A brain cell atlas integrating single-cell transcriptomes across human brain regions.

While single-cell technologies have greatly advanced our comprehension of human brain cell types and functions, studies including large numbers of donors and multiple brain regions are needed to extend our understanding of brain cell heterogeneity. Integrating atlas-level single-cell data presents a chance to reveal rare cell types and cellular heterogeneity across brain regions. Here we present the Brain Cell Atlas, a comprehensive reference atlas of brain cells, by assembling single-cell data from 70 human and 103 mouse studies of the brain throughout major developmental stages across brain regions, covering over 26.3 million cells or nuclei from both healthy and diseased tissues. Using machine-learning based algorithms, the Brain Cell Atlas provides a consensus cell type annotation, and it showcases the identification of putative neural progenitor cells and a cell subpopulation of PCDH9high microglia in the human brain. We demonstrate the gene regulatory difference of PCDH9high microglia between hippocampus and prefrontal cortex and elucidate the cell-cell communication network. The Brain Cell Atlas presents an atlas-level integrative resource for comparing brain cells in different environments and conditions within the Human Cell Atlas.

Surface Hydroxylation-Induced Electrostatic Forces Thicken Water Films on Quartz.

Aqueous films on mineral surfaces control the physical, chemical, and biological transport processes in the atmosphere, soil, and rocks. Despite the importance of thin films for various research and engineering fields, there are still unanswered questions regarding the roles of the different forces affecting the nature of water films. One of these, the focus of this study, is the development of abnormally thick water films on quartz surfaces. In this study, we developed a density-functional-theory-based model to describe the time-dependent evolution of water films and identify the governing forces responsible for thickening films. We simulated the diffusion of water vapor from ambient air toward mineral surfaces and the formation and thickening of water films at various relative humidity values. Our model predicts an abnormal water film thickness on a hydroxylated quartz surface compared to a surface free of hydroxylation, which explains experimental observations. We further used the model to understand the key interaction forces at different stages of water film formation and thickening. Our model suggests that the attractive hydrogen bonding and van der Waals forces initiate a seed layer of water, and the electrostatic forces, generated by the hydroxylated and thus charged surface, lead to the thickening of water films. This generalizable model can provide insights into the peculiarities of water film development on various mineral surfaces.

Toward Low-Voltage and High-Sensitivity Direct X-ray Detectors Based on Thick Bulk Heterojunction Organic Device.

Organic semiconducting materials are promising for the fabrication of flexible ionizing radiation detectors for imaging because of their tissue equivalence, simple large-scale processing, and mass production. However, it is challenging to achieve high-sensitivity detection for organic direct detectors prepared by low-cost solution processing because of the compromise between thickness and carrier transport. In this study, high-performance organic direct X-ray detectors were fabricated by building a micrometer-thick bulk heterojunction (BHJ) using poly(3-hexylthiophene-2,5-diyl) (P3HT):(6,6)-phenyl c71 butyric acid methyl ester. A 5 µm BHJ film was fabricated by drop-casting and enhanced crystallization of P3HT using binary solvents and high-boiling-point additives to improve the charge carrier mobility. Furthermore, this organic direct X-ray detector has a sensitivity of >654.26 µC Gyair s-1 and a self-powered response. Because of the architecture of the thick active layer and the energy cascade in this diode detector, it has a very low dark current of 46.26 pA at -2 V. A fast and efficient approach was developed for fabricating thick, highly mobile organic BHJ films for high-performance direct X-ray detectors. It has great potential for application in a new generation of flexible and portable large-area flat-panel detectors.

Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity.

Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.

Patch-seq: Advances and Biological Applications.

Multimodal analysis of gene-expression patterns, electrophysiological properties, and morphological phenotypes at the single-cell/single-nucleus level has been arduous because of the diversity and complexity of neurons. The emergence of Patch-sequencing (Patch-seq) directly links transcriptomics, morphology, and electrophysiology, taking neuroscience research to a multimodal era. In this review, we summarized the development of Patch-seq and recent applications in the cortex, hippocampus, and other nervous systems. Through generating multimodal cell type atlases, targeting specific cell populations, and correlating transcriptomic data with phenotypic information, Patch-seq has provided new insight into outstanding questions in neuroscience. We highlight the challenges and opportunities of Patch-seq in neuroscience and hope to shed new light on future neuroscience research.

A primate nigrostriatal atlas of neuronal vulnerability and resilience in a model of Parkinson's disease.

The degenerative process in Parkinson's disease (PD) causes a progressive loss of dopaminergic neurons (DaNs) in the nigrostriatal system. Resolving the differences in neuronal susceptibility warrants an amenable PD model that, in comparison to post-mortem human specimens, controls for environmental and genetic differences in PD pathogenesis. Here we generated high-quality profiles for 250,173 cells from the substantia nigra (SN) and putamen (PT) of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonian macaques and matched controls. Our primate model of parkinsonism recapitulates important pathologic features in nature PD and provides an unbiased view of the axis of neuronal vulnerability and resistance. We identified seven molecularly defined subtypes of nigral DaNs which manifested a gradient of vulnerability and were confirmed by fluorescence-activated nuclei sorting. Neuronal resilience was associated with a FOXP2-centered regulatory pathway shared between PD-resistant DaNs and glutamatergic excitatory neurons, as well as between humans and nonhuman primates. We also discovered activation of immune response common to glial cells of SN and PT, indicating concurrently activated pathways in the nigrostriatal system. Our study provides a unique resource to understand the mechanistic connections between neuronal susceptibility and PD pathophysiology, and to facilitate future biomarker discovery and targeted cell therapy.

Synthesis and Characterization of Photoswitchable Dithienylethene-Based Chiral Bisoxazoline Compounds with Bidirectional Visible-Light Control.

In this paper, we have successfully synthesized dithienylethene-based chiral bisoxazoline ligands with bidirectional photoswitching capabilities under visible light irradiation and proposed a strategy for adjusting the conjugation system length in sensitizer groups. The detailed experimental procedures and the characterization data are presented in the main text and the Supporting Information. Despite their moderate photoswitching rates, these ligands provide a promising approach towards developing fully visible light-responsive chiral catalysts.

Visible-light-induced reactions of methylenecyclopropanes (MCPs).

Diverse, visible-light-induced transformations of methylenecyclopropanes (MCPs) have been reported in recent years, attracting significant attention from synthetic chemists. As readily accessible strained molecules, MCPs have sufficient reactivity to selectively generate different target products, through reactions with various radical species upon visible-light irradiation under regulated reaction conditions. These transformations can be classified into three subcategories of reaction pathway, forming ring-opened products, cyclopropane derivatives, and alkynes. These products include pharmaceutical intermediates and polycyclic/heterocyclic compounds that are challenging to obtain using traditional methods. This review summarizes the recent advancements in this field.

Adult neurogenesis in the primate hippocampus.

Adult hippocampal neurogenesis (AHN) is crucial for learning, memory, and emotion. Deficits of AHN may lead to reduced cognitive abilities and neurodegenerative disorders, such as Alzheimer's disease. Extensive studies on rodent AHN have clarified the developmental and maturation processes of adult neural stem/progenitor cells. However, to what extent these findings apply to primates remains controversial. Recent advances in next-generation sequencing technologies have enabled in-depth investigation of the transcriptome of AHN-related populations at single-cell resolution. Here, we summarize studies of AHN in primates. Results suggest that neurogenesis is largely shared across species, but substantial differences also exist. Marker gene expression patterns in primates differ from those of rodents. Compared with rodents, the primate hippocampus has a higher proportion of immature dentate granule cells and a longer maturation period of newly generated granule cells. Future research on species divergence may deepen our understanding of the mechanisms underlying adult neurogenesis in primates.

Identification of visual cortex cell types and species differences using single-cell RNA sequencing.

The primate neocortex exerts high cognitive ability and strong information processing capacity. Here, we establish a single-cell RNA sequencing dataset of 133,454 macaque visual cortical cells. It covers major cortical cell classes including 25 excitatory neuron types, 37 inhibitory neuron types and all glial cell types. We identified layer-specific markers including HPCAL1 and NXPH4, and also identified two cell types, an NPY-expressing excitatory neuron type that expresses the dopamine receptor D3 gene; and a primate specific activity-dependent OSTN + sensory neuron type. Comparisons of our dataset with humans and mice show that the gene expression profiles differ between species in relation to genes that are implicated in the synaptic plasticity and neuromodulation of excitatory neurons. The comparisons also revealed that glutamatergic neurons may be more diverse across species than GABAergic neurons and non-neuronal cells. These findings pave the way for understanding how the primary cortex fulfills the high-cognitive functions.

Deciphering the core seed endo-bacteriome of the highland barley in Tibet plateau.

Highland barley (Hordeum vulgare var. nudum (L.) Hook.f., qingke) has unique physical and chemical properties and good potential for industrial applications. As the only crop that can be grown at high altitudes of 4200-4500 m, qingke is well adapted to extreme habitats at high altitudes. In this study, we analysed the seed bacterial community of 58 genotypes of qingke grown in different regions of Tibet, including qingke landraces, modern cultivars, and winter barley varieties, and characterised endophytic bacterial communities in seeds from different sources and the core endo-bacteriome of qingke. This study aim to provide a reference for the application of seed endophytes as biological inoculants for sustainable agricultural production and for considering microbe-plant interactions in breeding strategies. A total of 174 qingke seed samples from five main agricultural regions in Tibet were collected and subjected to investigation of endophytic endo-bacteriome using high-throughput sequencing and bioinformatics approaches. The phyla of endophytic bacteria in qingke seeds from different sources were similar; however, the relative proportions of each phylum were different. Different environmental conditions, growth strategies, and modern breeding processes have significantly changed the community structure of endophytic bacteria in seeds, among which the growth strategy has a greater impact on the diversity of endophytic bacteria in seeds. Seeds from different sources have conserved beneficial core endo-bacteriome. The core endo-bacteriome of qingke seeds dominated by Enterobacteriaceae may maintain qingke growth by promoting plant growth and assisting plants in resisting pests and diseases. This study reveals the core endo-bacteriome of qingke seeds and provides a basis for exploiting the endophytic endo-bacteriome of qingke seeds.

Linking transcriptomes with morphological and functional phenotypes in mammalian retinal ganglion cells.

Retinal ganglion cells (RGCs) are the brain's gateway to the visual world. They can be classified into different types on the basis of their electrophysiological, transcriptomic, or morphological characteristics. Here, we characterize the transcriptomic, morphological, and functional features of 472 high-quality RGCs using Patch sequencing (Patch-seq), providing functional and morphological annotation of many transcriptomic-defined cell types of a previously established RGC atlas. We show a convergence of different modalities in defining the RGC identity and reveal the degree of correspondence for well-characterized cell types across multimodal data. Moreover, we complement some RGC types with detailed morphological and functional properties. We also identify differentially expressed genes among ON, OFF, and ON-OFF RGCs such as Vat1l, Slitrk6, and Lmo7, providing candidate marker genes for functional studies. Our research suggests that the molecularly distinct clusters may also differ in their roles of encoding visual information.

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning.

Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.

1,1-Dimethylhydrazine adsorption on intrinsic, vacancy, and N-doped graphene: a first-principle study.

Graphene and its derivatives have been widely used in the area of high-sensitivity sensing materials for small-molecule gases. Based on first-principle calculations, the present study systematically investigated the adsorption of 1,1-dimethylhydrazine on intrinsic graphene, graphene with vacancy defects, and nitrogen-doped graphene. The adsorption effects, when 1,1-dimethylhydrazine takes on different orientations, were determined separately, and the specific adsorption energy and charge transfer were calculated accordingly. The results reveal that the 1,1-dimethylhydrazine adsorption on intrinsic graphene, graphene with vacancy defects, and nitrogen-doped graphene falls into physical adsorption. Besides, both vacancy defect and nitrogen doping help enhance the adsorption but the effect of vacancy defect is superior to that of nitrogen doping.

Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations.

The extent to which neurogenesis occurs in adult primates remains controversial. In this study, using an optimized single-cell RNA sequencing pipeline, we profiled 207,785 cells from the adult macaque hippocampus and identified 34 cell populations comprising all major hippocampal cell types. Analysis of their gene expression, specification trajectories and gene regulatory networks revealed the presence of all key neurogenic precursor cell populations, including a heterogeneous pool of radial glia-like cells (RGLs), intermediate progenitor cells (IPCs) and neuroblasts. We identified HMGB2 as a novel IPC marker. Comparison with mouse single-cell transcriptomic data revealed differences in neurogenic processes between species. We confirmed that neurogenesis is recapitulated in ex vivo neurosphere cultures from adult primates, further supporting the existence of neural precursor cells (NPCs) that are able to proliferate and differentiate. Our large-scale dataset provides a comprehensive adult neurogenesis atlas for primates.

[Effect of elevated atmospheric CO2 concentration and temperature on volatile halogenated organic compound content in soils of Schima superba and Cunninghamia lanceolata seedlings.] / 大气CO2浓度和温度升高对木荷和杉木幼苗土壤卤代烃含量的影响.

Global changes caused by the increases of atmospheric CO2 concentration and temperature have important effects on soil biogeochemical processes. The synthesis and release of volatile halogenated organic compounds (VOXs) is an important pathway for soil to participate in the global material cycle and energy flow. In this study, Schima superba and Cunninghamia lanceolata seedlings in the southern subtropics were selected as the research objects. Four treatments, including control (CK), elevated CO2 concentration (EC), elevated temperature (ET) and elevated both factors (EC+ET) were set up. The effects of EC and ET on soil VOXs formation were studied by an open-top chamber system coupled with a purging and trapping gas chromatography/mass spectrometry. The results showed that VOXs content in the soil of S. superba seedlings was 0.065-0.252 ng·g-1, which was higher than that of C. lanceolata (0.038-0.136 ng·g-1). At the EC, ET and EC+ET treatments, VOXs contents were reduced in soils of both species. The effect of ET was the most significant, with the decrease rates of 74.2% and 72.1% in both soils, respectively. The change of VOXs content with increasing temperature mainly attributed to the changes of soil moisture and nitrogen content. The content of VOXs in the soils of S. superba seedlings decreased more than that of C. lanceolata under different treatments. In CK, EC, ET and EC+ET treatment, bromodichloromethane (BDCM) (27.5%, 36.7%, 32.9%, 32.6%) and tetrachloromethane (TCM) (9.0%, 16.8%, 22.7%, 15.8%) were the main VOXs in the soil of S. superba seedlings, respectively, while BDCM and dibromomethane (DBM) were the main VOXs in the soil of C. lanceolata seedlings. BDCM accounted for 31.9%, 38.2%, 40.9% and 37.2% of the VOXs content in each treatment, and DBM accounted for 17.9%, 16.5%, 19.2% and 16.0% of the VOXs content, respectively. Simulating elevated atmospheric CO2 concentration and temperature was conducive to more comprehensive reflection of the ecological effect of global climate change, and it could provide data support for improving the VOCs flux model.

Identification of TPBG-Expressing Amacrine Cells in DAT-tdTomato Mouse.

Purpose: Neurons are the bricks of the neuronal system and experimental access to certain neuron subtypes will be of great help to decipher neuronal circuits. Here, we identified trophoblast glycoprotein (TPBG)-expressing GABAergic amacrine cells (ACs) that were selectively labeled in DAT-tdTomato transgenic mice. Methods: Retina and brain sections were prepared for immunostaining with antibodies against various biomarkers. Patch-sequencing was performed to obtain the transcriptomes of tdTomato-positive cells in DAT-tdTomato mice. Whole-cell recordings were conducted to identify responses to light stimulation. Results: Tyrosine hydroxylase immunoreactive cells were colocalized with tdTomato-positive cells in substantia nigra pars compacta, but not in the retina. Transcriptomes collected from tdTomato-positive cells in retinas via Patch-sequencing exhibited the expression of marker genes of ACs (Pax6 and Slc32a1) and marker genes of GABAergic neurons (Gad1, Gad2, and Slc6a1). Immunostaining with antibodies against relevant proteins (GAD67, GAD65, and GABA) also confirmed transcriptomic results. Furthermore, tdTomato-positive cells in retinas selectively expressed Tpbg, a marker gene for distinct clusters molecularly defined, which was proved with TPBG immunoreactivity in fluorescently labeled cells. Finally, tdTomato-positive cells recorded showed ON-OFF responses to light stimulation. Conclusions: Ectopic expression occurs in the retina but not in the substantia nigra pars compacta in the DAT-tdTomato mouse, and fluorescently labeled cells in the retina are TPBG-expressing GABAergic ACs. This type of transgenic mice has been proved as an ideal tool to achieve efficient labeling of a distinct subset of ACs that selectively express Tpbg.

Spectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrass.

The perennial native switchgrass adapts better than other plant species do to marginal soils with low plant-available nutrients, including those with low phosphorus (P) content. Switchgrass roots and their associated microorganisms can alter the pools of available P throughout the whole soil profile making predictions of P availability in situ challenging. Plant P homeostasis makes monitoring of P limitation via measurements of plant P content alone difficult to interpret. To address these challenges, we developed a machine-learning model trained with high accuracy using the leaf tissue chemical profile, rather than P content. By applying this learned model in field trials across two sites with contrasting extractable soil P, we observed that actual plant available P in soil was more similar than expected, suggesting that adaptations occurred to alleviate the apparent P constraint. These adaptations come at a metabolic cost to the plant that have consequences for feedstock chemical components and quality. We observed that other biochemical signatures of P limitation, such as decreased cellulose-to-lignin ratios, were apparent, indicating re-allocation of carbon resources may have contributed to increased P acquisition. Plant P allocation strategies also differed across sites, and these differences were correlated with the subsequent year's biomass yields.

The Morita-Baylis-Hillman reaction for non-electron-deficient olefins enabled by photoredox catalysis.

A strategy for overcoming the limitation of the Morita-Baylis-Hillman (MBH) reaction, which is only applicable to electron-deficient olefins, has been achieved via visible-light induced photoredox catalysis in this report. A series of non-electron-deficient olefins underwent the MBH reaction smoothly via a novel photoredox-quinuclidine dual catalysis. The in situ formed key ß-quinuclidinium radical intermediates, derived from the addition of olefins with quinuclidinium radical cations, are used to enable the MBH reaction of non-electron-deficient olefins. On the basis of previous reports, a plausible mechanism is suggested. Mechanistic studies, such as radical probe experiments and density functional theory (DFT) calculations, were also conducted to support our proposed reaction pathways.