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Abstract Comparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: 1) Analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and 2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole-genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.

Severe winters have occurred frequently in mid-latitude Eurasia during the past decade. Simulations with a 100-member ensemble of an atmospheric model detect an influence of declining Arctic sea-ice cover. Over the past decade, severe winters occurred frequently in mid-latitude Eurasia 1 , 2 , despite increasing global- and annual-mean surface air temperatures 3 . Observations suggest that these cold Eurasian winters could have been instigated by Arctic sea-ice decline 2 , 4 , through excitation of circulation anomalies similar to the Arctic Oscillation 5 . In climate simulations, however, a robust atmospheric response to sea-ice decline has not been found, perhaps owing to energetic internal fluctuations in the atmospheric circulation 6 . Here we use a 100-member ensemble of simulations with an atmospheric general circulation model driven by observation-based sea-ice concentration anomalies to show that as a result of sea-ice reduction in the Barents–Kara Sea, the probability of severe winters has more than doubled in central Eurasia. In our simulations, the atmospheric response to sea-ice decline is approximately independent of the Arctic Oscillation. Both reanalysis data and our simulations suggest that sea-ice decline leads to more frequent Eurasian blocking situations, which in turn favour cold-air advection to Eurasia and hence severe winters. Based on a further analysis of simulations from 22 climate models we conclude that the sea-ice-driven cold winters are unlikely to dominate in a warming future climate, although uncertainty remains, due in part to an insufficient ensemble size.

Although infection by SARS-CoV-2, the causative agent of coronavirus pneumonia disease (COVID-19), is spreading rapidly worldwide, no drug has been shown to be sufficiently effective for treating COVID-19. We previously found that nafamostat mesylate, an existing drug used for disseminated intravascular coagulation (DIC), effectively blocked Middle East respiratory syndrome coronavirus (MERS-CoV) S protein-mediated cell fusion by targeting transmembrane serine protease 2 (TMPRSS2), and inhibited MERS-CoV infection of human lung epithelium-derived Calu-3 cells. Here we established a quantitative fusion assay dependent on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein, angiotensin I converting enzyme 2 (ACE2) and TMPRSS2, and found that nafamostat mesylate potently inhibited the fusion while camostat mesylate was about 10-fold less active. Furthermore, nafamostat mesylate blocked SARS-CoV-2 infection of Calu-3 cells with an effective concentration (EC)50 around 10 nM, which is below its average blood concentration after intravenous administration through continuous infusion. On the other hand, a significantly higher dose (EC50 around 30 μM) was required for VeroE6/TMPRSS2 cells, where the TMPRSS2-independent but cathepsin-dependent endosomal infection pathway likely predominates. Together, our study shows that nafamostat mesylate potently inhibits SARS-CoV-2 S protein-mediated fusion in a cell fusion assay system and also inhibits SARS-CoV-2 infection in vitro in a cell-type-dependent manner. These findings, together with accumulated clinical data regarding nafamostat’s safety, make it a likely candidate drug to treat COVID-19.

This study investigated ice cloud formation associated with marine bioaerosols over the Southern Ocean (SO) using a combination of cloud particle sensor (CPS) sonde observations, satellite products, reanalysis data, and backward trajectory analysis. The CPS sonde detected ice clouds at temperatures higher than −10°C in the mid‐troposphere near an atmospheric river at high‐latitudes over the SO. Backward trajectory analyses indicated that a mid‐latitude air mass with a high concentration of atmospheric dimethylsulfide (DMS) in the atmospheric boundary layer (<1 km) arrived at the ice cloud formation layer over the high‐latitudes. The DMS in the boundary layer began to increase under high wave conditions, coincident with the highest chlorophyll‐a concentrations in the ocean. These results suggest that bioaerosols emitted from the ocean over the mid‐latitudes acted as ice‐nucleating particles for ice cloud formation over high‐latitudes. Plain Language Summary Polar region clouds play a key role in Earth's climate. Knowledge of the cloud phase (i.e., liquid water, ice, or mixed) is important for determining the surface heat budget because the reflection of solar radiation at the cloud top depends on cloud phase. Although the development of numerical climate models allows the investigation of clouds globally, there still is a cloud phase (water or ice) bias in the models. Therefore, an observational study is required to investigate cloud formation environments. During a cruise in the SO by a research ship, ice clouds were observed at relatively high temperatures in the mid‐troposphere at high‐latitudes. Analysis of the trajectory of the air mass at the ice formation height indicated that the air mass had traveled from the surface in the mid‐latitudes to the mid‐troposphere over high‐latitudes. Biogenic material emitted from the ocean under strong wind and high wave conditions was transferred to the air mass near the surface in the mid‐latitudes and eventually reached the mid‐troposphere at the observation point. These results suggest that marine biogenic material transported from the mid‐latitudes influenced ice cloud formation under relatively high temperatures. Key Points A cloud particle sensor sonde measured ice clouds at air temperatures higher than −10 °C in the mid‐troposphere near an atmospheric river Mid‐latitude air mass with high dimethylsulfide (DMS) in the boundary layer reached the ice cloud formation layer over high‐latitudes Simulated high surface atmospheric DMS was associated with observed high chlorophyll‐a concentration under simulated high wave conditions

Identification of orthologous or paralogous relationships of coding genes is fundamental to all aspects of comparative genomics. For accurate identification of orthologs among deeply diversified bilaterian lineages, precise estimation of gene trees is indispensable, given the complicated histories of genes over millions of years. By estimating gene trees, orthologs can be identified as members of an orthogroup, a set of genes descended from a single gene in the last common ancestor of all the species being considered. In addition to comparisons with a given species tree, purposeful taxonomic sampling increases the accuracy of gene tree estimation and orthogroup identification. Although some major phylogenetic relationships of bilaterians are gradually being unraveled, the scattering of published genomic data among separate web databases is becoming a significant hindrance to identification of orthogroups with appropriate taxonomic sampling. By integrating more than 250 metazoan gene models predicted in genome projects, we developed a web tool called ORTHOSCOPE to identify orthogroups of specific protein-coding genes within major bilaterian lineages. ORTHOSCOPE allows users to employ several sequences of a specific molecule and broadly accepted nodes included in a user-specified species tree as queries and to evaluate the reliability of estimated orthogroups based on topologies and node support values of estimated gene trees. A test analysis using data from 36 bilaterians was accomplished within 140 s. ORTHOSCOPE results can be used to evaluate orthologs identified by other stand-alone programs using genome-scale data. ORTHOSCOPE is freely available at https://www.orthoscope.jp or https://github.com/jun-inoue/orthoscope (last accessed December 28, 2018).

Influence of low Arctic sea‐ice minima in early autumn on the wintertime climate over Eurasia is investigated. Observational evidence shows that significant cold anomalies over the Far East in early winter and zonally elongated cold anomalies from Europe to Far East in late winter are associated with the decrease of the Arctic sea‐ice cover in the preceding summer‐to‐autumn seasons. Results from numerical experiments using an atmospheric general circulation model support these notions. The remote response in early winter is regarded as a stationary Rossby wave generated thermally through an anomalous turbulent heat fluxes as a result of anomalous ice‐cover over the Barents‐Kara Seas in late autumn, which tends to induce an amplification of the Siberian high causing colder conditions over the Far East. The late‐winter cold anomalies over Eurasia are also reproduced in our experiment, which is associated with the negative phase of the North Atlantic Oscillation.

Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post–teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70–80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.

NF-κB was first identified in 1986 as a B cell-specific transcription factor inducing immunoglobulin κ light chain expression. Subsequent studies revealed that NF-κB plays important roles in development, organogenesis, immunity, inflammation, and neurological functions by spatiotemporally regulating cell proliferation, differentiation, and apoptosis in several cell types. Furthermore, studies on the signal pathways that activate NF-κB led to the discovery of TRAF family proteins with E3 ubiquitin ligase activity, which function downstream of the receptor. This discovery led to the proposal of an entirely new signaling mechanism concept, wherein K63-ubiquitin chains act as a scaffold for the signaling complex to activate downstream kinases. This concept has revolutionized ubiquitin studies by revealing the importance of the nonproteolytic functions of ubiquitin not only in NF-κB signaling but also in a variety of other biological systems. TRAF6 is the most diverged among the TRAF family proteins, and our studies uncovered its notable physiological and pathological functions.

The Antarctic Peninsula of West Antarctica was one of the most rapidly warming regions on the Earth during the second half of the 20th century. Changes in the atmospheric circulation associated with remote tropical climate variabilities have been considered as leading drivers of the change in surface conditions in the region. However, the impacts of climate variabilities over the mid-latitudes of the Southern Hemisphere on this Antarctic warming have yet to be quantified. Here, through observation analysis and model experiments, we reveal that increases in winter sea surface temperature (SST) in the Tasman Sea modify Southern Ocean storm tracks. This, in turn, induces warming over the Antarctic Peninsula via planetary waves triggered in the Tasman Sea. We show that atmospheric response to SST warming over the Tasman Sea, even in the absence of anomalous tropical SST forcing, deepens the Amundsen Sea Low, leading to warm advection over the Antarctic Peninsula. The Antarctic Peninsula sees some of the strongest warming of the whole continent over the last decades, the drivers of which are not well known. Here, the authors show that winter sea surface temperature increases in the Tasman sea lead to changes in Southern Ocean storm tracks that in turn warm the Antarctic Peninsula.

The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the contribution of each species to digestion. Here, we report single-cell transcriptomes of four protists species comprising the protist population in worldwide pest Coptotermes formosanus . Comparative transcriptomic analysis revealed that the expression patterns of the genes involved in wood digestion were different among species, reinforcing their division of roles in wood degradation. Transcriptomes, together with enzyme assays, also suggested that one of the protists, Cononympha leidyi , actively degrades chitin and assimilates it into amino acids. We propose that C. leidyi contributes to nitrogen recycling and inhibiting infection from entomopathogenic fungi through chitin degradation. Two of the genes for chitin degradation were further revealed to be acquired via lateral gene transfer (LGT) implying the importance of LGT in the evolution of symbiosis. Our single-cell-based approach successfully characterized the function of each protist in termite hindgut and explained why the gut community includes multiple species.