Digital Commons Network^™

High Throughput Analysis Of Leaf Chlorophyll Content In Sorghum Using Rgb, Hyperspectral, And Fluorescence Imaging And Sensor Fusion, Huichun Zhang, Yufeng Ge, Xinyan Xie, Abbas Atefi, Nuwan Wijewardane,, Suresh Thapa

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Leaf chlorophyll content plays an important role in indicating plant stresses and nutrient status. Traditional approaches for the quantification of chlorophyll content mainly include acetone ethanol extraction, spectrophotometry and high-performance liquid chromatography. Such destructive methods based on laboratory procedures are time consuming, expensive, and not suitable for high-throughput analysis. High throughput imaging techniques are now widely used for non-destructive analysis of plant phenotypic traits. In this study three imaging modules (RGB, hyperspectral, and fluorescence imaging) were, separately and in combination, used to estimate chlorophyll content of sorghum plants in a greenhouse environment. Color features, spectral indices, and chlorophyll fluorescence …

Sources Of Variability And Uncertainty In Food-Energy-Water Nexus Systems, Heydi Calderon-Ambelis, Deepak R. Keshwani

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A nexus approach contributes to the strategic allocation of resources to secure food, energy, and water for the world population. Integrated models considering the complex interactions across food, energy, and water (FEW) enhance decision-making and strategic planning towards resilience. However, a significant number of the existing integrated models leave unaddressed the inherent variability and uncertainty present in the FEW sectors. Here, we review the importance of characterizing variability over spatial and temporal scales and the importance of decreasing the uncertainty present within a FEW nexus systems. The review also discusses existing modeling tools that address variability and uncertainty on single …

Modeling Water Quantity And Quality Nonlinearities For Watershed Adaptability To Hydroclimate Extremes In Agricultural Landscapes, Juan Carlos Jaimes-Correa, Francisco Muñoz-Arriola, Shannon Bartelt-Hunt

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Changing water supplies and demands, inherent to climate fluctuations and human activities, are pushing for a paradigm shift in water management worldwide. The occurrence of extreme hydrometeorological and climate events such as extended wet periods and droughts, compounded with contaminants, impair the access to water resources, demanding novel designs, construction, and management across multiple hydrologic scales and biogeochemical processes. A constraint to studying hydrologic and biogeochemical disturbances and improving best management practices for water quantity and quality at the watershed scale resides in the suitable monitoring, data availability, and the creation of frameworks. We hypothesize that streamflow and contaminants, simulated …

Comparison Effect On Biogas Production From Vegetable And Fruit Waste With Rumen Digesta Through Co-Digestion Process, Anika Tasnim, Muhammad Rashed Al Mamun, Md Anwar Hossen, Md Towfiqur Rahman, Md Janibul Alam Soeb

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Biogas is the best renewable energy as it can be produced from any biomass for example any plant or living organism. The purpose of this research was to produce biomethane from co-digestion of vegetable and fruit waste with rumen digesta through anaerobic digestion process. In this research, two trials of experiment were conducted. Each trial has three different sample with different mixing ratios. Raw materials used in the experiment was rumen digesta of goat and cow, potato, capsicum, cucumbers, onions, radish, cauliflower, carrot, leafy vegetables, apple, banana, and papaya. In each sample, 1200 gram of raw materials were used. Hydraulic …

Influences Of Artificial Light On Mating Of Black Soldier Fly (Hermetia Illucens): A Review, Md Rabiul Awal, Md Masudur Rahman, Md Abdur Razzak Choudhury, Md Mehedi Hasan, Md Towfiqur Rahman, Md Fuad Mondal

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Black soldier fly (Hermetia illucens) is a potential insect species which can convert biodegradable materials and some indigestible organic waste into valuable biomass. Because of having good quality of fat and protein, its production and use in animal feed are being extended day by day. To fulfill the future demand re-searchers are trying to find out the successful mass rearing techniques of H. illucens in laboratory or indoor condition. However, the most critical part of H. illucens mass production is obtaining successful mating. This insect is very sensitive to light. It prefers direct sunlight for its …

Modeling The Evolution Of Herbicide Resistance In Weed Species With A Complex Life Cycle, K. Harrison Holmes, John L. Lindquist, Richard Rebarber, Rodrigo Werle, Melinda K. Yerka, Brigitte Tenhumberg

Brigitte Tenhumberg Papers

A growing number of weed species have evolved resistance to herbicides in recent years, which causes an immense financial burden to farmers. An increasingly popular method of weed control is the adoption of crops that are resistant to specific herbicides, which allows farmers to apply the herbicide during the growing season without harming the crop. If such crops are planted in the presence of closely related weed species, it is possible that resistance genes could transfer from the crop species to feral populations of the wild species via gene flow and become stably introgressed under ongoing selective pressure by the …

Exploring Higher-Order Conceptual Learning In An Arthropod With A Large Multisensory Processing Center, Kenna D. S. Lehmann, Fiona G. Shogren, Mariah Fallick, James Colton Watts, Daniel Schoenberg, Daniel D. Wiegmann, Verner P. Bingman, Eileen A. Hebets

School of Biological Sciences: Faculty Publications

Comparative cognition aims to understand the evolutionary history and current function of cognitive abilities in a variety of species with diverse natural histories. One characteristic often attributed to higher cognitive abilities is higher-order conceptual learning, such as the ability to learn concepts independent of stimuli—e.g., ‘same’ or ‘different’. Conceptual learning has been documented in honeybees and a number of vertebrates. Amblypygids, nocturnal enigmatic arachnids, are good candidates for higher-order learning because they are excellent associational learners, exceptional navigators, and they have large, highly folded mushroom bodies, which are brain regions known to be involved in learning and memory in insects. …

Reconstructed Evolutionary Patterns For Crocodile-Line Archosaurs Demonstrate Impact Of Failure To Log-Transform Body Size Data, Roger B. J. Benson, Pedro Godoy, Mario Bronzati, Richard J. Butler, William Gearty

School of Biological Sciences: Faculty Publications

No abstract provided.

The Ecology Of Wealth Inequality In Animal Societies, Eli D. Strauss, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Individuals vary in their access to resources, social connections and phenotypic traits, and a central goal of evolutionary biology is to understand how this variation arises and influences fitness. Parallel research on humans has focused on the causes and consequences of variation in material possessions, opportunity and health. Central to both fields of study is that unequal distribution of wealth is an important component of social structure that drives variation in relevant outcomes. Here, we advance a research framework and agenda for studying wealth inequality within an ecological and evolutionary context. This ecology of inequality approach presents the opportunity to …

Integrating Tropical Research Into Biology Education Is Urgently Needed, Ann E. Russell, T. Mitchell Aide, Elizabeth Braker, Carissa N. Ganong, Rebecca D. Hardin, Karen D. Holl, Sara C. Hotchkiss, Jeffrey A. Klemens, Erin K. Kuprewicz, Deedra Mcclearn, George Middendorf, Rebecca Ostertag, Jennifer S. Powers, Sabrina E. Russo, Jennifer L. Stynoski, Ursula Valdez, Charles G. Willis

School of Biological Sciences: Faculty Publications

Understanding tropical biology is important for solving complex problems such as climate change, biodiversity loss, and zoonotic pandemics, but biology curricula view research mostly via a temperatezone lens. Integrating tropical research into biology education is urgently needed to tackle these issues.

The tropics are engines of Earth systems that regulate global cycles of carbon and water, and are thus critical for management of greenhouse gases. Compared with higher-latitude areas, tropical regions contain a greater diversity of biomes, organisms, and complexity of biological interactions. The tropics house the majority of the world’s human population and provide important global commodities from species …

Functional Response Of Harmonia Axyridis To The Larvae Of Spodoptera Litura: The Combined Effect Of Temperatures And Prey Instars, Yasir Islam, Farhan Mahmood Shah, Ali Güncan, John Paul Delong, Xingmiao Zhou

School of Biological Sciences: Faculty Publications

Functional responses are central to predator–prey dynamics and describe how predation varies with prey abundance. Functional responses often are measured without regard to prey size (i.e., body mass) or the temperature dependence of feeding rates. However, variation in prey size within populations is ubiquitous, and predation rates are often both size and temperature-dependent. Here, we assessed functional responses of larvae and adult Harmonia axyridis on the 1st, 2nd, and 3rd instars of the prey Spodoptera litura across a range of temperatures (i.e., 15, 20, 25, 30, and 35◦C). The type and parameters of the functional responses were determined using logistic …

Pea Aphid Winged And Wingless Males Exhibit Reproductive, Gene Expression, And Lipid Metabolism Differences, Omid Saleh Ziabari, Qingyi Zhong, Swapna R. Purandare, Joel Reiter, Anthony J. Zera, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Alternative, intraspecific phenotypes offer an opportunity to identify the mechanistic basis of differences asso- ciated with distinctive life history strategies. Wing dimorphic insects, in which both flight-capable and flight- incapable individuals occur in the same population, are particularly well-studied in terms of why and how the morphs trade offflight for reproduction. Yet despite a wealth of studies examining the differences between fe- male morphs, little is known about male differences, which could arise from different causes than those acting on females. Here we examined reproductive, gene expression, and biochemical differences between pea aphid ( Acyrthosiphon pisum ) winged and wingless …

Social Networks In The Single Cell, Moira Rodriguez, Ana Martinez-Hottovy, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial DNA (mtDNA) can become damaged in many ways. A major repair mechanism is homologous recombination, which requires an undamaged DNA template. Presumably, this template comes from a different mitochondrion in the same cell. Plant mitochondria undergo fission and fusion to form transient networks which could allow the exchange of genetic information. To test this hypothesis, Chustecki et al. (2022) used msh1 mutants with defective DNA repair, and showed that mitochondrial interactions increased, revealing a link between the physical and genetic behavior of mitochondria.

Late Pleistocene Megafauna Extinction Leads To Missing Pieces Of Ecological Space In A North American Mammal Community, Felisa A. Smith, Emma A. Elliott Smith, Amelia Villaseñor, Catalina P. Tomé, S. Kathleen Lyons, Seth D. Newsome

School of Biological Sciences: Faculty Publications

The conservation status of large-bodied mammals is dire. Their decline has serious consequences because they have unique ecological roles not replicated by smaller-bodied animals. Here, we use the fossil record of the megafauna extinction at the terminal Pleistocene to explore the consequences of past biodiversity loss. We characterize the isotopic and body-size niche of a mammal community in Texas before and after the event to assess the influence on the ecology and ecological interactions of surviving species (>1 kg). Preextinction, a variety of C₄ grazers, C₃ browsers, and mixed feeders existed, similar to modern African savannas, with …

Fishing Regulations, Sexual Dimorphism, And The Life History Of Harvest, Lyndsie S. Wszola, Zachary S. Feiner, Christopher J. Chizinski, Jamilynn B. Poletto, John P. Delong

School of Biological Sciences: Faculty Publications

Freshwater recreational fisheries regulations are a vital tool for achieving social and ecological fisheries objectives. However, angler behavior and fish biology may interact to influence regulation efficacy in unexpected ways. We combined models of fish growth and angler behavior to explore how angler behavior interacts with fish life history to shape the probability of fish harvest given capture across ages, life stages, and sexes of walleye (Sander vitreus). Compared to females, males grew more quickly as juveniles, matured earlier, and reached smaller maximum sizes. Male walleye were therefore vulnerable to harvest for more of their reproductive lives than …

Forage Database: A Compilation Of Functional Responses For Consumers And Parasitoids, Stella Uiterwaal, Ian T. Lagerstrom, Shelby R. Lyon, John Delong

School of Biological Sciences: Faculty Publications

Functional responses, the relationships between consumer foraging rate and resource (prey) density, provide key insights into consumer–resource interactions while also being a major driver of population dynamics and food web structure. We present a global database of 2598 standardized functional responses and parameters extracted from the published literature. We refit the functional responses with a Type II model using standardized methods and report the fitted parameters along with data on experimental conditions, consumer and resource taxonomy and type, as well as the habitat and dimensionality of the foraging interaction. The consumer and resource species covered here are taxonomically diverse, from …

An Empiricist’S Guide To Using Ecological Theory, Tess N. Grainger, Athmanathan Senthilnathan, Po-Ju Ke, Matthew A. Barbour, Natalie T. Jones, John Delong, Sarah P. Otto, Mary I. O'Connor, Kyle E. Coblentz, Nikunj Goel, Jawad Sakarchi, Megan C. Szojka, Jonathan M. Levine, Rachel M. Germain

School of Biological Sciences: Faculty Publications

A scientific understanding of the biological world arises when ideas about how nature works are formalized, tested, refined, and then tested again. Although the benefits of feedback between theoretical and empirical research are widely acknowledged by ecologists, this link is still not as strong as it could be in ecological research. This is in part because theory, particularly when expressed mathematically, can feel inaccessible to empiricists who may have little formal training in advanced math. To address this persistent barrier, we provide a general and accessible guide that covers the basic, step-by-step process of how to approach, understand, and use …

Towards An Integrative View Of Virus Phenotypes, John P. Delong, Maitham A. Al-Sammak, Zeina Al-Ameeli, David Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack

School of Biological Sciences: Faculty Publications

Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus’s phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in …

Predator Functional Responses And The Biocontrol Of Aphids And Mites, John Delong, Stella Uiterwaal

School of Biological Sciences: Faculty Publications

Biocontrol with predators is a key tool for controlling agricultural pests and preserving the productive efficiency of crops. Determining which predators to use for biocontrol often involves measuring their functional response—the relationship between foraging rate and prey abundance, yet comparisons of functional responses across predators are complicated by differences in experimental procedures. Here we use a compilation of functional responses standardized for time and space units to illustrate key sources of variation in functional responses for predators being tested for control of aphids and mites. Our results show that arena size (as a proxy for habitat structure) is a crucial …

What Happens When Transition Metal Trichalcogenides Are Interfaced With Gold?, Archit Dhingra, Dmitri E. Nikonov, Alexey Lipatov, Alexander Sinitskii, Peter Dowben

Peter Dowben Publications

Transition metal trichalcogenides (TMTs) are two-dimensional (2D) systems with quasi-one-dimensional (quasi-1D) chains. These 2D materials are less susceptible to undesirable edge defects, which enhances their promise for low-dimensional optical and electronic device applications. However, so far, the performance of 2D devices based on TMTs has been hampered by contact-related issues. Therefore, in this review, a diligent effort has been made to both elucidate and summarize the interfacial interactions between gold and various TMTs, namely, In₄Se₃, TiS₃, ZrS₃, HfS₃, and HfSe₃. X-ray photoemission spectroscopy data, supported by the results …

A Biological And Chemical Approach To Restoring Water Quality: A Case Study In An Urban Eutrophic Pond, Levi J. Mckercher, Tiffany L. Messer, Aaron R. Mittelstet, Steve D. Comfort

School of Natural Resources: Faculty Publications

Efforts to improve water quality of eutrophic ponds often involve implementing changes to watershed management practices to reduce external nutrient loads. While this is required for long-term recovery and prevention, eutrophic conditions are often sustained through the recycling of internal nutrients already present within the waterbody. In particular, internal phosphorus bound to organic material and adsorbed to sediment has the potential to delay lake recovery for decades. Thus, pond and watershed management techniques are needed that not only reduce external nutrient loading but also mitigate the effects of internal nutrients already present. Therefore, our objective was to demonstrate a biological …

A Pivotal New Approach To Groundwater Quality Assessment, M. L. Cherry, T. Gilmore, T. Messer, Y. Li, J. Westrop

School of Natural Resources: Faculty Publications

No abstract provided.

Natural Environment: Protocol To Recover Pollen Grains On Bodies, Karl J. Reinhard, A. Barbosa

School of Natural Resources: Faculty Publications

No abstract provided.

Phenotypic And Genomic Diversification In Complex Carbohydrate-Degrading Human Gut Bacteria, Nicholas A. Pudlo, Karthik Urs, Ryan Crawford, Ali Pirani, Todd Atherly, Roberto Jimenez, Nicolas Terrapon, Bernard Henrissat, Daniel Peterson, Cherie Ziemer, Evan Snitkin, Eric C. Martens

Department of Food Science and Technology: Faculty Publications

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability …

Experimental Evaluation Of Ecological Principles To Understand And Modulate The Outcome Of Bacterial Strain Competition In Gut Microbiomes, Rafael R. Segura Munoz, Sara Mantz, Ines Martinez, Fuyong Li, Robert J. Schmaltz, Nicholas A. Pudlo, Karthik Urs, Eric C. Martens, Jens Walter, Amanda Ramer-Tait

Department of Food Science and Technology: Faculty Publications

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus …

Large-Scale Analyses Of Heat Shock Transcription Factors And Database Construction Based On Whole-Genome Genes In Horticultural And Representative Plants, Tong Yu, Yun Bai, Zhuo Liu, Zhiyuan Wang, Qihang Yang, Tong Wu, Shuyan Feng, Yu Zhang, Shaoqin Shen, Quang Li, Liqiang Gu, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf genes were …

Thermal Inactivation Of Salmonella On Chicken Wings Cooked In Domestic Convection And Air Fryer Ovens, Carmen Cano, Xinyao Wei, Cyril A. Etaka, Byron D. Chaves

Department of Food Science and Technology: Faculty Publications

Chicken wings are among the most popular poultry products for home and foodservice consumption. Poultry products must be handled and cooked safely to decrease the risk of foodborne salmonellosis for consumers. This study aims to validate the use of domestic appliances (convection and air fryer ovens) for the thermal inactivation of Salmonella on chicken wings. Wings (n = 3, 46.5 ± 4.3 g) were inoculated with a five-strain cocktail of Salmonella (ca. 8 log₁₀ CFU/wing) and cooked in a convection oven (179.4ºC) or an air fryer (176, 190, or 204ºC) for 2, 5, 10, 15, 20, 22, or 25 …

Recent Advances In Biosensors For Detection Of Covid-19 And Other Viruses, Shobhit K. Patel, Jaymit Surve, Juveriya Parmar, Kawsar Ahmed, Francis M. Bui, Fahad Ahmed Al-Zahrani

Department of Mechanical and Materials Engineering: Faculty Publications

This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and …

A Robot-Assisted Acoustofluidic End Effector, Jan Durrer, Prajwal Agrawal, Ali Ozgul, Stephen C.F. Neuhauss, Nitesh Nama, Daniel Ahmed

Department of Mechanical and Materials Engineering: Faculty Publications

Liquid manipulation is the foundation of most laboratory processes. For macroscale liquid handling, both do-it-yourself and commercial robotic systems are available; however, for microscale, reagents are expensive and sample preparation is difficult. Over the last decade, lab-on-a-chip (LOC) systems have come to serve for microscale liquid manipulation; however, lacking automation andmulti-functionality. Despite their potential synergies, each has grown separately and no suitable interface yet exists to link macro-level robotics with micro-level LOC or microfluidic devices. Here, we present a robot-assisted acoustofluidic end effector (RAEE) system, comprising a robotic arm and an acoustofluidic end effector, that combines robotics and microfluidic functionalities.We …

Assessment Of Design Quality And Developing A Methodological Model For Open Air Museums: A Study Of Wadi El-Hitan Protected Area, Khloud Khalid Eldamshiry

Architectural Engineering

Open air natural history museums acts as a distinct type of museum exhibiting its collections out of doors aiming to document earlier forms of life, ways of living, cultural habits and folk costumes. “Natural history Museums and cultural organizations have been recognized as a value for the vitality and character of cities which can be used as a tool for “urban regeneration”, that includes the challenge to achieve longterm, strategic reshaping of cities by using a powerful and unified technological system “spreadsheet based decision support system:” to plan for a future vision of the museum as an urban space that …