Patient factors associated with telehealth quality and experience among adults with chronic conditions

Objective

To evaluate patient-reported experiences of telehealth and disparities in access, use, and satisfaction with telehealth during the COVID-19 pandemic.

Materials and methods

We examined data from the fifth wave of the COVID-19 & Chronic Conditions (C3) study conducted between December 2020 and March 2021.

Results

Of the 718 participants, 342 (47.6%) reported having a telehealth visit within the past 4 months. Participants who had a recent telehealth visit were younger, reported worse overall health and chronic illness burden, and living below poverty level. Among participants who had a telehealth visit, 66.7% reported telephone visits and most participants (57.6%) rated telehealth quality as better-or-equal-to in-person visits. Inadequate health literacy was associated with lower likelihood of reporting telehealth quality and usefulness. In multivariable analyses, lower patient activation (adjusted odds ratio (AOR) 0.19, 95% CI, 0.05-0.59) and limited English proficiency (AOR 0.12, 95% CI, 0.03-0.47) were less likely to report telehealth as being better than in-person visits; lower patient activation (AOR 0.06, 95% CI, 0.003-0.41) and income below poverty level (AOR 0.36, 95% CI, 0.13-0.98) were associated with difficulty remembering telehealth visit information.

Discussion

Most participants reported usefulness and ease of navigating telehealth. Lower socioeconomic status, limited English proficiency, inadequate health literacy, lower educational attainment, and low patient activation are risks for poorer quality telehealth.

Conclusion

The COVID pandemic has accelerated the adoption of telehealth, however, disparities in access and self-reported visit quality persist. Since telemedicine is here to stay, we identify vulnerable populations and discuss potential solutions to reduce healthcare disparities in telehealth use.

Shaping nature outcomes in corporate settings

Transnational companies have substantive impacts on nature: a hallmark of living in the Anthropocene. Understanding these impacts through company provision of information is a precursor to holding them accountable for nature outcomes. The effect of increasing disclosures (of varying quality) is predicated on 'information governance', an approach that uses disclosure requirements to drive company behaviour. However, its efficacy is not guaranteed. We argue that three conditions are required before disclosures have the possibility to shape nature outcomes, namely: (1) radical traceability that links company actions to outcomes in particular settings; (2) developing organizational routines, tools and approaches that translate strategic intent to on-the-ground behaviour; and (3) mobilizing and aligning financial actors with corporate nature ambitions. While disclosure is key to each of these conditions, its limits must be taken into account and it must be nested in governance approaches that shape action, not just reporting. This article is part of the theme issue 'Bringing nature into decision-making'.

Photosynthesis and other factors affecting the establishment and maintenance of cnidarian-dinoflagellate symbiosis

Coral growth depends on the partnership between the animal hosts and their intracellular, photosynthetic dinoflagellate symbionts. In this study, we used the sea anemone Aiptasia, a laboratory model for coral biology, to investigate the poorly understood mechanisms that mediate symbiosis establishment and maintenance. We found that initial colonization of both adult polyps and larvae by a compatible algal strain was more effective when the algae were able to photosynthesize and that the long-term maintenance of the symbiosis also depended on photosynthesis. In the dark, algal cells were taken up into host gastrodermal cells and not rapidly expelled, but they seemed unable to reproduce and thus were gradually lost. When we used confocal microscopy to examine the interaction of larvae with two algal strains that cannot establish stable symbioses with Aiptasia, it appeared that both pre- and post-phagocytosis mechanisms were involved. With one strain, algae entered the gastric cavity but appeared to be completely excluded from the gastrodermal cells. With the other strain, small numbers of algae entered the gastrodermal cells but appeared unable to proliferate there and were slowly lost upon further incubation. We also asked if the exclusion of either incompatible strain could result simply from their cells' being too large for the host cells to accommodate. However, the size distributions of the compatible and incompatible strains overlapped extensively. Moreover, examination of macerates confirmed earlier reports that individual gastrodermal cells could expand to accommodate multiple algal cells. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Tools used to measure the impact of comorbidities on surgical outcomes in children with complex chronic conditions: A scoping review

AIM

To identify and describe assessment tools used to measure the impact of comorbidities on postoperative outcomes in children with complex chronic conditions (CCC).

METHOD

This was a scoping review using five electronic databases. The search was conducted in March 2022 by a medical librarian. There were no date or language restrictions. Included studies were full-text articles published in peer-reviewed journals that described a tool used to measure the impact of comorbidities in children with CCC to assess postoperative outcomes. A standardized data charting tool was used.

RESULTS

A total of 2157 articles were retrieved. Five studies reporting on six comorbidity measures met inclusion criteria. All were cohort studies and were secondary analyses of data from an administrative database (n = 4) or a patient registry (n = 1). Sample sizes ranged from 645 to 25 747 participants. One paper described the assessment of reliability. Only one form of validity - predictive validity - was assessed in three papers for five measures.

INTERPRETATION

Findings from this scoping review revealed a paucity of comorbidity assessment tools validated for use with children with CCC; significant conceptual and measurement challenges exist in the current scientific literature.

Redox active plant phenolic, acetosyringone, for electrogenetic signaling

Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H2O2) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a "pro-signaling molecule" that can be activated by its oxidation-in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O2 to form H2O2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed "pro-signal" dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.

Achieving Decentralized, Electrified, and Decarbonized Ammonia Production

The rapid reduction in the cost of renewable energy has motivated the transition from carbon-intensive chemical manufacturing to renewable, electrified, and decarbonized technologies. Although electrified chemical manufacturing technologies differ greatly, the feasibility of each electrified approach is largely related to the energy efficiency and capital cost of the system. Here, we examine the feasibility of ammonia production systems driven by wind and photovoltaic energy. We identify the optimal regions where wind and photovoltaic electricity production may be able to meet the local demand for ammonia-based fertilizers and set technology targets for electrified ammonia production. To compete with the methane-fed Haber-Bosch process, electrified ammonia production must reach energy efficiencies of above 20% for high natural gas prices and 70% for low natural gas prices. To account for growing concerns regarding access to water, geospatial optimization considers water stress caused by new ammonia facilities, and recommendations ensure that the identified regions do not experience an increase in water stress. Reducing water stress by 99% increases costs by only 1.4%. Furthermore, a movement toward a more decentralized ammonia supply chain driven by wind and photovoltaic electricity can reduce the transportation distance for ammonia by up to 76% while increasing production costs by 18%.

Critically assessing atavism, an evolution-centered and deterministic hypothesis on cancer

Cancer is most commonly viewed as resulting from somatic mutations enhancing proliferation and invasion. Some hypotheses further propose that these new capacities reveal a breakdown of multicellularity allowing cancer cells to escape proliferation and cooperation control mechanisms that were implemented during evolution of multicellularity. Here we critically review one such hypothesis, named "atavism," which puts forward the idea that cancer results from the re-expression of normally repressed genes forming a program, or toolbox, inherited from unicellular or simple multicellular ancestors. This hypothesis places cancer in an interesting evolutionary perspective that has not been widely explored and deserves attention. Thinking about cancer within an evolutionary framework, especially the major transitions to multicellularity, offers particularly promising perspectives. It is therefore of the utmost important to analyze why one approach that tries to achieve this aim, the atavism hypothesis, has not so far emerged as a major theory on cancer. We outline the features of the atavism hypothesis that, would benefit from clarification and, if possible, unification.

Corals survive severe bleaching event in refuges related to taxa, colony size, and water depth

Marine heatwaves are increasing in frequency and duration, threatening tropical reef ecosystems through intensified coral bleaching events. We examined a strikingly variable spatial pattern of bleaching in Moorea, French Polynesia following a heatwave that lasted from November 2018 to July 2019. In July 2019, four months after the onset of bleaching, we surveyed > 5000 individual colonies of the two dominant coral genera, Pocillopora and Acropora, at 10 m and 17 m water depths, at six forereef sites around the island where temperature was measured. We found severe bleaching increased with colony size for both coral genera, but Acropora bleached more severely than Pocillopora overall. Acropora bleached more at 10 m than 17 m, likely due to higher light availability at 10 m compared to 17 m, or greater daily temperature fluctuation at depth. Bleaching in Pocillopora corals did not differ with depth but instead varied with the interaction of colony size and Accumulated Heat Stress (AHS), in that larger colonies (> 30 cm) were more sensitive to AHS than mid-size (10-29 cm) or small colonies (5-9 cm). Our findings provide insight into complex interactions among coral taxa, colony size, and water depth that produce high spatial variation in bleaching and related coral mortality.

Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension

Nonenzymatic template-directed RNA copying requires catalysis by divalent metal ions. The primer extension reaction involves the attack of the primer 3'-hydroxyl on the adjacent phosphate of a 5'-5'-imidazolium-bridged dinucleotide substrate. However, the nature of the interaction of the catalytic metal ion with the reaction center remains unclear. To explore the coordination of the catalytic metal ion with the imidazolium-bridged dinucleotide substrate, we examined catalysis by oxophilic and thiophilic metal ions with both diastereomers of phosphorothioate-modified substrates. We show that Mg2+ and Cd2+ exhibit opposite preferences for the two phosphorothioate substrate diastereomers, indicating a stereospecific interaction of the divalent cation with one of the nonbridging phosphorus substituents. High-resolution X-ray crystal structures of the products of primer extension with phosphorothioate substrates reveal the absolute stereochemistry of this interaction and indicate that catalysis by Mg2+ involves inner-sphere coordination with the nonbridging phosphate oxygen in the pro-SP position, while thiophilic cadmium ions interact with sulfur in the same position, as in one of the two phosphorothioate substrates. These results collectively suggest that during nonenzymatic RNA primer extension with a 5'-5'-imidazolium-bridged dinucleotide substrate the interaction of the catalytic Mg2+ ion with the pro-SP oxygen of the reactive phosphate plays a crucial role in the metal-catalyzed SN2(P) reaction.

Biomolecular Interaction Analysis Quantification with a Low-Volume Microfluidic Chip and Particle Diffusometry

Microfluidic techniques are widely applied in biomolecular analysis and disease diagnostic assays. While the volume of the sample that is directly used in such assays is often only femto-to microliters, the "dead volume" of solutions supplied in syringes and tubing can be much larger, even up to milliliters, increasing overall reagent use and making analysis significantly more expensive. To reduce the difficulty and cost, we designed a new chip using a low volume solution for analysis and applied it to obtain real-time data for protein-protein interaction measurements. The chip takes advantage of air/aqueous two-phase droplet flow, on-chip rapid mixing within milliseconds, and a droplet capture method, that ultimately requires only 2 μL of reagent solution. The interaction is analyzed by particle diffusometry, a nonintrusive and precise optical detection method to analyze the properties of microparticle diffusion in solution. Herein, we demonstrate on-chip characterization of human immunodeficiency virus p24 antibody-antigen protein binding kinetics imaged via fluorescence microscopy and analyzed by PD. The measured kon and koff are 1 × 106 M-1 s-1 and 3.3 × 10-4 s-1, respectively, and agree with independent measurement via biolayer interferometry and previously calculated p24-antibody binding kinetics. This new microfluidic chip and the protein-protein interaction analysis method can also be applied in other fields that require low-volume solutions to perform accurate measurement, analysis, and detection.

Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.

Domestic dogs in indigenous Amazonian communities: Key players in Leptospira cycling and transmission?

BACKGROUND

Leptospirosis is the world's most common zoonotic disease. Mitigation and control rely on pathogen identification and understanding the roles of potential reservoirs in cycling and transmission. Underreporting and misdiagnosis obscure the magnitude of the problem and confound efforts to understand key epidemiological components. Difficulties in culturing hamper the use of serological diagnostics and delay the development of DNA detection methods. As a result, especially in complex ecosystems, we know very little about the importance of different mammalian host species in cycling and transmission to humans.

METHODOLOGY/PRINCIPAL FINDINGS

We sampled dogs from five indigenous Kichwa communities living in the Yasuní National Park in the Ecuadorian Amazon basin. Blood and urine samples from domestic dogs were collected to assess the exposure of these animals to Leptospira and to identify the circulating species. Microscopic Agglutination Tests with a panel of 22 different serovars showed anti-leptospira antibodies in 36 sampled dogs (75%), and 7 serogroups were detected. Two DNA-based detection assays revealed pathogenic Leptospira DNA in 18 of 19 dog urine samples (94.7%). Amplicon sequencing and phylogenetic analysis of 16S rRNA and SecY genes from 15 urine samples revealed genetic diversity within two of three different Leptospira species: noguchii (n = 7), santarosai (n = 7), and interrogans (n = 1).

CONCLUSIONS/SIGNIFICANCE

The high prevalence of antibodies and Leptospira DNA provides strong evidence for high rates of past and current infections. Such high prevalence has not been previously reported for dogs. These dogs live in the peridomestic environment in close contact with humans, yet they are free-ranging animals that interact with wildlife. This complex web of interactions may explain the diverse types of pathogenic Leptospira observed in this study. Our results suggest that domestic dogs are likely to play an important role in the cycling and transmission of Leptospira. Future studies in areas with complex ecoepidemiology will enable better parsing of the significance of genotypic, environmental, and host characteristics.

Symbiosis takes a front and center role in biology

All animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. While the recognition of this phenomenon has been slow in coming, it will impact most, if not all, subdisciplines of biology.

Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses

Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC257, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.

Exploring Ward Team Handoffs of Overnight Admissions: Key Lessons from Field Observations

BACKGROUND

The diagnostic process is a dynamic, team-based activity that is an important aspect of ward rounds in teaching hospitals. However, few studies have examined how academic ward teams operate in areas such as diagnosis in the handoff of overnight admissions during ward rounds. This study draws key lessons from team interactions in the handoff process during ward rounds.

OBJECTIVE

To describe how ward teams operate in the handoff of patients admitted overnight during ward rounds, and to characterize the role of the bedside patient evaluation in this context.

DESIGN

A qualitative ethnographic approach using field observations and documentary analysis.

PARTICIPANTS

Attending physicians, medical residents, and medical students on general medicine services in a single teaching hospital.

APPROACH

Thirty-five hours of observations were undertaken over a 4-month period. We purposively approached a diverse group of attendings who cover a range of clinical teaching experience, and obtained informed consent from all ward team members and observed patients. Thirty patient handoffs were observed across 5 ward teams with 45 team members. We conducted thematic analysis of researcher field notes and electronic health record documents using social cognitive theories to characterize the dynamic interactions occurring in the real clinical environment.

KEY RESULTS

Teams spent less time during ward rounds on verifying history and physical examination findings, performing bedside evaluations, and discussing differential diagnoses than other aspects (e.g., reviewing patient data in conference rooms) in the team handoff process of overnight admissions. Several team-based approaches to diagnosis and bedside patient evaluations were observed, including debriefing for learning and decision-making.

CONCLUSIONS

This study highlights potential strengths and missed opportunities for teaching, learning, and engaging directly with patients in the ward team handoff of patients admitted overnight. These findings may inform curriculum development, faculty training, and patient safety research.

Characteristics differentiating problem representation synthesis between novices and experts

BACKGROUND

Formulating a thoughtful problem representation (PR) is fundamental to sound clinical reasoning and an essential component of medical education. Aside from basic structural recommendations, little consensus exists on what characterizes high-quality PRs.

OBJECTIVES

To elucidate characteristics that distinguish PRs created by experts and novices.

METHODS

Early internal medicine residents (novices) and inpatient teaching faculty (experts) from two academic medical centers were given two written clinical vignettes and were instructed to write a PR and three-item differential diagnosis for each. Deductive content analysis described the characteristics comprising PRs. An initial codebook of characteristics was refined iteratively. The primary outcome was differences in characteristic frequencies between groups. The secondary outcome was characteristics correlating with diagnostic accuracy. Mixed-effects regression with random effects modeling compared case-level outcomes by group.

RESULTS

Overall, 167 PRs were analyzed from 30 novices and 54 experts. Experts included 0.8 fewer comorbidities (p < .01) and 0.6 more examination findings (p = .01) than novices on average. Experts were less likely to include irrelevant comorbidities (odds ratio [OR] = 0.4, 95% confidence interval [CI] = 0.2-0.8) or a diagnosis (OR = 0.3, 95% CI = 0.1-0.8) compared with novices. Experts encapsulated clinical data into higher-order terms (e.g., sepsis) than novices (p < .01) while including similar numbers of semantic qualifiers (SQs). Regardless of expertise level, PRs following a three-part structure (e.g., demographics, temporal course, and clinical syndrome) and including temporal SQs were associated with diagnostic accuracy (p < .01).

CONCLUSIONS

Compared with novices, expert PRs include less irrelevant data and synthesize information into higher-order concepts. Future studies should determine whether targeted educational interventions for PRs improve diagnostic accuracy.

Quantum control of exciton wave functions in 2D semiconductors

Excitons-bound electron-hole pairs-play a central role in light-matter interaction phenomena and are crucial for wide-ranging applications from light harvesting and generation to quantum information processing. A long-standing challenge in solid-state optics has been to achieve precise and scalable control over excitonic motion. We present a technique using nanostructured gate electrodes to create tailored potential landscapes for excitons in 2D semiconductors, enabling in situ wave function shaping at the nanoscale. Our approach forms electrostatic traps for excitons in various geometries, such as quantum dots, rings, and arrays thereof. We show independent spectral tuning of spatially separated quantum dots, achieving degeneracy despite material disorder. Owing to the strong light-matter coupling of excitons in 2D semiconductors, we observe unambiguous signatures of confined exciton wave functions in optical reflection and photoluminescence measurements. This work unlocks possibilities for engineering exciton dynamics and interactions at the nanometer scale, with implications for optoelectronic devices, topological photonics, and quantum nonlinear optics.

Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120

In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.

Oleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes

Lipogenesis is a vital but often dysregulated metabolic pathway. Here we use optical photothermal infrared imaging to quantify lipogenesis rates of isotopically labelled oleic acid and glucose concomitantly in live cells. In hepatocytes, but not adipocytes, we find that oleic acid feeding at 60 μM increases the number and size of lipid droplets (LDs) while simultaneously inhibiting storage of de novo synthesized lipids in LDs. Our results demonstrate alternate regulation of lipogenesis between cell types.

Multiannual patterns of genetic structure and mating type ratios highlight the complex bloom dynamics of a marine planktonic diatom

Understanding the genetic structure of populations and the processes responsible for its spatial and temporal dynamics is vital for assessing species' adaptability and survival in changing environments. We investigate the genetic fingerprinting of blooming populations of the marine diatom Pseudo-nitzschia multistriata in the Gulf of Naples (Mediterranean Sea) from 2008 to 2020. Strains were genotyped using microsatellite fingerprinting and natural samples were also analysed with Microsatellite Pool-seq Barcoding based on Illumina sequencing of microsatellite loci. Both approaches revealed a clonal expansion event in 2013 and a more stable genetic structure during 2017-2020 compared to previous years. The identification of a mating type (MT) determination gene allowed to assign MT to strains isolated over the years. MTs were generally at equilibrium with two notable exceptions, including the clonal bloom of 2013. The populations exhibited linkage equilibrium in most blooms, indicating that sexual reproduction leads to genetic homogenization. Our findings show that P. multistriata blooms exhibit a dynamic genetic and demographic composition over time, most probably determined by deeper-layer cell inocula. Occasional clonal expansions and MT imbalances can potentially affect the persistence and ecological success of planktonic diatoms.

Evolution of exploitation and replication of giant viruses and virophages

Tripartite biotic interactions are inherently complex, and the strong interdependence of species and often one-sided exploitation can make these systems vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation beyond the point where sustainable resource use is no longer possible. We used this general prediction to test the potential role of trait evolution for persistence in a tripartite microbial system consisting of a marine heterotrophic flagellate preyed upon by a giant virus, which in turn is parasitized by a virophage. Host and virophage may benefit from this interaction because the virophage reduces the harmful effects of the giant virus on the host population and the virophage can persist integrated into the host genome when giant viruses are scarce. We grew hosts and virus in the presence and absence of the virophage over ∼280 host generations and tested whether levels of exploitation and replication in the giant virus and/or virophage population evolved over the course of the experiment, and whether the changes were such that they could avoid overexploitation and extinction. We found that the giant virus evolved toward lower levels of replication and the virophage evolved toward increased replication but decreased exploitation of the giant virus. These changes reduced overall host exploitation by the virus and virus exploitation by the virophage and are predicted to facilitate persistence.

A single Prochlorococcus ecotype dominates the tropical Bay of Bengal with ultradian growth

The Bay of Bengal (BoB) spans >2.2 million km2 in the northeastern Indian Ocean and is bordered by dense populations that depend upon its resources. Over recent decades, a shift from larger phytoplankton to picoplankton has been reported, yet the abundance, activity, and composition of primary producer communities are not well-characterized. We analysed the BoB regions during the summer monsoon. Prochlorococcus ranged up to 3.14 × 105 cells mL-1 in the surface mixed layer, averaging 1.74 ± 0.46 × 105 in the upper 10 m and consistently higher than Synechococcus and eukaryotic phytoplankton. V1-V2 rRNA gene amplicon analyses showed the High Light II (HLII) ecotype formed 98 ± 1% of Prochlorococcus amplicons in surface waters, comprising six oligotypes, with the dominant oligotype accounting for 65 ± 4% of HLII. Diel sampling of a coherent water mass demonstrated evening onset of cell division and rapid Prochlorococcus growth between 1.5 and 3.1 div day-1, based on cell cycle analysis, as confirmed by abundance-based estimates of 2.1 div day-1. Accumulation of Prochlorococcus produced by ultradian growth was restricted by high loss rates. Alongside prior Arabian Sea and tropical Atlantic rates, our results indicate Prochlorococcus growth rates should be reevaluated with greater attention to latitudinal zones and influences on contributions to global primary production.

Using Natural Language Processing to Identify Stigmatizing Language in Labor and Birth Clinical Notes

INTRODUCTION

Stigma and bias related to race and other minoritized statuses may underlie disparities in pregnancy and birth outcomes. One emerging method to identify bias is the study of stigmatizing language in the electronic health record. The objective of our study was to develop automated natural language processing (NLP) methods to identify two types of stigmatizing language: marginalizing language and its complement, power/privilege language, accurately and automatically in labor and birth notes.

METHODS

We analyzed notes for all birthing people > 20 weeks' gestation admitted for labor and birth at two hospitals during 2017. We then employed text preprocessing techniques, specifically using TF-IDF values as inputs, and tested machine learning classification algorithms to identify stigmatizing and power/privilege language in clinical notes. The algorithms assessed included Decision Trees, Random Forest, and Support Vector Machines. Additionally, we applied a feature importance evaluation method (InfoGain) to discern words that are highly correlated with these language categories.

RESULTS

For marginalizing language, Decision Trees yielded the best classification with an F-score of 0.73. For power/privilege language, Support Vector Machines performed optimally, achieving an F-score of 0.91. These results demonstrate the effectiveness of the selected machine learning methods in classifying language categories in clinical notes.

CONCLUSION

We identified well-performing machine learning methods to automatically detect stigmatizing language in clinical notes. To our knowledge, this is the first study to use NLP performance metrics to evaluate the performance of machine learning methods in discerning stigmatizing language. Future studies should delve deeper into refining and evaluating NLP methods, incorporating the latest algorithms rooted in deep learning.

Quality improvement project demonstrating a sustained increase in the assessment and sampling of ascites for hospitalised patients with cirrhosis

Objective

Using quality improvement techniques, we aimed to improve the rate of assessment and sampling of ascitic fluid for the purpose of diagnosing spontaneous bacterial peritonitis in patients with cirrhosis admitted to the hospitalist service of our institution.

Design/methods

Based on stakeholder needs assessment, we implemented interventions targeting provider knowledge, procedure workflows and clinical decision support. We analysed key metrics during preintervention (September-December 2020), intervention roll-out (January-April 2021), postintervention (May-September 2021) and sustainability (September-December 2022) periods for admissions of patients with cirrhosis to our hospitalist service at Maine Medical Center, a 700-bed tertiary-care academic hospital in Portland, Maine, USA.

Results

Among patients with cirrhosis admitted to our service, documentation of assessment for paracentesis increased from a preintervention baseline of 60.1% to 93.5% (p<0.005) postintervention. For patients with ascites potentially amenable to paracentesis, diagnostic paracentesis rate increased from 59.7% to 93% (p<0.005), with the rate of paracentesis within 24 hours increasing from 52.6% to 77.2% (p=0.01). These improvements persisted during our sustainability period. Complication rate was low (1.2%) across all study periods.

Conclusion

Our quality improvement project led to a sustained improvement in the identification of patients with cirrhosis needing diagnostic paracentesis and an increased procedure completion rate. This improvement strategy serves as a model for needed work toward closing a national performance gap for patients with cirrhosis.

Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep-sea floor

The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.

On the impact of incomplete taxon sampling on the relative timing of gene transfer events

A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.

Energetics of the microsporidian polar tube invasion machinery

Microsporidia are eukaryotic, obligate intracellular parasites that infect a wide range of hosts, leading to health and economic burdens worldwide. Microsporidia use an unusual invasion organelle called the polar tube (PT), which is ejected from a dormant spore at ultra-fast speeds, to infect host cells. The mechanics of PT ejection are impressive. Anncaliia algerae microsporidia spores (3-4 μm in size) shoot out a 100-nm-wide PT at a speed of 300 μm/s, creating a shear rate of 3000 s-1. The infectious cargo, which contains two nuclei, is shot through this narrow tube for a distance of ∼60-140 μm (Jaroenlak et al, 2020) and into the host cell. Considering the large hydraulic resistance in an extremely thin tube and the low-Reynolds-number nature of the process, it is not known how microsporidia can achieve this ultrafast event. In this study, we use Serial Block-Face Scanning Electron Microscopy to capture 3-dimensional snapshots of A. algerae spores in different states of the PT ejection process. Grounded in these data, we propose a theoretical framework starting with a systematic exploration of possible topological connectivity amongst organelles, and assess the energy requirements of the resulting models. We perform PT firing experiments in media of varying viscosity, and use the results to rank our proposed hypotheses based on their predicted energy requirement. We also present a possible mechanism for cargo translocation, and quantitatively compare our predictions to experimental observations. Our study provides a comprehensive biophysical analysis of the energy dissipation of microsporidian infection process and demonstrates the extreme limits of cellular hydraulics.

Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying

2-Thiouridine (s2U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s2U:s2U compared to those with U:U pairs. Notably, the C═O···H-N hydrogen bond in the U:U pair is replaced with a C═S···H-N hydrogen bond in the s2U:s2U base pair. The thermodynamic stability of the s2U:s2U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s2U:s2U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s2U base pair outcompetes the slightly weaker s2U:s2U base pair. In addition, even if an s2U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s2U. Our findings suggest that s2U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.

Inconsistent dilution: experimental but not field evidence for a dilution effect in Daphnia-bacteria interactions

The dilution effect hypothesis, which suggests greater host biodiversity can reduce infectious disease transmission, occurs in many systems but is not universal. Most studies only investigate the dilution of a single parasite in a community, but many host communities have multiple parasites circulating. We studied a zooplankton host community with prior support for a dilution effect in laboratory- and field-based studies of a fungal parasite, Metschnikowia bicuspidata. We used paired experiments and field studies to ask whether dilution also occurred for a bacterial parasite, Pasteuria ramosa. We hypothesized that the similarities between the parasites might mean the dilution pattern seen in Metschnikowia would also be seen in Pasteuria. However, because Daphnia-Pasteuria interactions have strong host-parasite genotype specificity, dilution may be less likely if diluter host genotypes vary in their capacity to dilute Pasteuria. In a lab experiment, Pasteuria prevalence in susceptible Daphnia dentifera was reduced strongly by higher densities of D. pulicaria and marginally by higher densities of D. retrocurva. In a second experiment, different D. pulicaria genotypes had a similar capacity to dilute both Metschnikowia and Pasteuria, suggesting that Pasteuria's strong host-parasite genotype specificity should not prevent dilution. However, we found no evidence of an impact of the dilution effect on the size of Pasteuria epidemics in D. dentifera in Midwestern U.S. lakes. Our finding that a second parasite infecting the same host community does not show a similar dilution effect in the field suggests the impact of biodiversity can differ even among parasites in the same host community.

How does parasite environmental transmission stage concentration change before, during, and after disease outbreaks?

Outbreaks of environmentally transmitted parasites require that susceptible hosts encounter transmission stages in the environment and become infected, but we also know that transmission stages can be in the environment without triggering disease outbreaks. One challenge in understanding the relationship between environmental transmission stages and disease outbreaks is that the distribution and abundance of transmission stages outside of their hosts have been difficult to quantify. Thus, we have limited data about how changes in transmission stage abundance influence disease dynamics; moreover, we do not know whether the relationship between transmission stages and outbreaks differs among parasite species. We used digital PCR to quantify the environmental transmission stages of five parasites in six lakes in southeastern Michigan every 2 weeks from June to November 2021. At the same time, we quantified infection prevalence in hosts and host density. Our study focused on eight zooplankton host species (Daphnia spp. and Ceriodaphnia dubia) and five of their parasites from diverse taxonomic groups (bacteria, yeast, microsporidia, and oomycete) with different infection mechanisms. We found that parasite transmission stage concentration increased prior to disease outbreaks for all parasites. However, parasites differed significantly in the relative timing of peaks in transmission stage concentration and infection outbreaks. The "continuous shedder" parasites had transmission stage peaks at the same time as or slightly after the outbreak peaks. In contrast, parasites relying on host death for transmission ("obligate killers") had transmission stage peaks before outbreak peaks. For most parasites, lakes with outbreaks had higher spore concentrations than those without outbreaks, especially once an outbreak began; the exception was for a parasite, Pasteuria ramosa, with very strong genotypic specificity of infection. Overall, our results show that disease outbreaks are tightly linked to transmission stage concentration; outbreaks were preceded by increases in transmission stage concentration in the environment and then were fueled by the production of more transmission stages during the outbreak itself, with concentrations decreasing to pre-outbreak levels as outbreaks waned. Thus, tracking transmission stages in the environment improves our understanding of the drivers of disease outbreaks and reveals how parasite traits may affect these dynamics.

Gametic selection favours polyandry and selfing

Competition among pollen or sperm (gametic selection) can cause evolution. Mating systems shape the intensity of gametic selection by determining the competitors involved, which can in turn cause the mating system itself to evolve. We model the bidirectional relationship between gametic selection and mating systems, focusing on variation in female mating frequency (monandry-polyandry) and self-fertilisation (selfing-outcrossing). First, we find that monandry and selfing both reduce the efficiency of gametic selection in removing deleterious alleles. This means that selfing can increase mutation load, in contrast to cases without gametic selection where selfing purges deleterious mutations and decreases mutation load. Second, we explore how mating systems evolve via their effect on gametic selection. By manipulating gametic selection, polyandry can evolve to increase the fitness of the offspring produced. However, this indirect advantage of post-copulatory sexual selection is weak and is likely to be overwhelmed by any direct fitness effects of mating systems. Nevertheless, gametic selection can be potentially decisive for selfing evolution because it significantly reduces inbreeding depression, which favours selfing. Thus, the presence of gametic selection could be a key factor driving selfing evolution.

Opening a can of worms: a test of the co-infection facilitation hypothesis

Parasitic infections are a global occurrence and impact the health of many species. Coinfections, where two or more species of parasite are present in a host, are a common phenomenon across species. Coinfecting parasites can interact directly or indirectly via their manipulation of (and susceptibility to) the immune system of their shared host. Helminths, such as the cestode Schistocephalus solidus, are well known to suppress immunity of their host (threespine stickleback, Gasterosteus aculeatus), potentially facilitating other parasite species. Yet, hosts can evolve a more robust immune response (as seen in some stickleback populations), potentially turning facilitation into inhibition. Using wild-caught stickleback from 20 populations with non-zero S. solidus prevalence, we tested an a priori hypothesis that S. solidus infection facilitates infection by other parasites. Consistent with this hypothesis, individuals with S. solidus infections have 18.6% higher richness of other parasites compared to S. solidus-uninfected individuals from the same lakes. This facilitation-like trend is stronger in lakes where S. solidus is particularly successful but is reversed in lakes with sparse and smaller cestodes (indicative of stronger host immunity). These results suggest that a geographic mosaic of host-parasite co-evolution might lead to a mosaic of between-parasite facilitation/inhibition effects.

Cryogenian Origins of Multicellularity in Archaeplastida

Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.

Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability

An organism's phenotypes and fitness often depend on the interactive effects of its genome (Gh⁢o⁢s⁢t), microbiome (Gm⁢i⁢c⁢r⁢o⁢b⁢e), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured L⁢e⁢m⁢n⁢am⁢i⁢n⁢o⁢r (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.m⁢i⁢n⁢o⁢r fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.

Apical annuli are specialised sites of post-invasion secretion of dense granules in Toxoplasma

Apicomplexans are ubiquitous intracellular parasites of animals. These parasites use a programmed sequence of secretory events to find, invade, and then re-engineer their host cells to enable parasite growth and proliferation. The secretory organelles micronemes and rhoptries mediate the first steps of invasion. Both secrete their contents through the apical complex which provides an apical opening in the parasite's elaborate inner membrane complex (IMC) - an extensive subpellicular system of flattened membrane cisternae and proteinaceous meshwork that otherwise limits access of the cytoplasm to the plasma membrane for material exchange with the cell exterior. After invasion, a second secretion programme drives host cell remodelling and occurs from dense granules. The site(s) of dense granule exocytosis, however, has been unknown. In Toxoplasma gondii, small subapical annular structures that are embedded in the IMC have been observed, but the role or significance of these apical annuli to plasma membrane function has also been unknown. Here, we determined that integral membrane proteins of the plasma membrane occur specifically at these apical annular sites, that these proteins include SNARE proteins, and that the apical annuli are sites of vesicle fusion and exocytosis. Specifically, we show that dense granules require these structures for the secretion of their cargo proteins. When secretion is perturbed at the apical annuli, parasite growth is strongly impaired. The apical annuli, therefore, represent a second type of IMC-embedded structure to the apical complex that is specialised for protein secretion, and reveal that in Toxoplasma there is a physical separation of the processes of pre- and post-invasion secretion that mediate host-parasite interactions.

The Duckbot: A system for automated imaging and manipulation of duckweed

Laboratory automation can boost precision and reproducibility of science workflows. However, current laboratory automation systems are difficult to modify for custom applications. Automating new experiment workflows therefore requires development of one-off research platforms, a process which requires significant time, resources, and experience. In this work, we investigate systems to lower the threshold to automation for plant biologists. Our approach establishes a direct connection with a generic motion platform to support experiment development and execution from a computational notebook environment. Specifically, we investigate the use of the open-source tool-changing motion platform Jubilee controlled using Jupyter notebooks. We present the Duckbot, a machine customized for automating laboratory research workflows with duckweed, a common multicellular plant. The Duckbot comprises (1) a set of end-effectors relevant for plant biology, (2) software modules which provide flexible control of these tools, and (3) computational notebooks which make use of these tools to automate duckweed experiments. We demonstrate the Duckbot's functionality by automating a particular laboratory research workflow, namely, duckweed growth assays. The Duckbot supports setting up sample plates with duckweed and growth media, gathering image data, and conducting relevant data analysis. We discuss the opportunities and limitations for developing custom laboratory automation with this platform and provide instructions on usage and customization.

Infrared Nanoimaging of Hydrogenated Perovskite Nickelate Memristive Devices

Solid-state devices made from correlated oxides, such as perovskite nickelates, are promising for neuromorphic computing by mimicking biological synaptic function. However, comprehending dopant action at the nanoscale poses a formidable challenge to understanding the elementary mechanisms involved. Here, we perform operando infrared nanoimaging of hydrogen-doped correlated perovskite, neodymium nickel oxide (H-NdNiO3, H-NNO), devices and reveal how an applied field perturbs dopant distribution at the nanoscale. This perturbation leads to stripe phases of varying conductivity perpendicular to the applied field, which define the macroscale electrical characteristics of the devices. Hyperspectral nano-FTIR imaging in conjunction with density functional theory calculations unveils a real-space map of multiple vibrational states of H-NNO associated with OH stretching modes and their dependence on the dopant concentration. Moreover, the localization of excess charges induces an out-of-plane lattice expansion in NNO which was confirmed by in situ X-ray diffraction and creates a strain that acts as a barrier against further diffusion. Our results and the techniques presented here hold great potential for the rapidly growing field of memristors and neuromorphic devices wherein nanoscale ion motion is fundamentally responsible for function.

The impact of the COVID-19 pandemic on the Galapagos Islands' seafood system from consumers' perspectives

The COVID-19 pandemic's early stages severely impacted global fisheries, particularly areas heavily reliant on imported food and tourism like the Galapagos Islands, Ecuador. To contain the spread of the virus, a full lockdown was implemented. However, the collapse of the tourism industry precipitated the worst economic crisis in the history of this multiple-use marine protected area. This paper examines the impact of the pandemic's early stages on consumption patterns and seafood security in the Galapagos from consumers' perspective, drawing on online surveys conducted during the lockdown. Our findings revealed pre-existing seafood insecurity across the archipelago, further exacerbated by the pandemic on the least-populated island. Nevertheless, the seafood system displayed moderated resilience to the pandemic's socioeconomic disruptions. A variety of adaptive responses were adopted by Galapagos residents to cope with the lockdown. Consumers modified their seafood consumption habits, while fishers adapted their harvesting and marketing strategies. Such adaptive responses were shaped by the unique socioeconomic characteristics of each inhabited island and the ability of seafood suppliers to shift from a tourism- and export-oriented to a resident- and domestic-oriented market. This transition has created novel opportunities to foster a systemic transformation of the Galapagos seafood system to enhance its resilience against future crises caused by new pandemics, climate change, or other natural and anthropogenic drivers of change.

Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data

Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.

A Critical Analysis of Chemical and Electrochemical Oxidation Mechanisms in Li-Ion Batteries

Electrolyte decomposition limits the lifetime of commercial lithium-ion batteries (LIBs) and slows the adoption of next-generation energy storage technologies. A fundamental understanding of electrolyte degradation is critical to rationally design stable and energy-dense LIBs. To date, most explanations for electrolyte decomposition at LIB positive electrodes have relied on ethylene carbonate (EC) being chemically oxidized by evolved singlet oxygen (1O2) or electrochemically oxidized. In this work, we apply density functional theory to assess the feasibility of these mechanisms. We find that electrochemical oxidation is unfavorable at any potential reached during normal LIB operation, and we predict that previously reported reactions between the EC and 1O2 are kinetically limited at room temperature. Our calculations suggest an alternative mechanism in which EC reacts with superoxide (O2-) and/or peroxide (O22-) anions. This work provides a new perspective on LIB electrolyte decomposition and motivates further studies to understand the reactivity at positive electrodes.

Role of Low-Energy (<20 eV) Secondary Electrons in the Extraterrestrial Synthesis of Prebiotic Molecules

We demonstrate for the first time that Galactic cosmic rays with energies as high as ∼1010 eV can trigger a cascade of low-energy (<20 eV) secondary electrons that could be a significant contributor to the interstellar synthesis of prebiotic molecules whose delivery by comets, meteorites, and interplanetary dust particles may have kick-started life on Earth. For the energetic processing of interstellar ice mantles inside dark, dense molecular clouds, we explore the relative importance of low-energy (<20 eV) secondary electrons-agents of radiation chemistry-and low-energy (<10 eV), nonionizing photons-instigators of photochemistry. Our calculations indicate fluxes of ∼102 electrons cm-2 s-1 for low-energy secondary electrons produced within interstellar ices due to attenuated Galactic cosmic-ray protons. Consequently, in certain star-forming regions where internal high-energy radiation sources produce ionization rates that are observed to be a thousand times greater than the typical interstellar Galactic ionization rate, the flux of low-energy secondary electrons should far exceed that of nonionizing photons. Because reaction cross sections can be several orders of magnitude larger for electrons than for photons, even in the absence of such enhancement, our calculations indicate that secondary low-energy (<20 eV) electrons are at least as significant as low-energy (<10 eV) nonionizing photons in the interstellar synthesis of prebiotic molecules. Most importantly, our results demonstrate the pressing need for explicitly incorporating low-energy electrons in current and future astrochemical simulations of cosmic ices. Such models are critically important for interpreting James Webb Space Telescope infrared measurements, which are currently being used to probe the origins of life by studying complex organic molecules found in ices near star-forming regions.

Evolution of biological cooperation: an algorithmic approach

This manuscript presents an algorithmic approach to cooperation in biological systems, drawing on fundamental ideas from statistical mechanics and probability theory. Fisher's geometric model of adaptation suggests that the evolution of organisms well adapted to multiple constraints comes at a significant complexity cost. By utilizing combinatorial models of fitness, we demonstrate that the probability of adapting to all constraints decreases exponentially with the number of constraints, thereby generalizing Fisher's result. Our main focus is understanding how cooperation can overcome this adaptivity barrier. Through these combinatorial models, we demonstrate that when an organism needs to adapt to a multitude of environmental variables, division of labor emerges as the only viable evolutionary strategy.

Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid

Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.

Phylogenomic position of eupelagonemids, abundant, and diverse deep-ocean heterotrophs

Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes, and only a single formal described species, Eupelagonema oceanica. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows that these two cells represent distinct subclades within eupelagonemids, each different from E. oceanica. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

Ensembl 2024

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.

The European Nucleotide Archive in 2023

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide Sequence Database Collaboration (INSDC). It serves the bioinformatics community worldwide via the submission, processing, archiving and dissemination of sequence data. The ENA supports data types ranging from raw reads, through alignments and assemblies to functional annotation. The data is enriched with contextual information relating to samples and experimental configurations. In this article, we describe recent progress and improvements to ENA services. In particular, we focus upon three areas of work in 2023: FAIRness of ENA data, pandemic preparedness and foundational technology. For FAIRness, we have introduced minimal requirements for spatiotemporal annotation, created a metadata-based classification system, incorporated third party metadata curations with archived records, and developed a new rapid visualisation platform, the ENA Notebooks. For foundational enhancements, we have improved the INSDC data exchange and synchronisation pipelines, and invested in site reliability engineering for ENA infrastructure. In order to support genomic surveillance efforts, we have continued to provide ENA services in support of SARS-CoV-2 data mobilisation and have adapted these for broader pathogen surveillance efforts.