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Genetic Selection For Improved Production Efficiency In The Mature Dairy Herd, Maeve Williams

Theses

Improving dairy cow production efficiency is highly desirable because of its well-documented impact on profitability and sustainability. Long-term gains in dairy cow production efficiency have already been delivered through genetic selection. Nonetheless, achieving further improvements in production efficiency could cement the economic and environmental efficiency of the dairy industry, globally. To date, several components contributing to production efficiency have been overlooked, with many studies focusing on dairy cow production efficiency over short periods rather than lifetime efficiency. Therefore, the objectives of this thesis were to quantify the genetic variance components of complementary dairy cow efficiency metrics; including dry matter intake, …

Identification And Creation Of Novel Bacteriocins With Potential Food And Clinical Applications, David Lynch

Theses

Bacteriocins represent a heterogeneous group of small, ribosomal-synthesized, potent antibacterial peptides produced by bacteria, capable of inhibiting bacteria both closely related or indeed those from other genera than the producer. In addition to their role as food preservatives, bacteriocins have potent activity against medically significant pathogens and are considered attractive alternatives to antibiotics, due to their inherent heat stability, potency at nanomolar scale, resistance to proteases and low levels of acquired resistance in commercial applications. The aim of this thesis was to identify, purify and bioengineer novel bacteriocins from Staphylococcus and Lactic Acid Bacteria (LAB), with a view to expanding …

Performance Analysis Of Zero Trust In Cloud Native Systems, Simone Rodigari

Theses

Critical applications demand strong security implementations, low latency and high availability at constant rates, however, the performance of a software system is affected by the implementation of security. This research measures the performance overhead and possible mitigation in cloud native systems secured with a service mesh, which allows enabling security policies for the authentication, authorization and encryption of traffic within distributed systems. The side-car proxy is a core component of this architecture, acting as a policy enforcement point and intercepting networking communication from/to applications part of the mesh, consequently affecting the performance of applications hosted in the cloud. Physical resources …

Complete Genome Analysis Of African Swine Fever Virus Genotypes Ii, Ix And Xv From Domestic Pigs In Tanzania, Jean Nepomuscene Hakizimana, Clara Yona, Mariam R. Makange, Ester A. Kasisi, Christopher L. Netherton, Hans Nauwynck, Gerald Misinzo

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African swine fever (ASF) caused by ASF virus (ASFV) is an infectious transboundary animal disease notifiable to the World Organization for Animal Health causing high mortality in domestic pigs and wild boars threatening the global domestic pig industry. To date, twenty-four ASFV genotypes have been described and currently genotypes II, IX, X, XV and XVI are known to be circulating in Tanzania. Despite the endemic status of ASF in Tanzania, only one complete genome of ASFV from the country has been described. This study describes the first complete genome sequence of ASFV genotype XV. In addition, the first Tanzanian complete …

Assessment Of Biosecurity Practices Adoption In Broiler Farms In East Africa: Case Study Of Pwani Region In Tanzania, Rogia Saïdath Adéline Gomez

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Broiler farming in Tanzania is an important poultry sub-sector, providing employment and the much-de- manded meat hence, contributing to the income and nutrition of the population. However, for small to medium-scale producers the profitability has been hampered by high incidences of diseases and costs associated with their control. This study aimed to assess the biosecurity practices adopted by broiler farmers in the Pwani region, Tanzania. A struc- tured questionnaire was administered to 78 broiler farmers complemented with on-site observations. Data collected were related to the socio-demographic characteristics, the structure of broiler farms, the level of biosecurity in the farms as …

Bibliometric Analysis Of The State Of Research On Agroecology Adoption And Methods Used For Its Assessment., Theodore Nikiema, Eugène C. Ezin, Sylvain Kpenavoun Chogou

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As a sustainable and holistic approach to agriculture, agroecology has received considerable attention in recent years because of its potential to address the environmental, economic, and social challenges of agricultural systems. In order to identify key trends, influential authors, impactful journals, and emerging research themes surrounding the agroecological adoption topic, we performed a bibliometric analysis based on metadata from documents dealing with the topic and methods employed for its assessment over the period of January 1990 to July 2023, extracted from the Web of Science database. Based on the metadata of more than 1280 articles, our analyses show that the …

A Tutorial On Agricultural Iot: Fundamental Concepts, Architectures, Routing, And Optimization, Emmanuel Effah, Ousmane Thiare, Alexander Wyglinski

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This paper presents an in-depth contextualized tutorial on Agricultural IoT (Agri-IoT), covering the fundamental concepts, assessment of routing architectures and protocols, and performance optimization techniques via a systematic survey and synthesis of the related literature. The negative impacts of climate change and the increasing global population on food security and unemployment threats have motivated the adoption of the wireless sensor network (WSN)-based Agri-IoT as an indispensable underlying technology in precision agriculture and greenhouses to improve food production capacities and quality. However, most related Agri-IoT testbed solutions have failed to achieve their performance expectations due to the lack of an in-depth …

Nanoparticles In Soil Remediation: Challenges And Opportunities, Wei Wei New, Joseph Ekhebume Ogbezode, Paran Gani

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Nanoremediation emerges as a promising technology for mitigating soil contamination, encompassing various nanotechnology applications, including chemical degradation, Fenton-type oxidation, photocatalytic degradation, immobilization, and integration with bioremediation techniques like phytoremediation. In addressing soil pollution, the most extensively researched nanomaterials (NMs) are based on carbon, metal and metal oxide, nZVI, and other nanocomposites. Nevertheless, limitations accompany the use of NMs in soil remediation. To assess whether nanotechnology applications outweigh environmental threats, it is crucial to investigate potential effects of NMs on terrestrial vegetation, soil organisms, and human well-being. The impacts of NMs on ecology and the soil environment must be taken into …

Energy Status In Africa: Challenges, Progress And Sustainable Pathways, Maklewa Agoundedemba, Chang Ki Kim, Hyun-Goo Kim

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Access to modern energy is essential for socioeconomic development, yet Africa faces significant challenges in this regard. For example, Sub-Saharan Africa (SSA) is marked by economic underdevelopment and poverty largely due to the non-environmentally friendly energy used (wood, charcoal) and limited access to modern energy resources. Indeed, this review provides an overview of the African energy landscape; it provides a comprehensive renewables-focused energy pathway for developing a cleaner and more sustainable African energy system. It explores end-use sector electrification in both rural and urban areas in Africa. It emphasizes the rapid expansion of renewable generation, the challenges facing and solutions …

Assessing Structure, Species Diversity, And Carbon Stocks Across Altitudinal Gradients In Hugumbrda Grat-Kahsu Forest, Tigray, Ethiopia: Implications For Ecosystem Service Management, Haftu Abrha Mengesha, Soro Dodiomon, Victor Ongoma, Emiru Birhane, Shenafi Manaye Manaye

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The study area, affected by war and siege, necessitates a study of its current ecological sta-
tus. The objective of this study was to assess the present forest structure, species diversity,
and Total Biomass Carbon Stock (TBCS) in relation to environmental variables. The findings
shown 42 woody plant species, with 23 in the highland and 41 in the midland. No signifi-
cant difference in species abundance is observed between the highland and midland areas.
However, there are significant differences in the average diameter and height of trees
between the altitudinal classes. Additionally, diversity indices shown significant difference,
with the midland …

Modeling Impacts Of Climate Change On The Geographic Distribution And Abundances Of Tamarindus Indica In Tigray Region, Ethiopia, Yirga Gufi, Ashenafi Manaye, Berihu Tesfamariam, Haftu Abrha Mengesha, Musse Tesfaye, Sibhatleab Hintsa

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Tamarindus indica is a multipurpose dry land species in sub-Saharan that is traditionally used to build resilience into the farming system. The species is highly threatened and listed on the IUCN Red List. However, information on how climatic condition locally influences its ecological distribution is limited. This study investigates the current and future suitable habitat for the species in the Tigray region, in northern Ethiopia. A total of 220 species presence points and the number of T. indica within a 50 m × 50 m plot were collected. In addition, 19 bioclimatic variables, 3 topographic variables and soil data …

Effect Of Some Biopesticides Based On Essential Oil And Plant Extracts On Postharvest Mango Stem-End Rot Disease Caused By Lasiodiplodia Theobromae, Yefoungnigui Souleymane Yeo, Dio Dramane Dembele, Brahima Camara, Soualo Ouattara, Jean-Yves Rey, Diana Fernandez, Daouda Koné

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Lasiodiplodia species causing mango Stem-end rot disease (SER) are mainly controlled using synthetic products, which can harm humans and environmental health. Therefore, developing an eco-friendly control method, such as using plant extract products, is imperative. In this study, we evaluated the inhibitory effect of 3 biopesticides based on essential oils (ASTOUN 50 EC, FERCA 50 EC, and NECO 50 EC) at 300, 500, 700, 1000 ppm and Moringa oleifera leaves extracts (Methanolic and aqueous) at 5, 10, 15 and 20 g/250 ml on mycelial growth of Lasiodiplodia theobromae in vitro. Subsequently, 135 fruits (cv. Kent) per treatment …

Genetic Diversity Of Newcastle Disease Virus Involved In The 2021 Outbreaks In Backyard Poultry Farms In Tanzania, Charlie Frank Arthur N'Guessan Amoia, Jean N. Hakizimana, Nisha K. Duggal, Augustino A. Chengula, Mohammed A. Rohaim, Muhammad Munir, James Weger-Lucarelli, Gerald Misinzo

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Newcastle disease virus is a significant avian pathogen with the potential to decimate poultry populations all over the world and cause enormous economic losses. Distinct NDV genotypes are currently causing outbreaks worldwide. Due to the high genetic diversity of NDV, virulent strains that may result in a lack of vaccine protection are more likely to emerge and ultimately cause larger epidemics with massive economic losses. Thus, a more comprehensive understanding of the circulating NDV genotypes is critical to reduce Newcastle disease (ND) burden. In this study, NDV strains were isolated and characterized from backyard poultry farms from Tanzania, East Africa …

Bioresources In Organic Farming: Implications For Sustainable Agricultural Systems, Akinlolu Olalekan Akanmu, Olumayowa Mary Olow, Austin Tenthani Phiri, Drocelle Nirere, Adeyinka John Odebode, Noëlla Josiane Karemera Umuhoza, Michael Dare Asemoloye, Olubukola Oluranti Babalola

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Over the years, the practice of agriculture has transformed from the era of traditional to that of intensive agriculture in the bid to boost the production index that will satisfy the food needs of the globally growing population. However, the continuous and exaggerated use of chemical fertilizers and pesticides has resulted in major adverse impacts on food and environmental safety, whereas most traditional techniques for reclamation of natural soil nutrients, including shifting cultivation and polyculture, are no longer attractive measures of land rejuvenation. There is, therefore, the need for urgent evaluation and adoption of innovative methods of replenishing the agricultural …

Geospatial Characterization Of Climate-Smart Agroforestry In Two Contrasting Physiographic Zones Of Rwanda, Donatien Ntawuruhunga, Edwin Estomii Ngowi, Halima Omari Mangi, Raymond John Salanga, Mashisia Shikuku

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Efficient use of rich natural resources notably land, is one of the most important indicators of economic progress. The unmatched population growth with production has triggered increased demand for food. Nations have prioritized sustainable agriculture as a coping strategy. Climate-smart agroforestry (CSAF) can be one of the options to increase productivity, income, and food security, and stabilize the environment. CSAF denotes a practiced farming system of combining trees with crops or animals (AF) evolved in practices to enhance productivity and feed the food-insecure people while coping with the adverse effects of climate change. This study investigates the land suitability for …

Climate-Smart Agroforestry Systems And Practices: A Systematic Review Of What Works, What Doesn’T Work, And Why, Donatien Ntawuruhunga, Edwin Estomii Ngowi, Halima Omari Mangi, Raymond John Salanga, Kelvin Mashisia Shikuku

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he prevailing global environmental distress, particularly in rural areas, calls for the adoption of integrated sustainable rural development strategies like climate-smart agroforestry (CSA) practices. CSAF is a new name for an old farming practice among the world’s traditional farmers, a holistic approach to land use in which trees, crops, and sometimes animals are combined within a managed farmland, a sustainable farming system and practice, and a pathway toward the mitigation and adaptation of the biggest challenge of our times: climate change. CSAF systems and practices provide a range of goods and services vital for human well-being, particularly for people …

Bushmeat Consumption In Africa: A Microbiological Safety Challenge?, Gwladys Gloria Amen Ahouanse, Abdulsudi Issa-Zacharia, Nuria Majaliwa

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Objective: This review analyzed the microbiological safety of bushmeat consumed in Africa over the past decades. Methodology:Previous Studies mainly focused on large animals like antelopes and smaller ones like grasscutter. Most microbes studied were similar to those in domestic animal meat, except for rare pathogens such as Salmonella spp, E.coli. Sampling, experiments, and microbe prevalence varied among studies.Results:All studies confirmed the presence of zoonotic pathogens dangerous to human beings. Therefore, more investigations are needed, especially for the chronic and severe cases of pathogens, since only few studies have addressed the bushmeat's microbiological safety in Africa. Conclusion:Efforts should be made to …

Bauhinia Rufescens, Ocimum Basilicum And Salvadora Persica: A Review Of Their Chemical Compounds And Properties For Antimicrobial, Antioxidant And Cytotoxicity, Hissein Hassan Abdel-Razakh, Gaymary George Bakari, Cheol-Ho Pan, Abubakar Shaaban Hoza

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Bauhinia rufescens, Ocimum basilicum and Salvadora persica are well known plants used in African traditional medicine, especially in Chadian traditional medicine. They are mostly used in the treatment of infectious diseases, inflammatory diseases, fever, and so on. Studies using various in vitro and in vivo bioassay techniques support the scientific rationale for most of these usages. In this review, ethnobotanical uses, chemistry of natural products, and pharmacological and clinical data for these plants are presented

Molecular Epidemiological Survey Of Pathogenic Trypanosomes In Naturally Infected Cattle In Northern Côte D’Ivoire., Jean-Yves Ekra, Edouard K. N’Goran, Leonard E.G Mboera, Biégo Guillaume Gragnon, Koco Rita Nadège Assovié, Eliakunda Michael Mafie

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ovine trypanosomiasis is a significant health concern for livestock intensification in Côte d’Ivoire. This study aimed to determine the prevalence and distribution of pathogenic trypanosomes and identify the most infected cattle breed in northern Côte d'Ivoire. We examined 700 cattle and found that polymerase chain reaction (PCR) was more sensi- tive (12.3%) than microscopic observation (5.6%). Among the trypanosome species de- tected in naturally infected cattle, Trypanosoma vivax was 7.3%, Trypanosoma simiae tsavo was 6.7%, and Trypanosoma congolense was 0.4%. The overall prevalence of trypanosome infection in all cattle breeds was 12.3%, while the prevalence in individual breeds was 14.8%, …

Prevalence Of Bovine Trypanosomiasis In Côte D’Ivoire: Systematic Review And Meta-Analysis, Jean-Yves Ekra, Edouard K. N’Goran, Léonard E.G Mboera, Eliakunda M. Mafie

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Bovine trypanosomiasis is a parasitic disease caused by protozoans of the genus Trypanosoma . The disease cause economic losses in livestock production. In order to determine the status of research on this disease in Côte d’Ivoire, we used the systematic review method and meta-analysis. Three electronics databases, namely Google Scholar, PubMed and CrossRef were used to search for publications on trypanosomiasis prevalence that met our inclusion criteria. Twenty five articles were identified, 11 of which met the inclusion criteria. Bovine trypanosomiasis prevalence of 2.99% (95% confidence interval [CI]: 2.96% – 3.01%) to 25.28% (95% CI: 25.17% – 25.38%) were recorded …

Heat Stress Effects On Milk Yield Traits And Metabolites And Mitigation Strategies For Dairy Cattle Breeds Reared In Tropical And Sub-Tropical Countries, Vincent Habimana, Athumani Nguluma, Zabron Cuthibert Nziku, Gota Morota, Raphael Mrode, Sebastian Chenyambuga

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Heat stress is an important problem for dairy industry in many parts of the world owing to its adverse effects on productivity and profitability. Heat stress in dairy cattle is caused by an increase in core body temperature, which affects the fat production in the mammary gland. It reduces milk yield, dry matter intake, and alters the milk composition, such as fat, protein, lactose, and solids-not-fats percentages among others. Understanding the biological mechanisms of climatic adaptation, identifying and exploring signatures of selection, genomic diversity and identification of candidate genes for heat tolerance within indicine and taurine dairy breeds is an …

Genes And Models For Estimating Genetic Parameters For Heat Tolerance In Dairy Cattle, Vincent Habimana, Chinyere Charlotte Ekine-Dzivenu, Athumani Shabani Nguluma, Zabron Cuthibert Nziku, Gota Morota, Sebastian Wilson Chenyambuga, Raphael Mrode

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Dairy cattle are highly susceptible to heat stress. Heat stress causes a decline in milk yield, reduced dry matter intake, reduced fertility rates, and alteration of physiological traits (e.g., respiration rate, rectal temperature, heart rates, pulse rates, panting score, sweating rates, and drooling score) and other biomarkers (oxidative heat stress biomarkers and stress response genes). Considering the significant effect of global warming on dairy cattle farming, coupled with the aim to reduce income losses of dairy cattle farmers and improve production under hot environment, there is a need to develop heat tolerant dairy cattle that can grow, reproduce and produce …

Characterization And Pathogenicity Of Fusarium Species Causing Sugar Beet Root Rot In Morocco, Abdelaaziz Farhaoui, Nabila El Alami, Grace Gachara, Said Ezrari, Mohammed Khadiri, Abdessalem Tahiri, Zineb Belabess

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The sugar beet crop ranks second globally among the plant species grown mainly
for sugar production. In Morocco, the area under sugar beet farming occupies ap-
proximately 57,000 ha yielding more than 3 million tons of roots. However, sugar beet
root-tip rot (RTR) caused by Fusarium spp. dramatically reduces the anticipated yields,
the purity of the resulting juice, and the sugar concentration. The current study aimed
at identifying and characterizing the Fusarium species responsible for the root rot in
sugar beet grown in the Khenifra-Beni Mellal region of Morocco. In this survey, 69
isolates of Fusarium were sampled from sugar …

Microparticles As Viral Rna Carriers From Stool For Stable And Sensitive Surveillance, Emmanuel Kifaro, Mi Jung Kim, Seungwon Jung, Yoon-Ha Jang, Sungyeon Moon, Dong-Hun Lee, Chang-Seon Song, Gerald Misinzo, Sang Kyung Kim

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Since its discovery, polymerase chain reaction (PCR) has emerged as an important technol- ogy for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel mi- croparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction …

Associative Learning Contributes To The Persistence Of Fatigue-Like Behavior In Male Mice In A Model Of Cancer Survivorship, Elisabeth G Vichaya, Josephine K Darpolor, Phillip S Gross, Jessica M Molkentine, Daniel W Vermeer, Paola D Vermeer, John H Lee, Cullen M Taniguchi, Robert Dantzer

Faculty, Staff and Student Publications

Persistent fatigue is a debilitating side effect that impacts a significant proportion of cancer survivors for which there is not yet an FDA-approved treatment. While certainly a multi-factorial problem, persistent fatigue could be due, in part, to associations learned during treatment. Therefore, we sought to investigate the role of associative learning in the persistence of fatigue using a preclinical model of cancer survivorship. For this purpose, we used a murine model of human papilloma virus-related head and neck cancer paired with a curative regimen of cisplatin-based chemoradiation in male C57BL/6J mice. Fatigue-like behavior was assessed by measuring variations in voluntary …

Small Molecule Inhibitor Of Tau Self-Association In A Mouse Model Of Tauopathy: A Preventive Study In P301l Tau Jnpl3 Mice, Eliot J Davidowitz, Patricia Lopez, Heidy Jimenez, Leslie Adrien, Peter Davies, James G Moe

Faculty, Staff and Student Publications

Advances in tau biology and the difficulties of amyloid-directed immunotherapeutics have heightened interest in tau as a target for small molecule drug discovery for neurodegenerative diseases. Here, we evaluated OLX-07010, a small molecule inhibitor of tau self-association, for the prevention of tau aggregation. The primary endpoint of the study was statistically significant reduction of insoluble tau aggregates in treated JNPL3 mice compared with Vehicle-control mice. Secondary endpoints were dose-dependent reduction of insoluble tau aggregates, reduction of phosphorylated tau, and reduction of soluble tau. This study was performed in JNPL3 mice, which are representative of inherited forms of 4-repeat tauopathies with …

Artificial Intelligence-Driven Meta-Analysis Of Brain Gene Expression Identifies Novel Gene Candidates And A Role For Mitochondria In Alzheimer’S Disease, Caitlin A Finney, Fabien Delerue, Wendy A Gold, David A Brown, Artur Shvetcov

Faculty, Staff and Student Publications

Alzheimer's disease (AD) is the most common form of dementia. There is no treatment and AD models have focused on a small subset of genes identified in familial AD. Microarray studies have identified thousands of dysregulated genes in the brains of patients with AD yet identifying the best gene candidates to both model and treat AD remains a challenge. We performed a meta-analysis of microarray data from the frontal cortex (n = 697) and cerebellum (n = 230) of AD patients and healthy controls. A two-stage artificial intelligence approach, with both unsupervised and supervised machine learning, combined with a functional …

A Unified Mediation Analysis Framework For Integrative Cancer Proteogenomics With Clinical Outcomes, Licai Huang, James P Long, Ehsan Irajizad, James D Doecke, Kim-Anh Do, Min Jin Ha

Faculty, Staff and Student Publications

MOTIVATION: Multilevel molecular profiling of tumors and the integrative analysis with clinical outcomes have enabled a deeper characterization of cancer treatment. Mediation analysis has emerged as a promising statistical tool to identify and quantify the intermediate mechanisms by which a gene affects an outcome. However, existing methods lack a unified approach to handle various types of outcome variables, making them unsuitable for high-throughput molecular profiling data with highly interconnected variables.

RESULTS: We develop a general mediation analysis framework for proteogenomic data that include multiple exposures, multivariate mediators on various scales of effects as appropriate for continuous, binary and survival outcomes. …

Sparse Tree-Based Clustering Of Microbiome Data To Characterize Microbiome Heterogeneity In Pancreatic Cancer, Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert Jenq, Christine B Peterson

Faculty, Staff and Student Publications

There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with similar microbiome profiles. We propose a novel unsupervised clustering approach in the Bayesian framework that innovates over existing model-based clustering approaches, such as the Dirichlet multinomial mixture model, in three key respects: we incorporate feature selection, learn the appropriate number of clusters from the data, and integrate information on the tree structure relating the observed features. We compare the performance of our proposed method to …

Erratum: Cxcl12-Mediated Monocyte Transmigration Into Brain Perivascular Space Leads To Neuroinflammation And Memory Deficit In Neuropathic Pain, Chun-Lin Mai, Zhi Tan, Ya-Nan Xu, Jing-Jun Zhang, Zhen-Hua Huang, Dong Wang, Hui Zhang, Wen-Shan Gui, Jun Zhang, Zhen-Jia Lin, Ying-Tong Meng, Xiao Wei, Ying-Tao Jie, Peter M Grace, Long-Jun Wu, Li-Jun Zhou, Xian-Guo Liu

Faculty, Staff and Student Publications

In the original Figure 7E of our article, the authors mistakenly reused the GFAP immunostaining representative image of the Vehi+Sham group for the anti-CXCL12+Sham group. This is because an error occurred in converting the original purple fluorescence of GFAP for each group to red fluorescence during preparation of representative pictures of Figure 7E. Unfortunately, this error was not found in multiple revisions. The correct version of Figure 7E is shown below. The correction made in this Erratum does not affect the results and conclusions in this study. The authors apologize for any inconvenience the errors may have caused.