Miracle-dz/UniFAR-FTUs huggingface dataset:
Transposon Ecology: The Power of Community Ecology Methods on Genomic Transposable Element Data

Transposon Ecology: Initial Exploration of Community Ecology Methods on Genomic Transposable Element Data Brent Saylor University of Guelph, 2019 Advisors: Professor Karl Cottenie Professor T. Ryan Gregory More than half of the human genome is made up of self-replicating mobile sequences of DNA called transposable elements (TEs). Much of the research on TEs has focused on the molecular mechanisms by which they transpose, their mutagenic effects, and the influences of their activity on the evolution of the host genomes in which they reside. In the 1980s, the “selfish DNA” papers popularized the idea of TEs as parasites, an analogy that grew into the idea of the genome as an ecosystem in which TEs were equivalent to species. In this thesis, I put this idea to work by testing the effectiveness of community ecology methods at identifying community-level TE patterns and exploring the potential insights that this approach may provide. I used redundancy analysis, community phylogenetics, and the 4 corner analysis to analyze the relationship between the TE community, TE traits, and the genomic environment. Each of these methods was adaptable to genomic TE data. The redundancy analysis found that, on average, 50% of the differences between TE communities of 11 genomes were explained by where that community was positioned on the chromosome (spatial patterns). In the human genome, 60% of the differences between TE communities were explained by spatial patterns, of which 33% is explained by the chromatin state and the remaining 66% remained unexplained. I also showed that TE traits affected the differences in TE communities, with older TE families having more structure within genomes. Phylogenetic community ecology methods indicated that 17-30% of the TE communities in the Drosophila melanogaster genome were phylogenetically nonrandom. This pattern could indicate important community structuring assembly processes. Finally, the 4 corner analysis showed that the TE community spatial patterns are associated with TE-specific traits. This association with the traits of individual TEs, and not TE families, makes it possible to predict where new TEs may be found and which TEs might occur in new environments. Overall, this thesis represents the first systematic application of ecological methods per se to genomic TE data and assessment of their utility, and lays the groundwork for many future studies in transposon ecology.
Deteriorative changes in maize kernels due to Aspergillus flavus Link. and Fusarium verticillioides (Sacc.) Nirenberg

The study aimed at measuring changes in chemical composition of maize kernels due to Aspergillus flavus Link. and Fusarium verticillioides (Sacc.) Nirenberg infection. The samples of maize kernels were incubated at 28 °C for 7, 14, 21, and 28 days. The samples were analysed for mycotoxin, moisture, crude fat, crude protein, crude ash, and crude fibre. Maize kernels inoculated with A. flavus and F. verticillioides exhibited a significant decrease in crude fat. Aflatoxin B1 (AFB1) contamination increased in maize kernels inoculated with A. flavus, and fumonisin B1 (FB1) in kernels inoculated with F. verticillioides. Crude ash and crude fibre content showed no changes. Incubation time significantly affected AFB1 and FB1 contamination levels, moisture, crude fat, and crude protein contents. AFB1 and FB1 contamination were significantly correlated with crude fat degradation. The tested strains had similar deteriorative effects on maize kernels. The significant changes in the proximate composition were only observed in maize kernels with mycotoxin contamination above the regulatory limit of 10 µg kg−1, thus not fit for human consumption.
Novel mediation analysis of human plasma proteome and metabolome reveals mediators of improved glycemia after gastric bypass surgery

Molecular mechanisms by which Roux-en-Y gastric bypass (RYGB) improves glycemic control and metabolism in type 2 diabetes (T2D) remain incompletely understood. In the SLIMM-T2D trial, participants with T2D were randomized to RYGB or nonsurgical management and their fasting plasma proteome and metabolome were analyzed for up to 3 years. To identify analytes that mediate improvement in outcomes, we developed a high-throughput mediation analysis method (Hitman), which is significantly more powerful than existing methods. Top-ranking analyte mediators of glycemia improvement were growth hormone receptor and prolylhydroxyproline, which were more significant than any clinical mediator, including BMI. Beta-alanine and Histidine Metabolism (both including CNDP1) were top differentially regulated pathways, and Valine, Leucine and Isoleucine Degradation was also a top differentially-regulated pathway and a top mediator of improvement in insulin resistance. The identified analytes may serve as novel targets for T2D therapy. More broadly, Hitman can identify analyte mediators of outcomes in randomized trials for which high-throughput data are available.
Using genetics to differentiate patients with similar symptoms: application to inflammatory arthritis in the rheumatology outpatient clinic

Slow developing complex diseases are a clinical diagnostic challenge. Since genetic information is increasingly available prior to a patient’s first visit to a clinic, it might improve diagnostic accuracy. We aimed to devise a method to convert genetic information into simple probabilities discriminating between multiple diagnoses in patients presenting with inflammatory arthritis. We developed G-Prob, which calculates for each patient the genetic probability for each of multiple possible diseases. We tested this for inflammatory arthritis-causing diseases (rheumatoid arthritis, systemic lupus erythematosus, spondyloarthropathy, psoriatic arthritis and gout). After validating in simulated data, we tested G-Prob in biobank cohorts in which genetic data were linked to electronic medical records: - 1,200 patients identified by ICD-codes within the eMERGE database (n= 52,623); - 245 patients identified through ICD codes and review of medical records within the Partners Biobank (n=12,604); - 243 patients selected prospectively with final diagnoses by medical record review within the Partners Biobank (n=12,604). The calibration of G-Prob with the disease status was high (with regression coefficients ranging from 0.90-1.08 (ideal would be 1.00) in all cohorts. G-Prob’s discriminative ability was high in all cohorts with pooled Area Under the Curve (AUC)=0.69 [95%CI 0.67-0.71], 0.81 [95%CI 0.76-0.84] and 0.84 [95%CI 0.81-0.86]. For all patients, at least one disease could be ruled out, and in 45% of patients a most likely diagnosis could be identified with an overall 64% positive predictive value. In 35% of instances the clinician’s initial diagnosis was incorrect. Initial clinical diagnosis explained 39% of the variance in final disease prediction which improved to 51% (P<0.0001) by adding G-Prob genetic data. In conclusion, by converting genotypes into an interpretable probability value for five different inflammatory arthritides, we can better discriminate and diagnose rheumatic diseases. Genotypes available prior to a clinical visit could be considered part of patients’ medical history and potentially used to improve precision and diagnostic efficiency in clinical practice.
Experiences of the foster care process in the Republic of Ireland: retrospective accounts from biological children of foster carers

5 Chapter 1: Thesis Introduction.7 Chapter 2: Foster Care in Ireland.14 Chapter 3: The Sociology of Childhood and Foster Care.61 Chapter 4: Biological Children of Foster Carers: A Review of the Literature.88 Chapter 5: Methodology.110 Chapter 6: Findings and Analysis.130 Chapter 7: Conclusion and Recommendations.171 Bibliography.192 Appendices.213
Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast

The coordination of metabolism and growth with cell division is crucial for proliferation. While it has long been known that cell metabolism regulates the cell division cycle, it is becoming increasingly clear that the cell division cycle also regulates metabolism. In budding yeast, we previously showed that over half of all measured metabolites change concentration through the cell cycle indicating that metabolic fluxes are extensively regulated during cell cycle progression. However, how this regulation is achieved still remains poorly understood. Since both the cell cycle and metabolism are regulated to a large extent by protein phosphorylation, we here decided to measure the phosphoproteome through the budding yeast cell cycle. Specifically, we chose a cell cycle synchronisation strategy that avoids stress and nutrient-related perturbations of metabolism, and we grew the yeast on ethanol minimal medium to force cells to utilize their full biosynthetic repertoire. Using a tandem-mass-tagging approach, we found over 200 sites on metabolic enzymes and transporters to be phospho-regulated. These sites were distributed among many pathways including carbohydrate catabolism, lipid metabolism and amino acid synthesis and therefore likely contribute to changing metabolic fluxes through the cell cycle. Among all one thousand sites whose phosphorylation increases through the cell cycle, the CDK consensus motif and an arginine-directed motif were highly enriched. This arginine-directed R-R-x-S motif is associated with protein-kinase A, which regulates metabolism and promotes growth. Finally, we also found over one thousand sites that are dephosphorylated through the G1/S transition. We speculate that the phosphatase Glc7/ PP1, known to regulate both the cell cycle and carbon metabolism, may play an important role because its regulatory subunits are phospho-regulated in our data. In summary, our results identify extensive cell cycle dependent phosphorylation and dephosphorylation of metabolic enzymes and suggest multiple mechanisms through which the cell division cycle regulates metabolic signalling pathways to temporally coordinate biosynthesis with distinct phases of the cell division cycle.
Hospital-associated infections and the safety of alcohol hand gels in children

Viral infections are common in childhood and a usual cause for hospitalization. Viruses are easily transmitted among children both in pediatric wards and in other child care facilities, like child daycare centers. Hand hygiene is an important part of prevention of the transmission of viruses. Since hospitalization times are getting shorter, hospital-associated infections often manifest after discharge. The aim of the study was to evaluate the magnitude of hospital-associated infections during and after hospitalization in pediatric wards with a focus on the effect of the ward structure. Data were collected during two periods of two years in the pediatric infectious diseases ward in Oulu University Hospital; data collection in the latter period was done using electronic follow-up methods. A two-year study period was also carried out in University Children’s hospital in Basel and in North Karelia Central Hospital in Joensuu. Paper questionnaires and electronic questionnaires were compared as methods of doing continuous surveillance of hospital-associated infections during and after hospitalization. The safety of alcohol-based hand gels in children’s use was studied using alcometer measurements after hand rub. Experiences on the use of alcoholbased hand gels in child day-care centers were collected by interviewing the personnel with questionnaires. Altogether 5.8 to 17.5% of hospitalized children (N=7046) got a hospital-associated infection; 65 to 93% of the infections became evident after discharge. The number of hospital-associated infections was lowest in wards where single rooms and cohorting based on infection etiology were used. Increased risk for hospital-associated infection was associated with young age, longer hospitalization time and a shared room. A higher response rate was achieved with electronic follow-up compared with questionnaires on paper, 84 vs. 61%. The costs of follow-up were €13.61 and €15.07 per patient in electronic and conventional follow-up, respectively. Electronic followup decreased annual expenses by 17.1%. Alcohol-based hand gels were found to be safe in children’s use, as no absorption was detected despite several contacts between hands and mucous membranes. Personnel in child day-care centers were active in using hand rubs and found them useful and easy to use. Earlier, there had been one incident with fire when using matches while hands were still wet with alcohol. The majority of hospital-associated infections in children become evident after discharge, and electronic follow-up is useful in evaluating their magnitude. The number of hospital-associated infections can be decreased with single room bedding and careful infection control. Alcohol-based hand gels are safe in children’s hand hygiene.
Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas

Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.
Enhancement of solubilization and biodegradation of petroleum by biosurfactant from Rhodococcus erythropolis HX-2

Abstract The demand to repair areas contaminated with hydrocarbon products has led to the development of new technologies for the treatment of contaminants in an unconventional method, that is, no physical or chemical methods are used. Biosurfactants are amphiphilic biomolecules produced by microorganisms that can be used in environments contaminated by petroleum products due to their unexceptionable tensile properties. Petroleum degrading strain Rhodococcus erythropolis HX-2 was found to be an effective producer of biosurfactants. The resulting biosurfactant (named NK) exhibits high physicochemical properties in terms of surface activity. It is capable of reducing surface tension from 54.99 to 28.89 mN/m and critical micelle concentration (CMC) is 100 mg/L. NK was found to be a substitute for chemically synthesized surfactants because of its higher solubilization efficiency for petroleum and polycyclic aromatic hydrocarbons, superior to SDS, Tween 80, Triton X-100 and Rhamnolipid (a wide used biosurfactant). In addition, it exhibits favorable emulsion stability over a wide range of pH (3–10), temperature (20–100 °C) and salinity ranges (5–20 g/L). It was found that the addition of biosurfactant can improve the efficiency of petroleum degradation, therefore it has potential applications in bioremediation. Highlights Rhodococcus erythropolis HX-2 is an effective petroleum degrading strain. HX-2 is a potential source of biosurfactant production. The biosurfactant NK reduces surface tension and exhibits high emulsification activity. The biosurfactant NK is effective over a wide range of temperatures, pH and salinity. The biosurfactant NK shows high solubilization efficiency for petroleum as well as polycyclic aromatic hydrocarbons.
Development of tomato hybrids with multiple disease tolerance

Four lines and six testers were crossed to produce 24 F1 hybrids following Line x Tester technique to screen the material tolerant to blight and cucumber mosaic virus using integrated protocols of whole plant assay, mechanical inoculation and breeding. Check hybrid T-1359 was highly susceptible to late blight (LB) and early blight (EB) to the mark of 94 and 74% respectively and cucumber mosaic virus (CMV) with a 2.8 severity index. One hybrid Nagina x LB5 was scored tolerant to late blight with 35% infection, while four genotypes viz. LB3, LB2, LB4, LB7 and one hybrid Naqeeb x LB5 were tolerant to early blight with 28-30% infection and tolerant to cucumber mosaic virus with 2.1 severity index. Nonadditive gene action was pre-dominant in genetic control of blights, viral diseases, yield and all yield related traits. Genotype Roma, LB5 and LB6 were found to be good general combiner for late blight while Roma, Nagina and LB2 for early blight. A high yielding hybrid Naqeeb x LB6 was the best one with 37.55% tolerance to late blight and 33.33% high yielder than T1359. Most of the hybrids showed better tolerance to CMV as compared to T-1359. Identified good combiners can be used in heterosis and recombination breeding to develop high yielding and disease tolerant tomato genotypes.
NATURAL HERBICIDAL POTENTIAL OF SELECTED PLANTS ON GERMINATION AND SEEDLING GROWTH OF WEEDS

Use of synthetic herbicides is increasing globally. Application of heavy doses of herbicides is directly / indirectly causing negative impact on crop quality, human health and environment. Allelopathic weeds have wide application prospects in increasing crop production, plant protection and biological control. Current study was conducted to evaluate allelopathic activity of aqueous extracts of Carica papaya, Lantana camara, Rhazya stricta and Pinus roxburghii against selected weeds viz. Phalaris minor, Avena fatua, Chenopodium album, Euphorbia helioscopia and Rumex dentatus on filter paper, soil and agar at 100%, 75%, 50% and 0% concentration. Germination percentage (%), radicle length (cm) and plumule length (cm) were parameters to assess allelopathic potential. The STATISTIX 9 software was used to analyse data. Based on results, it was concluded that aqueous extract of R. stricta, P. roxburghii, C. papaya and L. camara possess potential inhibitory effects amongst which L. camara showed most prominant inhibitory effects towrads weeds. The germination and growth inhibition effects were found in order L. camara>P. roxburghii>R. stricta>C. papaya. Detailed field study is recommended to establish allelopathic potential of these species.
Evolution of the acoustic startle response of Mexican cavefish

The ability to detect threatening sensory stimuli and initiate an escape response is essential for survival and under stringent evolutionary pressure. In diverse fish species, acoustic stimuli activate Mauthner neurons, which initiate a stereotypical C-start escape response. This reflexive behavior is highly conserved across aquatic species and provides a model for investigating the neural mechanism underlying the evolution of escape behavior. Here, we define evolved differences in the C-start response between populations of the Mexican cavefish, Astyanax mexicanus. Cave populations of A. mexicanus inhabit in an environment devoid of light and macroscopic predation, resulting in evolved differences in diverse morphological and behavioral traits. We find that the C-start is present in multiple populations of cavefish and river-dwelling surface fish, but response kinematics and probability differ between populations. The Pachón population of cavefish have an increased response probability, a slower response and reduction of the maximum bend angle, revealing evolved differences between surface and cave populations. In two other independently evolved populations of cavefish, the response probability and the kinematics of the response differ from one another, as well as from surface fish, suggesting the independent evolution of differences in the C-start response. Investigation of surface-cave hybrids reveals a relationship between angular speed and peak angle, suggesting these two kinematic characteristics are related at the genetic or functional levels. Together, these findings provide support for the use of A. mexicanus as a model to investigate the evolution of escape behavior.
Molecular identification of blast resistance genes in rice genotypes using gene-specific markers

Molecular identification of major blast resistance (R ) genes in rice was performed in a group of 10 rice (Oryza sativa) genotypes from Egypt and Saudi Arabia using six DNA markers (T8042, NSB, YL153/YL154, RM3843, RM3330, and z4794) belonging to three classes: single-nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and insertion-deletions (InDels). The markers were chosen based on their linkage to six major R genes (Pit, Pib, Pi39 (t), Pi40 (t), Piz/Piz-t, and Pita /Pita2 ). The studied markers showed low allelic diversity, with the number of alleles identified in a single genotype ranging between two and nine alleles. The Egyptian genotype Eg-N-7 had two alleles of the Pi40 (t) gene, while the Saudi Arabian genotype Al-Ahsa1 had nine alleles that belonged to the seven R genes. The studied genotypes were also assessed for 19 agro-morphological traits. Analysis of variance of the studied traits showed significant differences among the genotypes. The putative associations between molecular markers and the agro-morphological traits were examined using associationmapping approach by employing the unified mixed model. Eight significant marker–trait associations were detected for eight agro-morphological traits (plant height, panicle length, sterility percentage, grain width, grain shape, elongation percentage, gelatinization temperature, and days to maturity). The phenotypic variance shown by each marker ranged between 43% and 65%. The findings of the current study will assist in identifying possible blast resistance genotypes for future rice breeding programs. Additionally, the results highlight the possible dual usage of specific markers in genotypic screening as well as in determining marker–trait associations.