Cellular Anatomy Research Articles

Diffusion kurtosis imaging, MAP-MRI and NODDI selectively track gray matter myelin density in the primate cerebral cortex

Abstract Diffusion magnetic resonance imaging (dMRI) has been widely used to model the trajectory of myelinated fiber bundles in the white matter. Increasingly, it is also used to evaluate the microstructure of the cerebral cortex gray matter. For example, in diffusion tensor imaging (DTI) of the cortex, fractional anisotropy (FA) correlates strongly with the anisotropy of cellular anatomy, while radial diffusivity (RD) tracks the anisotropy of myelinated fibers. However, no DTI parameter shows specificity to gray matter myelin density. Here, we show that three higher-order diffusion parameters—the mean diffusion kurtosis (MK), the Neurite Density Index (NDI) from neurite orientation dispersion and density imaging (NODDI), and the Non-Gaussian (NG) parameter from mean apparent propagator (MAP)-MRI—each track the laminar and regional myelin density of the primate cerebral cortex in fine detail. We carried out ultra-high-resolution, multi-shelled dMRI in ex-vivo marmoset monkey brains. We compared the spatial mapping of the MK, NDI, and ND diffusion parameters to the cortical myelin distribution of these brains, with the latter obtained in two ways: First, using histological sections finely co-registered to the MRI, and second using magnetization transfer ratio MRI scans (MTR), an established non-diffusion method for imaging myelin density. We found that, in contrast to DTI parameters, each of these higher-order diffusion measures captured the spatial variation of myelin density in the cortex. The demonstration that diffusion parameters exhibit both sensitivity and specificity for gray matter myelin density will allow dMRI to more effectively track human disease, in which myelinated and non-myelinated tissue compartments are affected differentially.

Integrated physiological response by four species of Rhodophyta to submarine groundwater discharge reveals complex patterns among closely-related species

Algal physiological ecology on submarine groundwater discharge (SGD) influenced reefs is likely shaped by intermittent, tidally-driven estuarine conditions that occur with SGD fluxes of fresh-to-brackish groundwater from the subterranean estuary to reef ecosystems. SGD is a common inconspicuous feature worldwide on reefs of basaltic high islands and continental margins. Yet, SGD-driven dynamics of algal physiology are not well understood. To understand how invasive species have physiologically outcompeted native species on many SGD-influenced reefs, physiology in tissue water potential (TWP) regulation, photosynthesis, nitrogen storage, and cellular anatomy were measured across a gradient of SGD-influence, for four Rhodophyte species. Compared with non-SGD conditions, SGD was associated with higher TWP, larger medulla cells with thinner walls, and thinner cortical cell walls for two invasives, Gracilaria salicornia and Acanthophora spicifera, higher photosynthetic rates in G. salicornia, greater nitrogen concentration for A. spicifera and G. salicornia, and increased δ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\delta$$\\end{document}15N ratios for A. spicifera, G. salicornia, and native Laurencia dendroidea. Distinct physiological strategies were measured for the two invasive species across the gradient of SGD-influence, and for L. dendroidea and Gracilaria perplexa offshore. This study illuminates species-specific physiological response, and how introduced opportunistic species may outcompete native species under conditions of SGD.

Unveiling universal aspects of the cellular anatomy of the brain

Recent cellular-level volumetric brain reconstructions have revealed high levels of anatomic complexity. Determining which structural aspects of the brain to focus on, especially when comparing with computational models and other organisms, remains a major challenge. Here we quantify aspects of this complexity and show evidence that brain anatomy satisfies universal scaling laws, establishing the notion of structural criticality in the cellular structure of the brain. Our framework builds upon understanding of critical systems to provide clear guidance in selecting informative structural properties of cellular brain anatomy. As an illustration, we obtain estimates for critical exponents in the human, mouse and fruit fly brains and show that they are consistent between organisms, to the extent that data limitations allow. Such universal quantities are robust to many of the microscopic details of the cellular structures of individual brains, providing a key step towards generative computational models of the cellular structure of the brain, and also clarifying in which sense one animal may be a suitable anatomic model for another.

Histological Characterisation of a Sheep Model of Mild Traumatic Brain Injury: A Pilot Study.

Large animal models of mild traumatic brain injury (mTBI) are needed to elucidate the pathophysiology of mechanical insult to a gyrencephalic brain. Sheep (ovis aries) are an attractive model for mTBI because of their neuroanatomical similarity to humans; however, few histological studies of sheep mTBI models have been conducted. We previously developed a sheep mTBI model to pilot methods for investigating the mechanical properties of brain tissue after injury. Here, we sought to histologically characterize the cortex under the impact site in this model. Three animals received a closed skull mTBI with unconstrained head motion, delivered with an impact stunner, and 3 sham animals were anesthetized but did not receive an impact. Magnetic resonance imaging (MRI) of the brain was performed before and after the impact and revealed variable degrees of damage to the skull and brain. Fluorescent immunohistochemistry revealed regions of hemorrhage in the cortex underlying the impact site in 2 of 3 mTBI sheep, the amount of which correlated with the degree of damage observed on the post-impact MRI scans. Labeling for microtubule-associated protein 2 and neuronal nuclear protein revealed changes in cellular anatomy, but, unexpectedly, glial fibrillary acidic protein and ionized calcium-binding adaptor molecule 1 labeling were relatively unchanged compared to sham animals. Our findings provide preliminary evidence of vascular and neuronal damage with limited glial reactivity and highlight the need for further in-depth histological assessment of large animal mTBI models.

SEGMENTATION OF LUNG CANCER IMAGE BASED ON CYTOLOGIC EXAMINATION USING THRESHOLDING METHOD

Lung cancer is the most dangerous cases which mostly attacks the man with the biggest causes of smoking. This cancer threatens the second largest death after heart attack, lung cancer cases increase significantly every year in various countries. Several methods have been established to detect lung cancer, including Computed Tomography of the thorax, sputum examination and cytology examination. The most decisive examination is through cytologic examination of the pleural fluid. However, the current state of biopsy performed by doctors does not always get a lot of specimens, making it difficult to determine the presence of cancer cells in the lungs. Cytological examination through the pleural fluid has difficulty in detecting cell images. The image of pleural fluid that has a high density between cells will produce an image with low detail, while an image with a low density will produce an image with high detail. Image segmentation is an important part in determining the cellular anatomy of pleural fluid to characterize images with cancer or normal categories. We propose the methodology of research by using group images to separate objects from other objects by highlighting important parts using image segmentation on pleural fluid of patients suspected of having lung cancer. Thresholding method used to see the comparison is Adaptive Thresholding, binary thresholding and Otsu Thresholding. The classification results of the three methods show a high accuracy of 99% on binary thresholding, then 97% accuracy on otsu thresholding and the lowest accuracy of 96% on adaptive thresholding, the three methods are considered to increase in proportion to the addition of the epoch parameter.

Genome Editing in Ferret Airway Epithelia Mediated by CRISPR/Nucleases Delivered with Amphiphilic Shuttle Peptides.

Gene editing strategies are attractive for treating genetic pulmonary diseases such as cystic fibrosis (CF). However, challenges have included the development of safe and effective vector systems for gene editing of airway epithelia and model systems to report their efficiency and durability. The domestic ferret (Mustela putorius furo) has a high degree of conservation in lung cellular anatomy with humans, and has served as an excellent model for many types of lung diseases, including CF. In this study, we evaluated the efficiency of amphiphilic shuttle peptide S10 for protein delivery and gene editing using SpCas9, and AsCas12a (Cpf1) ribonucleoproteins (RNPs). These approaches were evaluated in proliferating ferret airway basal cells, polarized airway epithelia in vitro, and lungs in vivo, by accessing the editing efficiency using reporter ferrets and measuring indels at the ferret CFTR locus. Our results demonstrate that shuttle peptides efficiently enable delivery of reporter proteins/peptides and gene editing SpCas9 or Cpf1 RNP complexes to ferret airway epithelial cells in vitro and in vivo. We measured S10 delivery efficiency of green fluorescent protein (GFP)-nuclear localization signal (NLS) protein or SpCas9 RNP into ferret airway basal cells and fully differentiated ciliated and nonciliated epithelial cells in vitro. In vitro and in vivo gene editing efficiencies were determined by Cas/LoxP-gRNA RNP-mediated conversion of a ROSA-TG Cre recombinase reporter using transgenic primary cells and ferrets. S10/Cas9 RNP was more effective, relative to S10/Cpf1 RNP at gene editing of the ROSA-TG locus. Intratracheal lung delivery of the S10 shuttle combined with GFP-NLS protein or D-Retro-Inverso (DRI)-NLS peptide demonstrated efficiencies of protein delivery that were ∼3-fold or 14-fold greater, respectively, than the efficiency of gene editing at the ROSA-TG locus using S10/Cas9/LoxP-gRNA. Cpf1 RNPs was less effective than SpCas9 at gene editing of LoxP locus. These data demonstrate the feasibility of shuttle peptide delivery of Cas RNPs to the ferret airways and the potential utility for developing ex vivo stem cell-based and in vivo gene editing therapies for genetic pulmonary diseases such as CF.

Role of Oxidative Stress in Retinal Disease and the Early Intervention Strategies: A Review.

The retina, owing to its cellular anatomy and physical location, is susceptible to generating reactive oxygen species (ROS), which are associated with several major retinal diseases. When ROS exceeds the body's natural antioxidants, the retina is in a state of oxidative stress, which is recognized as the pathogenesis of retinal diseases. The early stage of the pathogenic process is an adaptive change in which oxidative stress and endogenous defense mechanisms occur. If no treatment is applied, the retinal diseases will progress to the pathological stage with neuronal and vascular dysfunction or damage and even blindness. This review summarizes the role of oxidative stress in several common retinal diseases, including retinitis pigmentosa, age-related macular degeneration, diabetic retinopathy, glaucoma, and retinopathy of prematurity. In addition, we discuss the early intervention strategies for these diseases. An outline is provided to identify potential intervention targets for further research. Early intervention for retinal diseases is necessary and urgent and may offer hope to improve patients' quality of life through functional vision.

A comprehensive comparison of facial skin hydration based on capacitance and conductance measurements in Chinese women.

The aim of this study was to compare the data of conductance and capacitance measurements of facial skin hydration and to evaluate and discuss the advantages and disadvantages of the different approaches. We measured skin capacitance (Corneometer® CM 825) and skin conductance (Skicon-200EX®) on 30 pre-defined facial sites of 125 Chinese women, resulting in 3750 readings per device. The data were analysed and compared, and continuous colour maps were generated on a 3D avatar for capacitance, conductance, relative difference (Δ%) and correlation (R-value) by interpolating between the individual readings and converting the values to colours. This visualization allows a better interpretation of the results. The complexity of facial skin hydration is revealed by this approach. The similarities and discrepancies in the facial hydration maps are clearly apparent. Due to the superiority of the Skicon in measuring high hydration levels, differences in skin hydration were evident on the forehead compared with the Corneometer maps, which may be related to the more superficial measurement of the Skicon within the stratum corneum. Conversely, a greater understanding of the complexity of facial skin hydration in the nasolabial fold was obvious when using the Corneometer. The best congruence between the instruments was found at two specific but separated facial areas, one around the inner eye region and the other one on a line between the nasolabial sulcus and the oblique, lateral jaw. Interestingly, the data were not normally distributed for both instruments and they had opposite skews. All facial clusters were statistically different from each other (p< 0.001), except the cheek and jaw for the Skicon. Larger than expected percentage coefficients of variance were found for the Corneometer on some facial sites that might be explainable by differences in stratum corneum physiology and biochemistry. Corneometer values of 48 AU and Skicon values of 132 μS were taken as the cutoff for normally hydrated facial skin. Both devices have their advantages and disadvantages suggesting that bio-instrumental measurement of skin hydration is actually more complicated than commonly thought and that the different facial zones and the use of multiple instrumentation have not been adequately considered.

New holozoans with cellular resolution from the early Ediacaran Weng'an Biota, SW China

Embryo-like fossils from the early Ediacaran Weng'an Biota (SW China, 609 myr ago), widely interpreted as holozoans, potentially provide insights into the early evolutionary development of metazoans and the rise of the animal kingdom. However, the biodiversity of the embryo-like fossil assemblage is largely underestimated and its more precise phylogenetic affinities within the holozoan tree are still under debate. We describe a new species of embryo-like fossil, Ostiosphaera rara n. gen. n. sp., from the Ediacaran Weng'an Biota. These 3D, phosphatized specimens exhibit a spherical morphology, a thick ornamented envelope with a circular opening and a membrane-bound, multicellular inner body. In terms of biological characteristics, O. rara shows similarities with a number of extant and fossil analogues, including testate amoebae, unicellular green algae, the cellular slime mould Fonticuida and co-occurring Weng'an embryo-like fossils. Although the phylogenetic affinity of O. rara is difficult to constrain precisely based on the available evidence, it is reasonable to follow the holozoan interpretation for these fossils because they share the same grade complexity with co-occurring embryo-like fossils, such as Megasphaera and Helicoforamina , in terms of the combination of biological features. These new holozoans resemble asexual reproductive gemmules of fossil and living demosponges in size, morphology, circular opening and cellular anatomy. If this similarity reflects biological affinity rather than convergent evolution, this discovery would force us to rethink the evolutionary history of Precambrian sponges. Thematic collection: This article is part of the Advances in the Cambrian Explosion collection available at: https://www.lyellcollection.org/cc/advances-cambrian-explosion

A new experimental model for the investigation of sequential hermaphroditism

The stunning sexual transformation commonly triggered by age, size or social context in some fishes is one of the best examples of phenotypic plasticity thus far described. To date our understanding of this process is dominated by studies on a handful of subtropical and tropical teleosts, often in wild settings. Here we have established the protogynous New Zealand spotty wrasse, Notolabruscelidotus, as a temperate model for the experimental investigation of sex change. Captive fish were induced to change sex using aromatase inhibition or manipulation of social groups. Complete female-to-male transition occurred over 60 days in both cases and time-series sampling was used to quantify changes in hormone production, gene expression and gonadal cellular anatomy. Early-stage decreases in plasma 17β-estradiol (E2) concentrations or gonadal aromatase (cyp19a1a) expression were not detected in spotty wrasse, despite these being commonly associated with the onset of sex change in subtropical and tropical protogynous (female-to-male) hermaphrodites. In contrast, expression of the masculinising factor amh (anti-Müllerian hormone) increased during early sex change, implying a potential role as a proximate trigger for masculinisation. Collectively, these data provide a foundation for the spotty wrasse as a temperate teleost model to study sex change and cell fate in vertebrates.

Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques.

The combination of tissue clearing techniques with advanced optical microscopy facilitates the achievement of three-dimensional (3D) reconstruction of macroscopic specimens at high resolution. Whole mouse organs or even bodies have been analyzed, while the reconstruction of the human nervous system remains a challenge. Although several tissue protocols have been proposed, the high autofluorescence and variable post-mortem conditions of human specimens negatively affect the quality of the images in terms of achievable transparency and staining contrast. Moreover, homogeneous staining of high-density epitopes, such as neuronal nuclear antigen (NeuN), creates an additional challenge. Here, we evaluated different tissue transformation approaches to find the best solution to uniformly clear and label all neurons in the human cerebral cortex using anti-NeuN antibodies in combination with confocal and light-sheet fluorescence microscopy (LSFM). Finally, we performed mesoscopic high-resolution 3D reconstruction of the successfully clarified and stained samples with LSFM.

Cellular anatomy of the mouse primary motor cortex

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input–output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

THE BIOLOGY OF PERIOSTEAL REACTIONS

<h3>BACKGROUND</h3> The periosteum is a thin membrane that covers almost all bony surfaces in the human body. This membrane is attached to the underlying bone through type I collagen fibers known as Sharpey's fibers. The periosteum is organized into an inner cellular layer with significant osteoblastic potential and an outer fibrous layer. This osteoblastic potential can be stimulated by both physiologic processes in growth and fracture repair and by pathologic conditions. The characteristics of the periosteal responses are modulated by factors such as the type of initiating stimulus, age, and anatomic site. <h3>CASE REPORT</h3> Through illustrative cases, we will discuss the biologic bases for periosteal responses and the association of these radiologic presentations with pathophysiologic situations such as in inflammation and malignancy. <h3>DISCUSSION/CONCLUSIONS</h3> This poster will review the gross and cellular anatomy of the periosteal membrane and a range of periosteal responses. An understanding of bone and periosteal biology serves as a foundation for a radiologist to recognize patterns of periosteal responses and to decipher the causative stimuli.

New petrified calamitaleans from the Permian of the Parnaíba Basin, central-north Brazil, part III, with some concerns regarding anatomical features of Paleozoic petrified sphenophytes

A new petrified calamitalean is described from the Permian Motuca Formation, Parnaíba Basin, central-north Brazil. In contrast to all other three-dimensionally preserved Brazilian species, it represents a semi-self-supporting woody plant characterized by a distinctive branch system and cellular anatomy. Arthropitys buritiranensis sp. nov. is proposed to accommodate the new material. The branch architecture is composed of at least three types of branches: (i) principal woody side branches, (ii) up to three secondary woody branches per node, scattered along the stem or the principal side branches, and (iii) 8–11 leafy twigs per whorl, at every third, rarely the second node, without secondary growth. The wood is segmented into fascicular wedges and interfascicular rays, clearly visible only within the inner wood of the stem and woody branches. The tracheid walls of the secondary xylem have exclusively scalariform pits. Ray parenchyma cells have pitted horizontal walls. The new calamitalean was part of the riparian vegetation of tree ferns, calamitaleans and gymnosperms recorded in a distal fluvial plain setting. The wood shows irregular growth interruptions and, therefore, points to a seasonally dry climate that shaped even low latitude paleofloras of tropical Pangaea.

Disruption of left-right axis specification in Ciona induces molecular, cellular, and functional defects in asymmetric brain structures

BackgroundLeft-right asymmetries are a common feature of metazoans and can be found in a number of organs including the nervous system. These asymmetries are particularly pronounced in the simple central nervous system (CNS) of the swimming tadpole larva of the tunicate Ciona, which displays a chordate ground plan. While common pathway elements for specifying the left/right axis are found among chordates, particularly a requirement for Nodal signaling, Ciona differs temporally from its vertebrate cousins by specifying its axis at the neurula stage, rather than at gastrula. Additionally, Ciona and other ascidians require an intact chorionic membrane for proper left-right specification. Whether such differences underlie distinct specification mechanisms between tunicates and vertebrates will require broad understanding of their influence on CNS formation. Here, we explore the consequences of disrupting left-right axis specification on Ciona larval CNS cellular anatomy, gene expression, synaptic connectivity, and behavior.ResultsWe show that left-right asymmetry disruptions caused by removal of the chorion (dechorionation) are highly variable and present throughout the Ciona larval nervous system. While previous studies have documented disruptions to the conspicuously asymmetric sensory systems in the anterior brain vesicle, we document asymmetries in seemingly symmetric structures such as the posterior brain vesicle and motor ganglion. Moreover, defects caused by dechorionation include misplaced or absent neuron classes, loss of asymmetric gene expression, aberrant synaptic projections, and abnormal behaviors. In the motor ganglion, a brain structure that has been equated with the vertebrate hindbrain, we find that despite the apparent left-right symmetric distribution of interneurons and motor neurons, AMPA receptors are expressed exclusively on the left side, which equates with asymmetric swimming behaviors. We also find that within a population of dechorionated larvae, there is a small percentage with apparently normal left-right specification and approximately equal population with inverted (mirror-image) asymmetry. We present a method based on a behavioral assay for isolating these larvae. When these two classes of larvae (normal and inverted) are assessed in a light dimming assay, they display mirror-image behaviors, with normal larvae responding with counterclockwise swims, while inverted larvae respond with clockwise swims.ConclusionsOur findings highlight the importance of left-right specification pathways not only for proper CNS anatomy, but also for correct synaptic connectivity and behavior.

Foveal Pit Morphology Characterization: A Quantitative Analysis of the Key Methodological Steps.

Disentangling the cellular anatomy that gives rise to human visual perception is one of the main challenges of ophthalmology. Of particular interest is the foveal pit, a concave depression located at the center of the retina that captures light from the gaze center. In recent years, there has been a growing interest in studying the morphology of the foveal pit by extracting geometrical features from optical coherence tomography (OCT) images. Despite this, research has devoted little attention to comparing existing approaches for two key methodological steps: the location of the foveal center and the mathematical modelling of the foveal pit. Building upon a dataset of 185 healthy subjects imaged twice, in the present paper the image alignment accuracy of four different foveal center location methods is studied in the first place. Secondly, state-of-the-art foveal pit mathematical models are compared in terms of fitting error, repeatability, and bias. The results indicate the importance of using a robust foveal center location method to align images. Moreover, we show that foveal pit models can improve the agreement between different acquisition protocols. Nevertheless, they can also introduce important biases in the parameter estimates that should be considered.

Wood shrinkage during fossilisation and its significance for studying deep-time lignophytes

Silicified wood is one of the most frequent and insightful records of ancient life since the Devonian. Although cellular anatomy is often preserved in great detail, alterations of organic matter occur during fossilisation modifying tissue properties. Due to taphonomic pathways, plant tissues experience multiple changes, which may cause a tissue-volume reduction, including desiccation, microbial decay, charcoalification, coalification and mineralisation. Case studies from different geological ages, fossilisation backgrounds and palaeogeographic positions provide evidence of widely distributed but still underestimated shrinkage phenomena in fossil woods. Samples from seven Paleozoic to Cenozoic localities representing several geologic settings are analysed to understand putative shrinkage reasons. Volume reduction is more widespread in fossilised wood than commonly thought. Accordingly, quantitative data on cellular anatomy may be misleading, and cell size and shape modifications affect morphometric purposes, like the interpretation and identification of fossil species. Differences in preservation demonstrate the profound effects of microbial degradation, such as lacking tracheid secondary walls and decayed tissue constituents. Differential shrinkage of silicified wood and their encrustation by stromatolites help quantify volume loss during fossilisation. They provide graphically measurable, one- and two-dimensional parameters to assess percental volume loss. Our approach reveals essential shrinkage-related alterations independent of palaeoenvironment, plant material and host rock. Tissue contraction varies considerably: Unexpectedly, variability even occurs in wood from the same fossil site, the same strata and reflecting the same taphonomy. The results demonstrate that shrinkage needs to be taken into account in comparisons of morphometric data obtained from fossil and modern woods, irrespective of their particular provenance.

Single Nucleotide Polymorphism (SNP) Discovery and Association Study of Flowering Times, Crude Fat and Fatty Acid Composition in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping-by-Sequencing (GBS)

Rapeseed is the most important oil crop used in the food and biodiesel industries. In this study, based on single nucleotide polymorphism (SNP) identified from genotyping-by-sequencing (GBS), and an association study of flowering time, crude fat and fatty acid contents were investigated in 46 rapeseed mutant lines derived from gamma rays. A total of 623,026,394 clean data reads were generated with 6.6 million reads on average. A set of 37,721 filtered SNPs was used to perform gene ontology and phylogenetic analysis. Hierarchical cluster analysis of the rapeseed mutant lines gave eight groups based on flowering time and fatty acid compositions. Gene ontological analysis of the mutant lines showed that many genes displaying SNPs are involved in cellular processes, cellular anatomy, and binding. A total of 40 SNPs were significantly associated with flowering time (1 SNP), crude fat content (2 SNPs), and fatty acid content (37 SNPs). A total of 21 genes were annotated from fatty acid content SNPs; among them, nine genes were significantly enriched in reproductive processes, such as embryonic development, fruit development, and seed development. This study demonstrated that SNPs are efficient tools for mutant screening and it provides a basis that the improving the oil qualities of rapeseed.

Single-cell transcriptomes of mouse bladder urothelium uncover novel cell type markers and urothelial differentiation characteristics.

ObjectivesMuch of the information to date in terms of subtypes and function of bladder urothelial cells were derived from anatomical location or by the expression of a small number of marker genes. To have a comprehensive map of the cellular anatomy of bladder urothelial cells, we performed single‐cell RNA sequencing to thoroughly characterize mouse bladder urothelium.Materials and methodsA total of 18,917 single cells from mouse bladder urothelium were analysed by unbiased single‐cell RNA sequencing. The expression of the novel cell marker was confirmed by immunofluorescence using urinary tract infection models.ResultsUnsupervised clustering analysis identified 8 transcriptionally distinct cell subpopulations from mouse bladder urothelial cells. We discovered a novel type of bladder urothelial cells marked by Plxna4 that may be involved with host response and wound healing. We also found a group of basal‐like cells labelled by ASPM that could be the progenitor cells of adult bladder urothelium. ASPM+ urothelial cells are significantly increased after injury by UPEC. In addition, specific transcription factors were found to be associated with urothelial cell differentiation. At the last, a number of interstitial cystitis/bladder pain syndrome–regulating genes were found differentially expressed among different urothelial cell subpopulations.ConclusionsOur study provides a comprehensive characterization of bladder urothelial cells, which is fundamental to understanding the biology of bladder urothelium and associated bladder disease.

Reconstructing the Developmental Trajectories of Multiple Subtypes in Pulmonary Parenchymal Epithelial Cells by Single-Cell RNA-seq.

BackgroundSome lung diseases are cell type-specific. It is essential to study the cellular anatomy of the normal human lung for exploring the cellular origin of lung disease and the cell development trajectory.MethodsWe used the Seurat R package for data quality control. The principal component analysis (PCA) was used for linear dimensionality reduction. UMAP and tSNE were used for dimensionality reduction. Muonocle2 was used to extract lung epithelial cells to analyze the subtypes of epithelial cells further and to study the development of these cell subtypes.ResultsWe showed a total of 20154 high quality of cells from human normal lung tissue. They were initially divided into 17 clusters cells and then identified as seven types of cells, namely macrophages, monocytes, CD8 + T cells, epithelial cells, endothelial cells, adipocytes, and NK cells. 4240 epithelial cells were extracted for further analysis and they were divided into seven clusters. The seven cell clusters include alveolar cell, alveolar endothelial progenitor, ciliated cell, secretory cell, ionocyte cell, and a group of cells that are not clear at present. We show the development track of these subtypes of epithelial cells, in which we speculate that alveolar epithelial progenitor (AEP) is a kind of progenitor cells that can develop into alveolar cells, and find six essential genes that determine the cell fate, including AGER, RPL10, RPL9, RPS18, RPS27, and SFTPB.ConclusionWe provide a transcription map of human lung cells, especially the in-depth study on the development of epithelial cell subtypes, which will help us to study lung cell biology and lung diseases.