Lighting the way: Compelling open questions in photosynthesis research.

Photosynthesis - the conversion of energy from sunlight into chemical energy - is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research.

Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits.

In plant mitochondria, nicotinamide adenine dinucleotide-malic enzyme (NAD-ME) has a housekeeping function in malate respiration. In different plant lineages, NAD-ME was independently co-opted in C4 photosynthesis. In the C4 Cleome species, Gynandropsis gynandra and Cleome angustifolia, all NAD-ME genes (NAD-MEα, NAD-MEß1, and NAD-MEß2) were affected by C4 evolution and are expressed at higher levels than their orthologs in the C3 species Tarenaya hassleriana. In T. hassleriana, the NAD-ME housekeeping function is performed by two heteromers, NAD-MEα/ß1 and NAD-MEα/ß2, with similar biochemical properties. In both C4 species, this role is restricted to NAD-MEα/ß2. In the C4 species, NAD-MEα/ß1 is exclusively present in the leaves, where it accounts for most of the enzymatic activity. Gynandropsis gynandra NAD-MEα/ß1 (GgNAD-MEα/ß1) exhibits high catalytic efficiency and is differentially activated by the C4 intermediate aspartate, confirming its role as the C4-decarboxylase. During C4 evolution, NAD-MEß1 lost its catalytic activity; its contribution to the enzymatic activity results from a stabilizing effect on the associated α-subunit and the acquisition of regulatory properties. We conclude that in bundle sheath cell mitochondria of C4 species, the functions of NAD-ME as C4 photosynthetic decarboxylase and as a housekeeping enzyme coexist and are performed by isoforms that combine the same α-subunit with differentially adapted ß-subunits.

Ether lipid deficiency disrupts lipid homeostasis leading to ferroptosis sensitivity.

Ferroptosis is an iron-dependent form of regulated cell death associated with uncontrolled membrane lipid peroxidation and destruction. Previously, we showed that dietary dihomo-gamma-linolenic acid (DGLA; 20: 3(n-6)) triggers ferroptosis in the germ cells of the model organism, Caenorhabditis elegans. We also demonstrated that ether lipid-deficient mutant strains are sensitive to DGLA-induced ferroptosis, suggesting a protective role for ether lipids. The vinyl ether bond unique to plasmalogen lipids has been hypothesized to function as an antioxidant, but this has not been tested in animal models. In this study, we used C. elegans mutants to test the hypothesis that the vinyl ether bond in plasmalogens acts as an antioxidant to protect against germ cell ferroptosis as well as to protect from whole-body tert-butyl hydroperoxide (TBHP)-induced oxidative stress. We found no role for plasmalogens in either process. Instead, we demonstrate that ether lipid-deficiency disrupts lipid homeostasis in C. elegans, leading to altered ratios of saturated and monounsaturated fatty acid (MUFA) content in cellular membranes. We demonstrate that ferroptosis sensitivity in both wild type and ether-lipid deficient mutants can be rescued in several ways that change the relative abundance of saturated fats, MUFAs and specific polyunsaturated fatty acids (PUFAs). Specifically, we reduced ferroptosis sensitivity by (1) using mutant strains unable to synthesize DGLA, (2) using a strain carrying a gain-of-function mutation in the transcriptional mediator MDT-15, or (3) by dietary supplementation of MUFAs. Furthermore, our studies reveal important differences in how dietary lipids influence germ cell ferroptosis versus whole-body peroxide-induced oxidative stress. These studies highlight a potentially beneficial role for endogenous and dietary MUFAs in the prevention of ferroptosis.

Novel genes and sex differences in COVID-19 severity.

Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10-22 and P = 8.1 × 10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10-8) and ARHGAP33 (P = 1.3 × 10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.

All-fiber broadband spectral acousto-optic modulation of a tubular-lattice hollow-core optical fiber.

We demonstrate a broadband acousto-optic notch filter based on a tubular-lattice hollow-core fiber for the first time to our knowledge. The guided optical modes are modulated by acoustically induced dynamic long-period gratings along the fiber. The device is fabricated employing a short interaction length (7.7 cm) and low drive voltages (10 V). Modulated spectral bands with 20 nm half-width and maximum depths greater than 60% are achieved. The resonant notch wavelength is tuned from 743 to 1355 nm (612 nm span) by changing the frequency of the electrical signal. The results indicate a broader tuning range compared to previous studies using standard and hollow-core fibers. It further reveals unique properties for reconfigurable spectral filters and fiber lasers, pointing to the fast switching and highly efficient modulation of all-fiber photonic devices.

Tackling antibiotic contaminations in wastewater with novel Modified-MOF nanostructures: A study of molecular simulations and DFT calculations.

The contamination of wastewater with antibiotics has emerged as a critical global challenge, with profound implications for environmental integrity and human well-being. Adsorption techniques have been meticulously investigated and developed to mitigate and alleviate their effects. In this study, we have investigated the adsorption behaviour of Erythromycin (ERY), Gentamicin (GEN), Levofloxacin (LEVO), and Metronidazole (MET) antibiotics as pharmaceutical contaminants (PHCs) on amide-functionalized (RC (=O)NH2)/MIL-53 (Al) (AMD/ML53A), using molecular simulations and density functional theory (DFT) calculations. Based on our DFT calculations, it becomes apparent that the adsorption tendencies of antibiotics are predominantly governed by the presence of AMD functional groups on the adsorbent surface. Specifically, hydrogen bonding (HB) and van der Waals (vdW) interactions between antibiotics and AMD groups serve as the primary mechanisms facilitating adsorption. Furthermore, we have observed that the adsorption behaviors of these antibiotics are influenced by their respective functional groups, molecular shapes, and sizes. Our molecular simulations delved into how the AMD/ML53A surfaces interact with antibiotics as PHCs. Moreover, various chemical quantum descriptors based on Frontier Molecular Orbitals (FMO) were explored to elucidate the extent of AMD/ML53A adsorption and to assess potential alterations in their electronic properties throughout the adsorption process. Monte Carlo simulation showed that ERY molecules adsorb stronger to the adsorbent in acidic and basic conditions than other contaminants, with high energies: -404.47 kcal/mol in acidic and -6375.26 kcal/mol in basic environments. Molecular dynamics (MD) simulations revealed parallel orientation for the ERY molecule's adsorption on AMD/ML53A with 80% rejection rate. In conclusion, our study highlighted the importance of modeling in developing practical solutions for removing antibiotics as PHCs from wastewater. The insights gained from our calculations can facilitate the design of more effective adsorption materials, ultimately leading to a more hygienic and sustainable ecosystem.

Direct oral anticoagulants versus vitamin K antagonists in patients with atrial fibrillation and stage 5 chronic kidney disease under dialysis: A systematic review and meta-analysis of randomized controlled trials.

BACKGROUND: In patients with atrial fibrillation (AF) and normal or slightly impaired renal function, the use of direct oral anticoagulants (DOACs) is preferable to vitamin K antagonists (VKAs). However, in patients undergoing hemodialysis, the efficacy, and safety of DOACs compared with VKAs are still unknown. PURPOSE: To review current evidence about the safety and efficacy of DOACs compared to VKAs, in patients with AF and chronic kidney disease under hemodialysis. METHODS: We systematically searched PubMed, Scopus, and Cochrane databases for RCTs comparing DOACs with VKAs for anticoagulation in patients with AF on dialysis therapy. Outcomes of interest were: (1) stroke; (2) major bleeding; (3) cardiovascular mortality; and (4) all-cause mortality. Statistical analysis was performed using RevMan 5.1.7 and heterogeneity was assessed by I2 statistics. RESULTS: Three randomized controlled trials were included, comprising a total of 383 patients. Of these, 218 received DOACs (130 received apixaban; 88 received rivaroxaban), and 165 were treated with VKAs (116 received warfarin; 49 received phenprocoumon). The incidence of stroke was significantly lower in patients treated with DOACs (4.7%) compared with those using VKAs (9.5%) (RR 0.42; 95% CI 0.18-0.97; p = 0.04; I2 = 0%). However, the difference was not statistically significant in the case of ischemic stroke specifically (RR 0.42; 95% CI 0.17-1.04; p = 0.06; I2 = 0%). As for the major bleeding outcome, the DOAC group (11%) had fewer events than the VKA group (13.9%) but without statistical significance (RR 0.75; 95% CI 0.45-1.28; p = 0.29; I2 = 0%). There was no significant difference between groups regarding cardiovascular mortality (RR 1.23; 95% CI 0.66-2.29; p = 0.52; I2 = 13%) and all-cause mortality (RR 0.98; 95% CI 0.77-1.24; p = 0.84; I2 = 16%). CONCLUSION: This meta-analysis suggests that in patients with AF on dialysis, the use of DOACs was associated with a significant reduction in stroke, and a numerical trend of less incidence of major bleeding compared with VKAs, but in this case with no statistical significance. Results may be limited by a small sample size or insufficient statistical power.

Calculation of the geometry, absorption spectrum, and first hyperpolarizability of 4,5-dicyanoimidazole derivatives in solution. A multiscale ASEC-FEG study.

We investigate the effects of solvents on the geometry, absorption spectrum, and first hyperpolarizability of six push-pull molecules, each containing a 4,5-dicyanoimidazole group as an electron acceptor and a N,N-dimethylamino group as an electron donor, with systematically extended π-conjugated systems. Geometry optimizations in dichloromethane, methanol, water, and formamide under normal thermodynamic conditions were performed using the average solvent electrostatic configuration-free energy gradient method, which employs a discrete solvent model. The conformational structure of molecules is moderately affected by the environment, with the π-conjugated system becoming more planar in protic solvents. Solvent effects on the first hyperpolarizability result in marked increases that are in line with the red shifts of the absorption spectrum. The hyperpolarizability of smaller molecules within the set may be significantly influenced by the effects of geometry relaxation in highly polar protic solvents. The results illustrate the role of hydrogen bonds in the structure and electronic properties of push-pull molecules in protic environments. For smaller molecules, hydrogen bonds significantly contribute to enhancing the hyperpolarizability, but the effect of these specific interactions becomes less significant with the length of the π-conjugated system.

Thyroid axis participates in high-temperature-induced male sex reversal through its activation by the stress response.

Environmental changes alter the sex fate in about 15% of vertebrate orders, mainly in ectotherms such as fish and reptiles. However, the effects of temperature changes on the endocrine and molecular processes controlling gonadal sex determination are not fully understood. Here, we provide evidence that thyroid hormones (THs) act as co-players in heat-induced masculinization through interactions with the stress axis to promote testicular development. We first demonstrated that the thyroid axis (through thyroid-related genes and T3 levels) is highly active in males during the gonadal development in medaka (Oryzias latipes). Similarly, T3 treatments promoted female-to-male sex reversal in XX embryos. Subsequently, embryonic exposure to temperature-induced stress up-regulated the genes related to the thyroid and stress axes with a final increase in T3 levels. In this context, we show that blocking the stress axis response by the loss of function of the corticotropin-releasing hormone receptors suppresses thyroid-stimulating hormone expression, therefore, heat-induced activation of the thyroid axis. Thus, our data showed that early activation of the stress axis and, in consequence, the TH axis, too, leaves us with that both being important endocrine players in inducing female-to-male reversal, which can help predict possible upcoming physiological impacts of global warming on fish populations.

In situ three-dimensional spider web construction and mechanics.

Spiders are nature's engineers that build lightweight and high-performance web architectures often several times their size and with very few supports; however, little is known about web mechanics and geometries throughout construction, especially for three-dimensional (3D) spider webs. In this work, we investigate the structure and mechanics for a Tidarren sisyphoides spider web at varying stages of construction. This is accomplished by imaging, modeling, and simulations throughout the web-building process to capture changes in the natural web geometry and the mechanical properties. We show that the foundation of the web geometry, strength, and functionality is created during the first 2 d of construction, after which the spider reinforces the existing network with limited expansion of the structure within the frame. A better understanding of the biological and mechanical performance of the 3D spider web under construction could inspire sustainable robust and resilient fiber networks, complex materials, structures, scaffolding, and self-assembly strategies for hierarchical structures and inspire additive manufacturing methods such as 3D printing as well as inspire artistic and architectural and engineering applications.

Molecular identification and prevalence of plerocercoid larvae (Cestoda: Diphyllobothriidae) in some commercial fish species from Peru.

Diphyllobothriosis, a fish-borne zoonosis in South America, is mainly caused by the Pacific broad tapeworm Adenocephalus pacificus Nybelin, 1931, a parasite of considerable concern in fishery resources due to its impact on public health. A new diphyllobothrid, Diphyllobothrium sprakeri Hernández-Orts et al. Parasites Vectors 14:219, 2021, was recently described from sea lions from the Pacific Coast, but marine fish acting as intermediate hosts are unknown. The objective of this study was to confirm the presence of plerocercoid larvae of Diphyllobothriidae Lühe, 1910 (Cestoda: Diphyllobothriidea) in nine fish species of commercial importance in Peru. Of a total of 6999 fish (5861 Engraulis ringens, 853 Sciaena deliciosa, 6 Sciaena callaensis, 171 Scomber japonicus, 40 Trachurus murphyi, 40 Ariopsis seemanni, 18 Merluccius peruanus, 5 Sarda chiliensis, and 5 Coryphaena hippurus), 183 were infected with plerocercoid larvae, representing a total prevalence of 2.61% and a mean intensity of 3.2. Based on mtDNA cox1 sequences of 43 plerocercoids, a phylogenetic analysis revealed that 41 belong to A. pacificus and two to D. sprakeri. These findings are first molecular data for D. sprakeri larvae, and the infections of E. ringens and T. murphyi by plerocercoid larvae represent the first records of intermediate/paratenic hosts for this species. Hence, the findings of the current study enhance our understanding of the presence of diphyllobothriid species in commercial fish from the Southeastern Pacific Ocean and their potential impact on seafood safety for local human populations.

Carbon nitride based materials: more than just a support for single-atom catalysis.

Recently, the missing link between homogeneous and heterogeneous catalysis has been found and it was named single-atom catalysis (SAC). However, the SAC field still faces important challenges, one of which is controlling the bonding/coordination between the single atoms and the support in order to compensate for the increase in surface energy when the particle size is reduced due to atomic dispersion. Excellent candidates to meet this requirement are carbon nitride (CN)-based materials. Metal atoms can be firmly trapped in nitrogen-rich coordination sites in CN materials, which makes them a unique class of hosts for preparing single-atom catalysts (SACs). As one of the most promising two-dimensional supports to stabilize isolated metal atoms, CN materials have been increasingly employed for preparing SACs. Herein, we will cover the most recent advances in single-atoms supported by CN materials. In this review, the most important characterization techniques and the challenges faced in this topic will be discussed, and the commonly employed synthetic methods will be delineated for different CN materials. Finally, the catalytic performance of SACs based on carbon nitrides will be reviewed with a special focus on their photocatalytic applications. In particular, we will prove CN as a non-innocent support. The relationship between single-atoms and carbon nitride supports is two-way, where the single-atoms can change the electronic properties of the CN support, while the electronic features of the CN matrix can tune the catalytic activity of the single sites in photocatalytic reactions. Finally, we highlight the frontiers in the field, including analytical method development, truly controlled synthetic methods, allowing the fine control of loading and multi-element synthesis, and how understanding the two-way exchange behind single-atoms and CN supports can push this topic to the next level.

A-296G variant of THBS1 gene (rs1478605) is associated with a lower frequency of stroke in a Brazilian population with sickle cell anemia.

OBJECTIVES: Stroke is a devastating clinical outcome that significantly contributes to the morbidity and mortality of sickle cell anemia (SCA) patients. Despite its advantages in predicting stroke risk, transcranial Doppler screening has limitations that restrict its applicability, highlighting the need for emerging prognostic tools. Thrombospondin-1 plays a crucial role in endothelial injury, platelet adhesion, and nitric oxide metabolism and may be implicated in stroke pathophysiology. Here, we aimed to evaluate the association of THBS1 genetic variations with the occurrence of stroke in SCA patients MATERIALS AND METHODS: By real-time PCR, 512 SCA patients were fully genotyped for THBS1 A-296G (rs1478605) polymorphism RESULTS: THBS1 GG genotype was associated with a lower risk for stroke occurrence [odds ratio (OR): 0.30; 95% confidence interval (CI): 0.11-0.78; P = 0.011], although these findings were not consistent with multivariate logistic regression analysis (OR: 0.73, 95% CI: 0.12 - 4.37; P = 0.736). In agreement, the cumulative incidence of stroke for patients with AG/AA genotypes was higher when compared to the GG genotype (P = 0.018). However, the association was not maintained in the multivariate proportional hazards model (hazard ratio: 0.67, 95% CI: 0.12-3.61; P = 0.643) CONCLUSIONS: In summary, the present study shows that the THBS1 A-296G (rs1478605) polymorphism may be a potential modifier for stroke in SCA.

Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory.

Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood-brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering -3.31, -1.68, and -6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states' properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated.

Optimization of HS-SPME/GC-MS Method for Determining Volatile Organic Compounds and Sensory Profile in Cocoa Honey from Different Cocoa Varieties (Theobroma cacao L.).

This study aimed to develop an analytical method using HS-SPME/GC-MS to determine the volatile organic compound (VOC) profiles and evaluate the sensory attributes of cocoa honey from four cocoa varieties (CCN51, PS1319, SJ02, and Parazinho). Using a multivariate factorial experimental design, the HS-SPME/GC-MS method was optimized to determine the VOC profiles. Twenty previously trained tasters participated in the ranking descriptive analysis, while 108 consumers participated in the acceptance and purchase intention tests. A total of 84 volatile organic compounds were identified from various chemical classes, including acids, alcohols, aldehydes, esters, ketones, monoterpenes, oxygenated monoterpenoids, sesquiterpenes, and oxygenated sesquiterpenoids. Palmitic acid was the compound found in the highest concentration in all varieties (5.13-13.10%). Multivariate analysis tools identified key compounds for differentiation and grouping of the samples. The results revealed that the variety significantly influenced both the VOCs' concentrations and sensory profiles. The CCN51, PS1319, and SJ02 varieties exhibited the highest diversity of VOCs and sensory attributes. Notably, the SJ02 and CCN51 varieties demonstrated superior acceptability and purchase intention, with means ranging from 7.21 and 7.08 to 3.71 and 3.56, respectively. These results indicate their potential as promising sources of cocoa honey for the food industry.

Topsoil's magnetic and electrical properties in a volcanic and tropical region.

Environmental monitoring by measuring topsoil's magnetic and electrical properties is one practical, quick, and low-cost approach. This method has been used worldwide as a proxy for the presence of potentially toxic elements. However, additional research must be conducted on diverse soil types, geology, and climates. We determined the magnetic and electrical properties of urban and agricultural topsoils in a volcanic region and analyzed them as possible proxies of potentially toxic elements for environmental monitoring. To identify topsoil characteristics, we employed the measurements of magnetic susceptibility and hysteresis, electrical conductivity, total dissolved solids, power of hydrogen (pH), particle morphology, and element contents that were statistically analyzed to identify relevant properties. The result was able to differentiate volcanic soils from urban, industrial, and agricultural areas as well. The value of low-frequency magnetic susceptibility (χLF) in soils from urban areas is higher than 866.0±249.9 ×10-8 m3 kg-1, while the value of χLF in agricultural areas is 208.0±67.8 ×10-8 m3 kg-1. This is reinforced by the relationship between low-frequency and frequency-dependent magnetic susceptibility (χLF-χFD%) in samples from urban areas that fall within the same cluster dominated by coarse-grained magnetic minerals originating from anthropogenic processes. In contrast, the agricultural area forms a separate cluster primarily influenced by pedogenic processes from acid igneous rock minerals. Caution is required for interpreting the magnetic signal due to the high contents of lithogenic magnetic particles inherited from the parent materials of Andisols.

Amazon Biobank: a collaborative genetic database for bioeconomy development.

Biodiversity is proposed as a sustainable alternative for the economic development of high-biodiversity regions. Especially in the field of biodiversity genomics, the development of low-cost DNA sequencing opens an opportunity for new actors beyond academia to engage in genomic sequencing. However, it is challenging to adequately compensate non-academic actors such as local populations for their contribution to the innovation process, preventing better bioeconomy development. Although many repositories register genomic data to support biodiversity research, they do not facilitate the fair sharing of economic benefits. In this work, we propose the creation of the Amazon Biobank, a community-based genetic database. We employed blockchain to build a transparent and verifiable log of transactions involving genomic data, and we used smart contracts to implement an internal monetary system for all participants who collect, insert, process, store, and validate genomic data. We also used peer-to-peer solutions to allow users with commodity computers to collaborate with the storage and distribution of DNA files. By combining emerging technologies, Amazon Biobank provides adequate benefit-sharing among all participants that collaborate with data, knowledge, and computational resources. It also provides traceability and auditability, allowing easy association between biotechnological research and DNA data. In addition, the solution is highly scalable and less dependent on the trust deposited in any system player. Therefore, Amazon Biobank can become an important stepping stone to unlock the potential of bioeconomy in rich ecosystems such as the Amazon Rainforest.

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.

MOTIVATION: Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites but millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate and fast phylogenetic inference of resolvable phylogenetic features. RESULTS: We present the TopHap approach that determines spatiotemporally common haplotypes of common variants and builds their phylogeny at a fraction of the computational time of traditional methods. We develop a bootstrap strategy that resamples genomes spatiotemporally to assess topological robustness. The application of TopHap to build a phylogeny of 68 057 SARS-CoV-2 genomes (68KG) from the first year of the pandemic produced an evolutionary tree of major SARS-CoV-2 haplotypes. This phylogeny is concordant with the mutation tree inferred using the co-occurrence pattern of mutations and recovers key phylogenetic relationships from more traditional analyses. We also evaluated alternative roots of the SARS-CoV-2 phylogeny and found that the earliest sampled genomes in 2019 likely evolved by four mutations of the most recent common ancestor of all SARS-CoV-2 genomes. An application of TopHap to more than 1 million SARS-CoV-2 genomes reconstructed the most comprehensive evolutionary relationships of major variants, which confirmed the 68KG phylogeny and provided evolutionary origins of major and recent variants of concern. AVAILABILITY AND IMPLEMENTATION: TopHap is available at https://github.com/SayakaMiura/TopHap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A compendium of kinetic modulatory profiles identifies ferroptosis regulators.

Cell death can be executed by regulated apoptotic and nonapoptotic pathways, including the iron-dependent process of ferroptosis. Small molecules are essential tools for studying the regulation of cell death. Using time-lapse imaging and a library of 1,833 bioactive compounds, we assembled a large compendium of kinetic cell death modulatory profiles for inducers of apoptosis and ferroptosis. From this dataset we identify dozens of ferroptosis suppressors, including numerous compounds that appear to act via cryptic off-target antioxidant or iron chelating activities. We show that the FDA-approved drug bazedoxifene acts as a potent radical trapping antioxidant inhibitor of ferroptosis both in vitro and in vivo. ATP-competitive mechanistic target of rapamycin (mTOR) inhibitors, by contrast, are on-target ferroptosis inhibitors. Further investigation revealed both mTOR-dependent and mTOR-independent mechanisms that link amino acid metabolism to ferroptosis sensitivity. These results highlight kinetic modulatory profiling as a useful tool to investigate cell death regulation.

Cadence (steps/min) and relative intensity in 61 to 85-year-olds: the CADENCE-Adults study.

BACKGROUND: We previously demonstrated that a heuristic (i.e., evidence-based, rounded yet practical) cadence threshold of ≥ 100 steps/min was associated with absolutely-defined moderate intensity physical activity (i.e., ≥ 3 metabolic equivalents [METs]) in older adults 61-85 years of age. Although it was difficult to ascertain achievement of absolutely-defined vigorous (6 METs) intensity, ≥ 130 steps/min was identified as a defensible threshold for this population. However, little evidence exists regarding cadence thresholds and relatively-defined moderate intensity indicators, including ≥ 64% heart rate [HR] maximum [HRmax = 220-age], ≥ 40% HR reserve [HRR = HRmax-HRresting], and ≥ 12 Borg Scale Rating of Perceived Exertion [RPE]; or vigorous intensity indicators including ≥ 77%HRmax, ≥ 60%HRR, and ≥ 14 RPE. PURPOSE: To analyze the relationship between cadence and relatively-defined physical activity intensity and identify relatively-defined moderate and vigorous heuristic cadence thresholds for older adults 61-85 years of age. METHODS: Ninety-seven ostensibly healthy adults (72.7 ± 6.9 years; 49.5% women) completed up to nine 5-min treadmill walking bouts beginning at 0.5 mph (0.8 km/h) and progressing by 0.5 mph speed increments (with 2-min rest between bouts). Directly-observed (and video-recorded) steps were hand-counted, HR was measured using a chest-strapped monitor, and in the final minute of each bout, participants self-reported RPE. Segmented mixed model regression and Receiver Operating Characteristic (ROC) curve analyses identified optimal cadence thresholds associated with relatively-defined moderate (≥ 64%HRmax, ≥ 40%HRR, and ≥ 12 RPE) and vigorous (≥ 77%HRmax, ≥ 60%HRR, and ≥ 14 RPE) intensities. A compromise between the two analytical methods, including Youden's Index (a sum of sensitivity and specificity), positive and negative predictive values, and overall accuracy, yielded final heuristic cadences. RESULTS: Across all relatively-defined moderate intensity indicators, segmented regression models and ROC curve analyses identified optimal cadence thresholds ranging from 105.9 to 112.8 steps/min and 102.0-104.3 steps/min, respectively. Comparable values for vigorous intensity indicators ranged between126.1-132.1 steps/min and 106.7-116.0 steps/min, respectively. Regardless of the relatively-defined intensity indicator, the overall best heuristic cadence threshold aligned with moderate intensity was ≥ 105 steps/min. Vigorous intensity varied between ≥ 115 (greater sensitivity) or ≥ 120 (greater specificity) steps/min. CONCLUSIONS: Heuristic cadence thresholds align with relatively-defined intensity indicators and can be useful for studying and prescribing older adults' physiological response to, and/or perceived experience of, ambulatory physical activity. TRIAL REGISTRATION: Clinicaltrials.gov NCT02650258. Registered 24 December 2015.