From Cell Types to an Integrated Understanding of Brain Evolution: The Case of the Cerebral Cortex

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Maria Antonietta Tosches
Keyword(s):  
Developmental Biology ◽  
Cerebral Cortex ◽  
High Throughput ◽  
Neural Development ◽  
Brain Evolution ◽  
Cell Types ◽  
Annual Review ◽  
Publication Date ◽  
Structural Units

With the discovery of the incredible diversity of neurons, Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural units of nervous systems but also evolutionary units, because their identities are encoded in the genome. With the advent of high-throughput cellular transcriptomics, neuronal identities can be characterized and compared systematically across species. The comparison of neurons in mammals, reptiles, and birds indicates that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. Using the cerebral cortex as a case study, this review illustrates how comparing neuron types across species is key to reconciling observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Plant Cell Identity in the Era of Single-Cell Transcriptomics

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Kook Hui Ryu ◽  
Yan Zhu ◽  
John Schiefelbein
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Plant Cell ◽  
High Throughput ◽  
Online Publication ◽  
Plant Cells ◽  
Cell Types ◽  
Annual Review ◽  
Publication Date ◽  
Cell Identity

High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Pathogenic Mechanisms Underlying Idiopathic Pulmonary Fibrosis

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Benjamin J. Moss ◽  
Stefan W. Ryter ◽  
Ivan O. Rosas
Keyword(s):  
Epithelial Cell ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Cell Activation ◽  
Alveolar Epithelial Cell ◽  
Cell Types ◽  
Annual Review ◽  
Publication Date ◽  
Metabolic Dysfunction ◽  
Epithelial Repair

The pathogenesis of idiopathic pulmonary fibrosis (IPF) involves a complex interplay of cell types and signaling pathways. Recurrent alveolar epithelial cell (AEC) injury may occur in the context of predisposing factors (e.g., genetic, environmental, epigenetic, immunologic, and gerontologic), leading to metabolic dysfunction, senescence, aberrant epithelial cell activation, and dysregulated epithelial repair. The dysregulated epithelial cell interacts with mesenchymal, immune, and endothelial cells via multiple signaling mechanisms to trigger fibroblast and myofibroblast activation. Recent single-cell RNA sequencing studies of IPF lungs support the epithelial injury model. These studies have uncovered a novel type of AEC with characteristics of an aberrant basal cell, which may disrupt normal epithelial repair and propagate a profibrotic phenotype. Here, we review the pathogenesis of IPF in the context of novel bioinformatics tools as strategies to discover pathways of disease, cell-specific mechanisms, and cell-cell interactions that propagate the profibrotic niche. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Aging of the Retina: Molecular and Metabolic Turbulences and Potential Interventions

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Laura Campello ◽  
Nivedita Singh ◽  
Jayshree Advani ◽  
Anupam K. Mondal ◽  
Ximena Corso-Diaz ◽  
...  
Keyword(s):  
Healthy Aging ◽  
Cell Types ◽  
Lifestyle Changes ◽  
Annual Review ◽  
Past Century ◽  
Publication Date ◽  
Vision Science ◽  
Human Lifespan ◽  
Cellular Events ◽  
Age Related

Multifaceted and divergent manifestations across tissues and cell types have curtailed advances in deciphering the cellular events that accompany advanced age and contribute to morbidities and mortalities. Increase in human lifespan during the past century has heightened awareness of the need to prevent age-associated frailty of neuronal and sensory systems to allow a healthy and productive life. In this review, we discuss molecular and physiological attributes of aging of the retina, with a goal of understanding age-related impairment of visual function. We highlight the epigenome–metabolism nexus and proteostasis as key contributors to retinal aging and discuss lifestyle changes as potential modulators of retinal function. Finally, we deliberate promising intervention strategies for promoting healthy aging of the retina for improved vision. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Integrated Patterning Programs During Drosophila Development Generate the Diversity of Neurons and Control Their Mature Properties

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
Anthony M. Rossi ◽  
Shadi Jafari ◽  
Claude Desplan
Keyword(s):  
Stem Cells ◽  
Nervous System ◽  
Neural Stem Cells ◽  
Cell Types ◽  
Annual Review ◽  
Publication Date ◽  
Temporal Patterning ◽  
Long Time ◽  
Neuronal Types ◽  
And Control

During the approximately 5 days of Drosophila neurogenesis (late embryogenesis to the beginning of pupation), a limited number of neural stem cells produce approximately 200,000 neurons comprising hundreds of cell types. To build a functional nervous system, neuronal types need to be produced in the proper places, appropriate numbers, and correct times. We discuss how neural stem cells (neuroblasts) obtain so-called area codes for their positions in the nervous system (spatial patterning) and how they keep time to sequentially produce neurons with unique fates (temporal patterning). We focus on specific examples that demonstrate how a relatively simple patterning system (Notch) can be used reiteratively to generate different neuronal types. We also speculate on how different modes of temporal patterning that operate over short versus long time periods might be linked. We end by discussing how specification programs are integrated and lead to the terminal features of different neuronal types. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Emerging Capabilities for the High-Throughput Characterization of Structural Materials

2021 ◽  
Vol 51 (1) ◽  
Author(s):  
Daniel B. Miracle ◽  
Mu Li ◽  
Zhaohan Zhang ◽  
Rohan Mishra ◽  
Katharine M. Flores
Keyword(s):  
High Throughput ◽  
Materials Science ◽  
Structural Materials ◽  
Rapid Screening ◽  
Annual Review ◽  
Publication Date ◽  
Synthesis Methods ◽  
Alloy Development ◽  
Composition Gradients ◽  
Future Vision

Structural materials have lagged behind other classes in the use of combinatorial and high-throughput (CHT) methods for rapid screening and alloy development. The dual complexities of composition and microstructure are responsible for this, along with the need to produce bulk-like, defect-free materials libraries. This review evaluates recent progress in CHT evaluations for structural materials. High-throughput computations can augment or replace experiments and accelerate data analysis. New synthesis methods, including additive manufacturing, can rapidly produce composition gradients or arrays of discrete alloys-on-demand in bulk form, and new experimental methods have been validated for nearly all essential structural materials properties. The remaining gaps are CHT measurement of bulk tensile strength, ductility, and melting temperature and production of microstructural libraries. A search strategy designed for structural materials gains efficiency by performing two layers of evaluations before addressing microstructure, and this review closes with a future vision of the autonomous, closed-loop CHT exploration of structural materials. Expected final online publication date for the Annual Review of Materials Science, Volume 51 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

β-Arrestins as Important Regulators of Glucose and Energy Homeostasis

2021 ◽  
Vol 84 (1) ◽  
Author(s):  
Sai P. Pydi ◽  
Luiz F. Barella ◽  
Lu Zhu ◽  
Jaroslawna Meister ◽  
Mario Rossi ◽  
...  
Keyword(s):  
Energy Homeostasis ◽  
Cell Types ◽  
Mutant Mice ◽  
Whole Body ◽  
Annual Review ◽  
Publication Date ◽  
Cytoplasmic Proteins ◽  
New Findings ◽  
Novel Drugs ◽  
G Protein Coupled

β-Arrestin-1 and -2 (also known as arrestin-2 and -3, respectively) are ubiquitously expressed cytoplasmic proteins that dampen signaling through G protein–coupled receptors. However, β-arrestins can also act as signaling molecules in their own right. To investigate the potential metabolic roles of the two β-arrestins in modulating glucose and energy homeostasis, recent studies analyzed mutant mice that lacked or overexpressed β-arrestin-1 and/or -2 in distinct, metabolically important cell types. Metabolic analysis of these mutant mice clearly demonstrated that both β-arrestins play key roles in regulating the function of most of these cell types, resulting in striking changes in whole-body glucose and/or energy homeostasis. These studies also revealed that β-arrestin-1 and -2, though structurally closely related, clearly differ in their metabolic roles under physiological and pathophysiological conditions. These new findings should guide the development of novel drugs for the treatment of various metabolic disorders, including type 2 diabetes and obesity. Expected final online publication date for the Annual Review of Physiology, Volume 84 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Toward a Mechanistic Understanding of Bacterial Rod Shape Formation and Regulation

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Ethan C. Garner
Keyword(s):  
Developmental Biology ◽  
Online Publication ◽  
Complex Problem ◽  
Annual Review ◽  
Publication Date ◽  
Simple Shape ◽  
Shape Formation ◽  
Mechanistic Understanding

One of the most common bacterial shapes is a rod, yet we have a limited understanding of how this simple shape is constructed. While only six proteins are required for rod shape, we are just beginning to understand how they self-organize to build the micron-sized enveloping structures that define bacterial shape out of nanometer-sized glycan strains. Here, we detail and summarize the insights gained over the last 20 years into this complex problem that have been achieved with a wide variety of different approaches. We also explain and compare both current and past models of rod shape formation and maintenance and then highlight recent insights into how the Rod complex might be regulated. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Generating and Using Transcriptomically Based Retinal Cell Atlases

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Karthik Shekhar ◽  
Joshua R. Sanes
Keyword(s):  
Expression Patterns ◽  
Retinal Disease ◽  
Cell Types ◽  
Retinal Cell ◽  
Annual Review ◽  
Publication Date ◽  
Vertebrate Species ◽  
Retinal Cells ◽  
Vision Science ◽  
The Brain

It has been known for over a century that the basic organization of the retina is conserved across vertebrates. It has been equally clear that retinal cells can be classified into numerous types, but only recently have methods been devised to explore this diversity in unbiased, scalable, and comprehensive ways. Advances in high-throughput single-cell RNA-sequencing (scRNA-seq) have played a pivotal role in this effort. In this article, we outline the experimental and computational components of scRNA-seq and review studies that have used them to generate retinal atlases of cell types in several vertebrate species. These atlases have enabled studies of retinal development, responses of retinal cells to injury, expression patterns of genes implicated in retinal disease, and the evolution of cell types. Recently, the inquiry has expanded to include the entire eye and visual centers in the brain. These studies have enhanced our understanding of retinal function and dysfunction and provided tools and insights for exploring neural diversity throughout the brain. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Metabolic Gatekeepers of Pathological B Cell Activation

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Teresa Sadras ◽  
Lai N. Chan ◽  
Gang Xiao ◽  
Markus Müschen
Keyword(s):  
B Cells ◽  
B Cell ◽  
Cell Activation ◽  
Cell Types ◽  
Cell Receptor ◽  
Annual Review ◽  
Publication Date ◽  
B Cell Activation ◽  
Dna Double Strand Breaks ◽  
Increased Risk

Unlike other cell types, B cells undergo multiple rounds of V(D)J recombination and hypermutation to evolve high-affinity antibodies. Reflecting high frequencies of DNA double-strand breaks, adaptive immune protection by B cells comes with an increased risk of malignant transformation. In addition, the vast majority of newly generated B cells express an autoreactive B cell receptor (BCR). Thus, B cells are under intense selective pressure to remove autoreactive and premalignant clones. Despite stringent negative selection, B cells frequently give rise to autoimmune disease and B cell malignancies. In this review, we discuss mechanisms that we term metabolic gatekeepers to eliminate pathogenic B cell clones on the basis of energy depletion. Chronic activation signals from autoreactive BCRs or transforming oncogenes increase energy demands in autoreactive and premalignant B cells. Thus, metabolic gatekeepers limit energy supply to levels that are insufficient to fuel either a transforming oncogene or hyperactive signaling from an autoreactive BCR. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 16 is February 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Promoters and Antagonists of Phagocytosis: A Plastic and Tunable Response

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Spencer Freeman ◽  
Sergio Grinstein
Keyword(s):  
Developmental Biology ◽  
Environmental Factors ◽  
Therapeutic Intervention ◽  
Online Publication ◽  
Membrane Traffic ◽  
Annual Review ◽  
Publication Date ◽  
Physical Barriers ◽  
Inside Out

Recent observations indicate that, rather than being an all-or-none response, phagocytosis is finely tuned by a host of developmental and environmental factors. The expression of key phagocytic determinants is regulated via transcriptional and epigenetic means that confer memory on the process. Membrane traffic, the cytoskeleton, and inside-out signaling control the activation of phagocytic receptors and their ability to access their targets. An exquisite extra layer of complexity is introduced by the coexistence of distinct “eat-me” and “don't-eat-me” signals on targets and of corresponding “eat” and “don't-eat” receptors on the phagocyte surface. Moreover, assorted physical barriers constitute “don't-come-close-to-me” hurdles that obstruct the engagement of ligands by receptors. The expression, mobility, and accessibility of all these determinants can be modulated, conferring extreme plasticity on phagocytosis and providing attractive targets for therapeutic intervention in cancer, atherosclerosis, and dementia. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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