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The Cyberinfrastructure Training and Capacity Building in Climate and Environmental Sciences (CI-TRACS) program represents a pioneering initiative aimed at enhancing cyberinfrastructure proficiency within Hawaii’s academic community. This paper outlines the program’s comprehensive strategy, which integrates curriculum development, hands-on workshops, and professional growth opportunities to cultivate a robust foundation in CI practices. The initiative’s core objective is to elevate CI literacy, promote cross-disciplinary cooperation, and endorse the principles of open science. Significant contributions from the CI-TRACS program include a suite of educational materials and resources tailored for integration into higher education syllabi. Collaboration with the Hawaii Data Science Institute has been instrumental in nurturing a burgeoning network of data science professionals. The CI-TRACS program is instrumental in realizing the shared vision of equipping Hawaii’s emerging workforce with the sophisticated CI skills necessary to navigate and excel in the evolving landscape of climate and environmental sciences. 

Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g., hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher’s own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app 

Residential yards and gardens can have surprisingly high plant diversity. However, we still do not understand all the factors that drive diversity in individual gardens, or how gardens scale up to create larger patterns of urban biodiversity. For example, social interactions between neighbors could affect whether they mimic each other’s yard design, affecting spatial turnover in plant communities. Further, socio-economic differences between neighborhoods might result in distinct plant assemblages across a city. In this paper, we used fieldwork, GIS, and spatial statistics to examine the variability in front yard vegetation—both cultivated and spontaneous plants—in 870 yards in Chicago, Illinois (USA). Our goals were to understand diversity and spatial patterning of plant communities in residential neighborhoods and how they vary with scale, considering alpha, beta, and gamma diversity. We addressed the following questions: (1) How do alpha, beta, and gamma diversity of cultivated and spontaneous plants vary between neighborhoods with different socioeconomic characteristics? (2) Within neighborhoods, do we see spatial autocorrelation in front-yard plant communities? If so, do those spatial patterns affect plant diversity at the neighborhood scale? We found diverse plant communities and distinct spatial patterns across Chicago. Richness and composition of both spontaneous and cultivated plants differed between neighborhoods, with some differences explained by socioeconomic factors such as education. Spontaneous and cultivated plants showed significant spatial autocorrelation, although that spatial autocorrelation generally did not influence neighborhood-scale diversity. Knowledge of these spatial patterns and their socioeconomic drivers could be exploited to increase adoption of environmentally-friendly yard management practices across a city. 

The 3′ untranslated regions (UTRs) of positive-strand RNA plant viruses commonly contain elements that promote viral replication and translation. The ~700 nt 3′UTR of umbravirus pea enation mosaic virus 2 (PEMV2) contains three 3′ cap-independent translation enhancers (3′CITEs), including one (PTE) found in members of several genera in the family Tombusviridae and another (the 3′TSS) found in numerous umbraviruses and several carmoviruses. In addition, three 3′ terminal replication elements are found in nearly every umbravirus and carmovirus. For this report, we have identified a set of three hairpins and a putative pseudoknot, collectively termed “Trio”, that are exclusively found in a subset of umbraviruses and are located just upstream of the 3′TSS. Modification of these elements had no impact on viral translation in wheat germ extracts or in translation of luciferase reporter constructs in vivo. In contrast, Trio hairpins were critical for viral RNA accumulation in Arabidopsis thaliana protoplasts and for replication of a non-autonomously replicating replicon using a trans-replication system in Nicotiana benthamiana leaves. Trio and other 3′ terminal elements involved in viral replication are highly conserved in umbraviruses possessing different classes of upstream 3′CITEs, suggesting conservation of replication mechanisms among umbraviruses despite variation in mechanisms for translation enhancement. 

Despite the perceived value of extracurricular experience, higher education relies heavily on grade point average (GPA) as a measure of undergraduates’ academic success. When used as a singular standard assessment, GPA, which is based on student progress and completion of coursework, may inadvertently steer undergraduates away from valuable out-of-class experiences that might enhance their employability after graduation. With this premise in mind, the current study proposes to supplement GPA scores in an undergraduate Computer Science program with a wholistic assessment known as an Innovation, Competency, and Experience (ICE) score. The ICE score is a point system for documenting and rewarding students’ extracurricular activities, in addition to their GPA scores. We designed and developed a web-based technology platform called RadGrad to implement ICE scores and promote student engagement and participation in extracurricular activities. Preliminary data shows that over 36% of students started to use RadGrad, even though its use was completely voluntary. More than half of those students planned and participated in various extracurricular activities, ultimately earning ICE points. Importantly, the ICE score deployed through RadGrad demonstrates the potential value of a supplemental assessment to GPA, which can promote extracurricular experiences relevant to students’ future careers beyond coursework. 

Purpose As the field of Computer Science (CS) continues to diversify and expand, the need for undergraduates to explore career possibilities and develop personalized study paths has never been greater. This reality presents a challenge for CS departments. How do the students striving to become competent professionals in an ever-changing field of study? How do they do this efficiently and effectively? This study addresses such questions by introducing RadGrad, an online application combining features of social networks, degree planners and serious games. Design/methodology/approach RadGrad application is designed to promote participation in extracurricular activities, value real-world experience and provide guidance for students planning their degrees. What follows is an exploration of how the application was designed, along with an analysis of how students used it in its first year. Findings Findings suggest RadGrad helped students to participate in relevant community activities and take an active role in planning their degrees. Originality/value The paper describes the features of the application, introducing how the concept of Innovation, Competence and Experience (ICE) scores – rather than a GPAs – were used to motivate undergraduates to participate in extracurricular activities. Initial results suggest RadGrad and the concept ICE scores can be applied to any field where students are encouraged to gain real-world experience as part of their degree program. Lessons learned and future directions are discussed. 

ABSTRACT A diversity of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity to bacteria and archaea through recording “memories” of past viral infections. Recently, many novel CRISPR-associated proteins have been discovered via computational studies, but those studies relied on biased and incomplete databases of assembled genomes. We avoided these biases and applied a network theory approach to search for novel CRISPR-associated genes by leveraging subtle ecological cooccurrence patterns identified from environmental metagenomes. We validated our method using existing annotations and discovered 32 novel CRISPR-associated gene families. These genes span a range of putative functions, with many potentially regulating the response to infection. IMPORTANCE Every branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to “remember” past infections in order to better fight them in the future. There has been much interest among molecular biologists in CRISPR immunity because this system can be repurposed as a tool for precise genome editing. Recently, a number of comparative genomics approaches have been used to detect novel CRISPR-associated genes in databases of genomes with great success, potentially leading to the development of new genome-editing tools. Here, we developed novel methods to search for these distinct classes of genes directly in environmental samples (“metagenomes”), thus capturing a more complete picture of the natural diversity of CRISPR-associated genes. 

Abstract Background Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates. Results We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth. Conclusions Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.