A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.

Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.

Synthesis of Well-Ordered Mesoporous Aluminosilicates with High Aluminum Contents: The Challenge and the Promise.

SBA-15 has recently emerged as a potential material for the catalytic conversion of large molecules. Usually, SBA-15 has a low content of aluminum due to the conventional acidic synthesis medium. Although a few approaches have been adopted to prepare Al-SBA-15 with a high alumina content, it is still challenging to prepare well-ordered Al-SBA-15 with a high alumina content. Here, we demonstrate a facile synthesis process in neutral mediums for the grafting of Al into the framework of SBA-15. This approach relies mainly on the dissociation of Si-O-Si bonds and the polymerization of Si-O-Si/Al bonds promoted by sodium persulfate (SPS) in neutral mediums. In this way, well-ordered Al-SBA-15 with a high aluminum content and enhanced acidity was obtained. Results of X-ray fluorescence spectroscopy (XRF) showed an n(SiO2)/n(Al2O3) ratio of 13.7, much lower than that of the conventional sample (21.7) obtained in acidic medium. The characterization results indicated the presence of a well-ordered Al-containing mesophase with high hydrothermal stability. Notably, the Al content and the acidity of Al-SBA-15 can be tuned by changing the SPS amount.

High day- and night-time temperatures affect grain growth dynamics in contrasting rice genotypes.

Rice grain yield and quality are predicted to be highly vulnerable to global warming. Five genotypes including heat-tolerant and susceptible checks, a heat-tolerant near-isogenic line and two hybrids were exposed to control (31 °C/23 °C, day/night), high night-time temperature (HNT; 31 °C/30 °C), high day-time temperature (HDT; 38 °C/23 °C) and high day- and night-time temperature (HNDT; 38 °C/30 °C) treatments for 20 consecutive days during the grain-filling stage. Grain-filling dynamics, starch metabolism enzymes, temporal starch accumulation patterns and the process of chalk formation were quantified. Compensation between the rate and duration of grain filling minimized the impact of HNT, but irreversible impacts on seed-set, grain filling and ultimately grain weight were recorded with HDT and HNDT. Scanning electron microscopy demonstrated irregular and smaller starch granule formation affecting amyloplast build-up with HDT and HNDT, while a quicker but normal amylopast build-up was recorded with HNT. Our findings revealed temporal variation in the starch metabolism enzymes in all three stress treatments. Changes in the enzymatic activity did not derail starch accumulation under HNT when assimilates were sufficiently available, while both sucrose supply and the conversion of sucrose into starch were affected by HDT and HNDT. The findings indicate differential mechanisms leading to high day and high night temperature stress-induced loss in yield and quality. Additional genetic improvement is needed to sustain rice productivity and quality under future climates.

Identification of stable QTLs causing chalk in rice grains in nine environments.

KEY MESSAGE: A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10% of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13% of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.

Heterotic groups of tropical indica rice germplasm.

KEY MESSAGE: Four heterotic groups were identified for tropical indica rice germplasm to develop hybrid rice in the tropics based on two studies. Heterotic groups are of fundamental importance in hybrid crop breeding. This study investigated hybrid yield, yield heterosis and combining ability within and among groups based on genetic distance derived from single-nucleotide polymorphism markers. The main objectives of the study were to (1) evaluate the magnitude of yield heterosis among marker-based groups, (2) identify possible heterotic groups for tropical indica hybrid rice, and (3) validate heterotic patterns concluded from a previous study. Seventeen rice parents selected from improved indica germplasm from the tropics with high genetic divergence and 136 derived hybrids were evaluated in five environments. The hybrids had more yield than their parents with an average of 24.1 % mid-parent heterosis. Genotype × environment interaction was the major factor affecting variations in yield and yield heterosis, which raised a necessity and a challenge to develop heterotic rice hybrid adapted to different regions and seasons in the tropics. Yield, yield heterosis and combining ability were significantly increased in inter-group than in intra-group hybrids. Four heterotic groups and three promising hybridization patterns, which could be used in tropical hybrid rice breeding, were identified based on marker-based grouping, yield and yield heterosis analyses in the two studies. The study reveals that molecular markers analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid rice breeding.

Determination of heterotic groups for tropical Indica hybrid rice germplasm.

KEY MESSAGE: Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials. Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.

Vision sculpts a continuum of L2/3 cell types in the visual cortex during the critical period.

We previously reported that vision specifies Layer 2/3 (L2/3) glutamatergic cell-type identity in the primary visual cortex (V1). Using unsupervised clustering of single-nucleus RNA-sequencing data, we identified molecularly distinct L2/3 cell types in normal-reared (NR) and dark-reared (DR) mice, but the two sets exhibited poor correspondence. Here, we show that classification of cell types was confounded in DR by vision-dependent gene programs that are orthogonal to gene programs underlying cell-type identity. A focused clustering analysis successfully matches cell types between DR and NR, suggesting that cell identity-defining gene programs persist under vision deprivation but are overshadowed by vision-dependent transcriptomic variation. Using multi-tasking theory we show that L2/3 cell types form a continuum between three cell-archetypes. Visual deprivation markedly shifts this distribution along the continuum. Thus, dark-rearing markedly influences cell states thereby masking cell-type-identities and changes the distribution of L2/3 types along a transcriptomic continuum.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.

Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our predictions by comparing them with chromatin conformation data and causal enhancer perturbation experiments. Our study shows how controlling for gene co-expression enables robust enhancer-gene linkage using single-cell sequencing data.

Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors.

Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their 'surplus' genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms' phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism's morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.

Threshold effect of industrial agglomeration on carbon productivity in China's Yangtze River economic belt: a perspective of technical resourcing.

The Yangtze River Economic Belt's industrial layout is characterized by industrial agglomeration. However, industrial agglomeration, while promoting economic development, has an uncertain impact on the ecological environment. This research studies the threshold impacts of pollution-intensive industrial agglomeration and green-based industrial agglomeration on the carbon productivity of the Yangtze River Economic Belt through the panel threshold regression models to find the "optimal industrial agglomeration scale." The results of the "optimal industrial agglomeration scale" show that under the existing economic conditions, only if pollution-intensive industrial agglomeration is controlled within a reasonable range can it contribute to carbon productivity. Green-based industries can only enhance carbon productivity when the scale of agglomeration reaches a certain value. In addition, this paper also points out that along the Yangtze River Economic Belt, regions with high agglomeration of green industries should consider investing more technological resources in emerging technologies that use clean energy as a production condition. In contrast, regions with high agglomeration of pollution-intensive industries should focus on improving existing technologies in which traditional energy sources are used as production conditions to increased carbon productivity.

Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.

Single-cell technologies measure unique cellular signatures but are typically limited to a single modality. Computational approaches allow the fusion of diverse single-cell data types, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells, we devised single-nucleus methylcytosine, chromatin accessibility, and transcriptome sequencing (snmCAT-seq) and applied it to postmortem human frontal cortex tissue. We developed a cross-validation approach using multi-modal information to validate fine-grained cell types and assessed the effectiveness of computational data fusion methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility, and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling the prediction of cell types that are associated with diseases.

Impact of China's outward foreign direct investment on green total factor productivity in "Belt and Road" participating countries: a perspective of institutional distance.

The "Belt and Road" must be built not only as a road to prosperity but also as a green road. However, as China's outward foreign direct investment (OFDI) in "Belt and Road" participating countries has continued to increase, "China's pollution transfer" has also been wildly rendered. This article uses data from 21 European countries participating in the "Belt and Road" Initiative from 2009 to 2018. After calculating the institutional distance between each sample country and China using the Kogut-Singh index, this article focuses on using the threshold regression model to study the relationship between China's OFDI and the host country's green total factor productivity (GTFP). The empirical results prove that China's OFDI is green rather than accompanied by pollution transfer, which can promote GTFP in countries participating in the "Belt and Road" Initiative. However, this positive effect will gradually weaken as political institutional distance and economic institutional distance increase. Moreover, the expansion of OFDI can reduce the impact of institutional distance on GTFP in "Belt and Road" participating countries. Therefore, for "Belt and Road" participating countries that differ greatly from China in terms of their institutional environment, cooperation with China should be strengthened to reduce the impact of bilateral institutional differences.

Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes.

Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of neural circuits. By directly measuring multiple molecular signatures in thousands to millions of individual cells, single-cell sequencing methods can comprehensively characterize the diversity of brain cell types. These measurements uncover gene regulatory mechanisms that shape cellular identity and provide insight into developmental and evolutionary relationships between brain cell populations. Single-cell sequencing data can aid the design of tools for targeted functional studies of brain circuit components, linking molecular signatures with anatomy, connectivity, morphology, and physiology. Here, we discuss the fundamental principles of single-cell transcriptome and epigenome sequencing, integrative computational analysis of the data, and key applications in neuroscience.

Comprehensive analysis of single cell ATAC-seq data with SnapATAC.

Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

Shanyou 63: an elite mega rice hybrid in China.

Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shanyou 63, a mega rice hybrid, derived from the parents Zhenshan 97A and Minghui 63, was a milestone for China's hybrid rice development and production because of its high yield and wide adaptability. It was planted in 16 provinces of the country on 17% of the national hybrid rice area annually during the 29 years from 1984 to 2012. The hybrid and its parents have also been widely used for basic and agronomic studies related to rice heterosis, stress tolerance, molecular markers and genomics. We review the development of the hybrid and its parents and their major characteristics for the purpose of learning from the history and guiding future hybrid rice development. The history and development experience show that a successful hybrid rice variety should have multiple traits, including high yield, wide adaptability, resistances to major diseases, and high rice quality that meets the demands of consumers. From the breeding aspect, hybrid rice provides the advantage of combining elite traits or genes from different types of parents, such as those from subspecies of indica and japonica, into a single variety. Farmers prefer not only a variety with high yield potential, but also stable yields and local adaptability.

Orientational phase transitions and the assembly of viral capsids.

We present a Landau theory for large-l orientational phase transitions and apply it to the assembly of icosahedral viral capsids. The theory predicts two distinct types of ordering transitions. Transitions dominated by the l=6,10,12, and 18 icosahedral spherical harmonics resemble robust first-order phase transitions that are not significantly affected by chirality. The remaining transitions depend essentially on including mixed l states denoted as l=15+16 corresponding to a mixture of l=15 and l=16 spherical harmonics. The l=15+16 transition is either continuous or weakly first-order and it is strongly influenced by chirality, which suppresses spontaneous chiral symmetry breaking. The icosahedral state is in close competition with states that have tetrahedral, D_{5}, and octahedral symmetries. We present a group-theoretic method to analyze the competition between the different symmetries. The theory is applied to a variety of viral shells.

Genome-wide association study of outcrossing in cytoplasmic male sterile lines of rice.

Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcrossing in hybrid rice seed production. Based on 43,394 single nucleotide polymorphism markers, 217 cytoplasmic male sterile lines were assigned into two subpopulations and a mixed-group where the linkage disequilibrium decay distances varied from 975 to 2,690 kb. Genome-wide association studies (GWAS) were performed for stigma exsertion rate (SE), panicle enclosure rate (PE) and seed-setting rate (SSR). A total of 154 significant association signals (P < 0.001) were identified. They were situated in 27 quantitative trait loci (QTLs), including 11 for SE, 6 for PE, and 10 for SSR. It was shown that six of the ten QTLs for SSR were tightly linked to QTLs for SE or/and PE with the expected allelic direction. These QTL clusters could be targeted to improve the outcrossing of female parents in hybrid rice breeding. Our study also indicates that GWAS-base QTL mapping can complement and enhance previous QTL information for understanding the genetic relationship between outcrossing and its related traits.

Growth of metal-semiconductor core-multishell nanorods with optimized field confinement and nonlinear enhancement.

This paper describes a facile method for the synthesis of Au/AuAg/Ag2S/PbS core-multishell nanorods with double trapping layers. The synthesis, in sequence, involved deposition of Ag shells onto the surfaces of Au nanorod seeds, formation of AuAg shells by a galvanic replacement reaction, and overgrowth of the Ag2S shells and PbS shells. The resulting core-multishell nanorod possesses an air gap between the Au core and the AuAg shell. Together with the Ag2S shell, the air gap can efficiently trap light, causing strong field confinement and nonlinear enhancement. The as-prepared Au/AuAg/Ag2S/PbS core-multishell nanorods display distinct localized surface plasmon resonance and nonlinear optical properties, demonstrating an effective pathway for maneuvering the optical properties of nanocavities.

[Preparation of stearic acid solid lipid nanoparticles containing podophyllotoxin].

OBJECTIVE: To improve the therapeutic efficacy and reduce the adverse effect of podophyllotoxin (PPT) by wrapping it in stearic acid solid lipid nanoparticles. METHODS: Stearic acid solid lipid nanoparticles containing podophyllotoxin was prepared using modified microemulsion technique, whose morphology was examined by transmission electron microscope. High-performance of liquid chromatography was employed to determine the entrapment efficiency of PPT in the nanoparticles. RESULT: The entrapment efficiency of PPT in the nanoparticles was 85.6% and the mean diameter of the particles was 56.5+/-25.8 nm. CONCLUSION: The stearic acid solid lipid nanoparticles has high entrapment efficiency for PPT and is homogeneous in size, which can be a promising targeted preparation for epidermal delivery.

[Preparation and characterization of podophyllotoxin-dipalmitoylphosphatidylcholine proliposome].

OBJECTIVE: To prepare podophyllotoxin-dipalmitoylphosphatidylcholine (PPT-DPPC) proliposomes (PPT-DPPC-PL) for improvement of the stability of PPT-DPPC liposome. METHODS: Freeze-drying method was used to prepare PPT-DPPC-PL, and the particle morphology, size range, encapsulation efficiency and stability of PPT-DPPC liposome were investigated. RESULTS: After hydration of PPT-DPPC-PL, PPT-DPPC liposome appeared multivesicular under electron microscope and the particles were distributed homogeneously with an average particle size of 1.45+/-0.38 microm. The encapsulation efficiency of PPT was 72.3%, and after storage at 4 to 40 degrees Celsius; for 1 to 6 months, the proliposome remained stable. CONCLUSION: The prepared PPT-DPPC-PL particles by freeze-drying method are evenly distributed. The preparation method is relatively simple with higher embedding ratio and better stability.