Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes

Phylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be jointly lost or retained across the tree of life. Phylogenetic profiling has customarily been more widely used with prokaryotes than eukaryotes, because the method is thought to require many diverse genomes. There are now many eukaryotic genomes available, but these are considerably larger, and typical phylogenetic profiling methods require at least quadratic time as a function of the number of genes. We introduce a fast, scalable phylogenetic profiling approach entitled HogProf, which leverages hierarchical orthologous groups for the construction of large profiles and locality-sensitive hashing for efficient retrieval of similar profiles. We show that the approach outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the tool to reconstruct networks and query for interactors of the kinetochore complex as well as conserved proteins involved in sexual reproduction: Hap2, Spo11 and Gex1. HogProf enables large-scale phylogenetic profiling across the three domains of life, and will be useful to predict biological pathways among the hundreds of thousands of eukaryotic species that will become available in the coming few years. HogProf is available at https://github.com/DessimozLab/HogProf

Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile

A novel actinobacterium, strain DB165T, was isolated from cold waters of Llullaillaco Volcano Lake (6170 m asl) in Chile. Phylogenetic analysis based on 16S rRNA gene sequences identified strain DB165T as belonging to the genus Subtercola in the family Microbacteriaceae, sharing 97.4% of sequence similarity with Subtercola frigoramans DSM 13057T, 96.7% with Subtercola lobariae DSM 103962T, and 96.1% with Subtercola boreus DSM 13056T. The cells were observed to be Gram-positive, form rods with irregular morphology, and to grow best at 10–15 °C, pH 7 and in the absence of NaCl. The cross-linkage between the amino acids in its peptidoglycan is type B2γ; 2,4-diaminobutyric acid is the diagnostic diamino acid; the major respiratory quinones are MK-9 and MK-10; and the polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, 5 glycolipids, 2 phospholipids and 5 additional polar lipids. The fatty acid profile of DB165T (5% >) contains iso-C14:0, iso-C16:0, anteiso-C15:0, anteiso-C17:0, and the dimethylacetal iso-C16:0 DMA. The genomic DNA G+C content of strain DB165T was determined to be 65 mol%. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses presented in this study, strain DB165T (= DSM 105013T = JCM 32044T) represents a new species in the genus Subtercola, for which the name Subtercola vilae sp. nov. is proposed

Genome Sequence of the Native Apiculate Wine Yeast Hanseniaspora vineae T02/19AF

The use of novel yeast strains for winemaking improves quality and provides variety including subtle characteristic differences in fine wines. Here we report the first genome of a yeast strain native to Uruguay, Hanseniaspora vineae T02/19AF, which has been shown to positively contribute to aroma and wine quality.Fil: Giorello, Facundo M.. Universidad de la República; UruguayFil: Berná, Luisa. Instituto Pasteur de Montevideo; UruguayFil: Greif, Gonzalo. Instituto Pasteur de Montevideo; UruguayFil: Camesasca, Laura. Inst. de Investigaciones Biológicas Clemente Estable; UruguayFil: Salzman, Valentina. Instituto Pasteur de Montevideo; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Medina, Karina. Universidad de la Republica. Facultad de Química; UruguayFil: Robello, Carlos. Instituto Pasteur de Montevideo; UruguayFil: Gaggero, Carina. Inst. de Investigaciones Biológicas Clemente Estable; UruguayFil: Aguilar, Pablo S.. Instituto Pasteur de Montevideo; UruguayFil: Carrau, Francisco. Sección Enología; Urugua

The variation of the gravitational constant inferred from the Hubble diagram of Type Ia supernovae

We consider a cosmological model with a variable gravitational constant, G, based on a scalar-tensor theory. Using the recent observational data for the Hubble diagram of type Ia supernovae (SNeIa) we find a phenomenological expression describing the variation of G. The corresponding variation of the fine structure constant \alpha within multidimensional theories is also computed and is shown not to support known constraints on \Delta \alpha / \alpha.Comment: LaTeX, 12 pages, 3 figs. In the replaced version figures are added and some errors are correcte

An upper limit to the secular variation of the gravitational constant from white dwarf stars

A variation of the gravitational constant over cosmological ages modifies the main sequence lifetimes and white dwarf cooling ages. Using an state-of-the-art stellar evolutionary code we compute the effects of a secularly varying G on the main sequence ages and, employing white dwarf cooling ages computed taking into account the effects of a running G, we place constraints on the rate of variation of Newton's constant. This is done using the white dwarf luminosity function and the distance of the well studied open Galactic cluster NGC 6791. We derive an upper bound G'/G ~ -1.8 10^{-12} 1/yr. This upper limit for the secular variation of the gravitational constant compares favorably with those obtained using other stellar evolutionary properties, and can be easily improved if deep images of the cluster allow to obtain an improved white dwarf luminosity function.Comment: 15 pages, 4 figures, accepted for publication in JCA

Pkh-kinases control eisosome assembly and organization

Eisosomes help sequester a subgroup of plasma membrane proteins into discrete membrane domains that colocalize with sites of endocytosis. Here we show that the major eisosome component Pil1 in vivo is a target of the long-chain base (LCB, the biosynthetic precursors to sphingolipids)-signaling pathway mediated by the Pkh-kinases. Eisosomes disassemble if Pil1 is hyperphosphorylated (i) upon overexpression of Pkh-kinases, (ii) upon reducing LCB concentrations by inhibiting serine-palmitoyl transferase in lcb1-mutant cells or by poisoning the enzyme with myriocin, and (iii) upon mimicking hyperphosphorylation in pil1-mutant cells. Conversely, more Pil1 assembles into eisosomes if Pil1 is hypophosphorylated (i) upon reducing Pkh-kinase activity in pkh1 pkh2-mutant cells, (ii) upon activating Pkh-kinases by addition of LCBs, and (iii) upon mimicking hypophosphorylation in pil1-mutant cells. The resulting enlarged eisosomes show altered organization. Other data suggest that Pkh signaling and sphingolipids are important for endocytosis. Taken together with our previous results that link eisosomes to endocytosis, these observations suggest that Pkh-kinase signaling relayed to Pil1 may help regulate endocytic events to modulate the organization of the plasma membrane

Arabidopsis HAP2/GCS1 is a gamete fusion protein homologous to somatic and viral fusogens

Cell–cell fusion is inherent to sexual reproduction. Loss of HAPLESS 2/GENERATIVE CELL SPECIFIC 1 (HAP2/GCS1) proteins results in gamete fusion failure in diverse organisms, but their exact role is unclear. In this study, we show that Arabidopsis thaliana HAP2/GCS1 is sufficient to promote mammalian cell–cell fusion. Hemifusion and complete fusion depend on HAP2/GCS1 presence in both fusing cells. Furthermore, expression of HAP2 on the surface of pseudotyped vesicular stomatitis virus results in homotypic virus–cell fusion. We demonstrate that the Caenorhabditis elegans Epithelial Fusion Failure 1 (EFF-1) somatic cell fusogen can replace HAP2/GCS1 in one of the fusing membranes, indicating that HAP2/GCS1 and EFF-1 share a similar fusion mechanism. Structural modeling of the HAP2/GCS1 protein family predicts that they are homologous to EFF-1 and viral class II fusion proteins (e.g., Zika virus). We name this superfamily Fusexins: fusion proteins essential for sexual reproduction and exoplasmic merger of plasma membranes. We suggest a common origin and evolution of sexual reproduction, enveloped virus entry into cells, and somatic cell fusion

Use of a gas-operated ventilator as a noninvasive bridging respiratory therapy in critically Ill COVID-19 patients in a middle-income country

During the COVID-19 pandemic, there was a notable undersupply of respiratory support devices, especially in low- and middle-income countries. As a result, many hospitals turned to alternative respiratory therapies, including the use of gas-operated ventilators (GOV). The aim of this study was to describe the use of GOV as a noninvasive bridging respiratory therapy in critically ill COVID-19 patients and to compare clinical outcomes achieved with this device to conventional respiratory therapies. Retrospective cohort analysis of critically ill COVID-19 patients during the first local wave of the pandemic. The final analysis included 204 patients grouped according to the type of respiratory therapy received in the first 24 h, as follows: conventional oxygen therapy (COT), n = 28 (14%); GOV, n = 72 (35%); noninvasive ventilation (NIV), n = 49 (24%); invasive mechanical ventilation (IMV), n = 55 (27%). In 72, GOV served as noninvasive bridging respiratory therapy in 42 (58%) of these patients. In the other 30 patients (42%), 20 (28%) presented clinical improvement and were discharged; 10 (14%) died. In the COT and GOV groups, 68% and 39%, respectively, progressed to intubation (P ≤ 0.001). Clinical outcomes in the GOV and NIV groups were similar (no statistically significant differences). GOV was successfully used as a noninvasive bridging respiratory therapy in more than half of patients. Clinical outcomes in the GOV group were comparable to those of the NIV group. These findings support the use of GOV as an emergency, noninvasive bridging respiratory therapy in medical crises when alternative approaches to the standard of care may be justifiable

Challenge 6: Open Science: reproducibility, transparency and reliability

Open Science is becoming a new paradigm in scientific research and complex changes are being done. This new way in knowledge development requires a great transformation that will allow science to adapt efficiently and effectively to the urgency of the problems to be solved while ensuring the reproducibility, transparency and reliability of scientific results. This chapter analyzes the impact of this change of model, the challenges to be addressed and the expected benefits.Peer reviewe

A white dwarf cooling age of 8 Gyr for NGC 6791 from physical separation processes

NGC 6791 is a well studied open cluster1 that it is so close to us that can be imaged down to very faint luminosities. The main sequence turn-off age (~8 Gyr) and the age derived from the termination of the white dwarf cooling sequence (~6 Gyr) are significantly different. One possible explanation is that as white dwarfs cool, one of the ashes of helium burning, 22Ne, sinks in the deep interior of these stars. At lower temperatures, white dwarfs are expected to crystallise and phase separation of the main constituents of the core of a typical white dwarf, 12C and 16O, is expected to occur. This sequence of events is expected to introduce significant delays in the cooling times, but has not hitherto been proven. Here we report that, as theoretically anticipated, physical separation processes occur in the cores of white dwarfs, solving the age discrepancy for NGC 6791.Comment: 3 pages, 2 figures, published in Natur