Digital Commons Network^™

From Tuberculosis Bedside To Bench: Ube2b Splicing As A Potential Biomarker And Its Regulatory Mechanism, Mengyuan Lyu, Jian Zhou, Yanbing Zhou, Weelic Chong, Wei Xu, Hongli Lai, Lu Niu, Yang Hai, Xiaojun Yao, Sheng Gong, Qinglan Wang, Yi Chen, Yili Wang, Liyu Chen, Ganzi People's Hospital, Jiongjiong Zeng, Chengdi Wang, Binwu Ying

Student Papers, Posters & Projects

Alternative splicing (AS) is an important approach for pathogens and hosts to remodel transcriptome. However, tuberculosis (TB)-related AS has not been sufficiently explored. Here we presented the first landscape of TB-related AS by long-read sequencing, and screened four AS events (S100A8-intron1-retention intron, RPS20-exon1-alternaitve promoter, KIF13B-exon4-skipping exon (SE) and UBE2B-exon7-SE) as potential biomarkers in an in-house cohort-1. The validations in an in-house cohort-2 (2274 samples) and public datasets (1557 samples) indicated that the latter three AS events are potential promising biomarkers for TB diagnosis, but not for TB progression and prognosis. The excellent performance of classifiers further underscored the diagnostic value …

Multitrait Genome-Wide Analyses Identify New Susceptibility Loci And Candidate Drugs To Primary Sclerosing Cholangitis, Younghun Han, Jinyoung Byun, Catherine Zhu, Ryan Sun, Julia Y Roh, Heather J Cordell, Hyun-Sung Lee, Vikram R Shaw, Sung Wook Kang, Javad Razjouyan, Matthew A Cooley, Manal M Hassan, Katherine A Siminovitch, Trine Folseraas, David Ellinghaus, Annika Bergquist, Simon M Rushbrook, Andre Franke, Tom H Karlsen, Konstantinos N Lazaridis, Kathryn A. Mcglynn, Katherine A Mcglynn, Lewis R Roberts, Christopher I Amos, International Psc Study Group

Faculty, Staff and Students Publications

Primary sclerosing cholangitis (PSC) is a rare autoimmune bile duct disease that is strongly associated with immune-mediated disorders. In this study, we implemented multitrait joint analyses to genome-wide association summary statistics of PSC and numerous clinical and epidemiological traits to estimate the genetic contribution of each trait and genetic correlations between traits and to identify new lead PSC risk-associated loci. We identified seven new loci that have not been previously reported and one new independent lead variant in the previously reported locus. Functional annotation and fine-mapping nominated several potential susceptibility genes such as MANBA and IRF5. Network-based in silico drug …

Detection And Characterization Of Constitutive Replication Origins Defined By Dna Polymerase Epsilon, Roman Jaksik, David A Wheeler, Marek Kimmel

Center for Medical Ethics and Health Policy Staff Publications

Background: Despite the process of DNA replication being mechanistically highly conserved, the location of origins of replication (ORI) may vary from one tissue to the next, or between rounds of replication in eukaryotes, suggesting flexibility in the choice of locations to initiate replication. Lists of human ORI therefore vary widely in number and location, and there are currently no methods available to compare them. Here, we propose a method of detection of ORI based on somatic mutation patterns generated by the mutator phenotype of damaged DNA polymerase epsilon (POLE).

Results: We report the genome-wide localization of constitutive ORI in POLE-mutated …

Increased Floodplain Inundation In The Amazon Since 1980, Ayan Fleischmann, Fabrice Papa, Stephen K. Hamilton, Alice Fassoni-Andrade, Sly Wongchuig, Jhan Carlo Espinoza, Rodrigo Paiva, John Melack, Etienne Fluet-Chouinard, Rafael M. Almeida

School of Earth, Environmental, & Marine Sciences Faculty Publications

Extensive floodplains throughout the Amazon basin support important ecosystem services and influence global water and carbon cycles. A recent change in the hydroclimatic regime of the region, with increased rainfall in the northern portions of the basin, has produced record-breaking high water levels on the Amazon River mainstem. Yet, the implications for the magnitude and duration of floodplain inundation across the basin remain unknown. Here we leverage state-of-the-art hydrological models, supported by in situ and remote sensing observations, to show that the maximum annual inundation extent along the central Amazon increased by 26% since 1980. We further reveal increased flood …

Sperm Donor Attitudes And Experiences With Direct-To-Consumer Genetic Testing., Sascha Wodoslawsky, Joy Fatunbi, Rebecca Mercier, Andrea Mechanick Braverman

Department of Obstetrics and Gynecology Faculty Papers

OBJECTIVE: To identify factors influencing sperm donor willingness to participate in direct-to-consumer genetic testing, comfort with sharing genetically identifiable data in commercial genetic testing databases, and likelihood to donate sperm again.

DESIGN: Cross-sectional online anonymous survey.

SETTING: Multicenter, 2 large American sperm banks from July 1, 2020 to July10, 2021.

PATIENTS: Sperm donors from 1980 to 2020.

INTERVENTIONS: None.

MAIN OUTCOME MEASURES: Associations between donor demographic characteristics, donation history, and attitudes toward direct-to-consumer genetic testing.

RESULTS: A total of 396 donors completed the survey. Most donations (61.5%) occurred from 2010 to 2020, and 34.3% were nonidentified donations. Nonidentified donors were …

Role Of Ribosome Recycling Factor In Natural Termination And Translational Coupling As A Ribosome Releasing Factor, Yoshio Inokuchi, Fabio Quaglia, Akikazu Hirashima, Yoshihiro Yamamoto, Hideko Kaji, Akira Kaji

Department of Biochemistry and Molecular Biology Faculty Papers

The role of ribosome recycling factor (RRF) of E. coli was studied in vivo and in vitro. We used the translational coupling without the Shine-Dalgarno sequence of downstream ORF (d-ORF) as a model system of the RRF action in natural termination of protein synthesis. For the in vivo studies we used the translational coupling by the adjacent coat and lysis genes of RNA phage GA sharing the termination and initiation (UAAUG) and temperature sensitive RRF. The d-ORF translation was measured by the expression of the reporter lacZ gene connected to the 5'-terminal part of the lysis gene. The results showed …

Collins '02 Leads High School Research Trip To Galápagos Islands With Carstens '02, Chris Francis

News and Events (Discontinued Series)

No abstract provided.

Microrna Profiles In Intestinal Epithelial Cells In A Mouse Model Of Sepsis, Siqingaowa Caidengbate, Yuichi Akama, Anik Banerjee, Khwanchanok Mokmued, Eiji Kawamoto, Arong Gaowa, Louise D Mccullough, Motomu Shimaoka, Juneyoung Lee, Eun Jeong Park

Faculty, Staff and Student Publications

Sepsis is a systemic inflammatory disorder that leads to the dysfunction of multiple organs. In the intestine, the deregulation of the epithelial barrier contributes to the development of sepsis by triggering continuous exposure to harmful factors. However, sepsis-induced epigenetic changes in gene-regulation networks within intestinal epithelial cells (IECs) remain unexplored. In this study, we analyzed the expression profile of microRNAs (miRNAs) in IECs isolated from a mouse model of sepsis generated via cecal slurry injection. Among 239 miRNAs, 14 miRNAs were upregulated, and 9 miRNAs were downregulated in the IECs by sepsis. Upregulated miRNAs in IECs from septic mice, particularly …

Mitochondrial Phosphatidylethanolamine Modulates Ucp1 To Promote Brown Adipose Thermogenesis, Jordan M Johnson, Irfan J Lodhi, Et Al.

2020-Current year OA Pubs

Thermogenesis by uncoupling protein 1 (UCP1) is one of the primary mechanisms by which brown adipose tissue (BAT) increases energy expenditure. UCP1 resides in the inner mitochondrial membrane (IMM), where it dissipates membrane potential independent of adenosine triphosphate (ATP) synthase. Here, we provide evidence that phosphatidylethanolamine (PE) modulates UCP1-dependent proton conductance across the IMM to modulate thermogenesis. Mitochondrial lipidomic analyses revealed PE as a signature molecule whose abundance bidirectionally responds to changes in thermogenic burden. Reduction in mitochondrial PE by deletion of phosphatidylserine decarboxylase (PSD) made mice cold intolerant and insensitive to β3 adrenergic receptor agonist-induced increase in whole-body oxygen …

Does Structural Racism Influence How Black/African Americans Define Memory Loss And Cognitive Impairment? An Africana Phenomenological Study, Andre Pruitt

Dissertations and Theses

With the variety of research about dementia and Alzheimer's disease (AD), few studies have explored the effect of social structures, such as racism, on how Black/African Americans conceptualize memory loss, dementia, or AD. Furthermore, limited within the scholarship are the environmental factors and structural racism that are thought to influence cognitive impairments and meaning making about cognitive decline impacting Black/African Americans.

Most U.S. research centers on methodologies and epistemologies grounded in Eurocentric ways of knowing (objectivity, individuality, either/or logic). However, Eurocentric methodologies fail to acknowledge the cultural experiences with memory loss, cognitive impairment, dementia, and AD, as well as the …

Feasibility Of [18f]Fspg Pet For Early Response Assessment To Combined Blockade Of Egfr And Glutamine Metabolism In Wild-Type Kras Colorectal Cancer, Seong-Woo Bae, Jianbo Wang, Dimitra K Georgiou, Xiaoxia Wen, Allison S Cohen, Ling Geng, Mohammed Noor Tantawy, H Charles Manning

Faculty, Staff and Student Publications

Early response assessment is critical for personalizing cancer therapy. Emerging therapeutic regimens with encouraging results in the wild-type (WT) KRAS colorectal cancer (CRC) setting include inhibitors of epidermal growth factor receptor (EGFR) and glutaminolysis. Towards predicting clinical outcome, this preclinical study evaluated non-invasive positron emission tomography (PET) with (4S)-4-(3-[18F]fluoropropyl)-L-glutamic acid ([18F]FSPG) in treatment-sensitive and treatment-resistant WT KRAS CRC patient-derived xenografts (PDXs). Tumor-bearing mice were imaged with [18F]FSPG PET before and one week following the initiation of treatment with either EGFR-targeted monoclonal antibody (mAb) therapy, glutaminase inhibitor therapy, or the combination. Imaging was correlated with tumor volume and histology. In PDX …

Monitoring Resistance And Biochemical Studies Of Three Egyptian Field Strains Of Spodoptera Littoralis (Lepidoptera: Noctuidae) To Six Insecticides, Moataz A M Moustafa, Rasha I A Moteleb, Yehia F Ghoneim, Sameh Sh Hafez, Reham E Ali, Essam E A Eweis, Nancy N Hassan

Faculty, Staff and Student Publications

BACKGROUND:

METHODS: Laboratory bioassays were carried out using the leaf-dipping method to examine the susceptibility of the laboratory and field strains to the tested insecticides. Activities of detoxification enzymes were determined in an attempt to identify resistance mechanisms.

RESULTS: The results showed that LC

CONCLUSION: Our findings, along with other tactics, are expected to help with the resistance management of

2023-02-24, Board Of Regents, Murray State University

Board of Regents Meeting Minutes

No abstract provided.

“From This Invisible Archipelago”: The Oceanic Ecopoetics Of Craig Santos Perez, Mandy Bloomfield

School of Law, Humanities and Social Sciences

No abstract provided.

Design Power And Potential Future Of Global Organization Of Life, A. Fuat Fırat

Markets, Globalization & Development Review

In this essay I propose a definition of design to address its potential role in largely determining power relations in the future. Some foundational discussion of wealth, culturally constructed differently in different historical times, trends of corporatization in the contemporary world, and the birth of control society is presented to help understand the possibilities and difficulties of building future organizations of life. I invite discussions and dialogues to widen and deepen the concept of design power.

Marketing, Development, And The Question Of Meaning, Dominique Bouchet

Markets, Globalization & Development Review

Originally developed as a sales technique, marketing ended up playing an economic and political role globally. With the advent of globalization and sustainability issues, the importance given to the techniques of marketing in both analyses and in communication limits the possibility of mutual understanding and of social creativity. A profound understanding of what is at stake for society and culture is not what matters when the focus is on the ways to maintain the superficial link to the instrument of power.

The market plays a central role within the fields of marketing, economics and politics. Yet, questions of what the …

Pasture Land Management System Decision Support Software, G. E. Groover, S. R. Smith, N. D. Stone, J. J. Venuto, J. M. Galbraith

IGC Proceedings (1977-2023)

Controlled or rotational grazing provides benefits to producers and society through profitable and sound management of grazing land and livestock. Pasture land management system (PLMS) is a decision support system developed to help university, government, and professionals provide technical pasture management assistance to beef and dairy producers. The PLMS focuses on the balance between seasonal forage supply and nutrient demand in a dairy or beef cattle operation. It allows users to explore and compare alternatives (dividing fields into multiple paddocks, changing stocking rates, and forage species) through a visual display and embedded simulation. Users enter a description of the farm …

Forecast Of Herbage Production Under Continuous Grazing, K. Søegaard, J. Berntsen, K. A. Nielsen, I. Thysen

IGC Proceedings (1977-2023)

The utilization of pasture is very sensitive to oscillations in herbage growth. The farmer’s daily planning involves decisions on pasture use as well as on the amount and composition of supplement feeding. In this planning, expected daily growth rate is an important factor. Often the knowledge and experience about the growth rate is first available after changes in management should have been made. A different growth rate than expected should lead to changes in the grazing area or in the supplement feeding. Therefore, a simple model of grass/clover growth under grazing and irrigated conditions was developed. From spring 2004, the …

A Decision Support Tool For Seed Mixture Calculations, B. P. Berg, G. Hutton

IGC Proceedings (1977-2023)

Grassland species are normally seeded in mixtures rather than monocultures. In theory, seeding rates for mixtures are simply a sum of the amount of pure live seed (PLS) of each seed lot in the mix, an amount sufficient to ensure establishment and survival of each species. Mixtures can be complex because of the number of species used (especially in conservation and reclamation programs) and variations in seed purity and seed size. Soil limitations and seeding equipment settings need to be considered and in Canada, a metric conversion may be required. All these conditions make by-hand calculations of mixtures containing more …

Risk-Efficiency Assessment Of Haying, A. J. Romera, J. Hodgson, S. T. Morris, S. J. R. Woodward, W. D. Stirling

IGC Proceedings (1977-2023)

Pastoral livestock farms are complex, dynamic systems subject to many forms of external disturbance. Farm Management strategies are therefore typically designed to minimize system variation. The objective of this study was to explore the impacts of different haying policies, in terms of expected profit and risk, for cow-calf farms in the Salado Region of Argentina.

Environmental Clustering Of New Zealand Dairy Herds, J. R. Bryant, N. López-Villalobos, J. E. Pryce, C. W. Holmes

IGC Proceedings (1977-2023)

Previous studies have found that milk yield (a proxy for feeding level) and temperature-humidity index (THI) are important factors in explaining genotype x environment (G x E) interactions, indicating differences between the abilities of genotypes to forage or consume concentrates effectively or to cope with thermal stress (Ravagnolo and Misztal, 2000; Zwald et al., 2003). The objective of this study was to quantify and cluster (CL) herd environments within New Zealand (NZ) based on production levels, a summer heat load index (HLI) and geographical location.

Irish Dairy Farming: Effects Of Introducing A Maize Component On Grassland Management Over The Next 50 Years, A. J. Brereton, N. M. Holden

IGC Proceedings (1977-2023)

Typical management of Irish dairy units is based on a low-cost spring-calving strategy with 90% of annual feed derived from grass grown on the farm. Almost 70% of feed is from grazed grass managed by rotational grazing, the remainder is conserved forage and concentrates. The objectives of the work were to examine how the management system has to be modified when part of the dairy unit land is allocated to maize silage instead of grass silage production, and to examine how climate change over the next 50 years will impact on grass and maize management within the production system.

Autumn Root Reserves Of Lucerne Affected Shoot Yields During The Following Spring, D. J. Moot, E. I. Teixeira

IGC Proceedings (1977-2023)

Frequent grazing affects shoot yield of lucerne (Medicago sativa L.) by limiting radiation interception (Teixeira et al., 2005b) and the accumulation of endogenous reserves (C and N) in perennial storage organs like crowns and taproots (Teixeira et al., 2005a). In temperate regions, the impact of low level of perennial reserves is particularly evident during early-spring, when lucerne regrowth resumes after an overwintering period. The analysis of lucerne yield can be fragmented into its yield components of plant population, shoots per plant and yield per shoot (Volenec et al., 1987). The objective of this research was to quantify …

Lucerne Crown And Taproot Biomass Affected Early-Spring Canopy Expansion, E. I. Teixeira, D. J. Moot, A. L. Fletcher

IGC Proceedings (1977-2023)

Leaf area index (LAI) quantifies canopy expansion in crops and is used in lucerne (Medicago sativa L.) simulation models to predict daily PAR interception (PAR i). This then drives yield through radiation use efficiency (RUE) (Gosse et al., 1984). In perennial crops, like lucerne, the level of biomass stored in crown and taproot may affect canopy expansion in subsequent regrowth cycles (Avice et al., 1997). In temperate regions the impact of this is likely to be greatest in early-spring, when low temperatures delay development. The objective of the current research was to identify whether contrasting levels of winter biomass in …

Extending The Grazing Season With Turnips, P. Thomet, S. Kohler

IGC Proceedings (1977-2023)

A comparison of the actual feeding costs on 86 typical Swiss dairy farms confirmed that the production of hay and grass silage is very expensive with costs from the field to intake in the range of 20-25 Euro cents/kg of dry matter (DM). Options to extend the grazing season for dairy cows in the late autumn and early winter, and hence reduce winter feeding costs, would therefore be welcome (Penrose et al., 1996). The aim of the study was to compare the DM production potential of summer-seeded turnips with other brassicas and Italian ryegrass and to test whether dairy cows …

Milk Production Performance Based On Grazed Grassland In Switzerland, P. Thomet, H. Menzi

IGC Proceedings (1977-2023)

A common feature of profitable dairy systems is the use of large amounts of low cost feed. One approach to improve the competitive ability of the dairy production therefore is to promote grazing (Dillon et al., 1995). A comparison of the actual feeding costs on typical Swiss dairy farms showed that hay and grass silage were four times and concentrates seven times more expensive than grazed grass. A maximum utilisation of grazed grass can be achieved with a seasonal production system, which synchronises the cow’s feed requirements with pasture growth. This strategy was implemented and consistently optimised on an …

The Effect Of Inclusion Of A Range Of Supplementary Feeds On Herbage Intake, Total Dry Matter Intake And Substitution Rate In Grazing Dairy Cows, S. J. Morrison, D. C. Patterson, S. Dawson, C. P. Ferris

IGC Proceedings (1977-2023)

The milk production potential of dairy cows has increased substantially over the past two decades. This development presents new challenges for managing dairy cows during grazing, particularly where the objective is to maximise the proportion of energy in the diet derived from forage. The objective of the current study was to explore supplementation strategies to maintain high total forage intakes from grazed grass supplemented with alternative forage supplements in dairy cows during the grazing season. A second objective of the study was to examine the effect of supplement on substitution rate (SR) and milk yield response.

White Clover Soil Fatigue: An Establishment Problem On Large And Intensive Dairy Farms, K. Søegaard, K. Møller

IGC Proceedings (1977-2023)

In recent years a new constraint, clover soil fatigue, has appeared for the establishment of white clover (Trifolium repens) in Denmark. Increasing dairy farm size has led to more intensive use of clover in crop rotation schemes in the grazing areas located at convenient distances from stables. It has become common practice to establish new clover/grass in the fields just after ploughing clover/grass swards, and soil fatigue is becoming more common. On fatigued land the clover plants emerge, then become stunted and eventually disappear within the same year. The problem tends to cover the full field area. Obviously, …

‘Reading The Cultural Landscape’ In The ‘Birthplace’ Of Modern Race/Racism: Using Hooks To Invite Students In As Critical Knowledge Producers & Co-Conspirators, Danielle Docka-Filipek

Feminist Pedagogy

No abstract provided.

Effect Of Farm Grass Cover At Turnout On The Grazing Management Of Spring Calving Dairy Cows, M. O'Donovan, L. Delaby, P. Defrance

IGC Proceedings (1977-2023)

Early spring grazing is an objective for most Irish dairy farmers. If more grass is included in the diet of the cow in early lactation, the profitability of the farm system can be increased. Post turnout, dairy cow feeding management varies with the amount of farm grass cover (FC) available. Experiments on the consequences of different FC at turnout require large resources and all scenarios cannot be accounted for. Consequently, a decision support system, Pâtur’IN (Delaby et al., this volume), was used to describe the effects of various FC at turnout on grazing management in spring.