HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome.

Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.

Investigation on hydrodynamic lubrication effect of micro groove seal in pharmaceutical kettle.

To improve the lubrication conditions of the seal in the pharmaceutical kettles, a specific shape groove with micrometer level on the sealing end face is set up to fully utilize the fluid dynamic pressure effect under given working conditions. A numerical model is developed to solve the pressure distribution in the micro groove, where any groove shape can be used. The numerical form of the model is derived using the principle of mass conservation without considering the film thickness derivative term, and the coordinate transformation is introduced to adapt to the curved shape of the groove. The cavitation phenomenon is taken into account in the flow field of the seal, and the JFO cavitation model is introduced to modify the Reynolds equation. The diversity of groove shapes is considered, and the node adsorption method is adopted to approximate the groove shape. The model is established based on the principle of mass conservation, which can adapt to any different groove shapes and has a strong scalability. By mathematical modeling and solving, the performances of the micro groove seal under different groove shapes are analyzed, providing a basis for the micro groove design of seal in pharmaceutical kettles.

Phase noise estimation based white light scanning interferometry for high-accuracy surface profiling.

White light scanning interferometry (WLSI) has been an extremely powerful technique in precision measurements. In this work, a phase noise estimation based surface recovery algorithm is proposed, which can significantly improve the measurement accuracy by decreasing the noise level in phase map coming from the systemic and environmental disturbances. The noise existed in phase map is firstly researched in spectrum domain and defined as the linear combination of complex terms at each angular wavenumber. Afterwards, based on the theoretical linearity of the phase distribution, the surface features can be redefined through establishing the function with respect to phase noise. By applying least square estimation (LSE), a spectral coefficient is defined to determine the optimal estimation of phase noise that represents the best statistical consistency with the actual case, from which a more accurate surface after removing most phase noise will then be generated. In order to testify the noise elimination ability of the proposed method, a nano-scale step height standard (9.5nm±1.0nm) is scanned, and the measurement result 9.49nm with repeatability 0.17nm is successfully achieved. Moreover, a leading edge of an aero-engine blade is also tested to investigate the potential of this method in industrial inspections. The measurement comparison with AFM is also displayed.

Phase-error-compensation-based surface recovery algorithm using spectrum selection for white light interferometry.

White light interferometry is a well-established surface recovery technique. In this paper, a white light signal processing algorithm based on phase error compensation using spectrum selection is proposed. The derived nonlinear phase distribution from the correlogram is modeled as the combination of random errors and systemic deviations. By developing a new, to the best of our knowledge, recovery algorithm, the phase noise can be separated from the linear map and significantly attenuated. Based on the proposed algorithm, the spectrum features of white light LEDs and halogen lamps are investigated in detail. The inner products defined by three selected points are employed to generate a coefficient to evaluate the linearity of an unwrapped phase map within a certain spectrum region. The optimal spectrum range corresponding to the best measurement performance can then be located where the coefficient approximates 1 and the spectrum energy stays relatively high. The simulations are carried out under different levels of SNR and scan step noises, which show that the new method can effectively reduce additional disturbance from the recovered topography. In experiments, the system with the proposed method is first calibrated by a step height standard (VLSI, 182.7±2.0nm) with the repeatability of 0.44 nm. A silicon wafer and three roughness standards are also tested to further verify the robustness of the new method.

SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants.

The dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. To study the quasispecies features and the intra-host evolution of SARS-CoV-2, we collected nine confirmed patients and sequenced the haplotypes of spike gene using a single-molecule real-time platform. Fourteen samples were extracted from sputum, nasopharyngeal swabs, or stool, which in total produced 283,655 high-quality circular consensus sequences. We observed a stable quasispecies structure that one master mutant (mean abundance ∼0.70), followed by numerous minor mutants (mean abundance ∼1.21 × 10-3). Under high selective pressure, minor mutants may obtain a fitness advantage and become the master ones. The later predominant substitution D614G existed in the minor mutants of more than one early patient. An epidemic variant had a possibility to be independently originated from multiple hosts. The mutant spectrums covered ∼85% amino acid variations of public genomes (GISAID; frequency ≥ 0.1) and likely provided an advantage mutation pool for the current/future epidemic variants. Notably, 32 of 35 collected antibody escape substitutions were preexistent in the early quasispecies. Virus populations in different tissues/organs revealed potentially independent replications. The quasispecies complexity of sputum samples was significantly lower than that of nasopharyngeal swabs (P = 0.02). Evolution analysis revealed that three continuous S2 domains (HR1, CH, and CD) had undergone a positive selection. Cell fusion-related domains may play a crucial role in adapting to the intrahost immune system. Our findings suggested that future epidemiologic investigations and clinical interventions should consider the quasispecies information that has missed by routine single consensus genome. IMPORTANCE RNA virus population in a host does not consist of a consensus single haplotype but rather an ensemble of related sequences termed quasispecies. The dynamics of quasispecies afford SARS-CoV-2 a great ability on genetic fitness during intrahost evolution. The process is likely achieved by changing the genetic characteristics of key functional genes, such as the spike glycoprotein. Previous studies have applied the next-generation sequencing (NGS) technology to evaluate the quasispecies of SARS-CoV-2, and results indicated a low genetic diversity of the spike gene. However, the NGS platform cannot directly obtain the full haplotypes without assembling, and it is also difficult to predict the extremely low-frequency variations. Therefore, we introduced a single-molecule real-time technology to directly obtain the haplotypes of the RNA population and further study the quasispecies features and intrahost evolution of the spike gene.

Multiprobe scanning probe microscope using a probe-array head.

We have developed a microelectromechanical system (MEMS)-based multiprobe scanning probe microscope (SPM) to improve imaging efficiency. The SPM head contains seven identical MEMS probes, and each of them integrates a displacement sensor and a Z-axis actuator. Force constant mode is designed based on the force feedback strategy rather than on the position feedback strategy for this kind of SPM head. A nano-measuring machine is equipped with the lateral XY scanners, which can reach a motion range of 25 mm × 25 mm. After calibration, the measurement of one-dimensional grating has been made to demonstrate the capability of multiprobe scanning.

Copy number gain of pro-inflammatory genes in patients with HBV-related acute-on-chronic liver failure.

BACKGROUND: Host genetic factors such as single nucleotide variations may play a crucial role in the onset and progression of HBV-related acute-on-chronic liver failure (ACLF). However, the underlying genomic copy number variations (CNVs) involved in the pathology are currently unclear. METHODS: We genotyped two cohorts with 389 HBV-related ACLF patients and 391 asymptomatic HBV carriers (AsCs), and then carried out CNV-based global burden analysis and a genome-wide association study (GWAS). RESULTS: For 1874 rare CNVs, HBV-related ACLF patients exhibited a high burden of deletion segments with a size of 100-200 kb (P value = 0.04), and the related genes were significantly enriched in leukocyte transendothelial migration pathway (P value = 4.68 × 10-3). For 352 common CNVs, GWAS predicted 17 significant association signals, and the peak one was a duplication segment located on 1p36.13 (~ 38 Kb, P value = 1.99 × 10-4, OR = 2.66). The associated CNVs resulted in more copy number of pro-inflammatory genes (MST1L, DEFB, and HCG4B) in HBV-related ACLF patients than in AsC controls. CONCLUSIONS: Our results suggested that the impact of host CNV on HBV-related ACLF may be through decreasing natural immunity and enhancing host inflammatory response during HBV infection. The findings highlighted the potential importance of gene dosage on excessive hepatic inflammation of this disease.

A high-performance and flexible thermoelectric generator based on the solution-processed composites of reduced graphene oxide nanosheets and bismuth telluride nanoplates.

The fabrication of a flexible thermoelectric generator (TEG) with both high power output and good flexibility has drawn considerable attention. Solution-processed inorganic nanocrystals have good processibility in interface to retain excellent electrical properties of nanocrystals and can be processed into thin films on a flexible substrate by an easy scale-up printing or coating method. However, a high-performance TEG device based on inorganic solution-processed materials also poses challenges when it comes to flexibility of the whole device. Herein, flexible planar TEG devices are fabricated by printing an ink mixture comprising solution-processed bismuth telluride (Bi2Te3) nanoplates with reduced-graphene oxide (rGO) nanosheets onto flexible polyimide substrates. The interface treatment by hot ethylenediamine and the appropriate amount of rGO contribute to the high electrical properties of the material. Also, when rGO nanosheets of 1% mass ratio are added, the optimum power output of the corresponding rGO/Bi2Te3 TEG device with six elements reaches ∼1.72 µW at a temperature difference of 20 K. Moreover, owing to the contribution from flexible rGO nanosheets, the suitable thickness of each element, and the artful connection of elements with a soft copper wire in the devices, the 1% rGO/Bi2Te3 TEG device was found to be robust, and its electrical resistance merely changes by 2% after bending 1000 cycles on 5 mm in bending. These inorganic-based TEGs with both high performance and good flexibility will promote the development of new generation energy devices in the field of flexible electronics.

Calibration of position and orientation for point light source synchronously with single image in photometric stereo.

In this paper, a calibration method for non-isotropic point light source is developed, which is capable of calibrating position and orientation of the point light source with a single image synchronously. Based on the bidirectional reflectance distribution function (BRDF), the relationship between the shape of observed surface and the recorded grayscale image is firstly investigated in a more accurate way. Based on this model, a cost function is proposed to evaluate the estimation error, and a new cumulative, error-free iteration method is designed to recursively estimate the point light source parameters. The average simulation rebuilding root mean square error (RMSE) is below 0.9. The experiments are performed by calibrating a point light source in a photometric stereo measurement system, and the corresponding RMSE is below 1.2 in the unit of grayscale. Further analysis shows one image is enough to achieve the precision calibration using our proposed method.

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization.

Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many aspects of the biomineralization process and its evolutionary origin remain unknown. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms that underlie its production of shells and pearls are not fully understood. We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins, chondroitin sulfotransferases, and regulatory elements. Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre suggests that elements of chitin- and collagen-based matrices have deep roots and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems.

The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.

Identification of stable QTLs for seed oil content by combined linkage and association mapping in Brassica napus.

Seed oil content is an important agricultural trait in rapeseed breeding. Although numerous quantitative trait locus (QTL) have been identified, most of them cannot be applied in practical breeding mainly due to environmental instability or large confidence intervals. The purpose of this study was to identify and validate high quality and more stable QTLs by combining linkage mapping and genome-wide association study (GWAS). For linkage mapping, we constructed two F2 populations from crosses of high-oil content (∼50%) lines 6F313 and 61616 with a low-oil content (∼40%) line 51070. Two high density linkage maps spanned 1987cM (1659 bins) and 1856cM (1746 bins), respectively. For GWAS, we developed more than 34,000 high-quality SNP markers based on 227 accessions. Finally, 40 QTLs and 29 associations were established by linkage and association mapping in different environments. After merging the results, 32 consensus QTLs were obtained and 7 of them were identified by both mapping methods. Seven overlapping QTLs covered an average confidence interval of 183kb and explained the phenotypic variation of 10.23 to 24.45%. We further developed allele-specific PCR primers to identify each of the seven QTLs. These stable QTLs should be useful in gene cloning and practical breeding application.

Overexpression of CHMP7 from rapeseed and Arabidopsis causes dwarfism and premature senescence in Arabidopsis.

Endosomal sorting complexes required for transport (ESCRT) are well known in mammalians and yeast and plays an essential role in the formation of multi-vesicular bodies. Accumulating evidence has shown that ESCRT proteins contribute to proper plant development. CHMP7 (charged multi-vesicular body protein 7) is an ESCRT-III-related protein and functions in the endosomal sorting pathway in humans. However, its function in plants has not been explored in detail. In this study, we isolate the putative homolog of CHMP7 from rapeseed, BnCHMP7, which contains eight exons and encodes a protein consisting of 423 amino acid residues. Compared with the wild-type, overexpression of BnCHMP7 in Arabidopsis disturbs plant growth and decreases seed yield. Moreover, the transgenic plants also display early leaf senescence and hypersensitivity to dark treatment due to defects in autophagic degradation. Further study showed that BnCHMP7 is highly expressed in leaves and that YFP-BnCHMP7 is predominantly localized in endosome. Compared with human CHMP7, we found that BnCHMP7 not only interacts with ESCRT-III subunits SNF7.2 (CHMP4B), but also with VPS2.2 and CHMP1B. As expected, microarray analysis revealed that the expression of ESCRT transport genes is significantly affected. Additionally, the expression of some genes that are involved in senescence, protein synthesis and protein degradation is also altered in BnCHMP7-overexpressing plants. Taken together, BnCHMP7 encodes an endosome-localized protein, which causes dwarfism and leaf senescence as an ESCRT-III-related component.

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.

Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.

PTGBase: an integrated database to study tandem duplicated genes in plants.

Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available.

The genome sequence of the orchid Phalaenopsis equestris.

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful.

The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.

Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

Genome sequence of the cultivated cotton Gossypium arboreum.

The complex allotetraploid nature of the cotton genome (AADD; 2n = 52) makes genetic, genomic and functional analyses extremely challenging. Here we sequenced and assembled the Gossypium arboreum (AA; 2n = 26) genome, a putative contributor of the A subgenome. A total of 193.6 Gb of clean sequence covering the genome by 112.6-fold was obtained by paired-end sequencing. We further anchored and oriented 90.4% of the assembly on 13 pseudochromosomes and found that 68.5% of the genome is occupied by repetitive DNA sequences. We predicted 41,330 protein-coding genes in G. arboreum. Two whole-genome duplications were shared by G. arboreum and Gossypium raimondii before speciation. Insertions of long terminal repeats in the past 5 million years are responsible for the twofold difference in the sizes of these genomes. Comparative transcriptome studies showed the key role of the nucleotide binding site (NBS)-encoding gene family in resistance to Verticillium dahliae and the involvement of ethylene in the development of cotton fiber cells.