Mistranslating the genetic code with leucine in yeast and mammalian cells.

Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide anticodon variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare and more common mistranslating tRNA variants. We investigated three rare human tRNALeu variants that mis-incorporate Leu at phenylalanine or tryptophan codons. Expression of each tRNALeu anticodon variant in neuroblastoma cells caused defects in fluorescent protein production without significantly increased cytotoxicity under normal conditions or in the context of proteasome inhibition. Using tRNA sequencing and mass spectrometry we confirmed that each tRNALeu variant was expressed and generated mistranslation with Leu. To probe the flexibility of the entire genetic code towards Leu mis-incorporation, we created 64 yeast strains to express all possible tRNALeu anticodon variants in a doxycycline-inducible system. While some variants showed mild or no growth defects, many anticodon variants, enriched with G/C at positions 35 and 36, including those replacing Leu for proline, arginine, alanine, or glycine, caused dramatic reductions in growth. Differential phenotypic defects were observed for tRNALeu mutants with synonymous anticodons and for different tRNALeu isoacceptors with the same anticodon. A comparison to tRNAAla anticodon variants demonstrates that Ala mis-incorporation is more tolerable than Leu at nearly every codon. The data show that the nature of the amino acid substitution, the tRNA gene, and the anticodon are each important factors that influence the ability of cells to tolerate mistranslating tRNAs.

Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae).

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.

Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales.

Premise: We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in generating long-read sequencing data determine which steps may be necessary for optimizing output and results. Methods: Four species of Calochortus (Liliaceae) were sequenced. Modifications made to sodium dodecyl sulfate (SDS) extractions and cleanup protocols included grinding with a mortar and pestle, using cut or wide-bore tips, chloroform cleaning, bead cleaning, eliminating short fragments, and using highly purified DNA. Results: Steps taken to maximize read length can decrease overall output. Notably, the number of pores in a flow cell is correlated with the overall output, yet we did not see an association between the pore number and the read length or the number of reads produced. Discussion: Many factors contribute to the overall success of a Nanopore sequencing run. We showed the direct impact that several modifications to the DNA extraction and cleaning steps have on the total sequencing output, read size, and number of reads generated. We show a tradeoff between read length and the number of reads and, to a lesser extent, the total sequencing output, all of which are important factors for successful de novo genome assembly.

Time to Radiation after Oncoplastic Reduction versus After Lumpectomy.

Prior studies contrasting oncoplastic reduction (OCR) to traditional lumpectomy have validated oncoplastic reduction surgery with similar survival and oncological outcomes. The purpose of this study was to evaluate if there was a significant difference in the time to initiation of radiation therapy after OCR in comparison with the standard breast-conserving therapy (lumpectomy). Methods: The patients included were from a database of breast cancer patients who all underwent postoperative adjuvant radiation after either OCR or lumpectomy at a single institution between 2003 and 2020. Patients who experienced delays in radiation for nonsurgical reasons were excluded. Comparisons were made between the groups in the time to radiation and complication rates. Results: A total of 487 patients underwent breast-conserving therapy, with 220 having undergone OCR and 267 lumpectomy patients. There was no significant difference in days to radiation between patient cohorts (60.5 OCR, 56.2 lumpectomy, P = 0.059). There was a significant difference in the number of complications between OCR and lumpectomy patients (20.4% OCR, 2.2% lumpectomy, P < 0.001). However, of patients who had complications, there was no significant difference in the number of days to radiation (74.3 OCR, 69.3 lumpectomy, P = 0.732). Conclusions: Compared with lumpectomy, OCR was not associated with an increased time to radiation but was associated with higher complications. Statistical analysis did not reveal surgical technique or complications to be independent, significant predictors of increased time to radiation. Surgeons should be aware that although complications may remain higher in OCR, this does not necessarily translate to delays in radiation.

Genotyping for HLA risk alleles versus patch tests to diagnose anti-seizure medication induced cutaneous adverse drug reactions.

Aim: To provide a comparison of genotyping for HLA risk alleles versus patch testing to determine which of these two tests is a better diagnostic tool for cutaneous hypersensitivity reactions caused by anti-seizure medication. Methods: A literature study was performed in PubMed to assess the sensitivity and specificity of HLA genotyping and patch tests for identifying anti-seizure medication induced cutaneous hypersensitivity reactions. Results: This study shows that HLA-B*15:02 genotyping shows high sensitivity for carbamazepine-induced SJS/TEN, especially in Han Chinese and Southeast Asian patients (66.7-100.0%) whereas the sensitivity of patch tests (0.0-62,5%), HLA-A*31:01 (0-50%) and HLA-B*15:11 (18.2-42.9%) are lower. On the contrary, for carbamazepine and phenytoin induced DRESS, patch tests (respectively 70.0-88.9% and 14.3-70.0%) show higher sensitivity than HLA tests (0-66.7% and 0-12.7%). Also for lamotrigine-induced DRESS patch tests perform better than HLA-B*15:02 (33.3-40.0 versus 0%). For anti-seizure medication induced MPE and for oxcarbazepine-induced SCARs more studies are needed. Conclusion: Use of HLA-B genotyping may aid clinicians in the diagnosis of carbamazepine, phenytoin, lamotrigine and oxcarbazepine induced SJS/TEN, particularly in Han Chinese and Southeast Asian patients. On the other hand, patch tests seem to perform better in the diagnosis of carbamazepine and phenytoin induced DRESS.

Systematic identification of tRNA genes in Drosophila melanogaster.

Transfer RNAs (tRNAs) are ubiquitous adapter molecules that link specific codons in messenger RNA (mRNA) with their corresponding amino acids during protein synthesis. The tRNA genes of Drosophila have been investigated for over half a century but have lacked systematic identification and nomenclature. Here, we review and integrate data within FlyBase and the Genomic tRNA Database (GtRNAdb) to identify the full complement of tRNA genes in the D. melanogaster nuclear and mitochondrial genomes. We apply a logical and informative nomenclature to all tRNA genes, and provide an overview of their characteristics and genomic features.

Distinct Stress-Dependent Signatures of Cellular and Extracellular tRNA-Derived Small RNAs.

The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA-derived small RNAs (tDRs) play pivotal roles in stress responses. However, RNA modifications present on tDRs are barriers to accurately quantifying tDRs using traditional small RNA sequencing. Here, AlkB-facilitated methylation sequencing is used to generate a comprehensive landscape of cellular and extracellular tDR abundances in various cell types during different stress responses. Extracellular tDRs are found to have distinct fragmentation signatures from intracellular tDRs and these tDR signatures are better indicators of different stress responses than miRNAs. These distinct extracellular tDR fragmentation patterns and signatures are also observed in plasma from patients on cardiopulmonary bypass. It is additionally demonstrated that angiogenin and RNASE1 are themselves regulated by stressors and contribute to the stress-modulated abundance of sub-populations of cellular and extracellular tDRs. Finally, a sub-population of extracellular tDRs is identified for which AGO2 appears to be required for their expression. Together, these findings provide a detailed profile of stress-responsive tDRs and provide insight about tDR biogenesis and stability in response to cellular stressors.

Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures.

Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson-Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.

Pulp De-epithelialization for Venous Outflow Augmentation after Digital Replantation.

Traumatic amputation injuries account for a substantial portion of emergency department visits. This includes digital amputations that may be considered for replantation. Following surgery, venous congestion is the most common cause of replant failure. To address this, several methods have been proposed to augment venous outflow. In this article, a simple and straightforward method that can be utilized to establish or augment venous outflow in cases of venous insufficiency is described. This method entails de-epithelization of the replanted digit pulp skin with use of postoperative anticoagulation. The area can be further expanded or stimulated to increase bleeding as needed and is allowed to heal by secondary intention. This method allows for reliable venous outflow with relative ease of implementation.

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes.

tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- and clade-specific models, greatly improving tRNAscan-SE's ability to identify and classify both typical and atypical tRNAs. We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model. Comparative model scoring has also enhanced the program's ability to detect tRNA-derived SINEs and other likely pseudogenes. For the first time, tRNAscan-SE also includes fast and highly accurate detection of mitochondrial tRNAs using newly developed models. Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon. These enhancements will provide researchers with more accurate and detailed tRNA annotation for a wider variety of tRNAs, and may direct attention to tRNAs with novel traits.

R2DT is a framework for predicting and visualising RNA secondary structure using templates.

Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world's largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .

Prevalence and extent of industry support for program directors of surgical fellowships in the United States.

BACKGROUND: Fellowship program directors have a considerable influence on the future practice patterns of their trainees. Multiple studies have demonstrated that industry can also exert substantial influence on the practice patterns of physicians as a whole. The purpose of this study is to quantify industry support of fellowship program directors across surgical subspecialties and to assess the prevalence of this support within specific subspecialties. METHODS: Fellowship program directors for acute care, breast, burn, cardio-thoracic, critical care, colon and rectal, endocrine, hepato-pancreato-biliary, minimally invasive, plastic, oncologic, pediatric, and vascular surgery for 2017 were identified using a previously described database. The Open Payments Database for 2017 was queried and data regarding general payments, research, associated research payments, and ownership were obtained. The national mean and median payouts to nonfellowship program director surgeons were used to determine subspecialties with substantial industry support. RESULTS: Five hundred and seventy-six fellowship program directors were identified. Of these, 77% of the fellowship program directors had a presence on the Open Payments Database. The subspecialties with the most fellowship program directors receiving any industry payment, regardless of amount, included vascular (93.5%), cardio-thoracic (92.8%), minimally invasive surgery (90.5%), plastics (85.3%), and colon and rectal (81.0%). The subspecialty with the greatest mean payment was minimally invasive surgery (21,175 US dollars); the greatest median payment was vascular (1,871 US dollars). The 3 most common types of payments were for general compensation (31.4%), consulting fees (28.7%), and travel and lodging (14.7%). Vascular surgery had the greatest percentage of fellowship program directors receiving research payments (48%). The greatest amount paid to any individual fellowship program director was 382,368 US dollars. Excluding outliers, fellowship program directors received substantially more payments than those received on average by general surgeons. CONCLUSION: The majority of fellowship program directors receive some industry support. Most payments are for compensation for noncontinuing medical education related services and consulting fees. Certain specialties were more likely to have industry payments than others. Overall, only a minority of fellowship program directors received research support from industry. We advocate for transparent discussions between fellowship program directors and their trainees to help foster healthy academic-industry collaborations.

Frequency of Toxoplasma gondii and Risk Factors Associated with the Infection in Stray Dogs and Cats of Panama.

Stray animals such as dogs and cats have an important role in maintaining the transmission cycles and dissemination of Toxoplasma gondii. Therefore, the objective of this study was to evaluate the frequency of T. gondii in stray dogs and cats in six different regions of Panama and determine risk factors associated with the dynamics of infection in each of the studied regions. Data were obtained using serological tests for the detection of anti-T. gondii IgG and IgM antibodies. The results of this study revealed an overall infection frequency of 23.73%. The infection frequencies found in dog and cat populations were 25.70% and 21.93% respectively, showing no statistically significant difference. Risk factor correlations suggested different infection dynamics depending on the region analyzed. The San Miguelito, North and West regions were more associated with positive cases in dogs with an age range greater than 13 months. Conversely, the Metro, Central and East regions were more associated with negative cases in cats with age ranging between 0 and 5 months. Infection of the parasite in stray animals can be influenced by intrinsic characteristics of each region, which can potentiate different risk factors associated with the different routes of transmission.

Major Outcomes With Personalized Dialysate TEMPerature (MyTEMP): Rationale and Design of a Pragmatic, Registry-Based, Cluster Randomized Controlled Trial.

BACKGROUND: Small randomized trials demonstrated that a lower compared with higher dialysate temperature reduced the average drop in intradialytic blood pressure. Some observational studies demonstrated that a lower compared with higher dialysate temperature was associated with a lower risk of all-cause mortality and cardiovascular mortality. There is now the need for a large randomized trial that compares the effect of a low vs high dialysate temperature on major cardiovascular outcomes. OBJECTIVE: The purpose of this study is to test the effect of outpatient hemodialysis centers randomized to (1) a personalized temperature-reduced dialysate protocol or (2) a standard-temperature dialysate protocol for 4 years on cardiovascular-related death and hospitalizations. DESIGN: The design of the study is a pragmatic, registry-based, open-label, cluster randomized controlled trial. SETTING: Hemodialysis centers in Ontario, Canada, were randomized on February 1, 2017, for a trial start date of April 3, 2017, and end date of March 31, 2021. PARTICIPANTS: In total, 84 hemodialysis centers will care for approximately 15 500 patients and provide over 4 million dialysis sessions over a 4-year follow-up. INTERVENTION: Hemodialysis centers were randomized (1:1) to provide (1) a personalized temperature-reduced dialysate protocol or (2) a standard-temperature dialysate protocol of 36.5°C. For the personalized protocol, nurses set the dialysate temperature between 0.5°C and 0.9°C below the patient's predialysis body temperature for each dialysis session, to a minimum dialysate temperature of 35.5°C. PRIMARY OUTCOME: A composite of cardiovascular-related death or major cardiovascular-related hospitalization (a hospital admission with myocardial infarction, congestive heart failure, or ischemic stroke) captured in Ontario health care administrative databases. PLANNED PRIMARY ANALYSIS: The primary analysis will follow an intent-to-treat approach. The hazard ratio of time-to-first event will be estimated from a Cox model. Within-center correlation will be considered using a robust sandwich estimator. Observation time will be censored on the trial end date or when patients die from a noncardiovascular event. TRIAL REGISTRATION: www.clinicaltrials.gov; identifier: NCT02628366.

CONTEXTE: De petits essais à répartition aléatoire ont montré que l'utilisation d'un dialysat à basse température réduisait le risque d'hypotension intra-dialytique. De même, certaines études observationnelles ont démontré qu'un dialysat à basse température était associé à un plus faible risque de mortalité toute cause ou d'origine cardiovasculaire. Le temps est venu de procéder à un vaste essai à répartition aléatoire comparant les effets d'un dialysat à basse température et à température standard sur les principaux résultats cardiovasculaires. OBJECTIF: Répartir aléatoirement des centres d'hémodialyse ambulatoire pour qu'ils suivent pendant quatre ans (i) un protocole personnalisé de dialysat à basse température ou (ii) un protocole de dialysat à température standard, et tester l'effet sur les hospitalisations et la mortalité attribuables à des événements cardiovasculaires. TYPE D'ÉTUDE: Un essai clinique à répartition aléatoire en grappes. CADRE: Le 1er février 2017, des centres d'hémodialyse de l'Ontario (Canada) ont été répartis aléatoirement en vue d'un essai qui a débuté le 3 avril 2017 et qui se poursuivra jusqu'au 31 mars 2021. PARTICIPANTS: Quatre-vingt-quatre centres d'hémodialyse qui prendront en charge environ 15 500 patients pendant les quatre ans de suivi. INTERVENTION: Les centres d'hémodialyse ont été répartis aléatoirement (1:1) pour offrir (i) un protocole personnalisé de dialysat à température réduite ou (ii) un protocole de dialysat à 36,5°C. Pour le protocole personnalisé, les infirmières règlent la température du dialysat entre 0,5 et 0,9°C sous la température corporelle du patient mesurée avant la dialyse, jusqu'à une température minimale de 35,5°C. PRINCIPAUX RÉSULTATS: Un ensemble d'hospitalisations attribuables à un événement cardiovasculaire majeur (accident ischémique cérébral non fatal, infarctus du myocarde ou insuffisance cardiaque congestive) et de décès d'origine cardiovasculaire consignés dans les bases de données de santé de l'Ontario. PRINCIPALE ANALYSE ENVISAGÉE: L'analyse primaire adoptera une approche fondée sur l'intention de traiter. Un modèle de Cox servira à estimer le rapport de risque du temps écoulé jusqu'au premier événement. La corrélation intra-centre sera prise en compte à l'aide d'un estimateur sandwich robuste. Le temps d'observation sera censuré à la date de fin de l'essai ou au moment d'un décès non lié à un événement cardiovasculaire.

tRNAviz: explore and visualize tRNA sequence features.

Transfer RNAs (tRNAs) are ubiquitous across the tree of life. Although tRNA structure is highly conserved, there is still significant variation in sequence features between clades, isotypes and even isodecoders. This variation not only impacts translation, but as shown by a variety of recent studies, nontranslation-associated functions are also sensitive to small changes in tRNA sequence. Despite the rapidly growing number of sequenced genomes, there is a lack of tools for both small- and large-scale comparative genomics analysis of tRNA sequence features. Here, we have integrated over 150 000 tRNAs spanning all domains of life into tRNAviz, a web application for exploring and visualizing tRNA sequence features. tRNAviz implements a framework for determining consensus sequence features and can generate sequence feature distributions by isotypes, clades and anticodons, among other tRNA properties such as score. All visualizations are interactive and exportable. The web server is publicly available at http://trna.ucsc.edu/tRNAviz/.

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.

Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole genomes. The newly developed version 2.0 has incorporated advanced methodologies with improved probabilistic search software and a suite of new gene models, enabling better functional classification of predicted genes. This chapter describes the use of the UNIX command-driven and online web versions, illustrating different search modes and options.