Life Sciences Commons^™

Democratizing Bioinformatics Through Easily Accessible Software Platforms For Non-Experts In The Field, Konstantinos Krampis

Publications and Research

No abstract provided.

Critical Agronomic Practices For Establishing The Recently Domesticated Perennial Herbaceous Forage Legume Tedera In Mediterranean-Like Climatic Regions In Western Australia, Daniel Real

Grain and Other Field Crops Research Articles

Tedera is a Mediterranean perennial herbaceous forage legume that remains green during summer and autumn with minimal leaf drop when grown in the medium to low rainfall zones of Western Australia. This unique attribute allows out-of-growing-season grazing that can complement the traditional grazing system based on winter annual species. Tedera is a traditional rangeland forage in the Canary Islands, where it recruits naturally from seed. Now, following its domestication, an agronomy package needs to be developed to allow reliable establishment of commercial plantings. From 2017 to 2020, experiments were conducted at Cunderdin, Dandaragan, Three Springs, Manjimup, and Merredin in WA …

Smokejumper Obituary: Houston, Douglas Wayne “Doug” (Redmond 1973), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Early Evidence Of The Sars-Cov-2 B.1.1.529 (Omicron) Variant In Community Wastewater: United States, November–December 2021, Amy Kirby, Rory M. Welsh, Zachary Marsh, Davida S. Smyth, Et Al.

Biology Faculty Publications (Archived)

Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater — United States, November–December 2021

Covers: California, Colorado, New York City, Houston

Preliminary Evidence That Lectins In Infant Soy Formula Apparently Bind Bovine Milk Exosomes And Prevent Their Absorption In Healthy Adults, Ezra Mutai, Alice Kah Hui Ngu, Janos Zempleni

Department of Nutrition and Health Sciences: Faculty Publications

Background: Milk exosomes and their microRNA (miR) cargos are bioavailable. The content of exosomes and miRs is negligible in infant formulas compared to human milk, and dietary depletion of exosomes led to changes in bacterial communities and impaired gut health in juvenile mice. Adverse effects of formula feeding may be compounded by using soy formulas due to exosome binding by abundant lectins in that matrix. The purpose of this study was to assess the bioavailability of milk exosomes and their miR cargos added to soy formula in adults, as well as the potential role of soy lectins in exosome …

Territory Holders Are More Aggressive Towards Older, More Dangerous Floaters, Walter H. Piper, Katherine R. Lee, Brian Hoover

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Animals that show aggression often risk injury and incur steep energetic costs. Thus, aggression should occur at such times and towards such opponents as to maximize fitness. We tested hypotheses predicting adaptive territorial aggression in the common loon, a species in which ease of observation of territory owners and floaters (prebreeders) seeking to evict them provide a rare window onto owner-floater competition. As predicted, older, more competitive floaters (4-year-olds and upwards) tended to intrude into territories that had produced chicks the previous year (and, hence, were of high quality). Older floaters also showed predicted increases in aggression and territorial yodeling, …

Serotype-Specific Effectiveness Against Pneumococcal Carriage And Serotype Replacement After Ten-Valent Pneumococcal Conjugate Vaccine (Pcv10) Introduction In Pakistan, Muhammad Imran Nisar, Fyezah Jehan, Shahira Shahid, Sheraz Ahmed, Sadia Shakoor, Furqan Kabir, Aneeta Hotwani, Sahrish Muneer, Farah Khalid, Sajid Muhammad, Asad Ali, Najeeha Talat Iqbal

Department of Paediatrics and Child Health

Objective: Pakistan was one of the first South-Asian countries to introduce the ten-valent pneumococcal conjugate vaccine (PCV10) at the national level, using a 3+0 schedule without catchup, in 2013.
Methods: From 2014-18, fifteen children Matiari, Sindh, and nasopharyngeal swabs were collected. The samples were cultured, and pneumococcus was further serotyped through multiplex PCR at the Aga Khan University Hospital as per the method described by the Centers for Disease Control and Prevention, USA.
Results: Pneumococcus was detected in 2370/3140 (75%) children. Vaccine type (VT) and non-vaccine type (NVT) serotypes were carried by 379 and 1990 children. There was a significant …

Pparα And Pparγ Activation Is Associated With Pleural Mesothelioma Invasion But Therapeutic Inhibition Is Ineffective, M. Lizeth Orozco Morales, Catherine A. Rinaldi, Emma De Jong, Sally M. Lansley, Joel P. A. Gummer, Bence Olasz, Shabarinath Nambiar, Danika E. Hope, Thomas H. Casey, Y. C. Gary Lee, Connull Leslie, Gareth Nealon, David M. Shackleford, Andrew K. Powell, Marina Grimaldi, Patrick Balaguer, Rachael M. Zemek, Anthony Bosco, Matthew J. Piggott, Alice Vrielink, Richard A. Lake, W. Joost Lesterhuis

Research outputs 2022 to 2026

Mesothelioma is a cancer that typically originates in the pleura of the lungs. It rapidly invades the surrounding tissues, causing pain and shortness of breath. We compared cell lines injected either subcutaneously or intrapleurally and found that only the latter resulted in invasive and rapid growth. Pleural tumors displayed a transcriptional signature consistent with increased activity of nuclear receptors PPARα and PPARγ and with an increased abundance of endogenous PPAR-activating ligands. We found that chemical probe GW6471 is a potent, dual PPARα/γ antagonist with anti-invasive and anti-proliferative activity in vitro. However, administration of GW6471 at doses that provided sustained plasma …

Sebasthian Varas – Covid 19 Oral History Project, Sebasthian Varas, Institute Of Child Nutrition. Child Nutrition Archives.

Oral History Project (all interviews)

Since 2009, Sebasthian Varas has worked for Canyons School District in Utah as the director for Nutrition Services. He is responsible for providing leadership and direction in matters pertaining to child nutrition programs for 33,000 students. He manages 43 schools and 275 employees.

Melissa Campbell And John Dupre - Covid 19 Oral History Project, Melissa Campbell, Institute Of Child Nutrition. Child Nutrition Archives.

Oral History Project (all interviews)

During 2022 the Child Nutrition Archives conducted multiple interviews investigating how child nutrition professionals dealt with the Covid 19 pandemic and its effects on the operations of school feeding programs. This interview examines the response of the Louisiana Department of Education Child Nutrition Programs.

Effect Of Seeding Rates On Productivity And Quality Of Alfalfa In Northern Area Of Korea, Jong Geun Kim, C. Liu, S. N. Wei, Y. F. Li, E. C. Jeong, H. J. Kim

IGC Proceedings (1977-2023)

Alfalfa cultivation in South Korea is not common. There are many reasons, but low productivity has been extremely limited. Although alfalfa growth was poor due to boron deficiency in the soil, the problem has recently been solved. Nevertheless, the cultivation of alfalfa is not expanding. About 200,000 tonnes of alfalfa hay are imported every year. Therefore, this study was conducted to find a way to replace imported hay by expanding alfalfa cultivation in Korea. Alfalfa (P5444) was sown in northern part of South Korea (Pyeongchang). Alfalfa was sown in September 2018 with different seeding rates (20, 30 and 40 kg/ha) …

Effect Of Prompt-Delayed Packaging And Ensiling Time On Fermentation And Aerobic Stability Of Soybean Curd Residue, Ajmal Wali, Takeshi Tsuruta, Naoki Nishino

IGC Proceedings (1977-2023)

Wet soybean curd residue (SCR) obtained from two tofu factories (F1 and F2) was anaerobically stored with or without added beet pulp (BP). Sealing was performed on the day of tofu production (prompt sealing [PS]) or 2 days after SCR was piled and unprocessed (delayed sealing [DS]). Predominant lactic acid fermentation was observed regardless of the sealing time and BP addition. Acinetobacter spp. were the most abundant (> 67%) bacteria in pre-ensiled SCR, regardless of the factory and sealing time. In PS silage, the abundances of typical lactic acid-producing bacteria, such as Lactobacillus, Pediococcus, and Streptococcus spp. reached …

Effect Of Native Grassland Intensification Over Cattle Performance, N. Caram, F. Casalás, M. Cadenazzi, R. Zanoniani, P. Boggiano

IGC Proceedings (1977-2023)

The objective was to evaluate the effect of different levels of intensification in native grassland over cattle live weight gain (LWG), stocking rate (SR) and average daily gain (ADG) in Uruguay. The study was carried out in 7.8 ha in Paysandú, between winter 2015 and autumn 2019. Experiment was a randomized complete block design, with 4 replicates. The four treatments applied were native grassland (NG), NG overseeded with Trifolium pratense (6 kg.ha^-1) and Lotus tenuis (6 kg.ha^-1) + 40 kg.ha^-1 of P₂O₅ (NGO), NG fertilized with 60 kg.ha^-1 of N + …

Relationship Between Exchangeable Acidity And Persistence Of Orchardgrass (Dactylis Glomerata) In Temperate Pastures Under Different Management, H. Kakihara, S. Ogura

IGC Proceedings (1977-2023)

Orchardgrass is a high productive, highly nutritive grass, but its persistence is low under acid soil condition. Therefore, to obtain the information on the effect of soil acidity on the persistence of orchardgrass in acid soil grasslands, we investigated the relationship between exchangeable acidity (y₁) and orchardgrass in sown pastures. Eight temperate pastures (four cutting meadows [CMs] and four cattle grazing pastures [GPs]) were used for vegetation survey and soil samplings. Six or three line transects (50 m each) were fixed in each meadow or pasture, and measurement location (three quadrats 20 cm×20 cm in size and 50 …

Productivity Of Grasslands In Wielkopolska In Conditions Of Weather Variables Changes In The Last 34 Years, B. Golińska, M. Czerwiński, P. Goliński

IGC Proceedings (1977-2023)

The purpose of this study was the assessment of the effect of climatic changes since 1985 on the productivity of grasslands in Wielkopolska region (Poland). The weather data (precipitation sum, mean, maximum and minimum air temperature, insolation, relative air humidity and wind speed) were collected from 1985 to 2018 at five weather stations located in the region that belong to the Institute of Meteorology and Water Management. Using this data, trends of Standardized Precipitation Evapotranspiration Index (SPEI) were determined. Grassland productivity was estimated from data collected by the Central Statistical Office, that refer to meadow hay production for each commune …

The Diversity Of Poisonous Plant Patches In The Arid Rangelands Of Namaqualand, South Africa, T. Jamalie, M. I. Samuels, C. F. Cupido, F. L. Müller, W. L. Engelbrecht, T. Dube, R. S. Knight

IGC Proceedings (1977-2023)

The Namaqualand region in South Africa is part of the richest arid biodiversity hotspot in the world. Plant distribution and diversity here are impacted by various biophysical and anthropogenic factors. In these landscapes, poisonous plant patches, which pose serious threats to livestock, are widespread but their contribution to the regions biodiversity are not fully understood. This study assessed their plant diversity and compared its matrix. This study was conducted in the semi-arid to arid Steinkopf pastoral area located in Namaqualand where livestock is still herded daily. Twenty-five paired sites were selected based on the dominance of poisonous plants within the …

Isotopic Δ15N Signature Of Grass-Alone And Grass-Legume Tropical Pastures To Estimate Sources Of Nitrogen To Grasses In Farmer Managed Pastures, Daniel M. Villegas, J. Velasquez, J. Arango, K. Obregon, Idupulapati M. Rao, G. Rosas, A. Oberson

IGC Proceedings (1977-2023)

Vast areas of tropical forest have been converted into pastures sown with introduced grasses (Urochloa spp.). The majority of pastures exist in some stage of degradation, which has dramatic ecological and economic consequences. Our objective was to determine isotopic ¹⁵N signature of grass alone and grass-legume pastures to estimate sources of nitrogen (N) to grasses in farmer managed pastures. This work contributes to enhancing the sustainability of tropical pastures in forest margins through the integration of legumes. The overarching hypothesis tested was that legumes associated with grasses will improve nutrient supply via symbiotic fixation and mobilization of soil …

Landscape-Level Impacts Of Mesquite Canopy Cover On Herbaceous Species Composition, D. B. Murray, C. E. Cooper

IGC Proceedings (1977-2023)

Woody encroachment of mesquite (Prosopis) and acacia (Acacia) species into grasslands has widespread and ongoing impacts on grassland ecosystems. Changes in the herbaceous layer are associated with changes in the canopy cover of these sparse-canopied species, which do not exclude the herbaceous component, but often change species composition under the canopy relative to surrounding open areas. These effects are often differential based on productivity of the site and herbaceous species composition of the grassland. Here we investigated landscape-scale changes in the herbaceous composition resulting from changes in canopy cover of honey mesquite (Prosopis glandulosa) …

Interactive Effects Of Drought And Fire On Co-Existing Woody And Herbaceous Communities In A Temperate Mesic Grassland, R. Keen, J. Nippert, E. Tooley, K. O’Keefe, S. Bachle, M. Sandwick

IGC Proceedings (1977-2023)

Increased drought and woody encroachment are likely to have substantial and interactive effects on grassland carbon and water cycling in the future. However, we currently lack necessary information to accurately predict grassland responses to drought-by-fire interactions in areas experiencing woody encroachment. A more thorough understanding of these interactive effects on grass-shrub physiology would improve the effectiveness of demographic vegetation models and refine predictions of future changes in grassland ecosystem function. To this end, we constructed passive rainout shelters over mature Cornus drummondii shrubs and co-existing grasses in two fire treatments (1-year and 4-year burn frequency) at the Konza Prairie Biological …

Interacting Effects Of Disease And Weather Variability On Rangeland Biodiversity Associated With Black-Tailed Prairie Dog (Cynomys Ludovicianus) Colonies, Courtney J. Duchardt, J. D. Hennig, D. Pellatz

IGC Proceedings (1977-2023)

Rangeland ecosystems worldwide are experiencing novel pressures during the Anthropocene, including land conversion, disease dynamics, non-native species, and climate change. These issues can be compounded in rangelands occupied by burrowing rodents. Often considered keystone species important for maintaining rangeland biodiversity, these species often experience widespread control efforts because of their potential to reduce forage for livestock. We examined the effects of climatic variation and disease on bird communities associated with a North American burrowing rodent, the black-tailed prairie dog (Cynomys ludovicianus). Following an outbreak of sylvatic plague (Yersinia pestis) in the prairie dog population, we observed …

Influence Of Grazing Intensity On Nutrient Concentrations In Grass Tissue: Evidence From Two Savannah Grass Species, C. Munyati

IGC Proceedings (1977-2023)

High grazing intensity can accelerate the recycling of animal nutrients on savannah rangelands through the deposition of dung and, subsequently, nutrient mineralisation, uptake and concentration in grass tissue. The actual magnitude of this influence can vary depending on the grazing system. This study derived grazing system-dependent magnitudes of the influence of grazing intensity on concentrations of major (N, P, K, Ca, Mg, Na) and trace (B, Co, Cu, Cr, Fe, Mn, Mo, Ni, Se, Zn) animal nutrients in above ground grass tissue. Two grass species were examined: Brachiaria nigropedata, a decreaser, and Eragrostis lehmanniana, an increaser. For the …

Proteomic Analysis Of Epididymal And Ejaculated Sperm And Respective Fluids, Saulo Menegatti Zoca, Emmalee J. Northrop-Albrecht, Julie Walker, Robert A. Cushman, George Perry

SDSU Beef Day 2022 Summary Publication

Study Description:

Ejaculated and epididymal semen was collected from mature Angus bulls (n = 9), and then centrifuged to separate sperm and fluid. Fluids were collected and sperm pellets were resuspended in a high ionic solution and vortexed to remove loosely attached proteins. Sperm samples were centrifuged, and the supernatant was collected. Samples collected for protein analysis were snap frozen in liquid nitrogen and stored at -80 ºC. Protein analysis was performed by liquid chromatography with tandem mass spectrometry (LCMS/MS). Yearling Angus cross bulls (n = 40) were used for sperm cultures. Ejaculated (n = 20) and epididymal (n = …

Results Of A Phase 1, Randomized, Placebocontrolled First-In-Human Trial Of Griffithsin Formulated In A Carrageenan Vaginal Gel, Natalia Teleshova, Maria J. Keller, José A. Fernández Romero, Barbara A. Friedland, George W. Creasy, Marlena G. Plagianos, Laurie Ray, Patrick Barnable, Larisa Kizima, Aixa Rodriguez, Nadjet Cornejal, Claudia Melo, Gearoff Cruz Rodriguez, Sampurna Mukhopadhyay, Giulia Calenda, Shweta U. Sinkar, Thierry Bonnaire, Asa Wesenberg, Shimin Zhang, Kyle Kleinbeck, Kenneth Palmer, Mohcine Alami, Barry R. O'Keefe, Patrick Gillevet, Hong Hur, Yupu Liang, Gabriela Santone, Raina N. Fichorova, Tamara Kalir, Thomas M. Zydowsky

Publications and Research

HIV pre-exposure prophylaxis (PrEP) is dominated by clinical therapeutic antiretroviral (ARV) drugs. Griffithsin (GRFT) is a non-ARV lectin with potent anti-HIV activity. GRFT’s preclinical safety, lack of systemic absorption after vaginal administration in animal studies, and lack of cross-resistance with existing ARV drugs prompted its development for topical HIV PrEP. We investigated safety, pharmacokinetics (PK), pharmacodynamics (PD), and immunogenicity of PC-6500 (0.1% GRFT in a carrageenan (CG) gel) in healthy women after vaginal administration. This randomized, placebo-controlled, parallel group, double-blind first-in-human phase 1 study enrolled healthy, HIV-negative, non-pregnant women aged 24–45 years. In the open label period, all participants (n …

Voluntary Workplace Genomic Testing: Wellness Benefit Or Pandora's Box?, Kunal Sanghavi, Betty Cohn, Anya E R Prince, W Gregory Feero, Kerry A Ryan, Kayte Spector-Bagdady, Wendy R Uhlmann, Charles Lee, J Scott Roberts, Debra J H Mathews

Faculty Research 2022

Consumer interest in genetic and genomic testing is growing rapidly, with more than 26 million Americans having purchased direct-to-consumer genetic testing services. Capitalizing on the increasing comfort of consumers with genetic testing outside the clinical environment, commercial vendors are expanding their customer base by marketing genetic and genomic testing services, including testing for pharmacogenomic and pathogenic variants, to employers for inclusion in workplace wellness programs. We describe the appeal of voluntary workplace genomic testing (wGT) to employers and employees, how the ethical, legal, and social implications literature has approached the issue of genetic testing in the workplace in the past, …

A Biological Condition Gradient For Caribbean Coral Reefs: Part Ii. Numeric Rules Using Sessile Benthic Organisms, Deborah L. Santavy, Susan K. Jackson, Benjamin Jessup, Christina Horstmann, Caroline Rogers, Ernesto Weil, Alina Szmant, David Cuevas Miranda, Brian K. Walker, Christopher Jeffrey, David Ballantine, William S. Fisher, Randy Clark, Hector Ruiz Torres, Brandi Todd, Sandy Raimondo

Marine & Environmental Sciences Faculty Articles

The Biological Condition Gradient (BCG) is a conceptual model used to describe incremental changes in bio- logical condition along a gradient of increasing anthropogenic stress. As coral reefs collapse globally, scientists and managers are focused on how to sustain the crucial structure and functions, and the benefits that healthy coral reef ecosystems provide for many economies and societies. We developed a numeric (quantitative) BGC model for the coral reefs of Puerto Rico and the US Virgin Islands to transparently facilitate ecologically meaningful management decisions regarding these fragile resources. Here, reef conditions range from natural, undisturbed conditions to severely altered or …

Self-Conscious Emotions And The Right Fronto-Temporal And Right Temporal Parietal Junction, Adriana Lavarco, Nathira Ahmad, Qiana Archer, Matthew Pardillo, Ray Nunez Castaneda, Anthony Minervini, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

For more than two decades, research focusing on both clinical and non-clinical populations has suggested a key role for specific regions in the regulation of self-conscious emotions. It is speculated that both the expression and the interpretation of self-conscious emotions are critical in humans for action planning and response, communication, learning, parenting, and most social encounters. Empathy, Guilt, Jealousy, Shame, and Pride are all categorized as self-conscious emotions, all of which are crucial components to one’s sense of self. There has been an abundance of evidence pointing to the right Fronto-Temporal involvement in the integration of cognitive processes underlying the …

What Are The Primary Cues Used By Mammalian Predators To Locate Freshwater Turtle Nests? A Critical Review Of The Evidence, Gregory A. Geller, Scott L. Parker

Biology

Turtle biologists have long been interested in the biotic and abiotic factors that influence the detection of freshwater turtle nests by mammalian predators. Increased knowledge of nest predation dynamics may help develop conservation strategies to increase turtle nesting success by altering or reducing the signal strength of predominant nest location cues. However, despite this long-standing interest, the related research has produced inconsistent and sometimes conflicting results across studies. Here we review much of the existing literature on freshwater turtle nest predation by mammalian predators and attempt to synthesize some general, underlying themes. Available data suggest that raccoons (Procyon lotor) primarily …

Dual Task Performance Is Associated With Amyloidosis In Cognitively Healthy Adults, Jason K. Longhurst, Jeffrey L. Cummings, Samantha E. John, Brach Poston, J. V. Rider, A. M. Salazar, V. R. Mishra, A. Ritter, J. Z. Caldwell, J. B. Miller, Jefferson W. Kinney, Merrill R. Landers

Brain Health Faculty Research

Background: Preclinical Alzheimer’s disease (AD) provides an opportunity for the study and implementation of interventions and strategies aimed at delaying, mitigating, and preventing AD. While this preclinical state is an ideal target, it is difficult to identify efficiently and cost-effectively. Recent findings have suggested that cognitive-motor dual task paradigms may provide additional inference. Objectives: Investigate the relationship between dual task performance and amyloidosis, suggestive of preclinical Alzheimer’s disease and whether dual task performance provides additional information beyond a cognitive composite, to help in the identification of amyloidosis. Design: Cross-sectional. Setting: Outpatient specialty brain health clinical research institution in the United …

Recent Advances In Our Molecular And Mechanistic Understanding Of Misfolded Cellular Proteins In Alzheimer’S Disease (Ad) And Prion Disease (Prd), Walter J. Lukiw

School of Medicine Faculty Publications

Naturally occurring neuron-abundant proteins including amyloid Aβ42 peptide and the microtubule-associated protein tau (MAPT) can, over time and under pathological situations, assume atypical conformations, altering their normal biological structure and function, and causing them to aggregate into insoluble and neurotoxic intracellular inclusions. These misfolded proteins ultimately contribute to the pathogenesis of several progressive, age-related and ultimately lethal human neurodegenerative disorders. The molecular mechanism of this pathological phenomenon of neuronal protein misfolding lends support to the ‘prion hypothesis’, which predicts that the aberrant folding of endogenous natural protein structures into unusual pathogenic isoforms can induce the atypical folding of other similar …

Maps Of Ticks (Acari: Argasidae, Ixodidae) For Austria And South Tyrol, Italy, Franz Rubel, Katharina Brugger

Harold W. Manter Laboratory of Parasitology: Library Materials

A first compilation of georeferenced tick locations in Austria and South Tyrol, Italy, is presented here. This allows the tick fauna to be examined in the various climatic regions of the European Alps. The dataset comprises 424 tick locations of Austria and 48 tick locations of South Tyrol, which were digitized from literature and visualized in the form of geographical maps. The tick fauna of Austria includes two species of Argasidae in the genera Argas and Carios and 15 species of Ixodidae in the genera Dermacentor, Haemaphysalis, and Ixodes, altogether 17 tick species. In addition, two species …