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Among RNAs, transfer RNAs (tRNAs) contain the widest variety of abundant post-transcriptional chemical modifications. These modifications are crucial for tRNAs to participate in protein synthesis, promoting proper tRNA structure and aminoacylation, facilitating anticodon:codon recognition, and ensuring the reading frame maintenance of the ribosome. While tRNA modifications were long thought to be stoichiometric, it is becoming increasingly apparent that these modifications can change dynamically in response to the cellular environment. The ability to broadly characterize the fluctuating tRNA modification landscape will be essential for establishing the molecular level contributions of individual sites of tRNA modification. The locations of modifications within individual tRNA sequences can be mapped using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). In this approach, a single tRNA species is purified, treated with ribonucleases and the resulting single-stranded RNA products are subject to LC-MS/MS analysis. The application of LC-MS/MS to study tRNAs is limited by the necessity of analyzing one tRNA at a time because the digestion of total tRNA mixtures by commercially available ribonucleases produces many short digestion products unable to be uniquely mapped back to a single site within a tRNA. We overcame these limitations by taking advantage of the highly structured nature of tRNAs to prevent the full digestion by single-stranded RNA specific ribonucleases. Folding total tRNA prior to digestion allowed us to sequence S. cerevisiae tRNAs with up to 97% sequence coverage for individual tRNA species by LC-MS/MS. This method presents a robust avenue for directly detecting the distribution of modifications in total tRNAs. 

Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N 2-methylguanosine, N 2, N 2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N 2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context. 

Indigenous Peoples across the Arctic have adapted to environmental change since time immemorial, yet recent climate change has imposed unprecedented and abrupt changes that affect the land and sea upon which communities rely. Co-created community-based observing programs offer an opportunity to harness the holistic breadth of knowledge in communities with the goal of tracking Arctic change while simultaneously supporting community priorities and local-scale needs. The Alaska Arctic Observatory and Knowledge Hub (AAOKH) is a network of Iñupiaq observers from northern Alaska coastal communities working in partnership with academic researchers. Here, we describe five core functions that have emerged through AAOKH, which include tracking long-term environmental changes; communicating Indigenous-led observations of the environment and their meaning; place-based and culturally relevant education; enabling scientific and Indigenous Knowledge exchange; and supporting community-led responses to environmental change. We outline and discuss specific actions and opportunities that have been used to increase knowledge exchange of AAOKH observations, make space for the next generation of Indigenous scholars, and create locally relevant data products and syntheses that can inform resource management and community planning. We also discuss our ongoing efforts to increasingly shift toward a knowledge coproduction framework as we plan to sustain AAOKH into the future.

 

The recent decline in wild populations of amphibians worldwide coincides with the period of rapid growth in the global trade of wildlife. The potential for pathogen transmission within and beyond the pet amphibian trade network makes it important to explore the attitudes and behavior of businesses involved in the industry. We surveyed US businesses involved in the pet amphibian trade industry to characterize their attitudes and behaviors and identify business characteristics that could influence percieved risk of pathogen transmission in trade. We found that amphibian businesses acquire their animals from a variety of sources (e.g., importers, wholesalers, retailers, breeders, hobbyists, wild), are aware of the threat of emerging pathogens, and are concerned about the potential spillover of pathogens from captive to wild populations. Attitudes and behaviors of businesses toward pathogens varied among business types (e.g., size of business, the share of amphibian sales, mode of business operation). Moreover, businesses expressed a strong interest in acquiring amphibians that are free of pathogens and indicated a willingness to pay a price premium to acquire certified disease‐free animals. Our results indicate that the US pet amphibian trade industry is willing to participate in healthy (clean) trade practices and increasing product prices may be one option to compensate for expenses. A government program to support pathogen‐free certification would likely facilitate implementation.

 

In 2009, Jones and Deitz published a tribe-level taxonomic revision and reclassification of the cryptic, arboreal leafhopper subfamily Ledrinae Kirschbaum, 1868 (Hemiptera: Cicadellidae), based on cladistic analyses of 235 morphological features for 75 cicadellid species. Their evolutionary reconstructions found strong node support for a monophyletic ingroup comprising five lineages—each morphologically and geographically cohesive—and also identified numerous traditionally placed taxa (sensu Oman et al 1990) that did not belong. In light of the robustness of their results, the authors recognized the five independent ingroup clades as tribes of Ledrinae, and described three of these as new. 

In late 2020, models predicted that a strong La Niña would take place for the first time since 2013, and we assessed whether physical and biological indicators in 2021 were similar to past La Niñas in the California Current Ecosystem (CCE). The Pacific Decadal Oscillation and Oceanic Niño Index indeed remained negative throughout 2021; the North Pacific Gyre Oscillation Index, however, remained strongly negative. The seventh largest marine heatwave on record was unexpectedly present from April to the end of 2021; however, similar to past La Niñas, this mass of warm water mostly remained seaward of the continental shelf. As expected from past La Niñas, upwelling and chlorophyll were mostly high and sea surface temperature was low throughout the CCE; however, values were close to average south of Point Conception. Similar to past La Niñas, abundances of lipid-rich, northern copepods off Oregon increased. In northern California, unlike past La Niñas, the body size of North Pacific krill (Euphausia pacifica) was close to average. Predictably, overall krill abundance was above average in far northern California but, unexpectedly, below average south of Cape Mendocino. Off Oregon, similar to past La Niñas, larval abundances of three of six coastal species rose, while five of six southern/offshore taxa decreased in 2021. Off California, as expected based on 2020, Northern Anchovy (Engraulis mordax) were very abundant, while Pacific Sardine (Sardinops sagax) were low. Similar to past La Niñas, market squid (Doryteuthis opalescens) and young of the year (YOY) Pacific Hake (Merluccius pacificus), YOY sanddabs (Citharichthysspp.), and YOY rockfishes (Sebastesspp.) increased. Southern mesopelagic (e.g., Panama lightfishVinciguerria lucetia, Mexican lampfishTriphoturus mexicanus) larvae decreased as expected but were still well above average, while northern mesopelagic (e.g., northern lampfishStenobrachius leucopsarus) larvae increased but were still below average. In line with predictions, most monitored bird species had above-average reproduction in Oregon and California. California sea lion (Zalophus californianus) pup count, growth, and weight were high given the abundant Anchovy forage. The CCE entered an enduring La Niña in 2021, and assessing the responses of various ecosystem components helped articulate aspects of the system that are well understood and those that need further study.

 

The first large‐scale, total‐evidence phylogeny of the owlflies (Neuroptera, Ascalaphidae) is presented. A combined morphological and molecular dataset was analysed under several analytical regimes for 76 exemplars of Myrmeleontiformia (Psychopsidae, Nymphidae, Nemopteridae, Myrmeleontidae, Ascalaphidae), including 57 of Ascalaphidae. At the subordinal level, the families were recovered in all analyses in the form Psychopsidae + (Nymphidae + (Nemopteridae + (Myrmeleontidae + Ascalaphidae). In the DNA‐only maximum‐likelihood analysis, Ascalaphidae were recovered as paraphyletic with respect to the Myrmeleontidae and the tribe Ululodini. In both the parsimony and Bayesian total‐evidence analyses, however, the latter with strong support, traditional Ascalaphidae were recovered as monophyletic, and in the latter, Stilbopteryginae were placed as the immediate sister group. The long‐standing subfamilies Haplogleniinae and Ascalaphinae were not recovered as monophyletic in any analysis, nor were several of the included tribes of non‐ululodine Ascalaphinae. The Ululodini were monophyletic and well supported in all analyses, as were the New World Haplogleniinae and, separately, the African/Malagasy Haplogleniinae. The remaining Ascalaphidae, collectively, were also consistently cohesive, but included a genus that until now has been placed in the Haplogleniinae,Protidricerus.Protidriceruswas discovered to express a well‐developed pleurostoma, a feature previously only encountered in divided‐eye owlflies. The feature traditionally used to differentiate the Haplogleniinae and Ascalaphinae, the entire or divided eye, can no longer be regarded as a spot‐diagnostic synapomorphy to separate these groups within the family. A new subfamilial classification based on these results is proposed and includes the following five subfamilies: Albardiinae, Ululodinae, Haplogleniinae, Melambrotinae and Ascalaphinae. In addition, the monophyletic containing group (Myrmeleontidae + (Palparidae + (Stilbopterygidae + Ascalaphidae))) is elevated to the rank of superfamily, as Myrmeleontoidea, in order to accommodate much‐needed taxonomic and nomenclatural restructuring anticipated to occur within the Ascalaphidae in the future. A list of genera included in each subfamily of Ascalaphidae is provided.