CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes.

Protein interactions are essential for cellular processes. In recent years there has been significant progress in computational prediction of 3D structures of individual protein chains, with the best-performing algorithms reaching sub-Ångström accuracy. These techniques are now finding their way into the prediction of protein interactions, adding to the existing modeling approaches. The community-wide Critical Assessment of Predicted Interactions (CAPRI) has been a catalyst for the development of procedures for the structural modeling of protein assemblies by organizing blind prediction experiments. The predicted structures are assessed against unpublished experimentally determined structures using a set of metrics with proven robustness that have been established in the CAPRI community. In addition, several advanced benchmarking databases provide targets against which users can test docking and assembly modeling software. These include the Protein-Protein Docking Benchmark, the CAPRI Scoreset, and the Dockground database, all developed by members of the CAPRI community. Here we present CAPRI-Q, a stand-alone model quality assessment tool, which can be freely downloaded or used via a publicly available web server. This tool applies the CAPRI metrics to assess the quality of query structures against given target structures, along with other popular quality metrics such as DockQ, TM-score and l-DDT, and classifies the models according to the CAPRI model quality criteria. The tool can handle a variety of protein complex types including those involving peptides, nucleic acids, and oligosaccharides. The source code is freely available from https://gitlab.in2p3.fr/cmsb-public/CAPRI-Q and its web interface through the Dockground resource at https://dockground.compbio.ku.edu/assessment/.

Odontogenic (hematogenic) or sinusopathy (contiguous) brain abscess: Case report.

Brain abscess is a rare infectious condition, affecting 0.4 to 0.9 per 100,000 individuals annually, with classic symptoms of fever, headache, and neurological deficits. The origin can be contiguous, hematogenous, due to ruptures of brain barriers, or cryptogenic. Dental infections, such as those related to Gemella morbillorum, are atypical, and when related to odontogenic sinusitis, it is normally unilateral. This report describes a case of peculiar brain abscess, of unconfirmed source, possibly involving sinusitis or periapical odontogenic lesion in an immunocompetent young woman. A 22-year-old patient presented with sinusitis showed by computed tomography, progressing to a brain abscess caused by multidrug-resistant Streptococcus sanguis. Additional cultures revealed Gemella morbillorum in maxillary sinusitis. Treatment involved stereotactic drainage, sinusotomy, and prolonged antibiotic therapy, with recurrence and surgical reintervention, in addition to prophylactic dental extraction and exerese of the brain cyst capsule. Brain abscess represents a significant medical challenge, often posing difficulties in pinpointing its primary infectious source despite the aid of comprehensive laboratory and imaging diagnostics, as evidenced in this case. Timely and targeted intervention in preceding infections assumes paramount importance for effective management, underscoring the indispensable role of a multidisciplinary healthcare team. Active patient engagement and adherence to treatment protocols are imperative to mitigate complications and foster favorable disease progression. Key words:Brain Abscess, Dental Focal Infection, Gemella, Sinusitis, Streptococcus sanguis.

Effects of a pro-resolving drug in COVID-19: preclinical studies to a randomized, placebo-controlled, phase Ib/IIa trial in hospitalized patients.

INTRODUCTION: Pro-resolving molecules may curb disease caused by viruses without altering the capacity of the host to deal with infection. AP1189 is a melanocortin receptor-biased agonist endowed with pro-resolving and anti-inflammatory activity. We evaluated the preclinical and early clinical effects of treatment with AP1189 in the context of COVID-19. METHODS: C57BL/6j mice were infected intranasally with MHV-A59 or hK18-ACE2 mice with SARS-CoV-2. AP1189 (10 mg·kg-1, BID, s.c.) was given to the animals from day 2 and parameters evaluated at day 5. Human PBMCs from health donors were infected with SARS-CoV-2 in presence or absence of AP1189 and production of cytokines quantified. In the clinical study, 6 patients were initially given AP1189 (100 mg daily for 14 days) and this was followed by a randomized (2:1), placebo-controlled, double-blind trial that enrolled 54 hospitalized COVID-19 patients needing oxygen support. The primary outcome was the time in days until respiratory recovery, defined as a SpO2 ≥ 93% in ambient air. RESULTS: Treatment with AP1189 attenuated pulmonary inflammation in mice infected with MHV-A59 or SARS-CoV-2 and decreased the release of CXCL10, TNF-α and IL-1ß by human PBMCs. Hospitalized COVID-19 patients already taking glucocorticoids took a median time of 6 days until respiratory recovery when given placebo versus 4 days when taking AP1189 (P = 0.017). CONCLUSION: Treatment with AP1189 was associated with less disease caused by beta-coronavirus infection both in mice and in humans. This is the first demonstration of the effects of a pro-resolving molecule in the context of severe infection in humans.

Identification of a DNA methylation episignature for recurrent constellations of embryonic malformations.

The term "recurrent constellations of embryonic malformations" (RCEM) is used to describe a number of multiple malformation associations that affect three or more body structures. The causes of these disorders are currently unknown, and no diagnostic marker has been identified. Consequently, providing a definitive diagnosis in suspected individuals is challenging. In this study, genome-wide DNA methylation analysis was conducted on DNA samples obtained from the peripheral blood of 53 individuals with RCEM characterized by clinical features recognized as VACTERL and/or oculoauriculovertebral spectrum association. We identified a common DNA methylation episignature in 40 out of the 53 individuals. Subsequently, a sensitive and specific binary classifier was developed based on the DNA methylation episignature. This classifier can facilitate the use of RCEM episignature as a diagnostic biomarker in a clinical setting. The study also investigated the functional correlation of RCEM DNA methylation relative to other genetic disorders with known episignatures, highlighting the common genomic regulatory pathways involved in the pathophysiology of RCEM.

PRKAG2-Related Lethal Congenital Glycogen Storage Disease of the Heart as Rare Cause of Fetal Hydrops With Bradycardia and Cardiomyopathy: Clinical Report and Literature Review.

Nonimmune foetal hydrops is a prenatal condition associated with significant perinatal mortality. It has so far been associated with over 200 chromosomal and monogenic conditions, most frequently chromosomal aneuploidies and RASopathies. Thorough clinical phenotyping and genetic evaluation are essential to determine the underlying etiology of this clinical entity and guide obstetrical and postnatal management. In this report, we describe the prenatal presentation and postnatal outcome of a pregnancy with Lethal Congenital Glycogen Storage Disease of the Heart, a rare autosomal dominant non lysosomal cardiac glycogenosis caused by a novel de novo likely pathogenic variant in the Protein Kinase AMP-Activated Non-Catalytic Subunit Gamma 2 (PRKAG2) gene, [NM_016203.3:c.1150A > G, p.(Arg384Gly)]. To this day, only six other molecularly confirmed prenatal presentations of this condition have been reported. This clinical report adds to the knowledge on the prenatal features, clinical evolution, molecular diagnosis and pathological findings of this disorder and underlines the clinical utility of comprehensive molecular testing in the investigation of nonimmune foetal hydrops and fetal cardiomyopathy.

The Enigma of Transcriptional Activation Domains.

Activation domains (ADs) of eukaryotic gene activators remain enigmatic for decades as short, extremely variable sequences which often are intrinsically disordered in structure and interact with an uncertain number of targets. The general absence of specificity increasingly complicates the utilization of the widely accepted mechanism of AD function by recruitment of coactivators. The long-standing enigma at the heart of molecular biology demands a fundamental rethinking of established concepts. Here, we review the experimental evidence supporting a novel mechanistic model of gene activation, based on ADs functioning via surfactant-like near-stochastic interactions with gene promoter nucleosomes. This new model is consistent with recent information-rich experimental data obtained using high-throughput synthetic biology and bioinformatics analysis methods, including machine learning. We clarify why the conventional biochemical principle of specificity for sequence, structures, and interactions fails to explain activation domain function. This perspective provides connections to the liquid-liquid phase separation model, signifies near-stochastic interactions as fundamental for the biochemical function, and can be generalized to other cellular functions.

Mandibular Gender Dimorphism: The Utility of Artificial Intelligence and Statistical Shape Modeling in Skeletal Facial Analysis.

BACKGROUND: In gender-affirming surgery, facial skeletal dimorphism is an important topic for every craniofacial surgeon. Few cephalometric studies have assessed this topic; however, they fall short to provide skeletal contour insights that direct surgical planning. Herein, we propose statistical shape modeling (SSM) as a novel tool for investigating mandibular dimorphism for young white individuals. METHODS: A single-center, retrospective study was performed using computed tomography (CT) scans of white individuals, aged 20 to 39 years old. AI-assisted, three-dimensional (3D) mandibles were reconstructed in Materialise Mimics v25.0. We used SSM to generate average 3D models for both genders. Relevant manual anthropometric measurements were taken for the SSMs and individual mandibles. Contour disparities were then represented using 3D overlays and heatmaps. Statistical analyses were performed using unpaired student t testing or Wilcoxon signed rank testing with 95% confidence interval as deemed appropriate by population-level normality assessment. RESULTS: Ninety-eight patients (53 females, 45 males) were included. Male mandibles showed greater bigonial width, intercondylar width, ramus height, and body length [p<0.005]. There was no statistically significant difference in the gonial angle measurements [p=0.62]. All relevant manual individual measurements demonstrated excellent concordance to their SSM counterparts. The 3D overlays of SSMs revealed squarer male chins with more lateral but less anterior projection than their female counterparts. Also, the female mandibles showed smoother transition at the gonial angle. CONCLUSIONS: SSM provides a novel tool to objectively evaluate volumetric and contour dimorphisms between genders. Moreover, this method can be automated, allowing for expedited comparisons between populations of interest compared to manual assessment. LEVEL OF EVIDENCE III: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors   www.springer.com/00266 . Bullet points about the importance of this work: Advancing Anthropometric Assessment: Statistical shape modeling (SSM) offers a cutting-edge approach to visualizing gender-specific skeletal anatomic differences for aesthetic and gender-affirming facial surgery. Expediting Comparative Analysis: The workflow established in this paper streamlines the evaluative process, enabling rapid morphologic comparisons between populations. Patient-Centered Care: This study establishes a foundation for the development of SSMs in individualized operative planning.

Endometabolic profiling of pigmented glacier ice algae: the impact of sample processing.

INTRODUCTION: Glacier ice algae, mainly Ancylonema alaskanum and Ancylonema nordenskiöldi, bloom on Greenland Ice Sheet bare ice surfaces. They significantly decrease surface albedo due to their purple-brown pigmentation, thus increasing melt. Little is known about their metabolic adaptation and factors controlling algal growth dynamics and pigment formation. A challenge in obtaining such data is the necessity of melting samples, which delays preservation and introduces bias to metabolomic analysis. There is a need to evaluate the physiological response of algae to melting and establish consistent sample processing strategies for metabolomics of ice microbial communities. OBJECTIVES: To address the impact of sample melting procedure on metabolic characterization and establish a processing and analytical workflow for endometabolic profiling of glacier ice algae. METHODS: We employed untargeted, high-resolution mass spectrometry and tested the effect of sample melt temperature (10, 15, 20 °C) and processing delay (up to 49 h) on the metabolome and lipidome, and complemented this approach with cell counts (FlowCam), photophysiological analysis (PAM) and diversity characterization. RESULTS AND CONCLUSION: We putatively identified 804 metabolites, with glycerolipids, glycerophospholipids and fatty acyls being the most prominent superclasses (> 50% of identified metabolites). Among the polar metabolome, carbohydrates and amino acid-derivatives were the most abundant. We show that 8% of the metabolome is affected by melt duration, with a pronounced decrease in betaine membrane lipids and pigment precursors, and an increase in phospholipids. Controlled fast melting at 10 °C resulted in the highest consistency, and is our recommendation for future supraglacial metabolomics studies.

Predicting the Future Focus of Orthognathic Surgery: Outcome-Driven Planning and Treatment With Function, Esthetics, and Occlusion as Key Indicators.

As an international group of orthognathic surgeons, we believe the next big thing in orthognathic surgery will be a clinical and research focus on patient-oriented outcomes and improved quality of life. We expect to see advances in diagnosis and treatment planning, materials development, and patient management.

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.

Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the information required to fully model biomolecular complexes at atomic resolution, particularly for large and heterogeneous assemblies. Integrative computational approaches have, therefore, gained popularity, complementing traditional experimental methods in structural biology. Here, we introduce HADDOCK2.4, an integrative modeling platform, and its updated web interface ( https://wenmr.science.uu.nl/haddock2.4 ). The platform seamlessly integrates diverse experimental and theoretical data to generate high-quality models of macromolecular complexes. The user-friendly web server offers automated parameter settings, access to distributed computing resources, and pre- and post-processing steps that enhance the user experience. To present the web server's various interfaces and features, we demonstrate two different applications: (i) we predict the structure of an antibody-antigen complex by using NMR data for the antigen and knowledge of the hypervariable loops for the antibody, and (ii) we perform coarse-grained modeling of PRC1 with a nucleosome particle guided by mutagenesis and functional data. The described protocols require some basic familiarity with molecular modeling and the Linux command shell. This new version of our widely used HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types.

Hyperspectral and Chlorophyll Fluorescence Analyses of Comparative Leaf Surfaces Reveal Cellular Influences on Leaf Optical Properties in Tradescantia Plants.

The differential effects of cellular and ultrastructural characteristics on the optical properties of adaxial and abaxial leaf surfaces in the genus Tradescantia highlight the intricate relationships between cellular arrangement and pigment distribution in the plant cells. We examined hyperspectral and chlorophyll a fluorescence (ChlF) kinetics using spectroradiometers and optical and electron microscopy techniques. The leaves were analysed for their spectral properties and cellular makeup. The biochemical compounds were measured and correlated with the biophysical and ultrastructural features. The main findings showed that the top and bottom leaf surfaces had different amounts and patterns of pigments, especially anthocyanins, flavonoids, total phenolics, chlorophyll-carotenoids, and cell and organelle structures, as revealed by the hyperspectral vegetation index (HVI). These differences were further elucidated by the correlation coefficients, which influence the optical signatures of the leaves. Additionally, ChlF kinetics varied between leaf surfaces, correlating with VIS-NIR-SWIR bands through distinct cellular structures and pigment concentrations in the hypodermis cells. We confirmed that the unique optical properties of each leaf surface arise not only from pigmentation but also from complex cellular arrangements and structural adaptations. Some of the factors that affect how leaves reflect light are the arrangement of chloroplasts, thylakoid membranes, vacuoles, and the relative size of the cells themselves. These findings improve our knowledge of the biophysical and biochemical reasons for leaf optical diversity, and indicate possible implications for photosynthetic efficiency and stress adaptation under different environmental conditions in the mesophyll cells of Tradescantia plants.

Characterization of a hydrothermally aged experimental alumina-toughened zirconia composite.

OBJECTIVES: To assess the effects of different aging protocols on chemical, physical, and mechanical properties of an experimental ATZ composite compared to a zirconia. METHODS: Disc-shaped specimens were obtained through uniaxial pressing of commercial powders (Tosoh), ATZ comprised of 80%ZrO2/20%Al2O3 (TZ-3YS20AB) and 3Y-TZP (3Y-SBE). The specimens of each material were divided into different groups according to the aging protocol: immediate, autoclave aging and hydrothermal reactor aging. The aging protocols were performed at 134 ºC for 20 h at 2.2 bar. Crystalline evaluations were performed using X-Ray Diffraction. The nanoindentation tests measured the elastic modulus (Em) and hardness (H). Biaxial flexural strength was performed, and Weibull statistics were used to determine the characteristic strength and Weibull modulus. The probability of survival was also determined. The Em and H data were analyzed by one-way ANOVA and Tukey test. RESULTS: Diffractograms revealed the presence of monoclinic phase in both materials after aging. The hydrothermal reactor decreased the Em for ATZ compared to its immediate condition; and the H for both ATZ and 3Y-TZP regarding their immediate and autoclave aging conditions, respectively. The aging protocols significantly increased the characteristic strength for ATZ, while decreased for 3Y-TZP. No difference regarding Weibull modulus was observed, except for 3Y-TZP aged in reactor. For missions of up to 500 MPa, both materials presented a high probability of survival (>99 %) irrespective of aging condition. SIGNIFICANCE: The synthesized ATZ composite exhibited greater physical and microstructural stability compared to 3Y-TZP, supporting potential application of the experimental material for long-span reconstructive applications.

Long-Read-Based Hybrid Genome Assembly and Annotation of Snow Algal Strain CCCryo 101-99 (cf. Sphaerocystis sp., Chlamydomonadales).

Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (nonobligate cryophilic) snow algae. Both can accumulate significant biomasses on glacier and snow habitats and play major roles in global climate dynamics. Despite their significance, genomic studies on these organisms remain scarce, hindering our understanding of their evolutionary history and adaptive mechanisms in the face of climate change. Here, we present the draft genome assembly and annotation of the psychrophilic snow algal strain CCCryo 101-99 (cf. Sphaerocystis sp.). The draft haploid genome assembly is 122.5 Mb in length and is represented by 664 contigs with an N50 of 0.86 Mb, a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 92.9% (n = 1,519), a maximum contig length of 5.3 Mb, and a guanine-cystosine (GC) content of 53.1%. In total, 28.98% of the genome (35.5 Mb) contains repetitive elements. We identified 417 noncoding RNAs and annotated the chloroplast genome. The predicted proteome comprises 14,805 genes with a BUSCO completeness of 97.8%. Our preliminary analyses reveal a genome with a higher repeat content compared with mesophilic chlorophyte relatives, alongside enrichment in gene families associated with photosynthesis and flagella functions. Our current data will facilitate future comparative studies, improving our understanding of the likely response of polar algae to a warming climate as well as their evolutionary trajectories in permanently cold environments.

CD5L is upregulated upon infection with Mycobacterium tuberculosis with no effect on disease progression.

Tuberculosis (TB) alone caused over a billion deaths in the last 200 years, making it one of the deadliest diseases to humankind. Understanding the immune mechanisms underlying protection or pathology in TB is key to uncover the much needed innovative approaches to tackle TB. The scavenger receptor cysteine-rich molecule CD5 antigen-like (CD5L) has been associated with TB, but whether and how CD5L shapes the immune response during the course of disease remains poorly understood. Here, we show an upregulation of CD5L in circulation and at the site of infection in C57BL/6 Mycobacterium tuberculosis-infected mice. To investigate the role of CD5L in TB, we studied the progression of M. tuberculosis aerosol infection in a recently described genetically engineered mouse model lacking CD5L. Despite the increase of CD5L during infection of wild-type mice, absence of CD5L did not impact bacterial burden, histopathology or survival of infected mice. Absence of CD5L associated with a modest increase in the numbers of CD4+ T cells and the expression of IFN-γ in the lungs of infected mice, with no major effect in overall immune cell dynamics. Collectively, this study confirms CD5L as a potential diagnostic biomarker to TB, showing no discernible impact on the outcome of the infection.

Predicting binding events in very flexible, allosteric, multi-domain proteins.

Knowledge of the structures formed by proteins and small ligands is of fundamental importance for understanding molecular principles of chemotherapy and for designing new and more effective drugs. Due to the still high costs and to the several limitations of experimental techniques, it is most often desirable to predict these ligand-protein complexes in silico, particularly when screening for new putative drugs from databases of millions of compounds. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology aimed at generating bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites. Validation was performed on the enzyme adenylate kinase (ADK), a paradigmatic example of proteins that undergo very large conformational changes upon ligand binding. By only exploiting the unbound structure and the putative binding sites of the protein, we generated a significant fraction of bound-like structures, which employed in ensemble-docking calculations allowed to find native-like poses of substrates, inhibitors, and catalytically incompetent binders. Our protocol provides a general framework for the generation of bound-like conformations of flexible proteins that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening for difficult targets, prediction of the impact of amino acid mutations on structure and dynamics, and protein engineering.

Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon.

The Least Nighthawk Chordeiles pusillus is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of C. pusillus to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050-2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Marajó island during favourable climatic conditions in the Pleistocene.

Photoswitchable Carbamazepine Analogs for Non-Invasive Neuroinhibition In Vivo.

A problem of systemic pharmacotherapy is off-target activity, which causes adverse effects. Outstanding examples include neuroinhibitory medications like antiseizure drugs, which are used against epilepsy and neuropathic pain but cause systemic side effects. There is a need of drugs that inhibit nerve signals locally and on-demand without affecting other regions of the body. Photopharmacology aims to address this problem with light-activated drugs and localized illumination in the target organ. Here, we have developed photoswitchable derivatives of the widely prescribed antiseizure drug carbamazepine. For that purpose, we expanded our method of ortho azologization of tricyclic drugs to meta/para and to N-bridged diazocine. Our results validate the concept of ortho cryptoazologs (uniquely exemplified by Carbazopine-1) and bring to light Carbadiazocine (8), which can be photoswitched between 400-590 nm light (using violet LEDs and halogen lamps) and shows good drug-likeness and predicted safety. Both compounds display photoswitchable activity in vitro and in translucent zebrafish larvae. Carbadiazocine (8) also offers in vivo analgesic efficacy (mechanical and thermal stimuli) in a rat model of neuropathic pain and a simple and compelling treatment demonstration with non-invasive illumination.

The Role of the Heterogeneous Catalyst to Produce Solketal from Biodiesel Waste: The Key to Achieve Efficiency.

The valorization of the large amount of crude glycerol formed from the biodiesel industry is of primordial necessity. One possible direction with high interest to the biorefinery sector is the production of fuel additives such as solketal, through the acetalization of glycerol with acetone. This is a chemical process that conciliates high sustainability and economic interest, since solketal contributes to the fulfillment of a Circular Economy Model through its use in biodiesel blends. The key to guarantee high efficiency and high sustainability for solketal production is the use of recovery and recyclable heterogeneous catalysts. Reported works indicate that high yields are attributed to catalyst acidity, mainly the ones containing Brönsted acidic sites. On the other hand, the catalyst stability and its recycling capacity are completely dependent of the support material and the acidic sites incorporation methodology. This review intends to conciliate the information spread on this topic and indicate the most assertive strategies to achieve high solketal production in short reaction time during various reaction cycles.

Giant viral signatures on the Greenland ice sheet.

BACKGROUND: Dark pigmented snow and glacier ice algae on glaciers and ice sheets contribute to accelerating melt. The biological controls on these algae, particularly the role of viruses, remain poorly understood. Giant viruses, classified under the nucleocytoplasmic large DNA viruses (NCLDV) supergroup (phylum Nucleocytoviricota), are diverse and globally distributed. NCLDVs are known to infect eukaryotic cells in marine and freshwater environments, providing a biological control on the algal population in these ecosystems. However, there is very limited information on the diversity and ecosystem function of NCLDVs in terrestrial icy habitats. RESULTS: In this study, we investigate for the first time giant viruses and their host connections on ice and snow habitats, such as cryoconite, dark ice, ice core, red and green snow, and genomic assemblies of five cultivated Chlorophyta snow algae. Giant virus marker genes were present in almost all samples; the highest abundances were recovered from red snow and the snow algae genomic assemblies, followed by green snow and dark ice. The variety of active algae and protists in these GrIS habitats containing NCLDV marker genes suggests that infection can occur on a range of eukaryotic hosts. Metagenomic data from red and green snow contained evidence of giant virus metagenome-assembled genomes from the orders Imitervirales, Asfuvirales, and Algavirales. CONCLUSION: Our study highlights NCLDV family signatures in snow and ice samples from the Greenland ice sheet. Giant virus metagenome-assembled genomes (GVMAGs) were found in red snow samples, and related NCLDV marker genes were identified for the first time in snow algal culture genomic assemblies; implying a relationship between the NCLDVs and snow algae. Metatranscriptomic viral genes also aligned with metagenomic sequences, suggesting that NCLDVs are an active component of the microbial community and are potential "top-down" controls of the eukaryotic algal and protistan members. This study reveals the unprecedented presence of a diverse community of NCLDVs in a variety of glacial habitats dominated by algae.

Condensation or Desublimation: Nanolevel Structural Look on Two Frost Formation Pathways on Surfaces with Different Wettabilities.

Processes of water condensation and desublimation on solid surfaces are ubiquitous in nature and essential for various industrial applications, which are crucial for their performance. Despite their significance, these processes are not well understood due to the lack of methods that can provide insight at the nanolevel into the very first stages of phase transitions. Taking advantage of synchrotron grazing-incidence wide-angle X-ray scattering (GIWAXS) and environmental scanning electron microscopy (ESEM), two pathways of the frosting process from supersaturated vapors were studied in real time for substrates with different wettabilities ranging from highly hydrophilic to superhydrophobic. Within GIWAXS, a fully quantitative structural and orientational characterization of the undergoing phase transition reveals the information on degree of crystallinity of the new phase and determines the ordering at the surfaces and inside the films at the initial stages of water/ice nucleation from vapor onto the substrates. The diversity of frosting scenarios, including direct desublimation from the vapor and two-stage condensation-freezing processes, was observed by both GIWAXS and ESEM for different combinations of substrate wettability and vapor supersaturations. The classical nucleation theory straightforwardly predicts the pathway of the phase transition for hydrophobic and superhydrophobic substrates. The case of hydrophilic substrates is more intricate because the barriers in Gibbs free energy for nucleating both liquid and solid embryos are close to each other and comparable to thermal energy kBT. At that end, classical nucleation theory allows concluding a relation between contact angles for ice and water embryos on the basis of the observed frosting pathway.