their functions and maintain chromosome stability. Two recently published works reported that FANCD2 localizes to discrete sites on mitotic chromosomes, as consequence of replication fork stalling. The FANC pathway proved to be required to promote BLM-mediated anaphase resolution of chromosome entanglements induced by replication stress. It has also been shown that chromosome entanglement derives from DNA intertwining at fragile sites and that FANCD2 specifically targets these sites. Collectively, our data highlight a new role for the FANC proteins in the prevention of chromosome instability and aneuploidy. These findings open new directions in understanding the mechanisms of chromosome fragility and the role of FANC proteins in preserving genome stability.