Miracle-dz/UniFAR-FTUs huggingface dataset:
The production of polyclonal, monoclonal and genetically-derived scFv antibody fragments for the detection of the ß-lactam antibiotic, cephalexin, in milk

This thesis describes the production of antibodies for the detection of cephalexin and their application in ELISA and Biacore ‘real-time’ surface plasmon resonance (SPR)-based biosensor assays. The use of antibiotics in food-producing animals has many beneficial effects (e.g. treatment of mastitis in dairy cattle). However, their use and misuse has also been implicated in the increased incidence of resistant microbial strains with the associated public health risks and economic losses for food processors. Antibiotic residues can adversely affect bacterial starter cultures used in the production of milk-based products such as cheese and yoghurts. The P-lactam antibiotic cephalexin was chosen as the target for the production of antibodies due to its generic cephem-based structure, solubility, and, in particular its use of this antibiotic in treatment of udder infections (e.g. mastitis). Cephalexin-protein conjugates were produced and used for the generation of polyclonal and monoclonal antibodies that were then purified and characterised by SDS-PAGE, Western blotting and ELISA. The specificity of these antibodies was determined and they were used in displacement immunoassays for the detection of the relevant antibiotic in ‘spiked’ samples of PBS and whole milk. Recombinant single chain Fv (scFv) antibody fragments were produced using phage-display technology. Naive and immune phage-display libraries were panned using cephalexin conjugates. In addition, a monoclonal antibody-secreting hybridoma cell line was used in the production of a phage-displayed recombinant scFv. The recombinant scFv (wild type) derived from the parental hybridoma cell was purified and characterised by SDS-PAGE, Western blotting and ELISA. Wild type scFv was subsequently used as a template for the production of a mutant scFv phage-displayed library using random mutagenesis and error-prone PCR.Mutant scFv antibodies were isolated, expressed and then purified using immobilised metal affinity chromatography (IMAC). Two mutant clones expressing scFv antibodies selected showed improved functional expression and assay performance when compared to wild type scFv. Comparative gene and amino-acid sequence analysis and protein modelling was carried out on wild type and selected mutant recombinant scFv antibodies and confirmed the presence of mutations in the framework and variable heavy chain complemetarity determining region amino acid sequences. All antibodies were evaluated in ELISA and Biacore assay formats for the detection of cephalexin in milk samples. The polyclonal, monoclonal and recombinant scFv antibodybased assays demonstrated varying sensitivity and reproducibility but achieved cephalexin detection below the legislated European Union maximum residue limit (EUMRL) in milk ( 10 0 Mgflig).
What was the source of the 2011 outbreak of Escherichia coli in Germany and France

Abstract: Shiga toxin-producing Escherichia coli (STEC) O104:H4 is a very rare cause of foodborne illness. In the European Union, sporadic cases have been previously linked to travel to North Africa, the Middle East and Central Asia. In Europe there have been cases of STEC O104:H21, which have led to the identification of cattle as an animal reservoir of this pathogen. In North America, an outbreak of STEC O104:H21 was linked to consumption of milk contaminated post-pasteurization. This case study summarizes the epidemiologic and laboratory investigations of the largest outbreak of E. coli O104:H4 that occurred in Germany and France during the summer of 2011 and discusses its implications. This outbreak became the deadliest outbreak of STEC ever recorded.
The mutability of staphyloccal biofilms

In their natural environment, bacteria are often found as sessile populations, known as biofilms, typified by surface adherence and extracellular matrix production. This growth phase confers broad spectrum antibiotic recalcitrance, through undefined mechanisms. This work sought to investigate a role for increased mutability ofstaphylococci in biofilms, as a contributing mechanism in biofilm antibiotic recalcitrance. Initially, a novel biofilm model for use with staphylococci was established that utilised cellulose disks and incorporated human plasma to promote bacterial surface adherence. This system was validated by demonstrating antibiotic recalcitrance, dissemination by D-amino acids, and similarities with transcriptional profiles of other biofilm models. Using this novel biofilm model, and the Sorbarod flow system, mutation frequencies (MFs) were determined for Staphylococcus aureus and Staphylococcus epidermidis in biofilms and compared with those in planktonic cultures. This revealed increases in MF of up to 68-fold compared with planktonic cultures. The role of oxidative stress in biofilm mutability was investigated by addition of antioxidants to biofilms. Here, MFs were reduced up to 5-fold, suggesting a role for oxidative damage. Transcriptional profiling of biofilms revealed upregulation of several genes involved in DNA repair, compared with planktonic cultures. Genes encoding antioxidant activity were also investigated; of these only sodA was upregulated. Staphyloxanthin biosysthetic genes, however, were downregulated. During these studies, S. aureus biofilms were found to generate phenotypic variants. White variants (WVs) and large pale variants (LPVs) were mostly found amongst cells shed from biofilms. WVs had lost biofilm forming capacity and had mutations in the alternative sigma factor, SigB. LPVs retained biofilm forming capacity, but the genetic basis of their variation remains undefined. In summary, I have shown that staphylococci exhibit enhanced mutability in biofilms, accelerating the emergence of antibiotic resistance and morphological variants. This may result from oxidative stress, causing the enhanced accumulation of mutations within the genome.
3D/1D COMPUTED FRACTIONAL FLOW RESERVE COMPARISON IN CORONARY ARTERY DISEASE

Fractional Flow Reserve (FFR) has become the gold standard for diagnosing coronary artery disease (CAD) since Gould et al. [11] claimed so whilst the most traditional way to measure FFR is invasive coronary angiography (ICA). Such modality is invasive and expense-costing according to DEFER (Deferral Versus Performance of PTCA in Patients Without Documented Ischemia) study [29], half of the patient underwent ICA has no ischemia risk at all. Thus non-invasive, cheap and reliable ways to alternate such operation is demanding and significant and FFRCFD is a promising candidate. By discretizing reconstructed coronary geometry from computed tomography angiography (CTA) and imposing circuit analogy coronary boundary condition, a finite element fluid solver or spectral element solver could reveal the velocity and pressure field inside coronary artery tree and hence FFR could be non-invasive acquired. Nonetheless, the computational cost to perform such method is prohibitive for most of the medical research centers or hospitals, greatly limiting the potential beneficiaries. The motivation of this work is to validate the accuracy of a one-dimensional (1D) reduced-order model of three-dimensional (3D) full order Navier-Stokes equations where the former one could be performed on a personal computer within a couple of minutes. The results show an agreement between high and low fidelity FFR from 3D and 1D pressure and velocity, demonstrating that the 1D solver could be used as a alternative to the 3D solver at fraction of the cost. Moreover, a sensitivity study is shown by varying parameters within a proper physiological range. Robustness of 1D solver has shown assuming proper outflow boundary conditions. This work also provides evidence that the 1D solver can be used reliably and efficiently in the clinical setting for FFR predictions. For my parents, Li-hong and Lai-qun.
Expression of Floral Fasciation in Gamma-ray Induced Gerbera jamesonii Mutants

In order to induce variations for floral traits in Gerbera jamesonii , seeds obtained from controlled crossing among white gerbera genotypes were irradiated with different doses of gamma rays (1 to 5 kR). Induced floral fasciations were observed in M 1 seed raised plants of gerbera. Ring-fasciation and linear-fasciation were observed in mutant types which lead to deformed and asymmetric flower heads which are mostly male and female sterile. Fasciated flowers are recurrent in the mutant types in comparison to spontaneous floral fasciation in wild type (normal) plants which occurs occasionally and is male and female fertile. An increase in the number and arrangement of vascular bundles in the stalks of fasciated capitula suggests alterations in the shoot apical meristem of the mutated plants. Different phenotypes of fasciated gerbera mutants suggest variable expressivity of the trait and attempts may be made to identify and utilize partially fertile fasciated genotypes in hybridization experiments with wild types for studying the genetic basis of fasciation. Fasciated gerberas can be propagated vegetatively to perpetuate their unusual forms and designated as cultivars of the specie
Invertebrate Palaeontology and Evolution

Preface. Macrofossils on CD--Rom. Part One: General Palaeontological Concepts. 1 Principles Of Palaeontology. 2 Evolution And The Fossil Record. 3 Major Events In The History Of Life. Part Two: Invertebrate Phyla. Sponges. 5 Cnidarians. 6 Bryozoans. 7 Brachiopods. 8 Molluscs. 9 Echinoderms. 10 Graptolites. 11 Arthropods. 12 Exceptional Faunas: Ichnology. Systematic Index. General Index
THE PROTEOMIC RESPONSE OF THE CARCINUS MAENAS Y-ORGAN OVER THE COURSE OF THE MOLT CYCLE

TITLE: The proteomic response of the Carcinus maenas Y-organ over the course of the molt cycle AUTHOR: ABSTRACT The proteomic response of the Carcinus maenas Y-organ over the course of the molt cycle Molting in arthropods is a complex process governed by regulatory mechanisms that have evolved and adapted over millennia to allow these animals to grow, despite being confined by a hardened exoskeleton. We isolated the molt-regulating Y-organs (YO) from the common shore crab Carcinus maenas at molt stages B, C 1-3 , C 4 , and D 0 to assess how changes in protein abundances might underline the unique physiology of each of these stages. We found that changes in protein abundance were most notable in the postmolt stages (B and C 1-3), where an increase in energy metabolism and the reactive oxygen species stress (ROS) response proteins was observed. An increase in triosephosphate isomerase and transketolase suggest that the postmolt YO is participating in triglycerides storage and is also actively recycling excess ribose sugars manufactured during the YO's previously activated state. We also propose as mechanism through which ROS-induced release of cyclophilin A may contribute to YO atrophy during postmolt through the remodeling of structural proteins such as collagen. We support the standing observation of YO atrophy during postmolt by drawing attention to hemolymph protein abundances, especially those of cryptocyanin isoforms, which dropped precipitously in intermolt (C 4) and remained at low abundances into early premolt (D 0). Finally, though our evidence is preliminary, we propose that future investigations into the YO proteome address the significance of the protein glutamate dehydrogenase. Glutamate dehydrogenase, a key enzyme involved in the formation of glutamate, represents a potential nutrient-sensing checkpoint that might be involved in YO activation. Historically, most attention has gone to the acute molt stages, where signaling mechanisms involved in the activation of the YO have been the focus. Here, we present data suggesting that other regulatory mechanism may be governing the atrophy the postmolt YO. A better understanding of crustacean physiology has the potential to benefit ecosystems and economies worldwide. AKNOWLEDGMENTS I would like to first and foremost thank my family for their unending support through all of life's ups and downs. I have been so fortunate to have so much love in my life from Mary, Paul, and Kailey Hamer. I can't imagine of a better group of people to have on my side as I've …
Proposing and Testing a Model of Corporate Social Responsibility as Consumer Marketing Derivative in Telecom Sector of Pakistan: A consumer Perspective

Modern businesses are expected to be socially responsible regardless of their industry of operation or country of abode. The age of economic globalization, efficiency in information transfer, and the desire to make our world a more sustainable place of abode for everyone have all combined together to make it even more so. Interestingly, it has now become apparent that corporate entities in both developed and developing economies of the world are conscious of their social responsibilities to all their stakeholders. This is certainly a step in the right direction; our world can only be a better place for this generation and future generations of all living objects to exist in, if we all as individuals and corporate entities were to take issues relating to social responsibility very seriously. The objective of the present study is to assess the corporate social responsibility (CSR) practices, relevant towards the domain of consumer marketing in relation to telecom (mobile phone operators) service sector of Pakistan. An attempt has been made to highlight the importance of CSR proposition towards organizations that is by adopting and incorporating the CSR inventiveness‘s will enhance the organizations profitability, growth and sustainability in a more competitive and constructive manner and which will earn them a stronger corporate identity with socially and business responsive organization stance and in return can attain customer retention on consistent basis at a marketplace.
Identification of growth-dependent genes involved in paraquat toxicity in Saccharomyces cerevisiae

Using the yeast strain library we established by overexpressing each gene essential for yeast growth, we comprehensively searched for genes affecting the sensitivity of yeast to paraquat. As a result, seven novel genes, UTP4, UTP25, SEC65, NDD1, TFB2, TIM23, and CCT6, were identified as conferring paraquat resistance in yeast via overexpression.
Direct and indirect effects of grazing constrain shrub encroachment in semi-arid Patagonian steppes

Question: What are the long-term effects of grazing exclusion on the population structure and dynamics of, and interactions among, three dominant shrub species? Location: Grass-shrub Patagonian steppe, Chubut, Argentina. Methods: Permanent plots were established in grazed paddocks and paddocks excluded from grazing in representative Patagonian rangelands. Shrub abundance, population size-structure, short-term (two 3-yr periods) and long-term (matrix models) population dynamics, and neighborhood interactions of three native and codominant shrub species (Mulinum spinosum, Senecio filaginoides and Adesmia volckmanni) were measured and analysed using different statistical approaches. Results: The total density of shrubs was 74% higher in paddocks excluded from grazing, owing mainly to increases in Mulinum (80%) and Senecio (68%) species. However, differences in size structure between ungrazed and grazed paddocks were only detected in Mulinum. Demographic rates differed between shrub species, time-periods and grazing conditions. In particular, recruitment in the short term (especially in wet years) and population growth rate in the long term (λ) were higher in paddocks excluded from grazing only in Mulinum populations. Senecio populations showed a marginal increase in recruitment and mortality independent of the grazing condition in the wet and dry period. Grazing exclusion modified the balance of neighborhood interactions among the three shrub species. In grazing-exclusion paddocks, there was a balance between positive and negative interspecific interactions, while in grazed paddocks there were more negative intraspecific and interspecific interactions, resulting in a net negative balance of neighborhood interactions. Conclusions: Our understanding of woody encroachment in arid rangelands can be informed through evaluation of direct and indirect effects of grazing exclusion on the abundance and demography of dominant woody species. In Patagonian arid steppes, the occurrence of woody encroachment in rangelands excluded from grazing can be explained by altered responses in plant-animal and plant-plant interactions among shrub species.
An Exploration of Fern Genome Space

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolutionacrossgreenplants, and shed lightongenetic and genomic features that characterize ferns, suchas their highchromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to2X) for six fern species fromthePolypodiales (Ceratopteris,Pteridium, Polypodium,Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of ferngenomescanprovide informationuseful for selectingapromisingcandidate fern species forwholegenomesequencing.Wealso describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
中国咖啡锈菌（Hemileia vastatrix）生理小种研究

对我国云南、海南和广东咖啡植区收集到的５８个咖啡锈菌菌株标本进行生理小种鉴定，鉴定出小种有７个。 各咖啡植区除共同出现Ⅱ号生理小种外，云南咖啡植区还出现Ⅰ，ＸＶ，ＸＸⅢ和ＸＸⅣ号生理小种；海南则出现Ⅵ和ＸＸⅡ号小种；广东咖啡栽培地区未发现有新的生理小种。 各咖啡植区新生成的生理小种种类有明显的不同。
Correlated activity and corticothalamic cell function in the early mouse visual system

Vision has long been the model for understanding cortical function. Great progress has been made in understanding the transformations that occur within some primary visual cortex (V1) layers, like the emergence of orientation selectivity in layer 4. Less is known about other V1 circuit elements, like the shaping of V1 input via corticothalamic projections, or the population structure of the cortico-cortical output in layer 2/3. Here, we use the mouse early visual system to investigate the structure and function of circuit elements in V1. We use two approaches: comparative physiology and optogenetics. We measured the structure of pairwise correlations in the output layer 2/3 using extracellular recordings. We find that despite a lack of organization in mouse V1 seen in other species, the specificity of connections preserves a correlation structure on multiple timescales. To investigate the role of corticogeniculate projections, we utilize a transgenic mouse line to specifically and reversibly manipulate these projections with millisecond precision. We find that activity of these cells results a mix of inhibition and excitation in the thalamus, is not spatiotemporally specific, and can affect correlated activity. Finally, we classify mouse thalamic cells according to stimuli used for cell classification in primates and cats, finding some, but not complete, homology to the processing streams of primate thalamus and further highlighting fundamentals of mammalian visual system organization. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Neuroscience First Advisor Diego Contreras
The antibacterial activity of some medicinal plants used in Meru Central District, Kenya

Five medicinal plants used by traditional medical health practitioners (TMP) in Meru central district namely: Piliostigma thonningii, Ajuga remota, Ocimum suave, Erythrina abyssinica and Harissonia abyssinica were investigated for their antibacterial activity against standard bacterial cultures namely; Staphylococcus aureus, Bacillus cereus, Escherichia coli and Pseudomonas aeruginosa . The antibacterial activity of the methanolic and water extracts was determined using the minimum bactericidal concentration (MBC) and minimum inhibitory concentration (MIC). Gram positive bacteria ( S. aureus and B. cereus ) were more susceptible to the plant extracts than Gram negative bacteria ( E. coli and P. aeruginosa ). The MIC and MBC of the positive control antibiotics (Ampicillin for gram positive and Gentamycin for gram negative) were less than 1mg/ml. The most susceptible bacteria was S. aureus followed by B. cereus while the most resistant was E. coli followed by P.aeruginosa . Methanolic extracts of P. thonningii stem and Ocimum suave leaves had the best antibacterial activity against the four bacterial species. There was no significant difference between the water and methanolic extracts of all the plants. These results justify the use of these plants by the traditional medical practitioners for management of bacterial conditions and further investigation on their safety and phytochemistry is needed.
EVALUATING DIETARY AMINO ACID ADEQUACY IN HORSES USING ISOTOPIC TECHNIQUES

OF DISSERTATION EVALUATING DIETARY AMINO ACID ADEQUACY IN HORSES USING ISOTOPIC TECHNIQUES Little is known about amino acid (AA) requirements in horses despite muscle mass accretion being of importance to an athletic species. Isotope methods for determining AA requirements and whole-body protein synthesis (WBPS) had not been previously used in growing horses. The first study herein was the first to apply isotope methods to determine WBPS in growing horses. In the study, weanling colts received two different levels of crude protein. Whole-body protein kinetics indicated that WBPS was greater when the weanlings were fed the diet with a greater crude protein content (P<0.05). The second study sought to determine a lysine requirement for yearling horses using the indicator AA oxidation (IAAO) method. Despite using six dietary levels of lysine; three above and three below the current recommendation, no breakpoint could be determined. Phenylalanine kinetics were not affected by lysine level (P>0.05), but plasma lysine increased linearly with lysine intake (P<0.0001). After comparing dietary AA intakes with current AA requirement recommendations, threonine was a candidate for the limiting AA in the diets used in the first two studies. The objective of the next two studies was to determine if threonine supplementation would increase WBPS. Weanling colts fed a grass forage and commercial concentrate were supplemented with threonine in one study, while adult mares fed a high fiber diet and low threonine concentrate were supplemented with threonine in the other study. In neither case were whole-body protein kinetics affected by threonine supplementation (P>0.05). However, multiple plasma AA concentrations were affected by supplementation (P<0.05) in both studies, suggesting that supplementation of a single AA can affect the metabolism of other AAs. The final study conducted was aimed at improving the IAAO method for use in horses. Intravenous isotope infusion was compared to a less invasive oral infusion. Both infusion methods produced stable plateaus and by calculation, the splanchnic extraction of phenylalanine was found to be 27%. Additional research is needed to determine AA requirements for horses. These studies add insight into equine AA requirements and metabolism and the confirmation of the oral isotope infusion method will allow future experiments to be less invasive.