Life Sciences Commons^™

Evidence Of Lactobacillus Strains Shared Between The Female Urinary And Vaginal Microbiota, Haley Atkins, Baani Sabharwal, Leah Boger, Natalie Stegman, Alexander Kula, Alan J. Wolfe, Swarnali Banerjee, Catherine Putonti

Biology: Faculty Publications and Other Works

Lactobacillus species are common inhabitants of the ‘healthy’ female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the …

Draft Genome Sequences For A Staphylococcus Aureus And A Staphylococcus Haemolyticus Isolate From Nasal Swab Samples From Healthy Females, Sandra Jablonska, Hannah Brown, Helen Appleberry, Catherine Putonti, Alex Kula

Biology: Faculty Publications and Other Works

Staphylococcus aureus and Staphylococcus haemolyticus are common members of the human microbiota, but they are also opportunistic pathogens. To identify antibiotic resistance in healthy individuals, we present the genome sequences of S. aureus 139 N-1 and S. haemolyticus 173 N-3, both isolated from nasal swab samples from asymptomatic female participants.

Heat Stress Changes The Bovine Methylome And Transcriptome And Investigation Of Two Novel Genetic Defects In Cattle, Rachel Renae Reith

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Heat stress is a major concern for livestock producers due to its negative impact on animal health and productivity. Heat stress does so by altering expression of genes through different regulatory mechanisms such as DNA methylation. Understanding how heat stress alters gene expression will help elucidate the genetic basis of physiological changes as well as identify targets for possible heat stress mitigation. The purpose of the first study was to understand how heat stress alters the adipose and skeletal muscle transcriptomes in zilpaterol-fed Brahman, as zilpaterol improves muscle growth and may mitigate the effects of heat stress. Differential expression and …

Measuring Activity Demands On Fatigue In Individuals With Parkinson's Disease, Laura R. Mccray, Kara M. Lee

Graduate Student Scholarship

The functional presentation of those with Parkinson's disease (PD) are complex, varying depending on cognition, physiological deficits, and support network. This study assesses the perceptions of fatigue across individuals with Parkinson's disease with different clinical presentations to guide clinicians in their selection of evidence-based interventions to facilitate greater functional outcomes. A mixed-methods design was used to collect data on the mental and physiological perceptions of fatigue, utilizing surveys and physiological measures such as heart rate. Participants were recruited from a community group targeting those with PD with inclusion criteria being a diagnosis of PD. Results for both heart rate and …

The Role Of Nr4a Transcription Factors In The Body And Their Effects In The Pancreatic Beta Cell, Jacob A. Herring

Theses and Dissertations

A central aspect of type 1 and type 2 diabetes is decreased functional β-cell mass which leads to systemic glucose dysregulation. Functional β-cell mass takes into account β-cell insulin secretion, β-cell proliferation, and β-cell survival. Several treatments are currently used to help maintain glucose levels in individuals with diabetes. However, cures for these diseases are not available due to inability to expand functional β-cell mass. Transcription factors control expression of target genes critical for various functions, and transcription factors that control β-cell function, proliferation and survival play a significant role in β-cell development and function. A more thorough examination of …

Identification Of Immune-Associated Biomarkers Of Diabetes Nephropathy Tubulointerstitial Injury Based On Machine Learning: A Bioinformatics Multi-Chip Integrated Analysis, Yaotan Li, Baoluo Hou, Yuxin Hu, Zhaoxi Dong, Jingyi Tang, Hongfang Liu, Weijing Liu

Faculty, Staff and Student Publications

BACKGROUND: Diabetic nephropathy (DN) is a major microvascular complication of diabetes and has become the leading cause of end-stage renal disease worldwide. A considerable number of DN patients have experienced irreversible end-stage renal disease progression due to the inability to diagnose the disease early. Therefore, reliable biomarkers that are helpful for early diagnosis and treatment are identified. The migration of immune cells to the kidney is considered to be a key step in the progression of DN-related vascular injury. Therefore, finding markers in this process may be more helpful for the early diagnosis and progression prediction of DN.

METHODS: The …

Ghcu, A Molecular Chaperone, Regulates Leaf Curling By Modulating The Distribution Of Kngh1 In Cotton, Lisha Xuan, Sunyi Yan, Yayao Zhang, Yiwen Cao, Xiaoran Li, Zhanfeng Si, Jieqiong Deng, Tianzhen Zhang, Yan Hu

Faculty, Staff and Student Publications

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial …

Genetic Analysis Of Seven Patients With Inherited Ichthyosis And Nagashima-Type Palmoplantar Keratoderma, Lin-Xi Zeng, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Inherited ichthyosis comprises a series of heterogeneous dermal conditions; it mainly manifests as widespread hyperkeratosis, xerosis and scaling of the skin. At times, overlapping symptoms require differential diagnosis between ichthyosis and several other similar disorders. The present study reports seven patients with confirmed or suspected to be associated with ichthyosis by conducting a thorough clinical and genetic investigation. Genetic testing was conducted using whole-exome sequencing, with Sanger sequencing as the validation method. The MEGA7 program was used to analyze the conservation of amino acid residues affected by the detected missense variants. The enrolled patients exhibited ichthyosis-like but distinct clinical manifestations. …

Fedgmmat: Federated Generalized Linear Mixed Model Association Tests

Faculty, Staff and Student Publications

Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for performing high-powered studies. As the sample sizes become more heterogeneous, complex statistical approaches, such as generalized linear mixed effects models, must be used to correct for the confounders that may bias results. On another front, due to the privacy concerns around Protected Health Information (PHI), genetic information is restrictively protected by sharing according to regulations such as Health Insurance Portability and Accountability Act (HIPAA). This limits data sharing …

High-Dimensional Multivariate Analysis Of Variance Via Geometric Median And Bootstrapping, Guanghui Cheng, Ruitao Lin, Liuhua Peng

Faculty, Staff and Student Publications

The geometric median, which is applicable to high-dimensional data, can be viewed as a generalization of the univariate median used in 1-dimensional data. It can be used as a robust estimator for identifying the location of multi-dimensional data and has a wide range of applications in real-world scenarios. This paper explores the problem of high-dimensional multivariate analysis of variance (MANOVA) using the geometric median. A maximum-type statistic that relies on the differences between the geometric medians among various groups is introduced. The distribution of the new test statistic is derived under the null hypothesis using Gaussian approximations, and its consistency …

Recommendations For The Revision Of Animal Units And Their Application In The Western Australian Rangelands, Ian Mclean, Sally Finch

Natural resources commissioned reports

This report provides recommendations for the practical application of a methodology for calculating and applying Animal Units in the rangelands of Western Australia.

Animal Units have evolved over time, in their definition, derivation and the size of the standard animals used. This has resulted in their being varying and inconsistent approaches within and across jurisdictions which has limited their application.

The Animal Unit methodology applied in this report is used in other rangeland and pastoral regions, it therefore progresses a nationally consistent approach.

The standard animals used in this methodology are:

• Animal Equivalent (AE), a 450 kg Bos taurus steer …

Towards Accurate Spatial Prediction Of Glossina Pallidipes Relative Densities At Country-Scale In Kenya, Stella Gachoki, Thomas A. Groen, Anton Vrieling, Andrew Skidmore, Daniel Masiga

All Peer-Reviewed Publications

Vector-borne diseases, like those transmitted by tsetse flies, pose a significant global public health threat. Reducing vector populations is a promising strategy for disease control, especially in the case of tsetse-transmitted African trypanosomiasis. However, the cost-effective implementation of large-scale vector surveillance and control measures face challenges due to the lack of spatially explicit and reliable maps identifying vector hotspots. In this study, we assessed the accuracy of predicting Glossina pallidipes relative densities across Kenya by linking constrained in-situ tsetse catch data from 660 traps across three Kenyan regions with readily available gridded satellite information (human population, land cover, soil properties, …

Offsetting, Paul Govind, Donna Houston, Michelle Mei Ling Lim, Andrew Mcgregor, Emily O'Gormon, Sandie Suchet-Pearson, Jonathan Symons

Research Collection Yong Pung How School Of Law

In Australia, the State of the Environment 2021 report (hereafter, SOE) revealed an unprecedented rate of biodiversity loss. 1 Yet development projects that will reduce biodiversity further continue to receive legal approval. Indeed, shortly after the release of the report, a new outer ring road was approved for construction in the state of Western Australia. 2 Land clearing undertaken as part of the project will result in significant loss of existing habitat for critically endangered western ringtail possums and endangered black cockatoos. This destruction was legitimized through the state government’s commitment to undertake “biodiversity offsetting,” whereby the loss of possum …

Effects Of Laccase And Transglutaminase On The Physicochemical And Functional Properties Of Hybrid Lupin And Whey Protein Powder, Teguh Santoso, Thao M. Ho, Geerththana Vinothsankar, Kirsi Jouppila, Tony Chen, Adrian Owens, Masoumeh Pourseyed Lazarjani, Mustafa M. Farouk, Michelle L. Colgrave, Don Otter, Rothman Kam, Thao T. Le

Research outputs 2022 to 2026

Plant-based protein is considered a sustainable protein source and has increased in demand recently. However, products containing plant-based proteins require further modification to achieve the desired functionalities akin to those present in animal protein products. This study aimed to investigate the effects of enzymes as cross-linking reagents on the physicochemical and functional properties of hybrid plant- and animal-based proteins in which lupin and whey proteins were chosen as representatives, respectively. They were hybridised through enzymatic cross-linking using two laccases (laccase R, derived from Rhus vernicifera and laccase T, derived from Trametes versicolor) and transglutaminase (TG). The cross-linking experiments were conducted …

Causes And Consequences Of Mitotic Chromosome Missegregation In Human Pluripotent Stem Cells, Chenhui Deng

Dartmouth College Ph.D Dissertations

Mitosis is a fundamental process that ensures the equal distribution of replicated chromosomes, which carry an organism's genetic material, into two daughter cells. The fidelity of mitosis is paramount, as errors in chromosome segregation result in aberrant chromosome numbers, including gains or losses, a state termed aneuploidy. Aneuploidy impacts a broad range of human conditions, including being one of the major hurdles in early human development where it is the primary cause of miscarriages and birth defects. Strikingly, more than 70% of human preimplantation embryos are aneuploid with mitotic chromosome segregation errors being the most common source of aneuploidy. However, …

Increased Co2 Levels During The First Half Of Incubation At High Altitude Modifies Embryonic Development Of Fertile Leghorn Breeder Eggs, Marco A. Juarez-Estrada, Erik I. Lopez-Ruiz, Sonia Lopez-Cordova, G. Tellez-Isaias, Omar F. Prado-Rebolledo

Political Science Faculty Publications and Presentations

The exchange of oxygen (O₂) and carbon dioxide (CO₂) within an incubator has a significant impact on embryonic development (ED) and hatching processes. This study examines the influence of non-ventilation (NV) conditions during the first ten days of incubation at high altitudes on Leghorn hens hatching eggs. Five hundred four hatching eggs were equally divided into three treatment groups and placed in twelve incubators (R = 4). The first group was subjected to standard ventilated conditions (V) during the setting phase. The ventilation inlet holes of the remaining incubators in the NV treatments were closed with …

Smokejumper Obituary: Clithero, Robert M. “Bob” (Missoula 1959), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Accessory Eyes And Dynamic Color Change In Palaemon Vulgaris, Nicholas Raymond Steichmann

Theses and Dissertations

Eyes are physiologically costly organs to produce and maintain, making the development of secondary eyes intriguing. Caridean shrimp possess reflecting superposition primary eyes, but some species across fourteen families possess an additional pair of eyes called accessory eyes along the dorso-posterior margin of the primary eyes. Secondary eyes are found in lizards, lampreys, and insects, where they often function as illumination detectors. Some shrimps may use accessory eyes to signal endocrine organs in their eyestalks to alter the pigmentation of their carapace providing better camouflage through disruptive coloration. To investigate the role of accessory eyes in dynamic color change we …

Leaf Development In The Reproductive Phase Of Arabidopsis: Investigating The Mechanics Of Cauline Leaf Identity And Bract Suppression, Darren Paul Manuela

Theses and Dissertations

Leaves in the reproductive phase subtend inflorescences or flowers and exhibit diverse morphological modifications specialized for reproductive success, such as attracting pollinators, protecting flowers/fruit, and photosynthesis. Using the model organism Arabidopsis, we investigated the development of these specialized leaves. In Arabidopsis, uniquely shaped cauline leaves subtend inflorescences, protect young floral buds and exhibit increased photosynthetic activity crucial for seed production. As form affects function, we analyzed gene expression patterns by RT-qPCR and GUS reporter genes in cauline leaves and examined mutant phenotypes with defective cauline leaf morphology. Our results reveal that redundant miR156-targeted SPLs function to promote cauline leaf identity …

Use Of Cobalt(Iii) And Copper(Ii) Complexes With Thiosemicarbazone Ligands And Berberine Chloride As Anti-Cancer Agents Against Triple Negative Breast Cancer, Duaa Rashad Alajroush

Chemistry & Biochemistry Theses & Dissertations

It is a worrying fact that chemotherapeutic options for treating triple negative breast cancer are limited in nature, including the use of inorganic pharmaceuticals such as cisplatin and its analogues. It has been reported that cisplatin has undesirable side effects when used as a chemotherapeutic drug. As such, there is a need to use non-platinum-containing complexes as chemotherapeutic agents. Based on that issue, it has been reported by our research group and others that cobalt- and copper-containing complexes have shown great potential in anti-cancer properties when compared to cisplatin. In this research project, the cytotoxic effects of the following complexes: …

Streaminghub - A Realtime Biosignal Processing Framework For Lab Scale Experimentation, Yasith Jayawardana

Computer Science Theses & Dissertations

In human subjects research, biosignals such as eye movements, heart rate, and brain activity, are often collected and analyzed to find patterns with tangible real-world implications. Modern advancements in technology have sparked interest towards analyzing biosignals in realtime. When developing such algorithms, one may expect to find free, open-source tools that provide easy access to live, recorded, and simulated data streams. Yet, biosignal interfaces are often vendor-specific, making cross-vendor biosignal streaming non-trivial. Likewise, reading biosignal datasets is also non-trivial, as their content may be arranged quite differently.

To combat this divide, we provide the scientific community with a realtime biosignal …

Dynamic Metabolic Flux Analysis Amidst Data Variability: Sphingolipid Biosynthesis Case Study In Arabidopsis Thaliana Cell Cultures, Abraham Boluwatife Osinuga

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Sphingolipids are pivotal for plant development and stress responses. Growing interest has been directed towards fully comprehending the regulatory mechanisms of the sphingolipid pathway. In this study, we explore its de novo biosynthesis and homeostasis in Arabidopsis thaliana cell cultures, shedding light on fundamental metabolic mechanisms. Employing ¹⁵N isotope labeling and quantitative dynamic modeling approach, we obtained data with notable variations and developed a regularized and constraint-based Dynamic Metabolic Flux Analysis (r-DMFA) framework to predict metabolic shifts due to enzymatic changes. Our analysis revealed key enzymes such as sphingoid-base hydroxylase (SBH) and long-chain-base kinase …

Development And Characterization Of Β-Cyclodextrin Inclusion Complexes With Enzalutamide For Easing Administration And Efficacy Of The Drug In Crpc, Meghana Kolli

Theses and Dissertations

Prostate cancer (PC) is prevalent among men in the US, often leading to castration-resistant prostate cancer (CRPC) with therapy. This is marked by androgen receptor (AR) overexpression, resistance, mutations, and splice variants. Enzalutamide (ENZ), a nonsteroidal antiandrogen, surpasses first-gen AR inhibitors like Bicalutamide. It's the go-to drug for CRPC. We explore ENZ for self-assembly complex formation, crucial for CRPC treatment. Using the solvent evaporation method, we developed β-cyclodextrin and ENZ self-assembly complexes (β-CD-ENZ). β-CD acts as both agent and solubilizer, FDA-approved and safe. Efficacy was tested on PC cell lines (C4-2B) and (22Rv1), including 3D cultures for cytotoxicity and a …

Triticale As A Source Of Resistance To Wheat Streak Mosaic Virus And Triticum Mosaic Virus, Marcos Winicius Goncalves De Souza

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) present a great threat to wheat production in the Great Plains area of the United States due to the loss of photosynthetic area causing reductions in crop yields. Effective control of these viruses is limited to a few available strategies including controlling volunteer wheat and using currently identified resistant genes to both the vector and viruses. While effective, these genes show temperature sensitivity and yield drag, and evidence that the vectors and viruses can overcome them has been found. Thus, new methods of genetic resistance are urgently needed. Field observations …

Utilization Of Probiotics To Compete With Clostridioides Difficile For Nutrient-Niches In A Variety Of In Vitro Contexts, April Elizabeth Johnson

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridium difficile is a major threat to public health and primarily affects at risk groups such as elderly, immunocompromised individuals, and individuals on antibiotics. Many decades of research have been conducted to figure out ways to exclude or reduce C. difficile colonization and toxin production. Two major proposed mechanisms for colonization resistance are production of secondary bile salts and competition for nutrients.

In Chapter 2, we found that antibiotic treatment disrupted bile salt metabolism increasing the levels of the primary bile salt cholate and decreasing the levels of deoxycholate, a secondary bile salt. However, bile salts were not required …

Establishing Marine Protected Areas In The Southern Ocean, Lessons For The Bbnj Agreement, Nengye Liu

Research Collection Yong Pung How School Of Law

This paper first gives a brief overview of the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR)’s struggle to establish Antarctic Marine Protected Areas (MPAs). The paper then addresses the question: what lessons can countries learn from CCAMLR's experience in establishing high seas MPAs under the Biodiversity in Areas Beyond National Jurisdiction (BBNJ) Agreement? The paper finds that the final text of the BBNJ Agreement did largely reflect CCAMLR's experience when it comes to MPAs. This is particularly so with respect to 1) clarification of the relationship between conservation and use; 2) the interpretation and application of a …

Private Management Of African Protected Areas Improves Wildlife And Tourism Outcomes But With Security Concerns In Conflict Regions, Sean Denny, Gabriel Englander, Patrick Hunnicutt

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Protected areas can conserve wildlife and benefit people when managed effectively. African governments increasingly delegate the management of protected areas to private, nongovernmental organizations, hoping that private organizations’ significant resources and technical capacities actualize protected areas’ potential. Does private sector management improve outcomes compared to a counterfactual of government management? We leverage the transfer of management authority from governments to African Parks (AP)—the largest private manager of protected areas in Africa—to show that private management significantly improves wildlife outcomes via reduced elephant poaching and increased bird abundances. Our results also suggest that AP’s management augments tourism, while the effect on …

Carbon-Based Nanocomposite Membranes For Membrane Distillation: Progress, Problems And Future Prospects, Chhabilal Regmi, Yuwaraj K. Kshetri, S. Ranil Wickramasinghe

Chemical Engineering Faculty Publications and Presentations

The development of an ideal membrane for membrane distillation (MD) is of the utmost importance. Enhancing the efficiency of MD by adding nanoparticles to or onto a membrane’s surface has drawn considerable attention from the scientific community. It is crucial to thoroughly examine state-of-the-art nanomaterials-enabled MD membranes with desirable properties, as they greatly enhance the efficiency and reliability of the MD process. This, in turn, opens up opportunities for achieving a sustainable water–energy–environment nexus. By introducing carbon-based nanomaterials into the membrane’s structure, the membrane gains excellent separation abilities, resistance to various feed waters, and a longer lifespan. Additionally, the use …

Impact Of Non-Thermal Plasma Generated Using Air And Nitrogen On Functional Properties Of Milk Protein Dispersions, Nikitha Modupalli, Md Mahfuzur Rahman

Food Science Faculty Publications and Presentations

This study focuses on improving the functionalities of milk protein concentrate (MPC) using a nonthermal plasma jet and plasma-activated water (PAW) with atmospheric air and nitrogen as source gases. The 5% and 10% MPC dispersions were directly treated with a plasma jet, and PAW was used to make the MPC dispersions. The dispersions were analyzed for changes in protein structure and functional properties. The treatment altered the secondary structure of MPC protein structure by increasing β-components and changing the order of random coils. The solubility of the PAW-treated 5% protein dispersions doubled due to plasma-induced modification of hydrophilic and covalent …

Characterizing The Quorum Sensing (Qs) System In The Model Eukaryote Chlamydomonas Reinhardtii, Kirstin Donnette Cutshaw

Theses and Dissertations

Group behaviors in microorganisms are often regulated by low-molecular weight molecules that enable them to sense population density, a signaling system known as quorum sensing (QS). QS in prokaryotes has provided insight into the role ‘social’ behaviors play in the bacterial world and refined our models of virulence, bacterial motility, and more. While less common, similar behaviors are observed in certain fungi, primarily yeasts, in which QS controls cell morphology, biofilm production, and other phenotypes. We have recently pursued the potential for QS to be more broadly distributed among unicellular eukaryotes, which could significantly alter our understanding of social behaviors …