Synthetic genomes unveil the effects of synonymous recoding.

Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers1-4. Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement-recoding-is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organism's genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.

Biochemical characterization of Fsa16295Glu from "Fervidibacter sacchari," the first hyperthermophilic GH50 with ß-1,3-endoglucanase activity and founding member of the subfamily GH50_3.

The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a ß-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as ß-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing ß-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.

Critical care nurse leaders' moral distress: A qualitative descriptive study.

BACKGROUND: Unit-based critical care nurse leaders (UBCCNL) play a role in exemplifying ethical leadership, addressing moral distress, and mitigating contributing factors to moral distress on their units. Despite several studies examining the experience of moral distress by bedside nurses, knowledge is limited regarding the UBCCNL's experience. RESEARCH AIM: The aim of this study was to gain a deeper understanding of the lived experiences of Alabama UBCCNLs regarding how they experience, cope with, and address moral distress. RESEARCH DESIGN: A qualitative descriptive design and inductive thematic analysis guided the investigation. A screening and demographics questionnaire and a semi-structured interview protocol were the tools of data collection. PARTICIPANT AND RESEARCH CONTEXT: Data were collected from 10 UBCCNLs from seven hospitals across the state of Alabama from February to July 2023. ETHICAL CONSIDERATIONS: This study was approved by the Institutional Review Board at the University of Alabama in Huntsville. Informed consent was obtained from participants prior to data collection. FINDINGS: UBCCNLs experience moral distress frequently due to a variety of systemic and organizational barriers. Feelings of powerlessness tended to precipitate moral distress among UBCCNLs. Despite moral distress resulting in increased advocacy and empathy, UBCCNLs may experience a variety of negative responses resulting from moral distress. UBCCNLs may utilize internal and external mechanisms to cope with and address moral distress. CONCLUSIONS: The UBCCNL's experience of moral distress is not dissimilar from bedside staff; albeit, moral distress does occur as a result of the responsibilities of leadership and the associated systemic barriers that UBCCNLs are privier to. When organizations allocate resources for addressing moral distress, they should be convenient to leaders and staff. The UBCCNL perspective should be considered in the development of future moral distress measurement tools and interventions. Future research exploring the relationship between empathy and moral distress among nurse leaders is needed.

Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert.

We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.

Critical care nurse leaders addressing moral distress: A qualitative study.

BACKGROUND: Moral distress (MD) occurs when clinicians are constrained from taking what they believe to be ethically appropriate actions. When unattended, MD may result in moral injury and/or suffering. Literature surrounding how unit-based critical care nurse leaders address MD in practice is limited. AIM: The aim of this study was to explore how ICU nurse leaders recognize and address MD among their staff. STUDY DESIGN: Qualitative descriptive with inductive thematic analysis. RESULTS: Five ICU nurse leaders participated in a one-time individual interview. Interview results suggest that (1) ICU nurse leaders can recognize and address MD among their staff and (2) nurse leaders experience MD themselves, which may be exacerbated by their leadership role and responsibilities. CONCLUSIONS: Further research is needed to develop interventions aimed at addressing MD among nurse leaders and equipping nurse leaders with the skills to identify and address MD within their staff and themselves. RELEVANCE TO CLINICAL PRACTICE: MD is an unavoidable phenomenon ICU nurse leaders are challenged with addressing in their day-to-day practice. As leaders, recognizing and addressing MD is a necessary task relating to mitigating burnout and turnover and addressing well-being among staff within the ICU.

Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting.

We present eight metatranscriptomic datasets of light algal and cyanolichen biological soil crusts from the Mojave Desert in response to wetting. These data will help us understand gene expression patterns in desert biocrust microbial communities after they have been reactivated by the addition of water.

The APPRISE Virtual Biobank for Infectious Diseases.

The Australian Partnership for Preparedness Research on InfectiouS disease Emergencies (APPRISE) has developed a virtual biobank to support infectious disease research in Australia. The virtual biobank (https://apprise.biogrid.org.au) integrates access to existing distributed infectious disease biospecimen collections comprising multiple specimen types, including plasma, serum, and peripheral blood mononuclear cells. Through the development of a common data model, multiple collections can be searched simultaneously via a secure web portal. The portal enhances the visibility and searchability of existing collections within their current governance and custodianship arrangements. The portal is easily scalable for integration of additional collections.

Promoting Competence in Nursing and Pharmacy Interprofessional Collaboration Through Telehealth Simulation.

ABSTRACT: Competence in interprofessional collaboration is essential for safe patient outcomes. This study examined the impact of an interprofessional telehealth pharmacology simulation on prelicensure nursing and pharmacy students' perceptions of interprofessional roles. A pretest-posttest design was used to compare participants' perceptions of interprofessional roles prior to and following the simulation. Data were collected using the Interdisciplinary Education Perception Scale (IEPS). Paired-samples t-tests showed statistically significant increases in scores for both the full IEPS (n = 99) and two subscales, Competency and Autonomy (n = 99) and Perception of Actual Cooperation (n = 99). Nurse educators should provide regular interprofessional experiences to foster learners' competence in interprofessional collaboration and communication.

Moral distress among nurse leaders: A qualitative systematic review.

Moral distress (MD) is well-documented within the nursing literature and occurs when constraints prevent a correct course of action from being implemented. The measured frequency of MD has increased among nurses over recent years, especially since the COVID-19 Pandemic. MD is less understood among nurse leaders than other populations of nurses. A qualitative systematic review was conducted with the aim to synthesize the experiences of MD among nurse leaders. This review involved a search of three databases (Medline, CINAHL, and APA PsychINFO) which resulted in the retrieval of 303 articles. PRISMA review criteria guided authors during the article review and selection process. Following the review, six articles were identified meeting review criteria and quality was assessed using the Critical Appraisal Skills Programme (CASP) Checklist for qualitative studies. No ethical review was required for this systematic review. The six studies included in this review originated from the United States, Brazil, Turkey, and Iran. Leadership roles ranged from unit-based leadership to executive leadership. Assigned quality scores based upon CASP criteria ranged from 6 to 9 (moderate to high quality). Three analytical themes emerged from the synthesis: (1) moral distress is consuming; (2) constrained by the system; and (3) adapt to overcome. The unique contributors of MD among nurse leaders include the leadership role itself and challenges navigating moral situations as they arise. The nurse leader perspective should be considered in the development of future MD interventions.

Evaluation of the Australian first few X household transmission project for COVID-19.

BACKGROUND: The Australian First Few X (FFX) Household Transmission Project for COVID-19 was the first prospective, multi-jurisdictional study of its kind in Australia. The project was undertaken as a partnership between federal and state health departments and the Australian Partnership for Preparedness Research on Infectious Disease Emergencies (APPRISE) and was active from April to October 2020. METHODS: We aimed to identify and explore the challenges and strengths of the Australian FFX Project to inform future FFX study development and integration into pandemic preparedness plans. We asked key stakeholders and partners involved with implementation to identify and rank factors relating to the strengths and challenges of project implementation in two rounds of modified Delphi surveys. Key representatives from jurisdictional health departments were then interviewed to contextualise findings within public health processes and information needs to develop a final set of recommendations for FFX study development in Australia. RESULTS: Four clear recommendations emerged from the evaluation. Future preparedness planning should aim to formalise and embed partnerships between health departments and researchers to help better integrate project data collection into core public health surveillance activities. The development of functional, adaptable protocols with pre-established ethics and governance approvals and investment in national data infrastructure were additional priority areas noted by evaluation participants. CONCLUSION: The evaluation provided a great opportunity to consolidate lessons learnt from the Australian FFX Household Transmission Project. The developed recommendations should be incorporated into future pandemic preparedness plans in Australia to enable effective implementation and increase local utility and value of the FFX platform within emergency public health response.

Decision-Making Strategies in Hospital Administrators in the Implementation of Nurse Residency Programs.

Current literature supports the creation and implementation of nurse residency programs to support new graduate nurses. The lack of this important postlicensure resource poses a problem for new graduate nurses who are seeking additional assistance and guidance during the transition to professional practice. This qualitative study revealed the factors, barriers, and benefits that influenced the decision-making process of nurse leaders in the implementation of nurse residency programs.

New Federal Efforts to Address Food and Nutrition Insecurity.

This JAMA Forum discusses the expansion and improvement of federal food and nutrition programs, such as the Supplemental Nutrition Assistance Program and the Special Supplemental Nutrition Program for Women, Infants, and Children, to combat food insecurity.

A Computational Approach to Identification of Candidate Biomarkers in High-Dimensional Molecular Data.

Complex high-dimensional datasets that are challenging to analyze are frequently produced through '-omics' profiling. Typically, these datasets contain more genomic features than samples, limiting the use of multivariable statistical and machine learning-based approaches to analysis. Therefore, effective alternative approaches are urgently needed to identify features-of-interest in '-omics' data. In this study, we present the molecular feature selection tool, a novel, ensemble-based, feature selection application for identifying candidate biomarkers in '-omics' data. As proof-of-principle, we applied the molecular feature selection tool to identify a small set of immune-related genes as potential biomarkers of three prostate adenocarcinoma subtypes. Furthermore, we tested the selected genes in a model to classify the three subtypes and compared the results to models built using all genes and all differentially expressed genes. Genes identified with the molecular feature selection tool performed better than the other models in this study in all comparison metrics: accuracy, precision, recall, and F1-score using a significantly smaller set of genes. In addition, we developed a simple graphical user interface for the molecular feature selection tool, which is available for free download. This user-friendly interface is a valuable tool for the identification of potential biomarkers in gene expression datasets and is an asset for biomarker discovery studies.

Virology and immune dynamics reveal high household transmission of ancestral SARS-CoV-2 strain.

BACKGROUND: Household studies are crucial for understanding the transmission of SARS-CoV-2 infection, which may be underestimated from PCR testing of respiratory samples alone. We aim to combine the assessment of household mitigation measures; nasopharyngeal, saliva, and stool PCR testing; along with mucosal and systemic SARS-CoV-2-specific antibodies, to comprehensively characterize SARS-CoV-2 infection and transmission in households. METHODS: Between March and September 2020, we obtained samples from 92 participants in 26 households in Melbourne, Australia, in a 4-week period following the onset of infection with ancestral SARS-CoV-2 variants. RESULTS: The secondary attack rate was 36% (24/66) when using nasopharyngeal swab (NPS) PCR positivity alone. However, when respiratory and nonrespiratory samples were combined with antibody responses in blood and saliva, the secondary attack rate was 76% (50/66). SARS-CoV-2 viral load of the index case and household isolation measures were key factors that determine secondary transmission. In 27% (7/26) of households, all family members tested positive by NPS for SARS-CoV-2 and were characterized by lower respiratory Ct values than low transmission families (Median 22.62 vs. 32.91; IQR 17.06-28.67 vs. 30.37-34.24). High transmission families were associated with enhanced plasma antibody responses to multiple SARS-CoV-2 antigens and the presence of neutralizing antibodies. Three distinguishing saliva SARS-CoV-2 antibody features were identified according to age (IgA1 to Spike 1, IgA1 to nucleocapsid protein (NP)), suggesting that adults and children generate distinct mucosal antibody responses during the acute phase of infection. CONCLUSION: Utilizing respiratory and nonrespiratory PCR testing, along with the measurement of SARS-CoV-2-specific local and systemic antibodies, provides a more accurate assessment of infection within households and highlights some of the immunological differences in response between children and adults.

An Update on Posterior Tarsal Tunnel Syndrome.

Posterior tarsal tunnel syndrome (PTTS) is an entrapment neuropathy due to compression of the tibial nerve or one of its terminal branches within the tarsal tunnel in the medial ankle. The tarsal tunnel is formed by the flexor retinaculum, while the floor is composed of the distal tibia, talus, and calcaneal bones. The tarsal tunnel contains a number of significant structures, including the tendons of 3 muscles as well as the posterior tibial artery, vein, and nerve. Focal compressive neuropathy of PTTS can originate from anything that physically restricts the volume of the tarsal tunnel. The variety of etiologies includes distinct movements of the foot, trauma, vascular disorders, soft tissue inflammation, diabetes mellitus, compression lesions, bony lesions, masses, lower extremity edema, and postoperative injury. Generally, compression of the posterior tibial nerve results in clinical findings consisting of numbness, burning, and painful paresthesia in the heel, medial ankle, and plantar surface of the foot. Diagnosis of PTTS can be made with the presence of a positive Tinel sign in combination with the physical symptoms of pain and numbness along the plantar and medial surfaces of the foot. Initially, patients are treated conservatively unless there are signs of muscle atrophy or motor nerve involvement. Conservative treatment includes activity modification, heat, cryotherapy, non-steroidal anti-inflammatory drugs, corticosteroid injections, opioids, GABA analog medications, tricyclic antidepressants, vitamin B-complex supplements, physical therapy, and custom orthotics. If PTTS is recalcitrant to conservative treatment, standard open surgical decompression of the flexor retinaculum is indicated. In recent years, a number of alternative minimally invasive treatment options have been investigated, but these studies have small sample sizes or were conducted on cadaveric models.

Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms.

The deadly toxin α-amanitin is a bicyclic octapeptide biosynthesized on ribosomes. A phylogenetically disjunct group of mushrooms in Agaricales (Amanita, Lepiota, and Galerina) synthesizes α-amanitin. This distribution of the toxin biosynthetic pathway is possibly related to the horizontal transfer of metabolic gene clusters among taxonomically unrelated mushrooms with overlapping habitats. Here, our work confirms that two biosynthetic genes, P450-29 and FMO1, are oxygenases important for amanitin biosynthesis. Phylogenetic and genetic analyses of these genes strongly support their origin through horizontal transfer, as is the case for the previously characterized biosynthetic genes MSDIN and POPB. Our analysis of multiple genomes showed that the evolution of the α-amanitin biosynthetic pathways in the poisonous agarics in the Amanita, Lepiota, and Galerina clades entailed distinct evolutionary pathways including gene family expansion, biosynthetic genes, and genomic rearrangements. Unrelated poisonous fungi produce the same deadly amanitin toxins using variations of the same pathway. Furthermore, the evolution of the amanitin biosynthetic pathway(s) in Amanita species generates a much wider range of toxic cyclic peptides. The results reported here expand our understanding of the genetics, diversity, and evolution of the toxin biosynthetic pathway in fungi.

Value of consultation in establishing a public health research network: lessons from APPRISE.

OBJECTIVES: To understand the challenges and benefits of an extensive consultation process relating to the establishment and ongoing funding of a novel, disseminated national research network for infectious disease preparedness. METHODS: We used a two-part modified Delphi process to identify and rank factors relating to the consultation process across the different stages of setting up a new research network. RESULTS: Research priorities for the new research network remained the same following consultation with a broad range of stakeholders. Broad networking and the establishment of a nationally recognised preparedness research network were clearly identified as the consultation's key strengths. The need for ongoing management of diverse expectations, particularly between researchers and public health practitioners, are clear challenges. Clarity on the distinct roles of researchers and decision makers are necessary to integrate research into a translational pathway. Researcher expectations for investigator-driven detailed inquiry must be balanced with expectations of routine public health activities and decision making. CONCLUSIONS: Consultation had a clear benefit for the development of a complex public health network with a focus on policy translation. Ongoing challenges include managing diverse expectations and recognising the need for continuing relationship management. Understanding the strengths and limitations of consultation to enable ongoing funding should inform the development of further collaborative research networks in multidisciplinary and translational contexts in health.

Characteristics, Comorbidities, and Data Gaps for Coronavirus Disease Deaths, Tennessee, USA.

As of March 2021, coronavirus disease (COVID-19) had led to >500,000 deaths in the United States, and the state of Tennessee had the fifth highest number of cases per capita. We reviewed the Tennessee Department of Health COVID-19 surveillance and chart-abstraction data during March 15‒August 15, 2020. Patients who died from COVID-19 were more likely to be older, male, and Black and to have underlying conditions (hereafter comorbidities) than case-patients who survived. We found 30.4% of surviving case-patients and 20.3% of deceased patients had no comorbidity information recorded. Chart-abstraction captured a higher proportion of deceased case-patients with >1 comorbidity (96.3%) compared with standard surveillance deaths (79.0%). Chart-abstraction detected higher rates of each comorbidity except for diabetes, which had similar rates among standard surveillance and chart-abstraction. Investing in public health data collection infrastructure will be beneficial for the COVID-19 pandemic and future disease outbreaks.