How Cortical Circuits Implement Cortical Computations: Mouse Visual Cortex as a Model

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
Cristopher M. Niell ◽  
Massimo Scanziani
Keyword(s):  
Visual Cortex ◽  
Cortical Neurons ◽  
Model Organism ◽  
Annual Review ◽  
Publication Date ◽  
Cortical Circuits ◽  
Cortical Function ◽  
Mouse Visual Cortex ◽  
The Brain ◽  
Insight Into

The mouse, as a model organism to study the brain, gives us unprecedented experimental access to the mammalian cerebral cortex. By determining the cortex's cellular composition, revealing the interaction between its different components, and systematically perturbing these components, we are obtaining mechanistic insight into some of the most basic properties of cortical function. In this review, we describe recent advances in our understanding of how circuits of cortical neurons implement computations, as revealed by the study of mouse primary visual cortex. Further, we discuss how studying the mouse has broadened our understanding of the range of computations performed by visual cortex. Finally, we address how future approaches will fulfill the promise of the mouse in elucidating fundamental operations of cortex. 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.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Development and Molecular Genetics of Marchantia polymorpha

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Takayuki Kohchi ◽  
Katsuyuki T. Yamato ◽  
Kimitsune Ishizaki ◽  
Shohei Yamaoka ◽  
Ryuichi Nishihama
Keyword(s):  
Model Organism ◽  
Land Plant ◽  
Marchantia Polymorpha ◽  
Annual Review ◽  
Publication Date ◽  
Molecular Tools ◽  
Genetic Redundancy ◽  
Morphological Differences ◽  
Evo Devo ◽  
Basal Position

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Diving into the world of alcohol teratogenesis: a review of zebrafish models of fetal alcohol spectrum disorder

2018 ◽  
Vol 96 (2) ◽  
pp. 88-97 ◽  
Author(s):  
Yohaan Fernandes ◽  
Desire M. Buckley ◽  
Johann K. Eberhart
Keyword(s):  
Fetal Alcohol Spectrum Disorder ◽  
Model Organism ◽  
Spectrum Disorder ◽  
Structural Defects ◽  
Craniofacial Skeleton ◽  
Fetal Alcohol ◽  
Embryonic Exposure ◽  
Fetal Alcohol Spectrum ◽  
The Brain ◽  
Insight Into

The term fetal alcohol spectrum disorder (FASD) refers to the entire suite of deleterious outcomes resulting from embryonic exposure to alcohol. Along with other reviews in this special issue, we provide insight into how animal models, specifically the zebrafish, have informed our understanding of FASD. We first provide a brief introduction to FASD. We discuss the zebrafish as a model organism and its strengths for alcohol research. We detail how zebrafish has been used to model some of the major defects present in FASD. These include behavioral defects, such as social behavior as well as learning and memory, and structural defects, disrupting organs such as the brain, sensory organs, heart, and craniofacial skeleton. We provide insights into how zebrafish research has aided in our understanding of the mechanisms of ethanol teratogenesis. We end by providing some relatively recent advances that zebrafish has provided in characterizing gene-ethanol interactions that may underlie FASD.

scholarly journals The Geometry of Information Coding in Correlated Neural Populations

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
Rava Azeredo da Silveira ◽  
Fred Rieke
Keyword(s):  
Neural Coding ◽  
Neural Population ◽  
Annual Review ◽  
Publication Date ◽  
Information Coding ◽  
Population Code ◽  
New Approach ◽  
Neural Populations ◽  
The Brain ◽  
Theoretical Developments

Neurons in the brain represent information in their collective activity. The fidelity of this neural population code depends on whether and how variability in the response of one neuron is shared with other neurons. Two decades of studies have investigated the influence of these noise correlations on the properties of neural coding. We provide an overview of the theoretical developments on the topic. Using simple, qualitative, and general arguments, we discuss, categorize, and relate the various published results. We emphasize the relevance of the fine structure of noise correlation, and we present a new approach to the issue. Throughout this review, we emphasize a geometrical picture of how noise correlations impact the neural code. 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.

scholarly journals Variations in photoreceptor throughput to mouse visual cortex and the unique effects on tuning

2020 ◽  
Author(s):  
I. Rhim ◽  
G. Coello-Reyes ◽  
I. Nauhaus
Keyword(s):  
Visual Cortex ◽  
Visual Field ◽  
Adaptive Filtering ◽  
Frequency Tuning ◽  
Cortical Circuits ◽  
Spatial Frequency Tuning ◽  
Upper Visual Field ◽  
Spatio Temporal ◽  
Mouse Visual Cortex ◽  
Common Laboratory

ABSTRACTVisual input to primary visual cortex (V1) depends on highly adaptive filtering in the retina. In turn, isolation of V1 computations to study cortical circuits requires control over retinal adaption and its corresponding spatio-temporal-chromatic output. Here, we first measure the balance of input to V1 from the three main photoreceptor opsins – M-opsin, S-opsin, and rhodopsin – as a function of light adaption and retinotopy. Results show that V1 is rod-mediated in common laboratory settings, yet cone-mediated in natural daylight, as evidenced by exclusive sensitivity to UV wavelengths via cone S-opsin in the upper visual field. Next, we show that cone-mediated V1 responds to 2.5-fold higher temporal frequencies than rod-mediated V1. Furthermore, cone-mediated V1 has smaller RFs, yet similar spatial frequency tuning. V1 responses in rod-deficient (Gnat1−/−) mice confirm that the effects are due to differences in photoreceptor contribution. This study provides foundation for using mouse V1 to study cortical circuits.

scholarly journals Reeling in the Zebrafish Cancer Models

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Alicia M. McConnell ◽  
Haley R. Noonan ◽  
Leonard I. Zon
Keyword(s):  
Cancer Biology ◽  
Model Organism ◽  
Transgenic Animals ◽  
Annual Review ◽  
Transgenic Zebrafish ◽  
Publication Date ◽  
Cancer Therapies ◽  
Cancer Models ◽  
Cancer Types ◽  
New Cancer Therapies

Zebrafish are rapidly becoming a leading model organism for cancer research. The genetic pathways driving cancer are highly conserved between zebrafish and humans, and the ability to easily manipulate the zebrafish genome to rapidly generate transgenic animals makes zebrafish an excellent model organism. Transgenic zebrafish containing complex, patient-relevant genotypes have been used to model many cancer types. Here we present a comprehensive review of transgenic zebrafish cancer models as a resource to the field and highlight important areas of cancer biology that have yet to be studied in the fish. The ability to image cancer cells and niche biology in an endogenous tumor make zebrafish an indispensable model organism in which we can further understand the mechanisms that drive tumorigenesis and screen for potential new cancer therapies. Expected final online publication date for the Annual Review of Cancer Biology, Volume 5 is March 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Regulation of Mitochondrial Ca2+ Uptake

2020 ◽  
Vol 83 (1) ◽  
Author(s):  
Elizabeth Murphy ◽  
Charles Steenbergen
Keyword(s):  
Cell Death ◽  
Genetic Alterations ◽  
Annual Review ◽  
Publication Date ◽  
Mitochondrial Matrix ◽  
Atp Production ◽  
The Past ◽  
Specific Manner ◽  
Insight Into ◽  
Disease Specific

Mitochondria are responsible for ATP production but are also known as regulators of cell death, and mitochondrial matrix Ca2+ is a key modulator of both ATP production and cell death. Although mitochondrial Ca2+ uptake and efflux have been studied for over 50 years, it is only in the past decade that the proteins responsible for mitochondrial Ca2+ uptake and efflux have been identified. The identification of the mitochondrial Ca2+ uniporter (MCU) led to an explosion of studies identifying regulators of the MCU. The levels of these regulators vary in a tissue- and disease-specific manner, providing new insight into how mitochondrial Ca2+ is regulated. This review focuses on the proteins responsible for mitochondrial transport and what we have learned from mouse studies with genetic alterations in these proteins. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Inferring cortical function in the mouse visual system through large-scale systems neuroscience

2016 ◽  
Vol 113 (27) ◽  
pp. 7337-7344 ◽  
Author(s):  
Michael Hawrylycz ◽  
Costas Anastassiou ◽  
Anton Arkhipov ◽  
Jim Berg ◽  
Michael Buice ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Large Scale ◽  
Model Organism ◽  
Building Blocks ◽  
Mammalian Brain ◽  
Cortical Function ◽  
Scientific Mission ◽  
Large Populations ◽  
Cell Type Specific ◽  
And Behavior

The scientific mission of the Project MindScope is to understand neocortex, the part of the mammalian brain that gives rise to perception, memory, intelligence, and consciousness. We seek to quantitatively evaluate the hypothesis that neocortex is a relatively homogeneous tissue, with smaller functional modules that perform a common computational function replicated across regions. We here focus on the mouse as a mammalian model organism with genetics, physiology, and behavior that can be readily studied and manipulated in the laboratory. We seek to describe the operation of cortical circuitry at the computational level by comprehensively cataloging and characterizing its cellular building blocks along with their dynamics and their cell type-specific connectivities. The project is also building large-scale experimental platforms (i.e., brain observatories) to record the activity of large populations of cortical neurons in behaving mice subject to visual stimuli. A primary goal is to understand the series of operations from visual input in the retina to behavior by observing and modeling the physical transformations of signals in the corticothalamic system. We here focus on the contribution that computer modeling and theory make to this long-term effort.

scholarly journals Neuronal adaptation reveals a suboptimal decoding of orientation tuned populations in the mouse visual cortex

2018 ◽  
Author(s):  
Miaomiao Jin ◽  
Jeffrey M. Beck ◽  
Lindsey L. Glickfeld
Keyword(s):  
Visual Cortex ◽  
Visual System ◽  
Cortical Neurons ◽  
Signal To Noise Ratio ◽  
Sensory Information ◽  
Orientation Discrimination ◽  
Signal To Noise ◽  
Neuronal Adaptation ◽  
Related Information ◽  
Mouse Visual Cortex

AbstractSensory information is encoded by populations of cortical neurons. Yet, it is unknown how this information is used for even simple perceptual choices such as discriminating orientation. To determine the computation underlying this perceptual choice, we took advantage of the robust adaptation in the mouse visual system. We find that adaptation increases animals’ thresholds for orientation discrimination. This was unexpected since optimal computations that take advantage of all available sensory information predict that the shift in tuning and increase in signal-to-noise ratio in the adapted condition should improve discrimination. Instead, we find that the effects of adaptation on behavior can be explained by the appropriate reliance of the perceptual choice circuits on target preferring neurons, but the failure to discount neurons that prefer the distractor. This suggests that to solve this task the circuit has adopted a suboptimal strategy that discards important task-related information to implement a feed-forward visual computation.

scholarly journals A Scalable and Modular Automated Pipeline for Stitching of Large Electron Microscopy Datasets

2021 ◽  
Author(s):  
Gayathri Mahalingam ◽  
Russel Torres ◽  
Daniel Kapner ◽  
Eric T Trautman ◽  
Tim Fliss ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Visual Cortex ◽  
High Throughput ◽  
Serial Section ◽  
Large Scale ◽  
Software Pipeline ◽  
Array Tomography ◽  
Automated Quality Control ◽  
Mouse Visual Cortex ◽  
The Brain

Serial section Electron Microscopy can produce high throughput imaging of large biological specimen volumes. The high-resolution images are necessary to reconstruct dense neural wiring diagrams in the brain, so called connectomes. A high fidelity volume assembly is required to correctly reconstruct neural anatomy and synaptic connections. It involves seamless 2D stitching of the images within a serial section followed by 3D alignment of the stitched sections. The high throughput of ssEM necessitates 2D stitching to be done at the pace of imaging, which currently produces tens of terabytes per day. To achieve this, we present a modular volume assembly software pipeline ASAP(Assembly Stitching and Alignment Pipeline) that is scalable and parallelized to work with distributed systems. The pipeline is built on top of the Render [18] services used in the volume assembly of the brain of adult Drosophila melanogaster [2]. It achieves high throughput by operating on the meta-data and transformations of each image stored in a database, thus eliminating the need to render intermediate output. The modularity of ASAP allows for easy adaptation to new algorithms without significant changes to the workflow. The software pipeline includes a complete set of tools to do stitching, automated quality control, 3D section alignment, and rendering of the assembled volume to disk. We also implemented a workflow engine that executes the volume assembly workflow in an automated fashion triggered following the transfer of raw data. ASAP has been successfully utilized for continuous processing of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex [1, 25]. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.

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