scholarly journals A Connectome of the Adult Drosophila Central Brain

2020 ◽  
Author(s):  
C. Shan Xu ◽  
Michal Januszewski ◽  
Zhiyuan Lu ◽  
Shin-ya Takemura ◽  
Kenneth J. Hayworth ◽  
...  
Keyword(s):  
Large Fraction ◽  
Large Data ◽  
Fruit Fly ◽  
Cell Types ◽  
Brain Regions ◽  
Central Complex ◽  
Data Set ◽  
New Methods ◽  
Central Brain ◽  
The Brain

AbstractThe neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete circuits of small animals, with hundreds of neurons, and selected circuits for larger animals. Here we (the FlyEM project at Janelia and collaborators at Google) summarize new methods and present the complete circuitry of a large fraction of the brain of a much more complex animal, the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses, and proofread such large data sets; new methods that define cell types based on connectivity in addition to morphology; and new methods to simplify access to a large and evolving data set. From the resulting data we derive a better definition of computational compartments and their connections; an exhaustive atlas of cell examples and types, many of them novel; detailed circuits for most of the central brain; and exploration of the statistics and structure of different brain compartments, and the brain as a whole. We make the data public, with a web site and resources specifically designed to make it easy to explore, for all levels of expertise from the expert to the merely curious. The public availability of these data, and the simplified means to access it, dramatically reduces the effort needed to answer typical circuit questions, such as the identity of upstream and downstream neural partners, the circuitry of brain regions, and to link the neurons defined by our analysis with genetic reagents that can be used to study their functions.Note: In the next few weeks, we will release a series of papers with more involved discussions. One paper will detail the hemibrain reconstruction with more extensive analysis and interpretation made possible by this dense connectome. Another paper will explore the central complex, a brain region involved in navigation, motor control, and sleep. A final paper will present insights from the mushroom body, a center of multimodal associative learning in the fly brain.

scholarly journals A Connectome and Analysis of the Adult Drosophila Central Brain

2020 ◽  
Author(s):  
Louis K. Scheffer ◽  
C. Shan Xu ◽  
Michal Januszewski ◽  
Zhiyuan Lu ◽  
Shin-ya Takemura ◽  
...  
Keyword(s):  
Large Fraction ◽  
Large Data ◽  
Fruit Fly ◽  
Cell Types ◽  
Large Data Sets ◽  
Data Sets ◽  
Central Brain ◽  
Chemical Synapses ◽  
New Procedures ◽  
Improved Methods

AbstractThe neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain.

scholarly journals A connectome and analysis of the adult Drosophila central brain

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Louis K Scheffer ◽  
C Shan Xu ◽  
Michal Januszewski ◽  
Zhiyuan Lu ◽  
Shin-ya Takemura ◽  
...  
Keyword(s):  
Large Fraction ◽  
Large Data ◽  
Fruit Fly ◽  
Cell Types ◽  
Large Data Sets ◽  
Data Sets ◽  
Central Brain ◽  
Chemical Synapses ◽  
New Procedures ◽  
Improved Methods

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain.

scholarly journals Functional divisions for visual processing in the central brain of flying Drosophila

2015 ◽  
Vol 112 (40) ◽  
pp. E5523-E5532 ◽  
Author(s):  
Peter T. Weir ◽  
Michael H. Dickinson
Keyword(s):  
Visual Processing ◽  
Visual Stimuli ◽  
Automated Analysis ◽  
Fruit Fly ◽  
Cell Types ◽  
Visual Responses ◽  
Behavioral Context ◽  
Central Brain ◽  
Brain Circuit ◽  
The Brain

Although anatomy is often the first step in assigning functions to neural structures, it is not always clear whether architecturally distinct regions of the brain correspond to operational units. Whereas neuroarchitecture remains relatively static, functional connectivity may change almost instantaneously according to behavioral context. We imaged panneuronal responses to visual stimuli in a highly conserved central brain region in the fruit fly, Drosophila, during flight. In one substructure, the fan-shaped body, automated analysis revealed three layers that were unresponsive in quiescent flies but became responsive to visual stimuli when the animal was flying. The responses of these regions to a broad suite of visual stimuli suggest that they are involved in the regulation of flight heading. To identify the cell types that underlie these responses, we imaged activity in sets of genetically defined neurons with arborizations in the targeted layers. The responses of this collection during flight also segregated into three sets, confirming the existence of three layers, and they collectively accounted for the panneuronal activity. Our results provide an atlas of flight-gated visual responses in a central brain circuit.

scholarly journals Location Matters: Navigating Regional Heterogeneity of the Neurovascular Unit

2021 ◽  
Vol 15 ◽  
Author(s):  
Louis-Philippe Bernier ◽  
Clément Brunner ◽  
Azzurra Cottarelli ◽  
Matilde Balbi
Keyword(s):  
Brain Function ◽  
Energy Demand ◽  
Neurovascular Unit ◽  
Cell Types ◽  
Brain Regions ◽  
Regional Heterogeneity ◽  
Regional Specialization ◽  
Multiple Cell ◽  
Cellular Components ◽  
The Brain

The neurovascular unit (NVU) of the brain is composed of multiple cell types that act synergistically to modify blood flow to locally match the energy demand of neural activity, as well as to maintain the integrity of the blood-brain barrier (BBB). It is becoming increasingly recognized that the functional specialization, as well as the cellular composition of the NVU varies spatially. This heterogeneity is encountered as variations in vascular and perivascular cells along the arteriole-capillary-venule axis, as well as through differences in NVU composition throughout anatomical regions of the brain. Given the wide variations in metabolic demands between brain regions, especially those of gray vs. white matter, the spatial heterogeneity of the NVU is critical to brain function. Here we review recent evidence demonstrating regional specialization of the NVU between brain regions, by focusing on the heterogeneity of its individual cellular components and briefly discussing novel approaches to investigate NVU diversity.

scholarly journals An Approach to Efficient Dictionary Utilization and Improved Data Compression Technique for LZW Algorithm

2020 ◽  
Vol 10 (2) ◽  
pp. 224-229
Keyword(s):  
Data Compression ◽  
Conventional Method ◽  
Large Data ◽  
Compression Algorithm ◽  
Case Scenario ◽  
Compression Technique ◽  
Data Set ◽  
New Methods ◽  
Lzw Algorithm ◽  
The Way

This paper proposes an improved data compression technique compared to existing Lempel-Ziv-Welch (LZW) algorithm. LZW is a dictionary-updation based compression technique which stores elements from the data in the form of codes and uses them when those strings recur again. When the dictionary gets full, every element in the dictionary are removed in order to update dictionary with new entry. Therefore, the conventional method doesn’t consider frequently used strings and removes all the entry. This method is not an effective compression when the data to be compressed are large and when there are more frequently occurring string. This paper presents two new methods which are an improvement for the existing LZW compression algorithm. In this method, when the dictionary gets full, the elements that haven’t been used earlier are removed rather than removing every element of the dictionary which happens in the existing LZW algorithm. This is achieved by adding a flag to every element of the dictionary. Whenever an element is used the flag is set high. Thus, when the dictionary gets full, the dictionary entries where the flag was set high are kept and others are discarded. In the first method, the entries are discarded abruptly, whereas in the second method the unused elements are removed once at a time. Therefore, the second method gives enough time for the nascent elements of the dictionary. These techniques all fetch similar results when data set is small. This happens due to the fact that difference in the way they handle the dictionary when it’s full. Thus these improvements fetch better results only when a relatively large data is used. When all the three techniques' models were used to compare a data set with yields best case scenario, the compression ratios of conventional LZW is small compared to improved LZW method-1 and which in turn is small compared to improved LZW method-2.

scholarly journals STAB: a spatio-temporal cell atlas of the human brain

2020 ◽  
Vol 49 (D1) ◽  
pp. D1029-D1037
Author(s):  
Liting Song ◽  
Shaojun Pan ◽  
Zichao Zhang ◽  
Longhao Jia ◽  
Wei-Hua Chen ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Temporal Dynamics ◽  
Cell Types ◽  
Brain Regions ◽  
Molecular Characteristics ◽  
Great Effort ◽  
Brain Functions ◽  
Spatio Temporal ◽  
The Brain

Abstract The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.

Three-Dimensional Time-Lapse Digital Movie Analysis of the Developing Fruit Fly Eye in Organ Culture

1997 ◽  
Vol 3 (S2) ◽  
pp. 1129-1130
Author(s):  
John Archie Pollock ◽  
Bejon T. Maneckshana ◽  
Teresa E. Leonardo
Keyword(s):  
Organ Culture ◽  
Compound Eye ◽  
Eye Development ◽  
Larval Instar ◽  
Three Dimensional ◽  
Fruit Fly ◽  
Time Lapse ◽  
Cell Types ◽  
Specific Cell ◽  
The Brain

The compound eye of the fruit fly, Drosophila melanogaster, is composed of a highly ordered array of facets (FIG. 1), each containing a precise set of neurons and supporting cells. The eye arises during the third larval instar from an undifferentiated epithelium, the eye imaginai disc, which is connected to the brain via the optic stalk (FIG. 2). During eye development, movement of the morphogenetic furrow, progressive recruitment of specific cell types and the growth of photoreceptor axons into the brain are each dynamic processes that are routinely studied indirectly in fixed tissues. While stereotyped development and the ‘crystalline’ like structure of the eye facilitates this analysis, certain experiments are hindered by the inability to observe developmental processes as they occur. To overcome this limitation, we have combined organ culture with advanced microscopy tools to enable the observation of eye development in living tissue.

scholarly journals Regulation and Modulation of pH in the Brain

2003 ◽  
Vol 83 (4) ◽  
pp. 1183-1221 ◽  
Author(s):  
MITCHELL CHESLER
Keyword(s):  
Intracellular Ph ◽  
Neural Activity ◽  
Extracellular Fluid ◽  
Cell Types ◽  
Brain Regions ◽  
Metabolic Products ◽  
Homeostatic Function ◽  
Acid Extrusion ◽  
Activity Dependent ◽  
The Brain

Chesler, Mitchell. Regulation and Modulation of pH in the Brain. Physiol Rev 83: 1183-1221, 2003; 10.1152/physrev.00010.2003.—The regulation of pH is a vital homeostatic function shared by all tissues. Mechanisms that govern H+ in the intracellular and extracellular fluid are especially important in the brain, because electrical activity can elicit rapid pH changes in both compartments. These acid-base transients may in turn influence neural activity by affecting a variety of ion channels. The mechanisms responsible for the regulation of intracellular pH in brain are similar to those of other tissues and are comprised principally of forms of Na+/H+ exchange, Na+-driven Cl-/HCO3- exchange, Na+-HCO3- cotransport, and passive Cl-/HCO3- exchange. Differences in the expression or efficacy of these mechanisms have been noted among the functionally and morphologically diverse neurons and glial cells that have been studied. Molecular identification of transporter isoforms has revealed heterogeneity among brain regions and cell types. Neural activity gives rise to an assortment of extracellular and intracellular pH shifts that originate from a variety of mechanisms. Intracellular pH shifts in neurons and glia have been linked to Ca2+ transport, activation of acid extrusion systems, and the accumulation of metabolic products. Extracellular pH shifts can occur within milliseconds of neural activity, arise from an assortment of mechanisms, and are governed by the activity of extracellular carbonic anhydrase. The functional significance of these compartmental, activity-dependent pH shifts is discussed.

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