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Abstract Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO3−) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2−) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO3−, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO2−, which disrupts denitrification causing N2O off gassing. 

A significant focus of the ISEE Professional Development Program (PDP) is identifying authentic STEM practices, so that educators and scientists can develop and assess these practices as intentionally as they would scientific content knowledge. In addition to the classic inquiry-based learning activities, PDP alumni also find themselves using and teaching these STEM practices in other contexts. Many PDP participants have benefited from recognizing "STEM practices" as its own category of specific skills and knowledge, allowing them to build these practices into their work intentionally, rather than simply expecting these skills to develop naturally as a by-product of learning STEM content. We present four instances where PDP lessons have been put to work by alumni of the program in this manner, either in teaching and mentoring students, performing real-world scientific research, or both. First, we consider two instances of alumni using their PDP training to inform the way they build authentic STEM practices into college classrooms and college mentorship, at the College of St. Scholastica and at UC Santa Cruz. Next, we describe a course-based undergraduate research experience (CURE) in which students learn and employ authentic STEM research practices at the University of Colorado at Boulder. Finally, we present an example of an alumna who has used her identification of widely-applicable STEM practices to broaden her own research horizons at Lawrence Berkeley National Laboratory. 

Ostensibly, the main goal of the ISEE Professional Development Program (PDP) is to teach scientists and engineers how to be intentional, inclusive educators by experiencing and designing inquiry-based learning activities. However, the PDP program has many indirect, positive effects on its participants as well, including building community and a sense of STEM identity, fluency to understand and discuss diversity, equity, and inclusion topics, and recognizing the importance of psychological safety in learning, academia, and industry. We present four narratives from past participants with underestimated minority identities, who discuss how the PDP program had a positive impact on their growth as scientists and engineers. In each case, the PDP provided critical tools, knowledge or support that enabled their success as graduate students and into their respective career and life journeys. 

Abstract RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.