Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins.

The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled.

Optical spatial differentiation enabled layer sensing of two-dimensional atomic crystals.

Zero-thickness model and slab model are two important models in the description of optical behaviors in two-dimensional atomic crystals. The predicted difference in optical behaviors between the two models is very small, which is difficult to distinguish by established measurement methods. Here, we present an optical spatial differentiation method to examine the difference in edge images of different graphene layers. The theoretical results show that the edge imaging is significantly different between the two different models. When the beam reflection is at the Brewster angle, different graphene layers are used to adjust the spatial differentiation. It is shown that the slab model is more sensitive to the number of graphene layers. The zero-thickness model is more suitable for one-dimensional optical differential operation. Moreover, the spatial differentiation plays the role of a band-pass filter. The high-frequency edge information components will pass through the filter, thus realizing layer-sensitive edge-enhanced imaging. In addition, we do not focus on the verification of the exact model, but only provide an alternative method to characterize the number of graphene layers based on two models, and also provide possibilities for achieving imaging edge detection by graphene differential operators. This study may provide a possible method for the optical characterization of two-dimensional atomic crystals.

Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation.

BACKGROUND: Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS: In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS: The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.

All-optical image edge detection based on the two-dimensional photonic spin Hall effect in anisotropic metamaterial.

Optical image processing based on the photonic spin Hall effect (SHE) has been gaining significant attention as a convenient and an accurate way for image edge detection. However, the recent edge imaging techniques depending on optical differentiation is mainly achieved by modulation of one-dimensional photonic SHE. Here, we theoretically predict the two-dimensional photonic SHE in the anisotropic metamaterial, and find that its longitudinal and transverse displacements exhibit spin-dependent property at filling factors with increasing incidence angle. As the transverse and in-plane displacements induced by the photonic SHE can be controlled by the filling factor of the crystal structure, the optical axis angle, and the incident angle, this intrinsical effect can be used to realize a tunable edge imaging. Interestingly, by changing the optical axis of the anisotropic metamaterial, the in-plane displacements are equal to the transverse displacements for a certain filling factor and the corresponding incident angle. Therefore, we propose a two-dimensional image edge detection method based on the photonic SHE in anisotropic metamaterial. Further numerical results validate the theoretical proposal.

[Optimization of ethanol reflux extraction process of Ziziphi Spinosae Semen- Schisandrae Sphenantherae Fructus based on network pharmacology combined with response surface methodology].

The present study optimized the ethanol extraction process of Ziziphi Spinosae Semen-Schisandrae Sphenantherae Fructus drug pair by network pharmacology and Box-Behnken method. Network pharmacology and molecular docking were used to screen out and verify the potential active components of Ziziphi Spinosae Semen-Schisandrae Sphenantherae Fructus, and the process evaluation indexes were determined in light of the components of the content determination under Ziziphi Spinosae Semen and Schisandrae Sphenantherae Fructus in the Chinese Pharmacopoeia(2020 edition). The analytic hierarchy process(AHP) was used to determine the weight coefficient of each component, and the comprehensive score was calculated as the process evaluation index. The ethanol extraction process of Ziziphi Spinosae Semen-Schisandrae Sphenantherae Fructus was optimized by the Box-Behnken method. The core components of the Ziziphi Spinosae Semen-Schisandrae Sphenantherae Fructus drug pair were screened out as spinosin, jujuboside A, jujuboside B, schisandrin, schisandrol, schisandrin A, and schisandrin B. The optimal extraction conditions obtained by using the Box-Behnken method were listed below: extraction time of 90 min, ethanol volume fraction of 85%, and two times of extraction. Through network pharmacology and molecular docking, the process evaluation indexes were determined, and the optimized process was stable, which could provide an experimental basis for the production of preparations containing Ziziphi Spinosae Semen-Schisandrae Sphenantherae Fructus.

Development, Status Quo, and Challenges to China's Health Informatization During COVID-19: Evaluation and Recommendations.

By applying advanced health information technology to the health care field, health informatization helps optimize health resource allocation, improve health care services, and realize universal health coverage. COVID-19 has tested the status quo of China's health informatization, revealing challenges to the health care system. This viewpoint evaluates the development, status quo, and practice of China's health informatization, especially during COVID-19, and makes recommendations to address the health informatization challenges. We collected, assessed, and evaluated data on the development of China's health informatization from five perspectives-health information infrastructure, information technology (IT) applications, financial and intellectual investment, health resource allocation, and standard system-and discussed the status quo of the internet plus health care service pattern during COVID-19. The main data sources included China's policy documents and national plans on health informatization, commercial and public welfare sources and websites, public reports, institutional reports, and academic papers. In particular, we extracted data from the 2019 National Health Informatization Survey released by the National Health Commission in China. We found that China developed its health information infrastructure and IT applications, made significant financial and intellectual informatization investments, and improved health resource allocations. Tested during COVID-19, China's current health informatization system, especially the internet plus health care system, has played a crucial role in monitoring and controlling the pandemic and allocating medical resources. However, an uneven distribution of health resources and insufficient financial and intellectual investment continue to challenge China's health informatization. China's rapid development of health informatization played a crucial role during COVID-19, providing a reference point for global pandemic prevention and control. To further promote health informatization, China's health informatization needs to strengthen top-level design, increase investment and training, upgrade the health infrastructure and IT applications, and improve internet plus health care services.

Mapping morphological shape as a high-dimensional functional curve.

Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000-4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of 'function' instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do.

Upstream development of Escherichia coli fermentation process with PhoA promoter using design of experiments (DoE).

In this work, a fed-batch fermentation development was performed with recombinant E. coli carrying the PhoA promoter system. The phosphate concentrations tested for this PhoA strain, 2.79 mM to 86.4 mM, were beyond the concentrations previously evaluated for cell growth and product titer. The results from the scouting work was used for design of experiments (DoE) where a range of phosphate levels from 27.1 mM to 86.4 mM was simultaneously evaluated with temperature, pH and DO set points. Definitive screening was used to evaluate these parameters simultaneously and the results indicate that fermentation temperature and phosphate content are the major contributors of product titer. The other factors tested such as pH had a minimal effect and DO had no impact on product titer.

RORγ Structural Plasticity and Druggability.

Retinoic acid receptor-related orphan receptor γ (RORγ) is a transcription factor regulating the expression of the pro-inflammatory cytokine IL-17 in human T helper 17 (Th17) cells. Activating RORγ can induce multiple IL-17-mediated autoimmune diseases but may also be useful for anticancer therapy. Its deep immunological functions make RORɣ an attractive drug target. Over 100 crystal structures have been published describing atomic interactions between RORɣ and agonists and inverse agonists. In this review, we focus on the role of dynamic properties and plasticity of the RORɣ orthosteric and allosteric binding sites by examining structural information from crystal structures and simulated models. We discuss the possible influences of allosteric ligands on the orthosteric binding site. We find that high structural plasticity favors the druggability of RORɣ, especially for allosteric ligands.

Identifying novel genetic determinants for oxidative stress tolerance in Candida glabrata via adaptive laboratory evolution.

Candida glabrata (C glabrata) is an important yeast of industrial and medical significance. Resistance to oxidative stress is an important trait affecting its robustness as a production host or virulence as a pathogenic agent, but current understanding of resistance mechanisms is still limited in this fungus. In this study, we rapidly evolved C glabrata population to adapt to oxidative challenge (from 80mM to 350mM of H2 O2 ) through short-term adaptive laboratory evolution. Adaptive mutants were isolated from evolved populations and subjected to phenotypic and omics analyses to identify potential mechanisms of tolerance to H2 O2 . Phenotypic characterizations revealed faster detoxification of H2 O2 and ability to initiate growth at a higher concentration of the oxidant in the isolated adaptive mutants compared with the wild type. Genome resequencing and genome-wide transcriptome analysis revealed multiple genetic determinants (eg, CAGL0E01243g, CAGL0F06831g, and CAGL0C00385g) that potentially contribute to enhanced H2 O2 resistance. Subsequent experimental verification confirmed that CgCth2 (CAGL0E01243g) and CgMga2 (CAGL0F06831g) are important in C glabrata tolerance to oxidative stress. Transcriptome profiling of adaptive mutants and bioinformatic analysis suggest that NADPH regeneration, modulation of membrane composition, cell wall remodeling, and/or global regulatory changes are involved in C glabrata tolerance to H2 O2 .

Characterization and expression patterns of ERK1 and ERK2 from Epinephelus coioides against Cryptocaryon irritans infection.

Mitogen-activated protein kinases (MAPKs), a group of serine-threonine protein kinases, play a crucial role in immunoreaction response to extra environmental stresses. In this study, two novel MAPKs, Ec-ERK1 and Ec-ERK2, were identified from Epinephelus coioides. Both Ec-ERK1 and Ec-ERK2 sequences contain a highly conserved Thr-Glu-Tyr (TEY) motif, an HRD domain, and an ATP binding loop containing GXGXXG. An analysis of phylogenetic relationships demonstrated that ERK amino acid sequences were conserved between different species indicating that the functions may be similar. Ec-ERK1 and Ec-ERK2 mRNA can be detected in all thirteen tissues examined, but the expression level is different in these tissues. The expression patterns of these two genes in E. coioides were also detected against Cryptocaryon irritans infection, which is capable of killing large numbers of fish in a short time and has a serious impact on aquaculture. The expression was up-regulated in most of the tissues examined, with the highest expressions of Ec-ERK1 (3.9 times) occurring in the head kidney and Ec-ERK2 (3.5 times) occurring in the spleen. There was no significant correlation between the expression of Ec-ERK1/Ec-ERK2 and the expression of nuclear factor kappaB (NF-kB). The results indicated the sequences and the characters of Ec-ERK1/ERK2 were conserved, Ec-ERK1/ERK2 showed tissue-specific expression patterns in healthy grouper, and their expressions were significantly varied post C. irritans infection, suggesting Ec-ERK1/ERK2 may play important roles in these tissues during pathogen-caused inflammation.

Two novel p38 MAPKs identified from Epinephelus coioides and their expression pattern in response to Cryptocaryon irritans infection.

P38 mitogen-activated protein kinases (MAPKs) are one of the most important central regulatory proteins response to extra environmental stresses. In this study, two novel p38 MAPKs, Ec-P38γ and Ec-P38δ, were identified from Epinephelus coioides, an economically important cultured fish in China and Southeast Asian counties. Both of Ec-p38γ and Ec-p38δ sequences contain a serine/threonine protein kinase (S_TKc) domain and a highly conserved Thr-Gly-Tyr (TGY) motif. Analysis of phylogenetic relationships illustrated that p38 amino acid sequences were conserved between different species indicating that the functions may be similar. The four subtypes of p38 (α, ß, γ, and δ) mRNA can be detected in all thirteen tissues examined, but the expression level is different in these tissues. The expression patterns of the four Ec-p38 subtypes in E. coioides were also detected response to Cryptocaryon irritans infection, one of the most important protozoan pathogens of marine fish. The expression of four p38 subtypes was up-regulated in the tissues examined, with the highest expressions of Ec-p38α (5.2 times) and Ec-p38δ (4.2 times) occurring in the skin, while Ec-p38ß (24.8 times) and γ (16.6 times) occurred in the spleen. There was no significantly correlation between the expression of Ec-p38γ/Ec-p38δ and the expression of nuclear factor kappaB (NF-kB). The results indicated the sequences and the characters of Ec-p38γ and Ec-p38δ were conserved, the p38 subtypes showed tissue-specific expression patterns in healthy grouper, and their expressions were significantly up-regulated post C. irritans infection, suggesting these p38 MAPKs may play important roles in these tissues during pathogen-caused inflammation.

Grouper (Epinephelus coioides) BCR signaling pathway was involved in response against Cryptocaryon irritans infection.

B cell antigen receptor (BCR) plays a crucial role in B cell development and antibody production. It comprises membrane immunoglobulin non-covalently associated with CD79a/CD79b heterodimer. After B cell activation, initial extracellular signals are transduced by BCR complex and amplified by two protein tyrosine kinases, LYN and SYK, which then trigger various pathways. In the present study, we cloned grouper genes for BCR accessory molecules, EcCD79a (669 bp) and EcCD79b (639 bp), as well as two protein tyrosine kinases, EcLYN (1482 bp) and EcSYK (1854 bp). Homology analysis showed that all four molecules had a relatively high amino acid identity compared with those in other animals. Among them, they all shared the highest identity with Takifugu rubripes (EcCD79a 49%, EcCD79b 52%, EcLYN 82% and EcSYK 77%). The conserved features and important functional residues were analyzed. Together with IgM and IgT, tissue distribution analysis showed that all six molecules were mainly expressed in immune organs, particularly systematic immune organs. In groupers infected with Cryptocaryon irritans, up-regulation of EcCD79a and b, EcIgM and EcIgT were not seen in the early stage skin and gill until 14-21 days. Up-regulation of EcCD79a was seen in head kidney at most time points, while EcCD79a and b were only significantly up-regulated in day 14 spleen. Significant up-regulation of EcIgT were seen in day 21 head kidney and day 1, day14 spleen. Significant up-regulation of EcIgM were seen in day 1 head kidney and 12 h spleen. In addition, two protein kinase genes, EcLYN and EcSYK, were up-regulated in the skin at most time points, which suggested that B cells may be activated at the skin local infection site.

Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater.

Understanding the transcriptional regulation of microRNAs (miRNAs) is extremely important for determining the specific roles they play in signaling cascades. However, precise identification of transcription factor binding sites (TFBSs) orchestrating the expressions of miRNAs remains a challenge. By combining accessible chromatin sequences of 12 cell types released by the ENCODE Project, we found that a significant fraction (~80%) of such integrated sequences, evolutionary conserved and in regions upstream of human miRNA genes that are independently transcribed, were preserved across cell types. Accordingly, we developed a computational method, Accessible and Conserved TFBSs Locater (ACTLocater), incorporating this chromatin feature and evolutionary conservation to identify the TFBSs associated with human miRNA genes. ACTLocater achieved high positive predictive values, as revealed by the experimental validation of FOXA1 predictions and by the comparison of its predictions of some other transcription factors (TFs) to empirical ChIP-seq data. Most notably, ACTLocater was widely applicable as indicated by the successful prediction of TF → miRNA interactions in cell types whose chromatin accessibility profiles were not incorporated. By applying ACTLocater to TFs with characterized binding specificities, we compiled a novel repository of putative TF → miRNA interactions and displayed it in ACTViewer, providing a promising foundation for future investigations to elucidate the regulatory mechanisms of miRNA transcription in humans.

[Service Middleware of Medical Information Integration and Exchange Based on HL7 and DICOM].

Medical information exchange and integration is the effective method to solve the interoperability and medical information island, and is the basis of medical information sharing. In this paper, we take medical texts and medical images as the basic integrated objects, DICOM, HL7 messages and datasets as the integrated units, efficient DI-COM, HL7 message construction and parsing methods as basis, design and realize a universal medical information integration and exchange service middleware. Experimental results show that the prototype system could perform medical information integration and exchange among relational database, HL7 and DICOM message, provide a feasible scheme to solve the medical information island and lay a good foundation for establishing the unified medical information integration and sharing platform. The middleware has been applied in the project named "development and demonstration of opened medical information integration system".

Two new species of Promonhystera Wieser, 1956 (Nematoda: Monhysterida: Xyalidae) from the South China Sea.

Two new species of free-living marine nematodes from the littoral sediment of the South China Sea are described as Promonhystera papilla sp. nov. and Promonhystera fluctispicula sp. nov. Both new species are characterized by striated cuticle; circular amphideal fovea; anterior sensilla in two circles, inner labial sensilla setiform; funnel-shaped buccal cavity; elongated spicules and conico-cylindrical tail. P. papilla sp. nov. is different from all known species of the genus by longer body length (more than 2.1mm versus less than 1.5 mm in other species), longer spicules (sp/a.b.d. = 4.14.6 versus 2.7) and males with three papilliform precloacal supplements and one small postcloacal papilla (versus absence) and gubernaculum boot-shaped. P. fluctispicula sp. nov. is similar to P. tricuspidata Wieser, 1956 in having similar waved spicules but differs from the latter species by tail conico-cylindrical (versus conical) and simple plate-like gubernaculum without tooth (versus gubernaculum with four distal teeth).

Two new species of the order Monhysterida (Nematoda) from the sea of China.

Two new marine nematode species belonging to the order Monhysterida are described from the sea of China. Halomonhysterazhangisp. nov. is characterized by its relatively small body size; short anterior sensory setae; small, circular amphidial fovea located at the level of buccal cavity base; funnel-shaped buccal cavity; an excretory-secretory system with a large ventral gland and opening as a very narrow canal just posterior to the level of cephalic setae; slightly curved slender spicules with cephalated proximal end and tapered distal end; rod-like gubernaculum without apophysis; two papilliform precloacal supplements just in front of the cloaca; conico-cylindrical tail with two ventral papillae, each with a seta; and distance between the vulva and anus slightly longer than the tail length. This is the first new species of epiphytic nematode reported in China. The second new species, Stylotheristusflagellicaudatussp. nov., has a relatively shorter body and longer tail; striated cuticle; The anterior sensilla arranged in two circles, the first circle consisting of six inner labial setiform papillae (3-4 µm) and the second circle consisting of 16 long setae (12-19 µm); a transversely oval amphideal fovea; a well-developed muscle around the funnel-shaped buccal cavity; short spicules and a gubernaculum composed of a single piece; and precloacal supplements absent. An updated key to all species of Halomonhystera and pictorial key to all species of Stylotheristus are also given.

Enhancing heat transfer efficiency in corrugated tube heat exchangers: A comprehensive approach through structural optimization and field synergy analysis.

In this paper, a precise and efficient method to optimize corrugated tube heat exchangers is proposed by combining computational fluid dynamics simulation with optimization. The optimization of tubular heat exchangers involves contradictory Colburn coefficient j, and the friction coefficient f, so it is a multi-objective optimization problem. The approximate model is obtained by an extreme learning machine, and the structure parameter of the heat exchanger is optimized by the nondominated sorting genetic algorithm-Ⅱ. Compared to the results between the original and optimized tube, the optimized structure Colburn coefficient increased by 5.1 % and the friction coefficient decreased by 9.3 %. Finally, the internal flow field is compared qualitatively from temperature, pressure, and velocity. The optimization effect is further emphasized by using the field synergy theory.

On-bead purification and nanodisc reconstitution of human chemokine receptor complexes for structural and biophysical studies.

Chemokine receptors, a subfamily of G-protein-coupled receptors (GPCRs), are responsible for cell migration during physiological processes as well as in diseases like inflammation and cancers. Here, we present a protocol for solubilizing, purifying, and reconstituting complexes of chemokine receptors with their ligands in "nanodiscs," soluble lipid bilayers that mimic the native environment of membrane receptors. The protocol yields chemokine receptor complexes with sufficient purity and yield for structural and biophysical studies and should be applicable to other GPCRs.