scholarly journals Neural Network Organization for Courtship Song Feature Detection in Drosophila

2020 ◽  
Author(s):  
Christa A. Baker ◽  
Claire McKellar ◽  
Aljoscha Nern ◽  
Sven Dorkenwald ◽  
Barry J. Dickson ◽  
...  
Keyword(s):  
Feature Detection ◽  
Frequency Tuning ◽  
Cell Types ◽  
Auditory Pathway ◽  
Courtship Song ◽  
Basis Set ◽  
Auditory Responses ◽  
Intermediate Layers ◽  
Wide Range ◽  
Feature Selectivity

ABSTRACTAnimals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to both challenges in comprehensively mapping the underlying circuits, particularly in large brains, and in characterizing tuning for behaviorally relevant features. Here, we take advantage of the small size, genetic tools, and connectomic resources for the Drosophila melanogaster brain to investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. By building a large collection of genetic enhancer lines, we identify 24 new cell types of the intermediate layers of the auditory pathway. Using a new connectomic resource, FlyWire, we map connections among these cell types, in addition to connections to known early and higher-order auditory neurons. We characterize auditory responses throughout this pathway, and find that the newly discovered neurons show diverse preferences for courtship song modes. However, rather than being sorted into separate streams, neurons with different preferences are highly interconnected. Among this population, frequency tuning is centered on frequencies present in song, whereas rate tuning is biased towards rates below those present in song, suggesting that these neurons form a basis set for the generation of pulse feature tuning downstream. Our study provides new insights into the organization of auditory coding within the Drosophila brain.

WAVEGUIDE-COAXIAL RESONATOR WITH WIDE-RANGE FREQUENCY TUNING AND INCREASED Q-FACTOR

2016 ◽  
Vol 75 (10) ◽  
pp. 887-894 ◽  
Author(s):  
R. I. Bilous ◽  
A. P. Motornenko ◽  
I. G. Skuratovskiy ◽  
O. I. Khazov
Keyword(s):  
Frequency Tuning ◽  
Q Factor ◽  
Coaxial Resonator ◽  
Wide Range

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

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 Energetics of mesoscale cell turbulence in two-dimensional monolayers

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shao-Zhen Lin ◽  
Wu-Yang Zhang ◽  
Dapeng Bi ◽  
Bo Li ◽  
Xi-Qiao Feng
Keyword(s):  
Kinetic Energy ◽  
Tumor Metastasis ◽  
Cell Types ◽  
Boltzmann Distribution ◽  
Scaling Exponent ◽  
Biological Processes ◽  
Two Dimensional ◽  
Cell Monolayers ◽  
Wide Range ◽  
Epithelial Cell Monolayers

AbstractInvestigation of energy mechanisms at the collective cell scale is a challenge for understanding various biological processes, such as embryonic development and tumor metastasis. Here we investigate the energetics of self-sustained mesoscale turbulence in confluent two-dimensional (2D) cell monolayers. We find that the kinetic energy and enstrophy of collective cell flows in both epithelial and non-epithelial cell monolayers collapse to a family of probability density functions, which follow the q-Gaussian distribution rather than the Maxwell–Boltzmann distribution. The enstrophy scales linearly with the kinetic energy as the monolayer matures. The energy spectra exhibit a power-decaying law at large wavenumbers, with a scaling exponent markedly different from that in the classical 2D Kolmogorov–Kraichnan turbulence. These energetic features are demonstrated to be common for all cell types on various substrates with a wide range of stiffness. This study provides unique clues to understand active natures of cell population and tissues.

Spatial-frequency and orientation tuning in psychophysical end-stopping

1998 ◽  
Vol 15 (4) ◽  
pp. 585-595 ◽  
Author(s):  
CONG YU ◽  
DENNIS M. LEVI
Keyword(s):  
Spatial Frequency ◽  
Frequency Tuning ◽  
Spatial Filter ◽  
Orientation Tuning ◽  
Maximal Strength ◽  
Facilitation Effect ◽  
Spatial Filters ◽  
Spatial Frequency Tuning ◽  
Spatial Frequencies ◽  
Wide Range

A psychophysical analog to cortical receptive-field end-stopping has been demonstrated previously in spatial filters tuned to a wide range of spatial frequencies (Yu & Levi, 1997a). The current study investigated tuning characteristics in psychophysical spatial filter end-stopping. When a D6 (the sixth derivative of a Gaussian) target is masked by a center mask (placed in the putative spatial filter center), two end-zone masks (placed in the filter end-zones) reduce thresholds. This “end-stopping” effect (the reduction of masking induced by end-zone masks) was measured at various spatial frequencies and orientations of end-zone masks. End-stopping reached its maximal strength when the spatial frequency and/or orientation of the end-zone masks matched the spatial frequency and/or orientation of the target and center mask, showing spatial-frequency tuning and orientation tuning. The bandwidths of spatial-frequency and orientation tuning functions decreased with increasing target spatial frequency. At larger orientation differences, however, end-zone masks induced a secondary facilitation effect, which was maximal when the spatial frequency of end-zone masks equated the target spatial frequency. This facilitation effect might be related to certain types of contour and texture perception, such as perceptual pop-out.

Df31 is a novel nuclear protein involved in chromatin structure in Drosophila melanogaster

2001 ◽  
Vol 114 (1) ◽  
pp. 37-47 ◽  
Author(s):  
G. Crevel ◽  
H. Huikeshoven ◽  
S. Cotterill
Keyword(s):  
Cell Types ◽  
Drosophila Embryo ◽  
Cell Fractionation ◽  
General Function ◽  
Structural Protein ◽  
Chromosomal Structure ◽  
Binding Characteristics ◽  
Wide Range ◽  
Cellular Dna

We originally isolated the Df31 protein from Drosophila embryo extracts as a factor which could decondense Xenopus sperm, by removing the sperm specific proteins and interacting with histones to facilitate their loading onto DNA. We now believe that this protein has a more general function in cellular DNA metabolism. The Df31 gene encodes a very hydrophilic protein with a predicted molecular mass of 18.5 kDa. Immunostaining showed that Df31 was present in a wide range of cell types throughout differentiation and in both dividing and non-dividing cells. In all cases the protein is present in large amounts, comparable with the level of nucleosomes. Injection of antisense oligonucleotides to lower the level of Df31 in embryos caused severe disruption of the nuclear structure. Large irregular clumps of DNA were formed, and in most cases the amount of DNA associated with each clump was more than that found in a normal nucleus. Immunofluorescence, cell fractionation, and formaldehyde cross-linking show that Df31 is associated with chromatin and that a significant fraction of it binds very tightly. It also shows the same binding characteristics when loaded onto chromatin in vitro. Chromatin fractionation shows that Df31 is tightly associated with nucleosomes, preferentially with oligonucleosomes. Despite this no differences were observed in the properties of nucleosomes loaded in the in vitro system in the presence and absence of Df31. These results suggest that Df31 has a role in chromosomal structure, most likely acting as a structural protein at levels of folding higher than that of nucleosomes.

Monaural inhibition in cat auditory cortex

1995 ◽  
Vol 73 (5) ◽  
pp. 1876-1891 ◽  
Author(s):  
M. B. Calford ◽  
M. N. Semple
Keyword(s):  
Auditory Cortex ◽  
Lateral Inhibition ◽  
Cortical Neurons ◽  
Frequency Tuning ◽  
Inhibitory Response ◽  
Forward Masking ◽  
Excitatory Response ◽  
Rate Level ◽  
Wide Range ◽  
Response Area

1. Several studies of auditory cortex have examined the competitive inhibition that can occur when appropriate sounds are presented to each ear. However, most cortical neurons also show both excitation and inhibition in response to presentation of stimuli at one ear alone. The extent of such inhibition has not been described. Forward masking, in which a variable masking stimulus was followed by a fixed probe stimulus (within the excitatory response area), was used to examine the extent of monaural inhibition for neurons in primary auditory cortex of anesthetized cats (barbiturate or barbiturate-ketamine). Both the masking and probe stimuli were 50-ms tone pips presented to the contralateral ear. Most cortical neurons showed significant forward masking at delays beyond which masking effects in the auditory nerve are relatively small compared with those seen in cortical neurons. Analysis was primarily concerned with such components. Standard rate-level functions were also obtained and were examined for nonmonotonicity, an indication of level-dependent monaural inhibition. 2. Consistent with previous reports, a wide range of frequency tuning properties (excitatory response area shapes) was found in cortical neurons. This was matched by a wide range of forward-masking-derived inhibitory response areas. At the most basic level of analysis, these were classified according to the presence of lateral inhibition, i.e., where a probe tone at a neuron's characteristic frequency was masked by tones outside the limits of the excitatory response area. Lateral inhibition was a property of 38% of the sampled neurons. Such neurons represented 77% of those with nonmonotonic rate-level functions, indicating a strong correlation between the two indexes of monaural inhibition; however, the shapes of forward masking inhibitory response areas did not usually correspond with those required to account for the "tuning" of a neuron. In addition, it was found that level-dependent inhibition was not added to by forward masking inhibition. 3. Analysis of the discharges to individual stimulus pair presentations, under conditions of partial masking, revealed that discharges to the probe occurred independently of discharges to the preceding masker. This indicates that even when the masker is within a neuron's excitatory response area, forward masking is not a postdischarge habituation phenomenon. However, for most neurons the degree of masking summed over multiple stimulus presentations appears determined by the same stimulus parameters that determine the probability of response to the masker.(ABSTRACT TRUNCATED AT 400 WORDS)

scholarly journals Wide range frequency tuning in vacuum electronic devices

2003 ◽  
Author(s):  
V.G. Baryshevsky ◽  
K.G. Batrakov ◽  
N.A. Belous ◽  
A.A. Gurinovich ◽  
A.S. Lobko ◽  
...  
Keyword(s):  
Frequency Tuning ◽  
Electronic Devices ◽  
Wide Range ◽  
Vacuum Electronic Devices

scholarly journals RNA-Seq Data-Mining Allows the Discovery of Two Long Non-Coding RNA Biomarkers of Viral Infection in Humans

2020 ◽  
Vol 21 (8) ◽  
pp. 2748 ◽  
Author(s):  
Ruth Barral-Arca ◽  
Alberto Gómez-Carballa ◽  
Miriam Cebey-López ◽  
María José Currás-Tuala ◽  
Sara Pischedda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Viral Infections ◽  
Umbilical Vein ◽  
Cell Types ◽  
Dermal Fibroblasts ◽  
Learning Approaches ◽  
Rna Seq ◽  
Wide Range ◽  
Healthy Control ◽  
Umbilical Vein Endothelial Cells

There is a growing interest in unraveling gene expression mechanisms leading to viral host invasion and infection progression. Current findings reveal that long non-coding RNAs (lncRNAs) are implicated in the regulation of the immune system by influencing gene expression through a wide range of mechanisms. By mining whole-transcriptome shotgun sequencing (RNA-seq) data using machine learning approaches, we detected two lncRNAs (ENSG00000254680 and ENSG00000273149) that are downregulated in a wide range of viral infections and different cell types, including blood monocluclear cells, umbilical vein endothelial cells, and dermal fibroblasts. The efficiency of these two lncRNAs was positively validated in different viral phenotypic scenarios. These two lncRNAs showed a strong downregulation in virus-infected patients when compared to healthy control transcriptomes, indicating that these biomarkers are promising targets for infection diagnosis. To the best of our knowledge, this is the very first study using host lncRNAs biomarkers for the diagnosis of human viral infections.

The Florey Lecture, 1988 - From egg to embryo: the initiation of cell differentiation in Amphibia

1989 ◽  
Vol 237 (1286) ◽  
pp. 11-25 ◽  
Keyword(s):  
Muscle Cell ◽  
Gene Activation ◽  
Cell Formation ◽  
Gene Promoter ◽  
Cell Types ◽  
Specific Gene ◽  
Embryonic Induction ◽  
Differentiated Cells ◽  
Wide Range ◽  
Muscle Genes

Some of the principles by which different cell types first arise at the beginning of animal development are illustrated by muscle cell formation in Amphibia. If the nucleus of a differentiated muscle cell is transplanted to an enucleated egg, some of the resulting embryos develop into tadpoles with a wide range of normally differentiated cells. These experiments show that genes undergo major changes in activity as a response to components of egg cytoplasm. Two fundamental mechanisms account for the regional activation of genes in early embryos. One involves the effect of localized ‘determinants’ in egg cytoplasm, and the other concerns cell interactions or embryonic induction. Both these mechanisms seem to be responsible for muscle cell formation in amphibian development. The old problem of embryonic induction has recently become accessible to analysis at the molecular level, especially in the case of the mesoderm or muscle-forming induction. This has been greatly facilitated by using a sensitive and quantitative assay to detect the first transcripts of muscle genes a few hours after the start of induction. The role of early events and of interactions among like cells during response to induction is discussed. In analysing specific gene activation following induction, DNA injection into fertilized eggs has shown that a very small part of the cardiac actin gene promoter is sufficient to enable it to respond to induction. Although the experimental work summarized here has been done on amphibian embryos, which are more suitable than other embryos for embryological manipulation, the conclusions reached are believed to be generally applicable to the development of other organisms.

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