Ancient gene transfer from algae to animals: Mechanisms and evolutionary significance

Background Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution

Insights into the Ecological Roles and Evolution of Methyl-Coenzyme M Reductase-Containing Hot Spring Archaea

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor

Bis{N,N-bis­[(diphenyl­phosphan­yl)meth­yl]aniline-κ2 P,P′}copper(I) tetra­fluoridoborate

In the cation of the title compound, [Cu(C32H29NP2)2]BF4, the CuI atom is four-coordinated in a distorted tetra­hedral geometry by four P atoms from two N,N-bis­[(diphenyl­phosphan­yl)meth­yl]aniline ligands. In the crystal, the cations are linked by C—H⋯π inter­actions, forming chains along the a axis. Intra­molecular C—H⋯N and inter­molecular C—H⋯F hydrogen bonds are also observed

Role of GLP-1 in the Hypoglycemic Effects of Wild Bitter Gourd

This study aimed to examine the role of GLP-1 in the hypoglycemic activity of wild bitter gourd (Momordica charantiaL., BG). In vitro, the GLP-1 secretion in STC-1, a murine enteroendocrine cell line, was dose dependently stimulated by water extract (WE), its fractions (WEL, &gt;3 kD and WES, &lt;3 kD), and a bitter compounds-rich fraction of BG. These stimulations were partially inhibited by probenecid, a bitter taste receptor inhibitor, and by U-73122, a phospholipase Cβ2 inhibitor. These results suggested that the stimulation might involve, at least in part, certain bitter taste receptors and/or PLCβ2-signaling pathway. Two cucurbitane triterpenoids isolated from BG, 19-nor-cucurbita-5(10),6,8,22-(E),24-pentaen-3β-ol, and 5β,19-epoxycucurbita-6,24-diene-3β,23ξ-diol (karavilagenine E,) showed relative high efficacy in the stimulation. In vivo, mice fed BG diet showed higher insulinogenic index in an oral glucose tolerance test. A single oral dose of WE or WES pretreatment significantly improved intraperitoneal glucose tolerance. A single oral dose of WES significantly decreased glucose and increased insulin and GLP-1 in serum after 30 min. This acute hypoglycemic effect of WES was abolished by pretreatment with exendin-9, a GLP-1 receptor antagonist. Our data provide evidence that BG stimulates GLP-1 secretion which contributes, at least in part, to the antidiabetic activity of BG through an incretin effect.</jats:p

Estimating the instant case fatality rate of COVID-19 in China

Objective: The outbreak of coronavirus disease 2019 (COVID-19) in China has been basically controlled. However, the global epidemic of COVID-19 is worsening. We established a method to estimate the instant case fatality rate (CFR) and cure rate of COVID-19 in China. Methods: A total of 82 735 confirmed cases released officially by the Chinese authorities from December 8, 2019 to April 18, 2020 were collected. The estimated diagnosis dates of deaths and cured cases were calculated based on the median cure time or median death time of individual cases. Following this, the instant CFR was calculated according to the number of deaths and cured cases on the same estimated diagnosis date. Results: In China,the instant CFR of COVID-19 was 3.8–14.6% from January 1 to January 17; itthen declined gradually and stabilized at 5.7% in April. The average CFR in China was 6.1 2.9%, while the CFR was 1.0 0.4% in China except Hubei Province. The cure rate of COVID-19 was 93.9 2.9% in China, and stabilized at 94.3%, while it was 99.0 0.4% in China except Hubei Province. Conclusions: The instant CFR of COVID-19 in China overall was much higher than that in China except Hubei Province. The CFR of COVID-19 in China was underestimated

Clathrin light chains negatively regulate plant immunity by hijacking the autophagy pathway.

The crosstalk between clathrin-mediated endocytosis (CME) and the autophagy pathway has been reported in mammals; however, the interconnection of CME with autophagy has not been established in plants. Here, we report that the Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopies Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants in both autoimmunity and nutrient sensitivity. Accordingly, the autophagy pathway is significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation, and degradation of GFP-ATG8h is significantly reduced in the clc2-1 clc3-1 mutant. Notably, simultaneous&nbsp;knockout of ATG8h and ATG8i by CRISPR-Cas9 results in enhanced resistance against Golovinomyces cichoracearum, supporting the functional relevance of the CLC2-ATG8h/8i interactions. In conclusion, our results reveal a link between the function of CLCs and the autophagy pathway in Arabidopsis

FeCl3 based Few-Layer Graphene Intercalation Compounds: Single Linear Dispersion Electronic Band Structure and Strong Charge Transfer Doping

Graphene has attracted great attentions since its first discovery in 2004. Various approaches have been proposed to control its physical and electronic properties. Here, we report that graphene based intercalation compounds is an efficient method to modify the electronic properties of few layer graphene (FLG). FeCl3 intercalated FLG were successfully prepared by two-zone vapor transport method. This is the first report on full intercalation for graphene samples. The features of the Raman G peak of such few-layer graphene intercalation compounds (FLGIC) are in good agreement with their full intercalation structures. The FLGIC presents single Lorentzian 2D peak, similar to that of single layer graphene, indicating the loss of electronic coupling between adjacent graphene layers. First principle calculations further reveal that the band structure of FLGIC is similar to single layer graphene but with strong doping effect due to the charge transfer from graphene to FeCl3. The successful fabrication of FLGIC opens a new way to modify properties of FLG for fundamental studies and future applications.Comment: 19 pages, 6 figures, accepted by Advanced Functional Material

A new species in Begonia sect. Diploclinium (Begoniaceae) from Guangxi, South China

Although Guangxi represents one of the distribution centres of begonias in China, the sect. Diploclinium (Wright) A. DC is not well documented herein. In this article, we illustrate a new species belonging to this section, Begonia fangchengensis Y.N.Huang, X.X. Feng &amp;amp; R.K.Li, which has been discovered in southern Guangxi. Begonia fangchengensis mostly resembles B. rotundilimba in elliptic leaf blade, palmate veins, dichasial cyme, three styles, axile placentation, and unequally 3-winged capsule. On the other hand, B. fangchengensis is characterized by creeping rhizome, pilose stipule, red and densely pilose petiole, pubescent leaf blade and pilose inflorescence bract, sparsely pilose ovary and the zygomorphic androecium, differing from the erect stem at anthesis, the green and densely villous petiole, the glabrous stipule, leaf blade, inflorescence bract, ovary and actinomorphic androecium in B. rotundilimba. Considering its small population size and narrow distribution, its conservation status is categorized as ‘Endangered (D)’ according to the IUCN Red List Categories and Criteria

γ\gamma-SUP: A clustering algorithm for cryo-electron microscopy images of asymmetric particles

Cryo-electron microscopy (cryo-EM) has recently emerged as a powerful tool for obtaining three-dimensional (3D) structures of biological macromolecules in native states. A minimum cryo-EM image data set for deriving a meaningful reconstruction is comprised of thousands of randomly orientated projections of identical particles photographed with a small number of electrons. The computation of 3D structure from 2D projections requires clustering, which aims to enhance the signal to noise ratio in each view by grouping similarly oriented images. Nevertheless, the prevailing clustering techniques are often compromised by three characteristics of cryo-EM data: high noise content, high dimensionality and large number of clusters. Moreover, since clustering requires registering images of similar orientation into the same pixel coordinates by 2D alignment, it is desired that the clustering algorithm can label misaligned images as outliers. Herein, we introduce a clustering algorithm $\gamma$-SUP to model the data with a $q$-Gaussian mixture and adopt the minimum $\gamma$-divergence for estimation, and then use a self-updating procedure to obtain the numerical solution. We apply $\gamma$-SUP to the cryo-EM images of two benchmark macromolecules, RNA polymerase II and ribosome. In the former case, simulated images were chosen to decouple clustering from alignment to demonstrate $\gamma$-SUP is more robust to misalignment outliers than the existing clustering methods used in the cryo-EM community. In the latter case, the clustering of real cryo-EM data by our $\gamma$-SUP method eliminates noise in many views to reveal true structure features of ribosome at the projection level.Comment: Published in at http://dx.doi.org/10.1214/13-AOAS680 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org