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Vibrio parahaemolyticus(VP) is a bacterial pathogen found in brackish and marine water that infects many marine organisms, such as oysters and shrimp. Consumption of raw or undercooked seafood contaminated withV. parahaemolyticusis a primary cause of seafood-borne gastroenteritis in humans. Due to increasing ocean temperatures,V. parahaemolyticuscontamination of oyster beds in the United States has spread up the east and west coasts to the northern-most states. Promising new research is exploring the isolation of bacteriophages againstV. parahaemolyticuswith a long-term goal to possibly decontaminate oyster beds, thereby expanding the harvest season and allowing for safer consumption of seafood. In this study, store-bought oysters harvested from the Chesapeake Bay in Virginia were used to isolate four bacteriophages with activity against a specificV. parahaemolyticusstrain. A standard double agar overlay plaque assay was used to identify phage activity. After phage isolation, the genomes were sequenced, and transmission electron microscopy (TEM) was performed to visualize the virions. The genomes and TEM images revealed four distinct phages. Three of the phages are distinct isolates that exhibit podovirus-like morphology with short tails and genome sizes of approximately 43 kbp. One phage has siphovirus-like morphology and is a mid-sized tailed phage with a genome size of 80 kbp. Although spot tests performed with the oyster homogenates on up to 10 differentV. parahaemolyticusstrains recovered activity across a wide range of hosts, plaque assays with the isolated phages showed limited host range. Future work will be necessary to determine the viability of using the bacteriophages for elimination ofV. parahaemolyticusin harvested oysters, treatment of aquaculture seed and spat, and/or the environment. 

Emerging satellite networks integrated with terrestrial and aerial systems form a key part of next-generation infrastructures supporting the Internet of Everything (IoE). This chapter outlines the current status of PQC-based authentication in integrated Space-Aerial-Terrestrial Networks (SATIN), highlighting the technical challenges in achieving quantum-resilient security within constrained and complex environments. While quantum computing necessitates migration to post-quantum cryptography (PQC), existing standards often demand resources that are unsuited for SATIN’s limited hardware and fragile links. We analyze leading NIST PQC signature and key encapsulation schemes in the SATIN context, evaluating trade-offs in computational cost, signature size, and protocol compatibility. Emerging directions, including broader algorithm evaluations, advanced protocol integrations (e.g., EMSS and NIST-PQC with terrestrial backbone, PQ group key management), and some alternative PQ technologies are discussed. Addressing these challenges requires advanced simulation and experimental frameworks to enable scalable, practical, and quantum-resilient secure communications in future integrated networks. 

Sustainable coffee production faces growing environmental and economic pressures, particularly under climate change and volatile markets. This study examines Honduran coffee farmers’ willingness to adopt sustainable land-sparing practices that integrate natural forests into production systems. Using a discrete choice experiment with 600 farmers in the Yoro region, we estimated preferences for carbon payments, coffee price premia, and technical training. Results show that financial incentives strongly influence adoption, with compensation requirements rising, the proportion of farmland allocated to forest increases. Farmers with higher incomes, existing forest cover, or prior experience with sustainable methods were more willing to participate. In contrast, lower-income farmers required greater payments due to risk aversion and opportunity costs. Findings highlight the importance of incentive structures that combine economic rewards with technical support, providing valuable insights for policies and programs that promote sustainable coffee landscapes in Central America. 

Abstract We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). C. campestris, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities. The species has served as a model parasite for studies of parasite biology, haustorium development, growth responses to chemical and light stimuli, gene content and expression, horizontal gene transfer, and interspecies RNA movement and has a recently developed transformation system. The 505 Mb (1C) genome is assembled into 31 chromosomes and supports annotation of 47,199 protein-coding genes, 214 small RNA loci (including 146 haustoria-specific miRNAs), and 3,238 interspecies mobile mRNA loci. C. campestris is a recent tetraploid with a high retention of duplicated genes and chromosomes, with less than 8% nucleotide divergence between homoeologous chromosomes. We also show that transformation of C. campestris with the RUBY marker system allows visualization of transformed Cuscuta-derived fluorescent mobile molecules that have entered the host stem. This genome, with an associated genome browser and BLAST server, will be of value for scientists performing fundamental research in a wide range of molecular, developmental, population, and evolutionary biology, as well as serve as a research tool for studying interspecies mobile molecules, generating genetic markers for species and genotype identification, and developing highly specific herbicides. 

In STEM disciplines, there has been a growing emphasis on implementing instructional changes in undergraduate education to enhance student success. Despite collecting different types of data, there are few applications of mid-project formative evaluations in instructional reform projects to explore faculty members' perceptions and interactions as change agents. This study conducted a formative evaluation focusing on a group of faculty participants involved in a project as part of a faculty learning community aimed at revising the chemistry curriculum at a public urban U.S. university, utilizing both qualitative and quantitative approaches. Using interview data, this study revealed that faculty participants in the reform project perceived their interactive involvement, as well as environmental changes and diverse student needs, as facilitators for their instructional improvement. Additionally, based on department-wide survey measures related to departmental culture and discussion networks for undergraduate education change, faculty participants in the reform efforts had more favorable perceptions of departmental culture about making changes and higher centrality scores within departmental discussion networks compared to their peer faculty members. Implications of these findings are discussed in relation to future project implementation and faculty development as change agents. 

ABSTRACT Municipal wastewater harbors diverse RNA viruses, which are responsible for many emerging and reemerging diseases in humans, animals, and plants. Although genomic sequencing can be a high-throughput approach for profiling the RNA virome in wastewater, wastewater processing methods often influence sequencing outcomes. Here, we systematically evaluated two wastewater processing methods, tangential-flow ultrafiltration (TFF) and Nanotrap Microbiome A Particles, for detecting the target RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via amplicon sequencing and characterizing the RNA virome using whole-transcriptome shotgun sequencing. Our results from paired comparison tests showed that the TFF and Nanotrap methods recovered similar SARS-CoV-2 variants at the lineage level (analysis of similarity [ANOSIM]R= −0.012,P= 0.874). Optimizing automated procedures for the Nanotrap method and concentration factors for the TFF method was critical for achieving high-depth and high-breadth coverage of the target virus genome. Notably, the two methods enriched distinct RNA viromes from the same wastewater samples (ANOSIMR= 0.260,P= 0.002), with TFF samples showing 22-fold and 7-fold higher relative abundances ofReoviridaeandCoronaviridae, respectively. These differences are likely due to the distinct virus concentration mechanisms employed by each method, which are influenced by liquid-solid partitioning of virus particles and interactions of viral surface proteins with ligands. Our findings underscore the importance of optimizing wastewater processing methods for genomic monitoring and have implications for broader environmental applications.IMPORTANCEWastewater genomic sequencing is an emerging technology for tracking viral infections within communities. However, different methods for concentrating viruses and extracting nucleic acids can influence the recoveries of RNA virome from wastewater. An in-depth understanding of virus concentration mechanisms and their impact on sequencing data quality and bioinformatic output would be critical to guide method selection and optimization. Specifically, this study systematically evaluated tangential-flow ultrafiltration and Nanotrap microbiome particles for their application to sequence SARS-CoV-2 and whole RNA virome from wastewater. Both methods yielded high-quality sequencing data for amplicon sequencing of SARS-CoV-2, but their outcomes diverged in the recovered RNA virome. We identified RNA viruses that are preferentially recovered by each of these two methods and proposed considerations of method selection for future studies of wastewater RNA virome. 

ABSTRACT Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found inBombella apis.B. apisis an important honey bee symbiont, found primarily in larvae, queens, and hive compartments.B. apisis found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However,B. apisappears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired byB. apisin its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types acrossB. apisstrains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the sameB. apisgenomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for eachB. apisstrain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that theB. apisCRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe. IMPORTANCEHoney bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacteriumBombella apis.B. apisis found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen’s digestive tract. The roles thatB. apismay serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity inB. apismay be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay betweenB. apisand its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host. 

Computational modeling of scientific systems is a powerful approach for fostering science and computational thinking (CT) proficiencies. However, the role of programming activities for this synergistic learning remains unclear. This paper examines alternative ways to engage with computational models (CM) beyond programming. Students participated in an integrated Science, Engineering, and Computational Modeling unit through one of three distinct instructional versions: Construct a CM, Interpret-and-Evaluate a CM, and Explore-and-Evaluate a simulation. Analyzing 188 student responses to a science+CT embedded assessment task, we investigate how science proficiency and instructional versions related to pseudocode interpretation and debugging performances. We found that students in the Explore-and-Evaluate a simulation outperformed students in the programming-based versions on the CT assessment items. Additionally, science proficiency strongly predicted students’ CT performance, unlike prior programming experience. These results highlight the promise of diverse approaches for fostering CT practices with implications for STEM+C instruction and assessment design. 

This paper presents an initiative aimed at integrating tailor-made micro-programming environments (MPEs) into middle school mathematics education to foster student learning and enhance computational thinking skills. We examine the effectiveness of MPEs in engaging students in computational thinking, aligning with mathematical practice standards, and usability in promoting interdisciplinary connections between mathematics and computing in the middle school setting. Findings suggest MPEs can advance computational thinking skills and enrich lesson alignment with educational standards. Most participants indicated approval of integrating MPEs into middle school classrooms.