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Electrochemical aptasensor for rapid detection of biothreats
No full textBiothreats—pathogenic agents capable of causing significant harm to humans, animals, or ecosystems—pose persistent and evolving risks to global health and security. These threats may arise naturally or be deliberately introduced, as in bioterrorism or biological warfare. While modern medical interventions have improved treatment outcomes, their effectiveness depends on the timely and accurate detection of pathogenic agents. Biosensors offer a promising solution for early detection by combining high sensitivity, specificity, and portability. Among them, electrochemical impedance spectroscopy (EIS)-based aptasensors enable label-free detection using aptamers—synthetic oligonucleotides that bind specific targets with high affinity.
This dissertation presents a comprehensive body of work focused on developing portable, robust biosensors for the detection of high-priority biothreat agents. A central contribution is the optimization of aptamer immobilization on nanoporous anodized aluminum oxide (NAAO) membranes using hetero-bifunctional crosslinkers, significantly improving surface coverage and sensing reproducibility. Additionally, the sensing mechanism of EIS within NAAO nanopores was refined across various sensor configurations to enhance sensitivity and response reliability. A compact, quarter-sized sensing platform was developed to automate fluid handling via peristaltic pumping while minimizing system footprint. The platform is compatible with airborne particle capture systems, enabling the detection of aerosolized biothreats by converting them into a liquid stream for analysis. Furthermore, a multiplexed biosensor system was introduced, capable of simultaneously detecting multiple pathogens—an essential feature given the unpredictable nature of biothreat exposure scenarios.
Throughout this work, biosensors were successfully developed and validated for the detection of five major biothreat agents: Ebola virus, SARS-CoV-2, Dengue virus, Marburg virus, and botulinum neurotoxin (BoNT). These innovations collectively advance the development of integrated, field-deployable diagnostic tools for real-time biothreat monitoring. The outcomes provide a strong foundation for future efforts in biosensor design, biodefense readiness, and public health surveillance
Concentration, Consolidation, and Foreign Ownership in US Agribusiness
No full textThere is regular interest among farmers, agribusinesses, and policymakers concerning the competitiveness of food and agricultural industries. It has also been of great interest to economists and has been researched for nearly a century as detailed by Crespi and MacDonald (2022) and recently studied to great extent by the US Department of Agriculture (MacDonald, Dong, and Fuglie 2023).
The purpose of this policy brief is neither to forge new research nor draw conclusions from the existing research, but rather to summarize the current state of concentration and ownership of agricultural and agriculture adjacent industries in the United States so that interested parties can debate and probe for answers within a common frame of reference. We begin with standard definitions that arise when speaking of competitive industry structure and then examine particular industries in a bit more detail in the following sections:
1. Frequently used Terminology when Discussing Concentration and Consolidation
2. Concentration in US Food and Agricultural Manufacturing and Adjacent Industries
3. Broiler Chicken, Pork, and Beef
4. Seeds
5. Grains and Oilseeds
6. Fertilizer
7. Farming<br/
Expression of sugarcane COBRA-Like genes, ScBC1 and ScBC1L2, increases plant biomass
No full textBackground Cellulose is a major determinant of plant biomass yield and quality, with significant industrial relevance. COBRA proteins are established regulators of cellulose deposition and cell wall organization; however, their roles in sugarcane (Saccharum spp.) growth and development remain uncharacterized. Results A genome-wide analysis identified 50 sugarcane COBRA genes grouped into 11 unigenes, with ScBC1 (Brittle Culm 1) and ScBC1L2 (Brittle Culm Like 2) highly expressed in stems. Phylogenetic analysis placed ScBC1 with secondary cell wall-associated genes, including maize ZmBK2, while ScBC1L2 clustered with primary cell wall-related genes. Transient expression of ScBC1 and ScBC1L2 in Nicotiana benthamiana increased leaf biomass and epidermal cell size, with ScBC1 having the strongest effect. Virus-induced gene silencing of ZmBK2 in maize reduced biomass, cellulose content, and cell area, and altered the expression of Cellulose Synthase (CesA) genes. Genes related to cell wall remodeling, including Expansin, β-Galactosidase, and Polygalacturonase, were differentially expressed in ZmBK2-silenced leaves, suggesting compensatory responses. Conclusions These findings indicate a conserved role of the ScBC1–ZmBK2 subclade in cellulose deposition and cell expansion, identifying ScBC1 as a promising target for improving sugarcane biomass.This article is published as Cardoso, S., Maloste, J.D., Souza, L.L. et al. Expression of sugarcane COBRA-Like genes, ScBC1 and ScBC1L2, increases plant biomass. BMC Plant Biol 26, 97 (2026). https://doi.org/10.1186/s12870-025-07910-yThis research was supported by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), grant numbers 88887.604041/2021-00 and 88887.916672/2023-00 (CAPES-PRINT Program). National Institute of Food and Agriculture (grant 7004470) and the Horticultural Sciences Department, University of Florida. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grants 408043/2022-9 and 305520/2021-0) and Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, grants 2014/06923-6, 2014/17486-6, 2016/24391-7, and BPE 2022/05041-6)
Effects of atmospheric CO2 levels on the susceptibility of maize to diverse pathogens
No full textRising atmospheric CO2 has profound implications for crop productivity and food security. Based on studies in C3 plants, elevated CO2 (eCO2) can shape plant-pathogen interactions, although the outcomes are often variable. The question of how eCO2 influences immunity and disease development in C4 plants, such as the globally important cereal crop maize (Zea mays L.), has not been systematically examined. We challenged maize plants grown under ambient CO2 (aCO2, 420 ppm) and eCO2 (550 ppm) with bacterial, viral, fungal, and oomycete pathogens. Plants grown in eCO2 were more susceptible to sugarcane mosaic virus, suggesting compromised antiviral defenses, less susceptible to Clavibacter nebraskensis, Exserohilum turcicum, and Colletotrichum graminicola, and susceptibility to Puccinia sorghi and Pythium sylvaticum was unchanged. Reduced susceptibility to C. nebraskensis was associated with enhanced basal immune responses. These results establish a foundation for dissecting eCO2-responsive defense mechanisms, and they highlight a critical need to understand how eCO2 will impact plant responses to microbes, pests, and abiotic stresses under future conditions.This preprint is from bioRxiv at doi:https://doi.org/10.64898/2025.12.31.69722
Elucidation of the bovine immune response to the live attenuated bacterial vaccines Brucella abortus strain RB51 and Bacillus Calmette-Guérin
No full textBovine brucellosis and bovine tuberculosis persist in domestic cattle in the United States and around the world. These chronic, zoonotic diseases cause economic concerns and pose significant risks to both animal and human health. In cattle, the Brucella abortus strain RB51 (RB51) and Bacillus Calmette-Guérin (BCG) vaccines are known to reduce incidence of bovine brucellosis and bovine tuberculosis, respectively, by conferring protective cell-mediated immunity. However, protection is not absolute, and additional knowledge of the bovine immune response to these live attenuated vaccines is needed. Therefore, the work presented in this dissertation was performed with the primary goal of further characterizing the immune responses induced by RB51 or BCG vaccination in cattle. This objective was investigated using a variety of immune assays, including flow cytometry, cytokine enzyme linked immunosorbent assays (ELISA), microscopy, and RNA sequencing. Initial work described BCG-specific memory T cell phenotypes capable of producing IFN-. Importantly, the phenotype of these memory cells was consistent with cell types that had previously been found to play a role in the response to Mycobacterium bovis. A follow-up study utilized a dual vaccination strategy to examine the differences among RB51, BCG, and RB51+BCG combination vaccinates. Of interest, the combination vaccination group showed enhanced CD4+ Th1 responses to BCG suggesting that there may be opportunities to improve the efficacy of BCG. Notably, additional analysis suggested that the genetic background of cattle may influence responses to RB51 and BCG vaccination. This observation was investigated further in the third study by evaluating breed-specific differences in innate immune parameters induced by RB51 and BCG, using cells from Herefords and Holsteins to model immune function in vitro. Breed-specific differences were observed in the in vitro responses to RB51 and BCG, suggesting that Herefords and Holsteins display differential immune responses to these vaccines, and imply that host genetic background may need to be considered when optimizing vaccination strategies in cattle. Collectively, the work in this dissertation provides novel, baseline evaluations of immune responses generated by the current RB51 and BCG vaccines. This work additionally highlights breed-specific immune responses and suggests further investigation of this immunological variation in the context of vaccine development and efficacy
AI-enabled microstructure design and process–structure–property mapping for organic electronics
No full textOrganic electronics represents a promising technology with versatile applications in renewable energy, flexible and wearable electronics, soft robotics, neuromorphic computing, and beyond. Despite significant progress over several decades of research, the technology is not mature enough for broad commercialization. Organic chemistry offers a wide range of possible material systems, and new material systems are continually being designed. Often, the device fabrication process involves multiple steps, and small changes in these steps can lead to very different microstructures. The relationship between material systems, processing conditions, microstructure, and device performance is complicated and hard to study. Additionally, there are several goals to optimize for: low cost, efficiency, stability, non-toxicity, environmental friendliness, safety, reliability, and compatibility with existing technologies.
This thesis addresses these challenges by developing a set of tools and workflows that facilitate the exploration, understanding, and prediction of the relationships between materials, processing, microstructure, and device behavior. First, the MicroGen3D framework generates realistic microstructures on demand using state-of-the-art generative modeling. Since the first challenge in studying structure–property relationships is simply having access to high-fidelity microstructures, this framework serves as a useful source of structures that would otherwise be difficult or costly to obtain. Building on this foundation, the thesis carries out extensive studies on structure-property mapping. High-throughput simulations, combined with data-driven surrogate modeling, enable the exploration of a wide range of microstructural and material parameter combinations. This approach reveals clear levers for improvement and offers practical design guidance. While much of this analysis is performed on two-dimensional microstructures, the insights remain useful and transferable to three-dimensional systems. The thesis also includes work showing how to minimize the heavy computational cost of realistic three-dimensional simulations by using the concept of representative volume elements (RVEs). This approach helps make large-scale 3D studies more practical and supports future three-dimensional studies.
Finally, the thesis presents work on reverse structure–property mapping. Using the transient current–time response, it is shown that device-level signals can act as a proxy for underlying microstructure, providing a possible path to estimate structural features without relying on expensive or slow imaging methods. Taken together, the thesis contributes to each stage of a potential end-to-end workflow: selecting a target property, inferring the required microstructural descriptors, generating candidate microstructures, predicting the associated processing conditions, and validating the outcome through forward modeling. This integrated view highlights how the individual components developed in this work can support future closed-loop design strategies for organic electronic devices
Artifact Removal and Image Restoration in AFM:A Structured Mask-Guided Directional Inpainting Approach
No full textAtomic Force Microscopy (AFM) enables high-resolution surface imaging at the nanoscale, yet the output is often degraded by artifacts introduced by environmental noise, scanning imperfections, and tip-sample interactions. To address this challenge, a lightweight and fully automated framework for artifact detection and restoration in AFM image analysis is presented. The pipeline begins with a classification model that determines whether an AFM image contains artifacts. If necessary, a lightweight semantic segmentation network, custom-designed and trained on AFM data, is applied to generate precise artifact masks. These masks are adaptively expanded based on their structural orientation and then inpainted using a directional neighbor-based interpolation strategy to preserve 3D surface continuity. A localized Gaussian smoothing operation is then applied for seamless restoration. The system is integrated into a user-friendly GUI that supports real-time parameter adjustments and batch processing. Experimental results demonstrate the effective artifact removal while preserving nanoscale structural details, providing a robust, geometry-aware solution for high-fidelity AFM data interpretation.This is a preprint from Zhang, Juntao, Angona Biswas, Jaydeep Rade, Charchit Shukla, Juan Ren, Anwesha Sarkar, Adarsh Krishnamurthy, and Aditya Balu. "Artifact Removal and Image Restoration in AFM: A Structured Mask-Guided Directional Inpainting Approach." arXiv preprint arXiv:2602.04051 (2026). doi: https://doi.org/10.48550/arXiv.2602.04051.This work was supported by the National Science Foundation (NSF) (CNS-2409359) and Iowa State University
Toward optimized genetic transformation techniques for soybean [Glycine max (L.) Merr.]
No full textSoybean (Glycine max) is an essential crop for food, feed, and biofuel, yet its recalcitrance to genetic transformation has long hindered functional genomics and trait improvement. In this thesis, we demonstrated Agrobacterium genome engineering with a novel tool, the CRISPR RNA-guide INTEGRATE system, and I explored multiple strategies to enhance Agrobacterium-mediated soybean transformation. First, the CRISPR RNA-guided INTEGRATE system was used to introduce precise genomic modifications in Agrobacterium rhizogenes strain K599. Disarmed K599 was generated and tested for its potential in plant transformation. In parallel, multiple factors were systematically evaluated in soybean transformation, including the use of a helper plasmid carrying additional vir genes (pKL2299A), constructs containing the maize REF1 peptide coding sequence, shortened co-cultivation periods, and alternative Agrobacterium strains such as EHA105 and disarmed K599 variants. While no single strategy achieved a dramatic increase in transformation efficiency, the findings still offered some critical information to guide future improvements. For example, the addition of a helper plasmid in Agrobacterium did not significantly improve soybean transformation efficiency, probably because the barrier was not related to T-DNA delivery. Also, expressing the maize REF1 in soybean failed to enhance regeneration, possibly due to structural features or interactions between the maize REF1 peptide and soybean receptors. Comparisons between RUBY marker-based constructs and bar selection further suggested that marker choice itself influences transformation outcomes. Additionally, shortening the co-cultivation period made no significant difference in transformation efficiency. At the end, there was only one experiment using an alternative Agrobacterium strain k599 for soybean transformation. Even though that was not enough to conclude whether K599 is better than EHA105 or not, it still showed that our disarmed K599 could be used for a soybean transformation system. Together, these findings underscore the complexity of soybean transformation and highlight the need for integrated solutions spanning strain engineering, construct optimization, and tissue culture refinement. The methodologies and insights presented here provide a foundation for advancing soybean transformation systems and can inform efforts in other recalcitrant crop species
Structural analysis of the SARS-CoV-2 exonuclease domain for the development of a resistant nucleotide analog inhibitor
No full textThe COVID-19 pandemic swept the world, took the lives of millions, and firmly cemented coronaviruses as a future threat to be observed and studied. The causative agent, SARS-CoV-2, has become an endemic virus, continuing to infect people globally. The enduring prevalence of SARS-CoV-2 has sparked a new need for preventative measures and treatments. Vaccination efforts have proven effective at minimizing severe symptoms in most patients, but treatment agents for those facing more severe infections have been limited. Many antivirals are nucleoside analogs, and one such antiviral is remdesivir, an adenosine analog that was approved for emergency use during the pandemic. However, the efficacy of remdesivir in clinical trials was much lower than in vitro studies. It was proposed that the unique coronavirus proofreading exonuclease, nsp14, was likely removing remdesivir from the product strand during replication, preventing the inhibitory action of remdesivir. To further develop our arsenal of antivirals effective against coronaviruses, it is necessary to overcome the hurdle of the exonuclease. To facilitate this, the parameters of the exonuclease active site were structurally characterized by cryo-electron microscopy, and the mechanism for excision was able to be determined by inspecting the interaction points between the active site and the 3′ end of the RNA. Then remdesivir was tested against the exonuclease and determined to be a substrate for nsp14 due to unique hydrogen bonds in the active site that allow it to be bound in an alternative method by the exonuclease compared to a normal nucleotide. With this new understanding, a new type of inhibitor, utilizing a substitution of the 3′-hydroxyl group with a phosphate, was created to test against the exonuclease. The 3′-phosphate RNA not only inhibits extension by the viral polymerase, but it also heavily resists extension by the exonuclease
Improving the strength of 3d-printed soil composites using xanthan gum
No full textThe rapid advancement in additive manufacturing, also known as 3D printing technology, has opened new possibilities for efficient and environmentally friendly building methods. Researchers have examined biopolymer-bound soil composites to assess their potential for use in 3D printing. This study evaluates the use of xanthan gum (XG), a sustainable, food-grade biopolymer, as a binder for kaolinite-based soils to enhance the shear strength and interlayer strength of 3D-printed structures. The overall mechanical performance with increasing xanthan gum content (0%, 1% and 2%) was evaluated using unconfined compressive strength (UCS). The interlayer bond properties and improvement were assessed to evaluate the effectiveness of XG in strengthening the interlayer weak interface associated with 3D-printed structures.
Results show an increase in UCS with the addition of xanthan gum at lower concentrations compared to untreated control specimens. A shift from brittle failure to ductile failure was observed with increasing XG content. The interlayer bond strength showed notable gains, with xanthan gum increasing the cohesion of the layers. Volumetric shrinkage, however, increased with increasing XG content. XG-clay mixes demonstrated good printability, making them well-suited for 3D printing applications. This study emphasizes the potential of xanthan gum as a sustainable binder for soil-based 3D printing. By enhancing both the mechanical strength and interlayer adhesion of printed structures, XG can be used to create more durable, eco-friendly construction materials