With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and... Show moreWith the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and gene expression information about cells in tissue sections at single cell resolution. Cell type classification of these spatially-resolved cells can be inferred by matching the spatial transcriptomics data to reference atlases derived from single cell RNA-sequencing (scRNA-seq) in which cell types are defined by differences in their gene expression profiles. However, robust cell type matching of the spatially-resolved cells to reference scRNA-seq atlases is challenging due to the intrinsic differences in resolution between the spatial and scRNA-seq data. In this study, we systematically evaluated six computational algorithms for cell type matching across four image-based spatial transcriptomics experimental protocols (MERFISH, smFISH, BaristaSeq, and ExSeq) conducted on the same mouse primary visual cortex (VISp) brain region. We find that many cells are assigned as the same type by multiple cell type matching algorithms and are present in spatial patterns previously reported from scRNA-seq studies in VISp. Furthermore, by combining the results of individual matching strategies into consensus cell type assignments, we see even greater alignment with biological expectations. We present two ensemble meta-analysis strategies used in this study and share the consensus cell type matching results in the Cytosplore Viewer (https://viewer.cytosplore.org) for interactive visualization and data exploration. The consensus matching can also guide spatial data analysis using SSAM, allowing segmentation-free cell type assignment. Show less
Hawrylycz, M.; Martone, M.E.; Ascoli, G.A.; Bjaalie, J.G.; Dong, H.W.; Ghosh, S.S.; ... ; Zingg, B. 2023
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain.... Show moreCharacterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain. Show less
Cackett, E.M.; Gelbord, J.; Barth, A.J.; De Rosa, G.; Edelson, R.; Goad, M.R.; ... ; Zaidouni, F. 2023
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals(1). Here, using high-throughput transcriptomic and epigenomic profiling of... Show moreThe primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals(1). Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations. Show less
Kara, E.; Mehdipour, M.; Kriss, G.A.; Cackett, E.M.; Arav, N.; Barth, A.J.; ... ; Zu, Y. 2021
The family Hahniidae is reported from Thailand for the first time. The genus Hexamatia gen. nov. and two new species, Hexamatia seekhaow gen. et sp. nov. and Hahnia ngai sp. nov., are described and... Show moreThe family Hahniidae is reported from Thailand for the first time. The genus Hexamatia gen. nov. and two new species, Hexamatia seekhaow gen. et sp. nov. and Hahnia ngai sp. nov., are described and illustrated. DNA sequences are provided for all the species reported here. The phylogenetic position of the novel genus Hexamatia gen. nov. and its relation to Hahnia are discussed. Based on these results, a new combination is proposed for Hexamatia senaria (Zhang, Li & Zheng, 2011) gen. et comb. nov. = Hahnia senaria. Known distribution of the species Hahnia saccata Zhang, Li & Zheng, 2011, originally described from China, is expanded. A brief review and notes on the taxonomy of the six-eyed hahniids are included. Show less
Rivera Quiroz, F.A.; Schilthuizen, M.; Petcharad, B.; Miller, J.A. 2020
Bilateral asymmetry in the genitalia is a rare but widely dispersed phenomenon in the animal tree of life. In arthropods, occurrences vary greatly from one group to another and there seems to be no... Show moreBilateral asymmetry in the genitalia is a rare but widely dispersed phenomenon in the animal tree of life. In arthropods, occurrences vary greatly from one group to another and there seems to be no common explanation for all the independent origins. In spiders, genital asymmetry appears to be especially rare. Most known species show almost perfectly symmetrical genitals with the right and left sides being mirror images of each other. However, some examples of asymmetric genitalia have been studied and many other reports are scattered in the taxonomic literature. Based on a broad literature survey, we found several species in thirteen families with evidence of genital asymmetry, mostly expressed only in females. Our review suggests that spider genital asymmetries, although rare, are more common than previously thought and taxonomic descriptions and illustrations are a useful but not entirely reliable tool for studying them. Here we also report on directional asymmetry in the liocranid spider Teutamus politus, the first known case of morphologically asymmetric male genitals in Entelegynae spiders. Generalities, evolution and categorization of asymmetry in spiders are further discussed. Show less
BackgroundMales of Opadometa are difficult to associate with conspecific females, and sex-matching errors may persist in the taxonomic literature. Recommended best practices for definitive sex... Show moreBackgroundMales of Opadometa are difficult to associate with conspecific females, and sex-matching errors may persist in the taxonomic literature. Recommended best practices for definitive sex matching in this genus suggest finding a male in the web of a female, or better yet, mating pairs.New informationA male Opadometa was observed hanging on a frame line of the web of a female Opadometa sarawakensis, a species for which the male was previously undescribed. This occurred during a tropical ecology field course held at the Danau Girang Field Centre in Sabah, Malaysia. A taxonomic description was completed as a course activity. Show less
