The athlete psychological well-being inventory: Factor equivalence with the sport injury-related growth inventory.

Until now, research on growth following sport injury has relied exclusively on retrospective reports and nomothetic measures drawn from other fields of research. Therefore, to more objectively explore growth following sport injury pre- and post-injury, rather than retrospectively, this study adapts and examines the psychometric properties of the Athlete Psychological Well-Being Inventory (APWBI), which can be used throughout the sport injury process (i.e., prior to and following sport injury). A sample of 164 athletes free from injury (71.3 % men; M age = 19.7 years, SD = 2.1) were compared to a sample of 168 athletes with history of previous injury (73.2 % men; M age = 19.7 years, SD = 2.1). Multigroup Confirmatory Factor Analysis demonstrated the measurement and factor equivalence between the APWBI and a retrospective measure, the Sport Injury-Related Growth Inventory (SIRGI). The APWBI also showed satisfactory to excellent internal consistency reliability for all its sub-dimensions ("sense of mastery", "positive relations with others", "responsibility for one's health", "self-awareness", "emotional ability", "purpose in life", "purpose in sport", and "body awareness") and for the total score. Analysis of the relationships with other self-report measures (i.e., the Positive Functioning Inventory, the Rosenberg's Self-Esteem Scale, and the Lie Scale) provided convergent and discriminant evidence to support the construct validity of the instrument. To conclude, the APWBI is a valid and reliable instrument for use within English-speaking athletes of various competitive levels (from local/county to international level).

AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.

MOTIVATION: Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree. RESULTS: We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as duplication, transfer, and loss probabilities for genome-scale datasets with hundreds of taxa. AVAILABILITY AND IMPLEMENTATION: GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.

Race and Ethnicity, Deprivation, and Infant Mortality in England, 2019-2022.

Importance: England has one of the highest infant mortality rates in Europe. Much of the variation in infant mortality rates between races and ethnicities may be due to socioeconomic factors, but how deprivation and race and ethnicity are associated with infant mortality is unclear. Objectives: To investigate the association of infant race and ethnicity with the infant mortality rate in England, adjusted for preterm birth and level of deprivation. Design, Setting, and Participants: This cohort study included children who died younger than 1 year of age, born at or after 22 weeks' gestation, occurring from April 1, 2019, to March 31, 2022, in England. Characteristics of the infant were derived from death notifications. Exposures: The racial and ethnic groups were derived from National Health Service data and were reported by the parents and characterized using the Office of National Statistics classification: Asian or Asian British (Bangladeshi, Chinese, Indian, Pakistani, or any other Asian background), Black or Black British (African, Caribbean, or any other Black background), multiracial (White and Asian, White and Black African, White and Black Caribbean, or any other multiracial background), White or White British (British, Irish, any other White background, or Gypsy or Irish Traveler), and other (Arab or any other racial or ethnic group). Main Outcomes and Measures: Risk of death for all racial and ethnic groups and relative risk of death compared with the reference group (White) were calcuated. Analyses were repeated, adjusting for deprivation, gestational age of infants, and region of England. Results: A total of 5621 infants who died younger than 1 year of age were reported to the National Child Mortality Database. A total of 2842 of 5130 infants (55.4%) were male; the median gestational age was 33 weeks (IQR, 25-38 weeks); of 5149 infants, 927 (18.0%) were Asian, 448 (8.7%) were Black, 3318 (64.4%) were White, 343 (6.7%) were multiracial, and 113 (2.2%) were from other racial and ethnic groups; and the median deprivation score was 4 (IQR, 3-5). In the unadjusted analysis, the relative risk of death compared with White infants was higher for Black (1.93 [95% CI, 1.75-2.13]) and Asian (1.67 [95% CI, 1.55-1.80]) infants. The population attributable risk fraction for all mortality rates among infants who were not White was 12.0% (95% CI, 10.3%-13.8%) (unadjusted), 9.8% (95% CI, 8.0%-11.7%) (adjusted for deprivation), 7.7% (95% CI, 5.9%-9.5%) (adjusted for gestational age at birth), and 12.8% (95% CI, 11.0%-14.5%) (adjusted for region of England). Conclusions and Relevance: This cohort study suggests that the proportion of infants who died before 1 year of age is associated with race and ethnicity, with a population attributable risk fraction of 12.0%. An overconservative adjustment for deprivation did not explain the overall patterns seen. Approximately half the population attributable risk fraction may be due to increased risk of preterm birth in Asian and Black communities. Work is needed to identify what can be done to reduce this incidence of infant mortality.

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.

A Multinational Case Series Describing Successful Treatment of Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection Caused by Omicron Sublineages With Prolonged Courses of Nirmatrelvir/Ritonavir.

The optimum treatment for persistent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not known. Our case series, across 5 hospitals in 3 countries, describes 11 cases where persistent SARS-CoV-2 infection was successfully treated with prolonged courses (median, 10 days [range, 10-18 days]) of nirmatrelvir/ritonavir (Paxlovid). Most cases (9/11) had hematological malignancy and 10 (10/11) had received CD20-depleting therapy. The median duration of infection was 103 days (interquartile range, 85-138 days). The majority (10/11) were hospitalized, and 7 (7/11) had severe/critical disease. All survived and 9 of 11 demonstrated viral clearance, almost half (4/9) of whom received nirmatrelvir/ritonavir as monotherapy. This case series suggests that prolonged nirmatrelvir/ritonavir has a role in treating persistent infection.

Routine Metagenomics Service for ICU Patients with Respiratory Infection.

Rationale: Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice. Objectives: Feasibility, performance, and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service. Methods: RMg was performed on 128 samples from 87 patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory ICUs at Guy's and St Thomas' NHS Foundation Trust, London. Measurements and Main Results: During the first 15 weeks, RMg provided same-day results for 110 samples (86%), with a median turnaround time of 6.7 hours (interquartile range = 6.1-7.5 h). RMg was 93% sensitive and 81% specific for clinically relevant pathogens compared with routine testing. Forty-eight percent of RMg results informed antimicrobial prescribing changes (22% escalation; 26% deescalation) with escalation based on speciation in 20 out of 24 cases and detection of acquired-resistance genes in 4 out of 24 cases. Fastidious or unexpected organisms were reported in 21 samples, including anaerobes (n = 12), Mycobacterium tuberculosis, Tropheryma whipplei, cytomegalovirus, and Legionella pneumophila ST1326, which was subsequently isolated from the bedside water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes (emm1-M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A), and Aspergillus fumigatus with multiple treatments and public health impacts. Conclusions: This pilot study illustrates the potential of RMg testing to provide benefits for antimicrobial treatment, infection control, and public health when provided in a real-world critical care setting. Multicenter studies are now required to inform future translation into routine service.

Salactin, a dynamically unstable actin homolog in Haloarchaea.

IMPORTANCE: Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.

Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae.

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.

Surge of lower respiratory tract group A streptococcal infections in England in winter 2022: epidemiology and clinical profile.

BACKGROUND: Following low incidence of invasive group A streptococcal (iGAS) infections during the COVID-19 pandemic, marked increases were noted in many countries during 2022, particularly in children. In November 2022, severe presentations of lower respiratory tract infections (LRTIs), including empyema, were notified by clinicians across the UK. UKHSA investigated this rise with the aim of informing clinical management and public health response. METHODS: We undertook a case-series analysis using multiple routine data sources, exempted from ethics approval or patient consent. We identified iGAS cases in England in children younger than 15 years with an LRTI reported between Oct 1 and Dec 21, 2022, using UKHSA laboratory surveillance data (GAS detected in LRT specimens) and notifications by clinicians and Health Protection Teams (HPTs). Symptoms, diagnoses, health-care interactions, and outcome (death or recovery) data were obtained from HPT case management notes, the National Child Mortality Database, and the NHS Digital Emergency Care Dataset. FINDINGS: We identified 147 cases of LRTI iGAS in children across England (77 [52%] male, 70 [48%] female; median age 4 years [IQR 2-6]). Predominant ethnicities were White (74 [65%] of 113 with known ethnicity) and Asian (18 [16%] of 113). Most reported symptoms were fever (90 [75%] of 120 children with ≥1 symptom) and cough (60 [50%] of 120), and 71 (48%) of all 147 children had a diagnosed respiratory viral coinfection (most commonly hMPV and RSV). 127 (86%) of children attended an emergency department, 31% (n=36/114 with onset date) at least twice within 21 days after symptom onset. 37 (25%) of 147 children died, with a median time from symptom onset to death of 4 days (IQR 3-7). Of 32 children with sample dates, 16 (84%) were tested for GAS on or after the day they died. Over half of deaths (21 [57%] of 37 deaths) occurred in the community after rapid deterioration, of whom 18 had previous contact with health-care services documented. INTERPRETATION: The UK saw an unusual rise in iGAS LRTIs in children in late 2022. One in four cases died, over half in the community. Non-specific symptoms, viral symptoms, or positive virology might have lowered suspicion of bacterial infection. Although the use of multiple available data sources expedited the analysis, varying data completeness limited interpretation. Our study highlights the need for earlier detection and identification of effective measures to prevent death. FUNDING: None.

ATP synthase evolution on a cross-braced dated tree of life.

The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.

The transit of oral premedication beyond the stomach in patients undergoing laparoscopic sleeve gastrectomy: a retrospective observational multicentre study.

BACKGROUND: Antiemetic and analgesic oral premedications are frequently prescribed preoperatively to enhance recovery after laparoscopic sleeve gastrectomy. However, it is unknown whether these medications transit beyond the stomach or if they remain in the sleeve resection specimen, thereby negating their pharmacological effects. METHODS: A retrospective cohort study was performed on patients undergoing laparoscopic sleeve gastrectomy and receiving oral premedication (slow-release tapentadol and netupitant/palonosetron) as part of enhanced recovery after bariatric surgery program. Patients were stratified into the Transit group (premedication absent in the resection specimen) and Failure-to-Transit group (premedication present in the resection specimen). Age, sex, body mass index, and presence of diabetes were compared amongst the groups. The premedication lead time (time between premedications' administration and gastric specimen resection), and the premedication presence or absence in the specimen was evaluated. RESULTS: One hundred consecutive patients were included in the analysis. Ninety-nine patients (99%) were morbidly obese, and 17 patients (17%) had Type 2 diabetes mellitus. One hundred patients (100%) received tapentadol and 89 patients (89%) received netupitant/palonosetron. One or more tablets were discovered in the resected specimens of 38 patients (38%). No statistically significant differences were observed between the groups regarding age, sex, diabetes, or body mass index. The median (Q1‒Q3) premedication lead time was 80 min (57.8‒140.0) in the Failure-to-Transit group and 119.5 min (85.0‒171.3) in the Transit group; P = 0.006. The lead time required to expect complete absorption in 80% of patients was 232 min (95%CI:180‒310). CONCLUSIONS: Preoperative oral analgesia and antiemetics did not transit beyond the stomach in 38% of patients undergoing laparoscopic sleeve gastrectomy. When given orally in combination, tapentadol and netupitant/palonosetron should be administered at least 4 h before surgery to ensure transition beyond the stomach. Future enhanced recovery after bariatric surgery guidelines may benefit from the standardization of premedication lead times to facilitate increased absorption. TRIAL REGISTRATION: Australian and New Zealand Clinical Trials Registry; number ACTRN12623000187640; retrospective registered on 22/02/2023.

Newborn Health and Child Mortality Across England.

Importance: Although the immediate impact of neonatal illness is well recognized, its wider and longer term outcomes on childhood mortality and the role of specific illnesses across childhood are unclear. Objective: To investigate how many deaths in childhood are associated with neonatal illness and the underlying conditions of the children who died. Design, Setting, and Participants: This population-based cohort study of children who died before age 10 years in England between April 1, 2019, and March 31, 2021, used data from the National Child Mortality Database. Data analysis was performed from September 2022 to May 2023. Exposure: Children who received care in a neonatal unit after birth plus those who died in the first day of life, before admission to a neonatal unit, were considered to have likely neonatal illness. Main Outcomes and Measures: The primary outcome was the relative risk (RR) of dying, stratified by likely neonatal illness and specific neonatal conditions. Comparisons were made using the χ2 or likelihood ratio test, as appropriate. Results: A total of 4829 children were included (median [IQR] age at death, 28 [2-274] days; 2606 boys [54.8%]; 2690 White children [64.0%]). Overall, 3456 children who died (71.6%) had evidence of likely neonatal illness. Children with neonatal illness were more likely to die before their tenth birthday than those without evidence of neonatal illness (RR, 13.82; 95% CI, 13.00-14.71). The estimated population-attributable risk fraction for neonatal illness among all deaths before age 10 years was 66.4% (95% CI, 64.9%-67.9%). Children with preceding neonatal illness who died were more likely to have underlying behavioral or developmental disorders (odds ratio [OR], 3.31; 95% CI, 2.47-4.42), chronic neurological disease (OR, 3.00; 95% CI, 2.51-3.58), and chronic respiratory disease (OR, 3.01; 95% CI, 2.43-3.73) than children without neonatal illness. Conclusions and Relevance: In this cohort study, most children who died before age 10 years had some evidence of neonatal illness, and they died of a range of causes, including infections and sudden, unexpected, unexplained death. These findings suggest that improvements to perinatal morbidity, an area with an existing evidence base for improvement, may have important impacts on child health across the next decade.

Changes in background characteristics and risk factors among SIDS infants in England: cohort comparisons from 1993 to 2020.

OBJECTIVES: Using the National Child Mortality Database, this work aims to investigate background characteristics and risk factors in the sleeping environment associated with sudden infant death syndrome (SIDS) and compare the prevalence with previous English SIDS case-control studies. DESIGN: Cohort of SIDS in 2020 compared with a combined analysis of two case-control studies conducted in 1993-1996 and 2003-2006. SETTING: England, UK PARTICIPANTS: 138 SIDS deaths in 2020 compared with 402 SIDS deaths and 1387 age-equivalent surviving controls, combined from previous studies. RESULTS: The increased vulnerability of SIDS infants identified in previous studies has become more marked. The infants who died in 2020 were younger (median=66 days (IQR: 34-118) vs 86 days (IQR: 52-148), p=0.003) with an increased prevalence of low birth weight (30.5% vs 21.6%, p=0.04) and preterm births (29.6% vs 19.3%, p=0.012). The excess of socioeconomically deprived families, male infants and high levels of maternal smoking during pregnancy were still evident. Among recent deaths, fewer infants were put down or found on their side; however, there was no significant change in the proportion of infants who were put down (15.6% vs 14.6%, p=0.81) and found prone (40.4% vs 35.3%, p=0.37), despite population wide risk reduction advice over three decades. The proportional increase observed in 2003-2006 of half the deaths occurring while sleeping next to an adult was maintained in 2020, and for the vast majority (90%), this was in hazardous circumstances (adult had consumed alcohol, smoked, slept on a sofa, or the infant was premature or low birth weight and less than 3 months old). More deaths also occurred when there was a disruption in infant care routine compared with previous observations (52.6% vs 20.7%, p<0.001). CONCLUSIONS: A more targeted approach is needed with vulnerable families emphasising the importance of sleeping infants on their back and proactive planning infant sleep when there are disruptions to the normal routine, in particular to avoid hazardous co-sleeping.

Defining eukaryotes to dissect eukaryogenesis.

The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.

Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance.

Rapid respiratory viral whole genome sequencing (WGS) in a clinical setting can inform real-time outbreak and patient treatment decisions, but the feasibility and clinical utility of influenza A virus (IAV) WGS using Nanopore technology has not been demonstrated. A 24 h turnaround Nanopore IAV WGS protocol was performed on 128 reverse transcriptase PCR IAV-positive nasopharyngeal samples taken over seven weeks of the 2022-2023 winter influenza season, including 25 from patients with nosocomial IAV infections and 102 from patients attending the Emergency Department. WGS results were reviewed collectively alongside clinical details for interpretation and reported to clinical teams. All eight segments of the IAV genome were recovered for 97/128 samples (75.8 %) and the haemagglutinin gene for 117/128 samples (91.4 %). Infection prevention and control identified nosocomial IAV infections in 19 patients across five wards. IAV WGS revealed two separate clusters on one ward and excluded transmission across different wards with contemporaneous outbreaks. IAV WGS also identified neuraminidase inhibitor resistance in a persistently infected patient and excluded avian influenza in a sample taken from an immunosuppressed patient with a history of travel to Singapore which had failed PCR subtyping. Accurate IAV genomes can be generated in 24 h using a Nanopore protocol accessible to any laboratory with SARS-CoV-2 Nanopore sequencing capacity. In addition to replicating reference laboratory surveillance results, IAV WGS can identify antiviral resistance and exclude avian influenza. IAV WGS also informs management of nosocomial outbreaks, though molecular and clinical epidemiology were concordant in this study, limiting the impact on decision-making.

On the potential roles of phosphorus in the early evolution of energy metabolism.

Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.

Navigating the Frontier of Synthetic Biology: An AI-Driven Analytics Platform for Exploring Research Trends and Relationships.

The field of synthetic biology has experienced rapid growth in recent years, leading to an overwhelming amount of literature that can make it difficult to comprehend the scope and trends of the discipline. In this study, we employ topic modeling to comprehensively map research topics within synthetic biology, revealing subtopics and their relationships, as well as trends over time. We utilize metadata to identify the most significant journals and countries in the field and discuss potential policy impact on the research output. In addition, we investigate co-authorship networks to analyze collaborations among authors, institutions, and countries. We believe that our findings could serve as a valuable resource for gaining a deeper understanding of synthetic biology and provide a foundation for analyzing other disciplines.

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.

ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria-where there is less certainty about the root position-ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.

Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge.

The deep sea is known to host novel bacteria with the potential to produce a diverse array of undiscovered natural products. Thus, understanding these bacteria is of broad interest in ecology and could also underpin applied drug discovery, specifically in the area of antimicrobials. Here, we isolate a new strain of Streptomyces from the tissue of the deep-sea sponge Polymastia corticata collected at a depth of 1869 m from the Gramberg Seamount in the Atlantic Ocean. This strain, which was given the initial designation A15ISP2-DRY2T, has a genome size of 9.29 Mb with a G+C content of 70.83 mol%. Phylogenomics determined that A15ISP2-DRY2T represents a novel species within the genus Streptomyces as part of the Streptomyces aurantiacus clade. The biosynthetic potential of A15ISP2-DRY2T was assessed relative to other members of the S. aurantiacus clade via comparative gene cluster family (GCF) analysis. This revealed a clear congruent relationship between phylogeny and GCF content. A15ISP2-DRY2T contains six unique GCFs absent elsewhere in the clade. Culture-based assays were used to demonstrate the antibacterial activity of A15ISP2-DRY2T against two drug-resistant human pathogens. Thus, we determine A15ISP2-DRY2T to be a novel bacterial species with considerable biosynthetic potential and propose the systematic name 'Streptomyces ortus' sp. nov.

Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome.

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.