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Protocol For Optimizing Production And Quality Control Of Infective Ecohiv Virions, Hammodah Rawhi Hammodah Alfar, Daphne N. Pariser, Harry Chanzu, Smita Joshi, Daniёlle M. Coenen, Joshua Lykins, Kanakanagavalli Shravani Prakhya, Mary Jane Potash, Wei Chao, Jennifer Kelschenbach, David J. Volsky, Kelly Metcalf-Pate

Saha Cardiovascular Research Center Faculty Publications

EcoHIV is a model of HIV infection that recapitulates aspects of HIV-1 pathology in mice. However, there are limited published protocols to guide EcoHIV virion production. Here, we present a protocol for producing infective EcoHIV virions and essential quality controls. We describe steps for viral purification, titering, and multiple techniques to analyze infection efficacy. This protocol produces high infectivity in C57BL/6 mice which will aid investigators in generating preclinical data.

Cell-Free, High-Density Lipoprotein-Specific Phospholipid Efflux Assay Predicts Incident Cardiovascular Disease, Masaki Sato, Edward B. Neufeld, Martin P. Playford, Yu Lei, Alexander V. Sorokin, Angel M. Aponte, Lita A. Freeman, Scott M. Gordon, Amit K. Dey, Kianoush Jeiran, Masato Hamasaki, Maureen L. Sampson, Robert D. Shamburek, Jingrong Tang, Marcus Y. Chen, Kazuhiko Kotani, Josephine L. C. Anderson, Robin P. F. Dullaart, Nehal N. Mehta, Uwe T. F. Tietge, Alan Thomas Remaley

Saha Cardiovascular Research Center Faculty Publications

BACKGROUND. Cellular cholesterol efflux capacity (CEC) is a better predictor of cardiovascular disease (CVD) events than HDL- cholesterol (HDL-C) but is not suitable as a routine clinical METHODS. We developed an HDL-specific phospholipid efflux (HDL-SPE) assay to assess HDL functionality based on whole plasma HDL apolipoprotein–mediated solubilization of fluorescent phosphatidylethanolamine from artificial lipid donor particles. We first assessed the association of HDL-SPE with prevalent coronary artery disease (CAD): study I included NIH severe-CAD (n = 50) and non-CAD (n = 50) participants, who were frequency matched for sex, BMI, type 2 diabetes mellitus, and smoking; study II included Japanese CAD …

A Lamprey Neural Cell Type Atlas Illuminates The Origins Of The Vertebrate Brain, Francesco Lamanna, Francisca Hervas-Sotomayor, A. Phillip Oel, David Jandzik, Daniel Sobrido-Cameán, Gabriel N. Santos-Durán, Megan L. Martik, Jan Stundl, Stephen A. Green, Thoomke Brüning, Katharina Mößinger, Julia Schmidt, Celine Schneider, Mari Sepp, Florent Murat, Jeramiah J. Smith, Marianne E. Bronner, María Celina Rodicio, Antón Barreiro-Iglesias, Daniel M. Medeiros, Detlev Arendt, Henrik Kaessmann

Markey Cancer Center Faculty Publications

The vertebrate brain emerged more than ~500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey—a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits—based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of cell types, tissue structures and gene expression programs of the ancestral vertebrate brain. However, our analyses also revealed …

Bacteroides Fragilis In The Gut Microbiomes Of Alzheimer’S Disease Activates Microglia And Triggers Pathogenesis In Neuronal C/Ebpβ Transgenic Mice, Yiyuan Xia, Yifan Xiao, Zi-Hao Wang, Ashfaqul M. Alam, John P. Haran, Beth A. Mccormick, Xiji Shu, Xiaochuan Wang, Keqiang Ye

Markey Cancer Center Faculty Publications

Gut dysbiosis contributes to Alzheimer’s disease (AD) pathogenesis, and Bacteroides strains are selectively elevated in AD gut microbiota. However, it remains unknown which Bacteroides species and how their metabolites trigger AD pathologies. Here we show that Bacteroides fragilis and their metabolites 12-hydroxy-heptadecatrienoic acid (12-HHTrE) and Prostaglandin E2 (PGE2) activate microglia and induce AD pathogenesis in neuronal C/EBPβ transgenic mice. Recolonization of antibiotics cocktail-pretreated Thy1-C/EBPβ transgenic mice with AD patient fecal samples elicits AD pathologies, associated with C/EBPβ/Asparaginyl endopeptidase (AEP) pathway upregulation, microglia activation, and cognitive disorders compared to mice receiving healthy donors’ fecal microbiota transplantation (FMT). Microbial 16S rRNA sequencing …

New Insights On The Differential Interaction Of Sulfiredoxin With Members Of The Peroxiredoxin Family Revealed By Protein-Protein Docking And Experimental Studies, Murli Mishra, Hong Jiang, Qiou Wei

Markey Cancer Center Faculty Publications

Sulfiredoxin (Srx) is the enzyme that restores the peroxidase activity of peroxiredoxins (Prxs) through catalyzing the reduction of hyperoxidized Prxs back to their active forms. This process involves protein-protein interaction in an enzyme-substrate binding manner. The integrity of the Srx-Prx axis contributes to the pathogenesis of various oxidative stress related human disorders including cancer, inflammation, cardiovascular and neurological diseases. The purpose of this study is to understand the structural and molecular biology of the Srx-Prx interaction, which may be of significance for prediction of target site for the novel drug-discovery. Homology modeling and protein-protein docking approaches were applied to examine …

Syne1 Mutation Is Associated With Increased Tumor Mutation Burden And Immune Cell Infiltration In Ovarian Cancer, Laura M. Harbin, Nan Lin, Frederick R. Ueland, Jill M. Kolesar

Markey Cancer Center Faculty Publications

SYNE1, a nuclear envelope protein critical for cellular structure and signaling, is downregulated in numerous malignancies. SYNE1 alterations are found in 10% of gynecologic malignancies and 5% of epithelial ovarian cancers. Previous studies demonstrated an association between SYNE1 mutation, increased tumor mutation burden (TMB), and immunotherapy response. This study evaluates the SYNE1 mutation frequency, association with TMB, and downstream effects of SYNE1 mutation in ovarian cancer. Genetic information, including whole-exome sequencing, RNA analysis, and somatic tumor testing, was obtained for consenting ovarian cancer patients at an academic medical center. Mutation frequencies were compared between the institutional cohort and The Cancer …

Unleashing The Potential Of 1,3-Diketone Analogues As Selective Lh2 Inhibitors, Juhoon Lee, Hou-Fu Guo, Shike Wang, Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Zhifeng Jing, Rae M. Sammons, Eun Jeong Cho, Pengyu Ren, G. Andrés Cisneros, Jonathan M. Kurie, Kevin N. Dalby

Markey Cancer Center Faculty Publications

Lysyl hydroxylase 2 (LH2) catalyzes the formation of highly stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs), thus promoting lung cancer metastasis through its capacity to modulate specific types of collagen cross-links within the tumor stroma. Using 1 and 2 from our previous high-throughput screening (HTS) as lead probes, we prepared a series of 1,3-diketone analogues, 1−18, and identified 12 and 13 that inhibit LH2 with IC50’s of approximately 300 and 500 nM, respectively. Compounds 12 and 13 demonstrate selectivity for LH2 over LH1 and LH3. Quantum mechanics/molecular mechanics (QM/MM) modeling indicates that the selectivity of 12 and 13 may stem from …

Self-Reported Consumption Of Bottled Water V. Tap Water In Appalachian And Non-Appalachian Kentucky, Jason W. Marion

Journal of Appalachian Health

Introduction: Quantitative studies on drinking water perceptions in Appalachia are limited. High-profile water infrastructure failures in the U.S. and Eastern Kentucky, coupled with human-made and natural disasters in the Appalachian Region, have likely impacted opinions regarding tap water.

Purpose: To use existing unexplored data to describe baseline tap water v. bottled water consumption in Kentucky.

Methods: Telephone-based cross-sectional data were obtained from the 2013 Kentucky Health Issues Poll (KHIP) directed by the Foundation for a Healthy Kentucky. Among many items in KHIP, self-reported consumption of bottled water over tap water, reasons for bottled water use, and demographic data were obtained. …

Evaluation Of A Faculty Fellows Program In Science Communication, Stacy Stanifer, Beverly Delidow, Kathy Rademacher, Luz Huntington-Moskos, Kelly Kennoy, Amanda Thaxton-Wiggins, Craig Wilmhoff, Ellen J. Hahn

Journal of Appalachian Health

Introduction: Science communication plays a crucial role in tackling pressing regional, national, and global health issues. Effective communication with various audiences is integral to dissemination of science findings.

Purpose: This study evaluates changes in self-efficacy and attitudes toward science communication skills over time and also assesses program outcomes and satisfaction with a Faculty Fellows in Science Communication (FFSC) program among faculty (N = 30) with interest in environmental health science and/or education in Appalachia Kentucky.

Methods: A mixed methods program evaluation was employed using longitudinal data on behaviors, attitudes, and program outcomes from three cohorts of Faculty Fellows who participated …

Scaling Up Of Site Carbon Dynamics To Predict The Carbon Dynamics In Kazakhstan, Central Asia, B. K. Wylie, Tagir Gilmanov, S. L. Stensaas, N. Z. Saliendra, D. A. Johnson, K. Akshalov, S. B. Frank, L. Zhang, R. F. Doyle, E. A. Laca, Montague W. Demment

IGC Proceedings (1977-2023)

Climate and management determine whether rangelands are net carbon sources or carbon sinks. Regional carbon dynamics of the Kazakh Steppe has not previously been documented. The objective of this study is to quantify the regional carbon flux dynamics of these extensive steppes.

A New System For Plant Experiments On Biodiversity Or Multi-Species Competition, John Connolly, L. Kirwan

IGC Proceedings (1977-2023)

Considerable discussion in recent years has focused on the design of competition and biodiversity experiments (Connolly et al., 2001a; Allison, 1999). Few agronomic experiments with >2 plant species have been conducted in greenhouse conditions (Gibson et al, 1999) or in the field (Connolly et al., 2001b). In many experiments the effects of density and initial species size have been confounded. The effects of species richness and evenness also are confounded frequently. The proposed system provides a framework of design and analysis, in which to address questions of function at community level and of structure and competition at …

Native Grasses Seeded Into A Cool-Season Pasture Encouraged By Low Resource Availability, J. E. Doll, R. L. Cates, R. D. Jackson

IGC Proceedings (1977-2023)

Native prairie of the Upper Midwest, which was dominated by warm-season (C₄) grasses, now exists as relatively small relict and restored patches (Curtis 1959). Re-introduction of natives into grazed agroecosystems would promote genetic, species, and landscape diversity. Extensive re-introduction of C₄ grasses will require a shift away from the paradigm of maximizing production because C₄ grasses have higher C:N ratios than C₃ grasses rendering them inferior forage species. Nonetheless, there is great interest amongst the grazing community of the Upper Midwest in establishing native grasses as a means of improving wildlife habitat and increasing belowground …

The Ag-Biota Project: A Preliminary Assessment Of Potential Indicators Of Biodiversity In Agricultural Grasslands, Gordon Purvis, A. Anderson, A. J. Helden, L. Kirwan

IGC Proceedings (1977-2023)

In compliance with European commitments to the Convention on Biological Diversity, the conservation and enhancement of biodiversity within agricultural land is a primary objective of current agri-environmental measures. However, there is a widespread lack of information concerning the effectiveness of agri-environmental schemes in Europe, (Kleijn & Sutherland, 2003). In large part, this is due to uncertainties about selection of appropriate biological indicators of biodiversity (Buchs, 2003; Duelli & Obrist, 2003).

Effects Of Plant Species Diversity In Multifunctional Grasslands On Avian Communities, K. K. Bakker, K. F. Higgins

IGC Proceedings (1977-2023)

Grasslands, planted or native sod, can provide multiple simultaneous functions (e.g., hay-forage production, biomass fuel products, bird nesting cover, soil and water conservation). Bird use of and abundance in grasslands is dependent on vegetation structure, size, and surrounding landscape (Bakker et al., 2002) but little is known about avian relationships to plant species diversity. We evaluated the relationship between plant species diversity and avian community structure in 5 grassland types. The results have application to grazing, haying, burning, and conservation practices applied to native and sown grassland stands and to conservation strategies for declining grassland bird populations.

Diversity And Adaptation Of Perennial Plants From North Africa: Legumes And Grasses, Aissa Abdelguerfi, M. Laouar, K. Abbas, M. M'Hammedi Bouzina

IGC Proceedings (1977-2023)

A variety of climates, soil types and reliefs characterise North Africa (Algeria, Morocco, and Tunisia). These natural conditions have produced a large diversity of environments, landscapes, plant formations and flora. Several factors have contributed to the spread of a wide floristic variety: the influence of the Mediterranean in the north and in the north-east, the Atlantic in the west, and the Sahara in the south, as well as the presence of mountain ranges, particularly the Rif, the Tell Atlas, the Sahara Atlas, the Middle Atlas, the High Atlas, and the Anti-Atlas. This diversity of landscapes, environments and ecosystems has generated …

Comparison Of Compositional Changes In Multi-Species Grass/Legume Mixture Experiments Across Three Nordic Countries (Iceland, Sweden And Finland) Over Two Years, Caroline Brophy, Anne-Maj Gustavsson, A. Helgadottir, Oiva Nissinen, J. Connolly

IGC Proceedings (1977-2023)

A multi-site experiment was established at 39 sites across Europe, Australia and Canada within COST Action 852 to: (1) assess the benefits of grass/legume mixtures over monocultures, (2) test the stability of mixtures and (3) evaluate the consistency of the observed patterns over broad environmental gradients. This paper compares the results from 3 Nordic sites using the same plant species: Korpa Experimental Station in Iceland, Lapland Research Station in Finland and Piteå in Sweden to investigate if compositional changes in mixtures are consistent across the sites.

Site Effects On The Composition Of Multi-Species Grass/Legume Mixtures During Sward Establishment, Rosemary P. Collins, M. Fothergill, John Connolly

IGC Proceedings (1977-2023)

Under the auspices of COST Action 852, a multi-site experiment investigated issues of community structure, function and their interrelationships in multi-species grass/legume mixtures (Collins et al., 2004; Sebastià et al., 2004). We describe the effects of 2 contrasting sites on forage yield and species composition during sward establishment.

Unplanned Fires And Sustainability Of A Semi-Arid Rangeland In South Africa, Hennie A. Snyman

IGC Proceedings (1977-2023)

Whether due to lightning or human negligence, large-scale unplanned fires affect large areas of the semi-arid southern African rangelands during the dormant winter (June-August) period (Everson 1999). These fires cause enormous fodder flow problems, and also influence ecosystem functioning (Snyman 2003). The short-term impact (2 years) of an unplanned fire on the sensitivity of above- and belowground productivity of a semi-arid rangeland was therefore investigated.

Effects Of Burning On Grassland Vegetation Cover On The Northeastern Side Of The Alborz Ranges In Iran, F. Amiri, M. R. Chaichi, A. Atrakchali

IGC Proceedings (1977-2023)

Golestan National Park is located on the northeastern side of the Alborz ranges, Golestan province, Iran. Because of the special vegetation cover and being located close to two wet and dry weather areas, this park is vulnerable to fire hazards. Between 1957 and 2004 more than 67 fires have been reported in the park. The international importance of the park requires a careful study on fire effects on vegetation cover, phytomass production, grass diversity and successional process after fires.

The Influence Of Tree Thinning And Subhabitat Differentiation On Panicum Maximum And Urochloa Mosambicensis Of A Bush Encroached Semi-Arid Savanna In South Africa, G. N. Smit

IGC Proceedings (1977-2023)

The productivity of grasses is most important for herbivores in extensive semi-arid savannas. In these areas an increase in woody plant abundance, commonly referred to as bush encroachment, suppresses grasses. This is the main reason why landowners often consider thinning or even total clearing of all woody plants. The aims of this study were to investigate the influence of different intensities of tree thinning and subhabitat differentiation on the grass layer of a semi-arid South African savanna.

The Effect Of Different Utilisation Methods On Composition Of Semi-Natural Grassland, J. Jančovič, L'. Vozár, L'. Jančovičová

IGC Proceedings (1977-2023)

There has been much research on application of mineral fertilisers to permanent grasslands to maximise production of above-ground phytomass (Folkman & Jančovič 1990), but the changes arising after exclusion of fertilisers have not been studied in Slovak Republic up to now despite current interest in low input ststems. This paper reports on the effects of cessation of fertiliser inputs for an eight-year period.

Impact Of The Agricultural Use On The Biodiversity Of A Festuca Rubra Meadow, I. Rotar, F. Păcirar, R. Vidican, N. Sima

IGC Proceedings (1977-2023)

Technological inputs into meadow ecosystems trigger significant changes in the sward. In this paper we present the effect of organic and mineral fertilisation on the biodiversity of a Festuca rubra meadow.

Long-Term Effect Of Levels Of N-, P-, K-Supply On The Shannon-Index For Two Pastures Located In Central Germany, Judith F. Oerlemans, W. Opitz Von Boberfeld

IGC Proceedings (1977-2023)

Intensive grassland production, including the use of mineral fertilisers, has degraded the botanical diversity of grassland communities seriously (Chapman, 2001). There is little information on optimal amounts of soil nutrient availability to maintain/regenerate species-rich grassland communities. This study in Central Germany aimed to quantify the long-term effect of different N-, P-, K-supply combinations on biodiversity, expressed in terms of the Shannon-Index (Sh-Id), of 2 pastures classified as Lolio-Cynosuretum.

The Effect Of Npk Fertilisation On Structure And Species Composition Of Grasslands, Frantisek Hrabě, Jiří Skládanka

IGC Proceedings (1977-2023)

Long-term research into the effect of N+PK nutrition enables an objective evaluation of the trend and rate of succession and a prediction of changes including production development in permanent grassland (Hrabě et al., 1991). Former research (Hrabě & Halva, 1993) and evaluation within an eco-system concept (Rychnovská et al., 1994) demonstrated marked changes in the species composition of grass communities with the application of N+PK fertilisation that did not correspond to the sward type and site conditions.

Effect Of Aspect And Animal Movement On A Temperate Mountain Grassland Structure, Sorkunde Mendarte, I. Amezaga, Isabel Albizu, A. Ibarra, Iker Mijangos, M. Onaindia

IGC Proceedings (1977-2023)

Mountain pasture systems are maintained by the combination of physical and environmental factors and human activity leading to highly complex ecosystems (Watkinson & Ormerod 2000). Differences between pastures are usually due to physical conditions and animal pressure (Fynn & O´Connor 2000). In extensive livestock production systems in the Basque Country (northern Spain), livestock graze in mountain pastures from May until October. This study examined the effect of aspect and animal movement on grassland structure.

Plant Functional Types And Grazing Management In Mediterranean Grassland: An 11-Year Synthesis, Marcelo Sternberg, Zalmen Henkin, Avi Perevolotsky, M. Gutman, Eugene D. Ungar

IGC Proceedings (1977-2023)

Mediterranean ecosystems have high seasonality in resource availability, high year-to-year rainfall variability, many annual plants in the forage and a long history of grazing and disturbance. These facts, and results of previous studies (Sternberg et al., 2000) suggested that stocking rates could be increased above those of traditional grazing. However, the long-term effects of intensive grazing on the vegetation were not fully known. This study aimed to evaluate the responses of plant functional types (PFT) and community structure to different regimes of cattle grazing in Mediterranean grassland, particularly at high stocking rates.

Floristic Composition And Species Richness Model In Winter Rangelands Of Northeastern Iran, Anahita Rashtian, Mansour Mesdaghi

IGC Proceedings (1977-2023)

Due to the variable annual rainfall, the plant communities of rangelands in northeastern of Iran are fluctuating and the productivity is highly variable. This ecosystem covers about 500,000 ha and is one of the important winter ranges in Iran. In this fluctuating ecosystem, species diversity and floristic composition are changing annually (Pabot, 1967). Under heavy grazing most of the range species were extinct, but under light and moderate grazing, species richness was improved, fitting with the humped-back model (Wilkinson, 1999). The objectives of this research were 1) to determine floristic composition in three vegetation types and 2) to show the …

Long-Term Trends Of Community Structures In Tall Grassland Vegetation Under Three Treatments In Northeastern Japan, M. Tsutsumi, S. Sakanoue, S. Takahashi, Y. Yamamoto, Y. Saito, S. Itano

IGC Proceedings (1977-2023)

In order to acquire fundamental knowledge on sustainable use and conservation of grasslands in an Asian monsoon climate, we have investigated since 1982 the vegetation of typical Japanese tall-grass, Miscanthus sinensis (Japanese plume-grass) dominant grassland. Three treatments, cattle-grazing, cutting and abandoning were carried out at the study site. We report the results of this research here, in particular focusing on the analysis of the changes in community structure and the influence of different utilization.

Is Biodiversity Declining In The Traditional Haymeadows Of Skye And Lochalsh, Scotland?, G. E. D. Tiley, D. G. L. Jones

IGC Proceedings (1977-2023)

Species-rich haymeadows have developed on crofts in the Isle of Skye and Lochalsh Districts of north-west Scotland as a result of a century or more of traditional land use. This has involved long rotations of late cutting for hay with aftermath grazing by cattle and short breaks for cropping. The traditional haymeadows are increasingly coming under threat from changes taking place in the countryside. A survey of the main haymeadows still remaining in Skye and Lochalsh was carried out during 2003 to assess the current botanical composition, management and conservation value, and to compare with earlier surveys.

Development Of Saline Vegetation On Embanked Grasslands At The Baltic Sea Coast After 10 Years Of Extensive Pasture Use, Renate Bockholt, S. Schmitz, S. Noel

IGC Proceedings (1977-2023)

Since the establishment of the National Park "Vorpommersche Boddenlandschaft" in 1992, the objective has been the restoration the grasslands, which was used intensively before. The soil type is a fine- sand gley. Management of embanked grasslands has been changed into extensive management. Fertilisation, renewal of the sward and water control by drainage have been stopped. Instead of the previous use of cutting for silage, mother cows (1 cattle/ ha) were grazing the areas extensively.