scholarly journals Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types

2019 ◽  
Author(s):  
Hanchuan Peng ◽  
Peng Xie ◽  
Lijuan Liu ◽  
Xiuli Kuang ◽  
Yimin Wang ◽  
...  
Keyword(s):  
Single Neuron ◽  
Morphological Diversity ◽  
Cell Types ◽  
Fluorescent Labeling ◽  
Computer Assisted ◽  
Large Set ◽  
Whole Brain ◽  
Wide Range ◽  
Neuronal Types ◽  
Organizational Rules

ABSTRACTEver since the seminal findings of Ramon y Cajal, dendritic and axonal morphology has been recognized as a defining feature of neuronal types. Yet our knowledge concerning the diversity of neuronal morphologies, in particular distal axonal projection patterns, is extremely limited. To systematically obtain single neuron full morphology on a brain-wide scale, we established a platform with five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We achieved sparse, robust and consistent fluorescent labeling of a wide range of neuronal types by combining transgenic or viral Cre delivery with novel transgenic reporter lines. We acquired high-resolution whole-brain fluorescent images from a large set of sparsely labeled brains using fluorescence micro-optical sectioning tomography (fMOST). We developed a set of software tools for efficient large-volume image data processing, registration to the Allen Mouse Brain Common Coordinate Framework (CCF), and computer-assisted morphological reconstruction. We reconstructed and analyzed the complete morphologies of 1,708 neurons from the striatum, thalamus, cortex and claustrum. Finally, we classified these cells into multiple morphological and projection types and identified a set of region-specific organizational rules of long-range axonal projections at the single cell level. Specifically, different neuron types from different regions follow highly distinct rules in convergent or divergent projection, feedforward or feedback axon termination patterns, and between-cell homogeneity or heterogeneity. Major molecularly defined classes or types of neurons have correspondingly distinct morphological and projection patterns, however, we also identify further remarkably extensive morphological and projection diversity at more fine-grained levels within the major types that cannot presently be accounted for by preexisting transcriptomic subtypes. These insights reinforce the importance of full morphological characterization of brain cell types and suggest a plethora of ways different cell types and individual neurons may contribute to the function of their respective circuits.

scholarly journals Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types

2020 ◽  
Author(s):  
Hanchuan Peng ◽  
Peng Xie ◽  
Lijuan Liu ◽  
Xiuli Kuang ◽  
Yimin Wang ◽  
...  
Keyword(s):  
Single Neuron ◽  
Morphological Diversity ◽  
Cell Types ◽  
Fluorescent Labeling ◽  
Computer Assisted ◽  
Large Set ◽  
Whole Brain ◽  
Wide Range ◽  
Neuronal Types ◽  
Organizational Rules

Abstract Ever since the seminal findings of Ramon y Cajal, dendritic and axonal morphology has been recognized as a defining feature of neuronal types. Yet our knowledge concerning the diversity of neuronal morphologies, in particular distal axonal projection patterns, is extremely limited. To systematically obtain single neuron full morphology on a brain-wide scale, we established a platform with five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We achieved sparse, robust and consistent fluorescent labeling of a wide range of neuronal types by combining transgenic or viral Cre delivery with novel transgenic reporter lines. We acquired high-resolution whole-brain fluorescent images from a large set of sparsely labeled brains using fluorescence micro-optical sectioning tomography (fMOST). We developed a set of software tools for efficient large-volume image data processing, registration to the Allen Mouse Brain Common Coordinate Framework (CCF), and computer-assisted morphological reconstruction. We reconstructed and analyzed the complete morphologies of 1,708 neurons from the striatum, thalamus, cortex and claustrum. Finally, we classified these cells into multiple morphological and projection types and identified a set of region-specific organizational rules of long-range axonal projections at the single cell level. Specifically, different neuron types from different regions follow highly distinct rules in convergent or divergent projection, feedforward or feedback axon termination patterns, and between-cell homogeneity or heterogeneity. Major molecularly defined classes or types of neurons have correspondingly distinct morphological and projection patterns, however, we also identify further remarkably extensive morphological and projection diversity at more fine-grained levels within the major types that cannot presently be accounted for by preexisting transcriptomic subtypes. These insights reinforce the importance of full morphological characterization of brain cell types and suggest a plethora of ways different cell types and individual neurons may contribute to the function of their respective circuits.

scholarly journals Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9690 ◽  
Author(s):  
Sérgio Ferreira-Cardoso ◽  
Pierre-Henri Fabre ◽  
Benoit de Thoisy ◽  
Frédéric Delsuc ◽  
Lionel Hautier
Keyword(s):  
Three Dimensional ◽  
Morphological Diversity ◽  
Ct Scanning ◽  
3D Models ◽  
Computer Assisted ◽  
Feeding Apparatus ◽  
Resource Exploitation ◽  
Masticatory Ability ◽  
Wide Range ◽  
Functional Shift

Background Ecological adaptations of mammals are reflected in the morphological diversity of their feeding apparatus, which includes differences in tooth crown morphologies, variation in snout size, or changes in muscles of the feeding apparatus. The adaptability of their feeding apparatus allowed them to optimize resource exploitation in a wide range of habitats. The combination of computer-assisted X-ray microtomography (µ-CT) with contrast-enhancing staining protocols has bolstered the reconstruction of three-dimensional (3D) models of muscles. This new approach allows for accurate descriptions of muscular anatomy, as well as the quick measurement of muscle volumes and fiber orientation. Ant- and termite-eating (myrmecophagy) represents a case of extreme feeding specialization, which is usually accompanied by tooth reduction or complete tooth loss, snout elongation, acquisition of a long vermiform tongue, and loss of the zygomatic arch. Many of these traits evolved independently in distantly-related mammalian lineages. Previous reports on South American anteaters (Vermilingua) have shown major changes in the masticatory, intermandibular, and lingual muscular apparatus. These changes have been related to a functional shift in the role of upper and lower jaws in the evolutionary context of their complete loss of teeth and masticatory ability. Methods We used an iodine staining solution (I2KI) to perform contrast-enhanced µ-CT scanning on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteaters. We reconstructed the musculature of the feeding apparatus of the three extant anteater genera using 3D reconstructions complemented with classical dissections of the specimens. We performed a description of the musculature of the feeding apparatus in the two morphologically divergent vermilinguan families (Myrmecophagidae and Cyclopedidae) and compared it to the association of morphological features found in other myrmecophagous placentals. Results We found that pygmy anteaters (Cyclopes) present a relatively larger and architecturally complex temporal musculature than that of collared (Tamandua) and giant (Myrmecophaga) anteaters, but shows a reduced masseter musculature, including the loss of the deep masseter. The loss of this muscle concurs with the loss of the jugal bone in Cyclopedidae. We show that anteaters, pangolins, and aardvarks present distinct anatomies despite morphological and ecological convergences.

scholarly journals Cross-Modality Coherent Registration of Whole Mouse Brains

2021 ◽  
Author(s):  
Hanchuan Peng ◽  
Lei Qu ◽  
Yuanyuan Li ◽  
Peng Xie ◽  
Lijuan Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Single Neuron ◽  
Cell Types ◽  
Brain Anatomy ◽  
Neuron Morphology ◽  
Brain Images ◽  
Whole Brain ◽  
Preparation Methods ◽  
Registration Method ◽  
3D Images

Abstract Recent whole brain mapping projects are collecting large-scale 3D images using powerful and informative modalities, such as STPT, fMOST, VISoR, or MRI. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modality image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulted from different sample preparation methods and imaging modalities. We introduced a cross-modality registration method, called mBrainAligner, which uses coherent landmark mapping as well as deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We also built a single cell resolution atlas using the fMOST modality, and used our method to generate whole brain map of 3D full single neuron morphology and neuron cell types.

scholarly journals Diversification of leech proboscis structure according to prey ingestion behavior

2020 ◽  
Author(s):  
Hee-Jin Kwak ◽  
Jung-Hyeuk Kim ◽  
Joo-Young Kim ◽  
Donggu Jeon ◽  
Doo-Hyung Lee ◽  
...  
Keyword(s):  
Circular Muscle ◽  
Morphological Diversity ◽  
Muscle Layer ◽  
Fluorescent Labeling ◽  
Behavioral Differences ◽  
Longitudinal Muscle Layer ◽  
Fluid Ingestion ◽  
External Pressures ◽  
Adult Feeding ◽  
Wide Range

Abstract Background Adaptive radiation is a phenomenon in which various organs are diversified morphologically or functionally as animals adapt to environmental inputs such as diet and circumstance. Although previous studies have addressed changes caused by various external pressures, the evidence for variation in invertebrates is not well known. Leeches comprise a carnivorous or ectoparasitic group of animals that feed on a wide range of prey. They exhibit a corresponding variety of ingestion behaviors and morphological diversity of mouthparts and gut specializations. However, research on the diversity of ingestion behaviors and the internal structure of feeding organs in leeches is little known. In this study, we use histological analyses, fluorescent labeling and immunohistochemistry to reveal the detailed proboscis structure in the family Glossiphoniidae, while also suggesting the diversification of proboscises.Results We identified the feeding behavior of rhynchobdellid leeches, which have the proboscises. Alboglossiphonia sp. swallows prey whole using its proboscis, whereas other leeches exhibit typical fluid-sucking behavior. Glossiphoniid leeches exhibit fluid ingestion behavior along with clear arrangement of longitudinal muscles, circular muscles surrounding the lumen, and radial muscles, while Alboglossiphonia sp., which displays macrophagous ingestion like salifid Barbronia sp., has a partial circular muscle distribution and spacious lumen that extends to longitudinal muscle layer. To address whether the different feeding behaviors are intrinsic, we investigated the behavioral patterns and muscle arrangements in the earlier developmental stage of glossiphoniid leeches. Juvenile Glossiphoniidae including the Alboglossiphonia sp. exhibit the fluid ingestion behavior and have the proboscis with the compartmentalized muscle layers.Conclusions Genetic, morphological and behavioral differences between juvenile and adult stages of Alboglossiphonia sp. suggest their adult feeding biology has diverged from ancestral glossiphoniid leeches, while retaining developmental vestiges of the typical juvenile feeding morphology currently observed across Glossiphoniidae. This study provides the characteristics of leeches with specific ingestion behaviors, and a comparison of structural differences that serves as the first evidence of the proboscis diversification.

scholarly journals A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality

2017 ◽  
Author(s):  
Tanya L. Daigle ◽  
Linda Madisen ◽  
Travis A. Hage ◽  
Matthew T. Valley ◽  
Ulf Knoblich ◽  
...  
Keyword(s):  
Cell Types ◽  
Single Copy ◽  
Brain Cell ◽  
Breeding Strategy ◽  
Mammalian Brain ◽  
Cell Populations ◽  
Large Set ◽  
Additional Advantage ◽  
Wide Range ◽  
Mouse Lines

SUMMARYModern genetic approaches are powerful in providing access to diverse types of neurons within the mammalian brain and greatly facilitating the study of their function. We here report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically-defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.

scholarly journals Syllabification of the Divine Comedy

2021 ◽  
Vol 14 (3) ◽  
pp. 1-26
Author(s):  
Andrea Asperti ◽  
Stefano Dal Bianco
Keyword(s):  
Text Processing ◽  
Solution Space ◽  
Generative Models ◽  
Divine Comedy ◽  
Point Of View ◽  
Computer Assisted ◽  
Wide Range ◽  
The Divine Comedy ◽  
Left And Right ◽  
Assisted Analysis

We provide a syllabification algorithm for the Divine Comedy using techniques from probabilistic and constraint programming. We particularly focus on the synalephe , addressed in terms of the "propensity" of a word to take part in a synalephe with adjacent words. We jointly provide an online vocabulary containing, for each word, information about its syllabification, the location of the tonic accent, and the aforementioned synalephe propensity, on the left and right sides. The algorithm is intrinsically nondeterministic, producing different possible syllabifications for each verse, with different likelihoods; metric constraints relative to accents on the 10th, 4th, and 6th syllables are used to further reduce the solution space. The most likely syllabification is hence returned as output. We believe that this work could be a major milestone for a lot of different investigations. From the point of view of digital humanities it opens new perspectives on computer-assisted analysis of digital sources, comprising automated detection of anomalous and problematic cases, metric clustering of verses and their categorization, or more foundational investigations addressing, e.g., the phonetic roles of consonants and vowels. From the point of view of text processing and deep learning, information about syllabification and the location of accents opens a wide range of exciting perspectives, from the possibility of automatic learning syllabification of words and verses to the improvement of generative models, aware of metric issues, and more respectful of the expected musicality.

scholarly journals A developmentally descriptive method for quantifying shape in gastropod shells

2020 ◽  
Vol 17 (163) ◽  
pp. 20190721
Author(s):  
J. Larsson ◽  
A. M. Westram ◽  
S. Bengmark ◽  
T. Lundh ◽  
R. K. Butlin
Keyword(s):  
Empirical Studies ◽  
Three Dimensional ◽  
Shell Shape ◽  
Large Set ◽  
Littorina Saxatilis ◽  
Shape Variation ◽  
Gastropod Shell ◽  
Geometric Morphometric ◽  
Wide Range ◽  
Descriptive Method

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

scholarly journals The atlas of RNase H antisense oligonucleotide distribution and activity in the CNS of rodents and non-human primates following central administration

2020 ◽  
Author(s):  
Paymaan Jafar-nejad ◽  
Berit Powers ◽  
Armand Soriano ◽  
Hien Zhao ◽  
Daniel A Norris ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Muscular Atrophy ◽  
Neurological Diseases ◽  
Cell Types ◽  
Rnase H ◽  
Central Administration ◽  
Spinal Motor Neurons ◽  
New Class ◽  
Wide Range ◽  
Therapeutic Development

Abstract Antisense oligonucleotides (ASOs) have emerged as a new class of drugs to treat a wide range of diseases, including neurological indications. Spinraza, an ASO that modulates splicing of SMN2 RNA, has shown profound disease modifying effects in Spinal Muscular Atrophy (SMA) patients, energizing efforts to develop ASOs for other neurological diseases. While SMA specifically affects spinal motor neurons, other neurological diseases affect different central nervous system (CNS) regions, neuronal and non-neuronal cells. Therefore, it is important to characterize ASO distribution and activity in all major CNS structures and cell types to have a better understanding of which neurological diseases are amenable to ASO therapy. Here we present for the first time the atlas of ASO distribution and activity in the CNS of mice, rats, and non-human primates (NHP), species commonly used in preclinical therapeutic development. Following central administration of an ASO to rodents, we observe widespread distribution and target RNA reduction throughout the CNS in neurons, oligodendrocytes, astrocytes and microglia. This is also the case in NHP, despite a larger CNS volume and more complex neuroarchitecture. Our results demonstrate that ASO drugs are well suited for treating a wide range of neurological diseases for which no effective treatments are available.

scholarly journals Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 389
Author(s):  
Pia Marter ◽  
Sixing Huang ◽  
Henner Brinkmann ◽  
Silke Pradella ◽  
Michael Jarek ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Morphological Diversity ◽  
Cell Types ◽  
Phylogenetic Position ◽  
Metagenome Analysis ◽  
New Family ◽  
Metagenome Sequencing ◽  
Axenic Strains ◽  
Reliable Classification ◽  
Metagenomic Assembly

Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.

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