scholarly journals Analysis of functional neuronal connectivity in the Drosophila brain

2012 ◽  
Vol 108 (2) ◽  
pp. 684-696 ◽  
Author(s):  
Zepeng Yao ◽  
Ann Marie Macara ◽  
Katherine R. Lelito ◽  
Tamara Y. Minosyan ◽  
Orie T. Shafer

Drosophila melanogaster is a valuable model system for the neural basis of complex behavior, but an inability to routinely interrogate physiologic connections within central neural networks of the fly brain remains a fundamental barrier to progress in the field. To address this problem, we have introduced a simple method of measuring functional connectivity based on the independent expression of the mammalian P2X2 purinoreceptor and genetically encoded Ca2+ and cAMP sensors within separate genetically defined subsets of neurons in the adult brain. We show that such independent expression is capable of specifically rendering defined sets of neurons excitable by pulses of bath-applied ATP in a manner compatible with high-resolution Ca2+ and cAMP imaging in putative follower neurons. Furthermore, we establish that this approach is sufficiently sensitive for the detection of excitatory and modulatory connections deep within larval and adult brains. This technically facile approach can now be used in wild-type and mutant genetic backgrounds to address functional connectivity within neuronal networks governing a wide range of complex behaviors in the fly. Furthermore, the effectiveness of this approach in the fly brain suggests that similar methods using appropriate heterologous receptors might be adopted for other widely used model systems.

mSphere ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Dianxiong Zou ◽  
Todd M. Hennessey

ABSTRACT Although many single-cell eukaryotes have served as classical model systems for chemosensory studies for decades, the major emphasis has been on chemoattraction and no chemorepellent receptor gene has been identified in any unicellular eukaryote. This is the first description of a gene that codes for a chemorepellent receptor in any protozoan. Integration of both depolarizing chemorepellent pathways and hyperpolarizing chemoattractant pathways is as important to chemoresponses of motile unicells as excitatory and inhibitory neurotransmitter pathways are to neurons. Therefore, both chemoattractant and chemorepellent pathways should be represented in a useful unicellular model system. Tetrahymena cells provide such a model system because simple behavioral bioassays, gene knockouts, biochemical analysis, and other approaches can be used with these eukaryotic model cells. This work can contribute to the basic understanding of unicellular sensory responses and provide insights into the evolution of chemoreceptors and possible chemorepellent approaches for preventing infections by some pathogenic protozoa. A conditioned supernatant from Tetrahymena thermophila contains a powerful chemorepellent for wild-type cells, and a gene called G37 is required for this response. This is the first genomic identification of a chemorepellent receptor in any eukaryotic unicellular organism. This conditioned supernatant factor (CSF) is small (<1 kDa), and its repellent effect is resistant to boiling, protease treatment, and nuclease digestion. External BAPTA eliminated the CSF response, suggesting that Ca2+ entry is required for the classical avoiding reactions (AR) used for chemorepulsion. A macronuclear G37 gene knockout (G37-KO) mutant is both nonresponsive to the CSF and overresponsive to other repellents such as quinine, lysozyme, GTP, and high potassium concentrations. All of these mutant phenotypes were reversed by overexpression of the wild-type G37 gene in a G37 overexpression mutant. Overexpression of G37 in the wild type caused increased responsiveness to the CSF and underresponsiveness to high K+ concentrations. Behavioral adaptation (by prolonged exposure to the CSF) caused decreases in responsiveness to all of the stimuli used in the wild type and the overexpression mutant but not in the G37-KO mutant. We propose that the constant presence of the CSF causes a decreased basal excitability of the wild type due to chemosensory adaptation through G37 and that all of the G37-KO phenotypes are due to an inability to detect the CSF. Therefore, the G37 protein may be the CSF receptor. The physiological role of these G37-mediated responses may be to both moderate basal excitability and detect the CSF as an indicator of high cell density growth. IMPORTANCE Although many single-cell eukaryotes have served as classical model systems for chemosensory studies for decades, the major emphasis has been on chemoattraction and no chemorepellent receptor gene has been identified in any unicellular eukaryote. This is the first description of a gene that codes for a chemorepellent receptor in any protozoan. Integration of both depolarizing chemorepellent pathways and hyperpolarizing chemoattractant pathways is as important to chemoresponses of motile unicells as excitatory and inhibitory neurotransmitter pathways are to neurons. Therefore, both chemoattractant and chemorepellent pathways should be represented in a useful unicellular model system. Tetrahymena cells provide such a model system because simple behavioral bioassays, gene knockouts, biochemical analysis, and other approaches can be used with these eukaryotic model cells. This work can contribute to the basic understanding of unicellular sensory responses and provide insights into the evolution of chemoreceptors and possible chemorepellent approaches for preventing infections by some pathogenic protozoa.


2019 ◽  
Author(s):  
Olof R. Nilsson ◽  
Laszlo Kari ◽  
Olivia Steele-Mortimer

AbstractOral infection of mice withSalmonellaTyphimurium is an important model system. In particular C57Bl/6 mice, which are susceptible toSalmonella, are used to study both systemic and gastrointestinal pathogenesis. Pretreatment with streptomycin disrupts the intestinal microbiota and results in colitis resembling human intestinalSalmonellosis. Oral gavage is typically used for delivery of both antibiotic and bacteria. Although convenient, this method requires a moderate level of expertise, can be stressful for experimental animals, and may lead to unwanted tracheal or systemic introduction of bacteria. Here, we demonstrate a simple method for oral infection of mice using small pieces of regular mouse chow inoculated with a known number of bacteria. Mice readily ate chow pieces containing up to 108CFUSalmonella, allowing for a wide range of infectious doses. In mice pretreated with streptomycin, infection with inoculated chow resulted in less variability in numbers of bacteria recovered from tissues compared to oral gavage, and highly consistent infections even at doses as low as 103Salmonella. Mice not treated with streptomycin, as well as resistant Nramp1 reconstituted C57Bl/6J mice, were also readily infected using this method. In summary, we show that foodborne infection of mice by feeding with pieces of chow inoculated withSalmonellaresults in infection comparable to oral gavage but represents a natural route of infection with fewer side effects and less variability among mice.


Author(s):  
Daniel J Lurie ◽  
Daniel Kessler ◽  
Danielle S Bassett ◽  
Richard F. Betzel ◽  
Michael Breakspear ◽  
...  

The brain is a complex dynamical system composed of many interacting sub-regions. Knowledge of how these interactions reconfigure over time is critical to a full understanding of the brain’s functional architecture, the neural basis of flexible cognition and behavior, and how neural systems are disrupted in psychiatric and neurological illness. The idea that we might be able to study neural and cognitive dynamics through analysis of neuroimaging data has catalyzed substantial interest in methods which seek to estimate moment-to-moment fluctuations in functional connectivity (often referred to as “dynamic” or time-varying connectivity; TVC). At the same time, debates have emerged regarding the application of TVC analyses to resting fMRI data, and about the statistical validity, physiological origins, and cognitive relevance of resting TVC. These and other unresolved issues complicate the interpretation of resting TVC findings and limit the insights which can be gained from this otherwise promising research area. This article reviews the current resting TVC literature in light of these issues. We introduce core concepts, define key terms, summarize current controversies and open questions, and present a forward-looking perspective on how resting TVC analyses can be rigorously applied to investigate a wide range of questions in cognitive and systems neuroscience.


2009 ◽  
Vol 56 (1) ◽  
Author(s):  
Olga Wesołowska ◽  
Krystyna Michalak ◽  
Jadwiga Maniewska ◽  
Andrzej B Hendrich

Model systems such as black lipid membranes or conventional uni- or multilamellar liposomes are commonly used to study membrane properties and structure. However, the construction and dimensions of these models excluded their direct optical microscopic observation. Since the introduction of the simple method of liposome electroformation in alternating electric field giant unilamellar vesicles (GUVs) have become an important model imitating biological membranes. Due to the average diameter of GUVs reaching up to 100 microm, they can be easily observed under a fluorescent or confocal microscope provided that the appropriate fluorescent probe was incorporated into the lipid phase during vesicle formation. GUVs can be formed from different lipid mixtures and they are stable in a wide range of physical conditions such as pH, pressure or temperature. This mini-review presents information about the methods of GUV production and their usage. Particularly, the use of GUVs in studying lipid phase separation and the appearance and behavior of lipid domains (rafts) in membranes is discussed but also other examples of GUVs use in membrane research are given. The experience of the authors in setting up the GUV-forming equipment and production of GUVs is also presented.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.


Author(s):  
S. Jelbart ◽  
K. U. Kristiansen ◽  
P. Szmolyan ◽  
M. Wechselberger

AbstractSingular exponential nonlinearities of the form $$e^{h(x)\epsilon ^{-1}}$$ e h ( x ) ϵ - 1 with $$\epsilon >0$$ ϵ > 0 small occur in many different applications. These terms have essential singularities for $$\epsilon =0$$ ϵ = 0 leading to very different behaviour depending on the sign of h. In this paper, we consider two prototypical singularly perturbed oscillators with such exponential nonlinearities. We apply a suitable normalization for both systems such that the $$\epsilon \rightarrow 0$$ ϵ → 0 limit is a piecewise smooth system. The convergence to this nonsmooth system is exponential due to the nonlinearities we study. By working on the two model systems we use a blow-up approach to demonstrate that this exponential convergence can be harmless in some cases while in other scenarios it can lead to further degeneracies. For our second model system, we deal with such degeneracies due to exponentially small terms by extending the space dimension, following the approach in Kristiansen (Nonlinearity 30(5): 2138–2184, 2017), and prove—for both systems—existence of (unique) limit cycles by perturbing away from singular cycles having desirable hyperbolicity properties.


Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1346
Author(s):  
Icksoo Lee

Numerous naturally occurring molecules have been studied for their beneficial health effects. Many compounds have received considerable attention for their potential medical uses. Among them, several substances have been found to improve mitochondrial function. This review focuses on resveratrol, (–)-epicatechin, and betaine and summarizes the published data pertaining to their effects on cytochrome c oxidase (COX) which is the terminal enzyme of the mitochondrial electron transport chain and is considered to play an important role in the regulation of mitochondrial respiration. In a variety of experimental model systems, these compounds have been shown to improve mitochondrial biogenesis in addition to increased COX amount and/or its enzymatic activity. Given that they are inexpensive, safe in a wide range of concentrations, and effectively improve mitochondrial and COX function, these compounds could be attractive enough for possible therapeutic or health improvement strategies.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Owen D. Jarman ◽  
Olivier Biner ◽  
John J. Wright ◽  
Judy Hirst

AbstractMitochondrial complex I (NADH:ubiquinone oxidoreductase) is a crucial metabolic enzyme that couples the free energy released from NADH oxidation and ubiquinone reduction to the translocation of four protons across the inner mitochondrial membrane, creating the proton motive force for ATP synthesis. The mechanism by which the energy is captured, and the mechanism and pathways of proton pumping, remain elusive despite recent advances in structural knowledge. Progress has been limited by a lack of model systems able to combine functional and structural analyses with targeted mutagenic interrogation throughout the entire complex. Here, we develop and present the α-proteobacterium Paracoccus denitrificans as a suitable bacterial model system for mitochondrial complex I. First, we develop a robust purification protocol to isolate highly active complex I by introducing a His6-tag on the Nqo5 subunit. Then, we optimize the reconstitution of the enzyme into liposomes, demonstrating its proton pumping activity. Finally, we develop a strain of P. denitrificans that is amenable to complex I mutagenesis and create a catalytically inactive variant of the enzyme. Our model provides new opportunities to disentangle the mechanism of complex I by combining mutagenesis in every subunit with established interrogative biophysical measurements on both the soluble and membrane bound enzymes.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sarah J. Brown ◽  
Ibrahim Boussaad ◽  
Javier Jarazo ◽  
Julia C. Fitzgerald ◽  
Paul Antony ◽  
...  

AbstractRecent evidence suggests neurogenesis is on-going throughout life but the relevance of these findings for neurodegenerative disorders such as Parkinson’s disease (PD) is poorly understood. Biallelic PINK1 mutations cause early onset, Mendelian inherited PD. We studied the effect of PINK1 deficiency on adult neurogenesis of dopaminergic (DA) neurons in two complementary model systems. Zebrafish are a widely-used model to study neurogenesis in development and through adulthood. Using EdU analyses and lineage-tracing studies, we first demonstrate that a subset of ascending DA neurons and adjacent local-projecting DA neurons are each generated into adulthood in wild type zebrafish at a rate that decreases with age. Pink1-deficiency impedes DA neurogenesis in these populations, most significantly in early adult life. Pink1 already exerts an early effect on Th1+ progenitor cells rather than on differentiated DA neurons only. In addition, we investigate the effect of PINK1 deficiency in a human isogenic organoid model. Global neuronal differentiation in PINK1-deficient organoids and isogenic controls is similar, but PINK1-deficient organoids display impeded DA neurogenesis. The observation of impaired adult dopaminergic neurogenesis in Pink1 deficiency in two complementing model systems may have significant consequences for future therapeutic approaches in human PD patients with biallelic PINK1 mutations.


2006 ◽  
Vol 52 (10) ◽  
pp. 1855-1863 ◽  
Author(s):  
Giulia Amicarelli ◽  
Daniel Adlerstein ◽  
Erlet Shehi ◽  
Fengfei Wang ◽  
G Mike Makrigiorgos

Abstract Background: Genotyping methods that reveal single-nucleotide differences are useful for a wide range of applications. We used digestion of 3-way DNA junctions in a novel technology, OneCutEventAmplificatioN (OCEAN) that allows sequence-specific signal generation and amplification. We combined OCEAN with peptide-nucleic-acid (PNA)-based variant enrichment to detect and simultaneously genotype v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) codon 12 sequence variants in human tissue specimens. Materials and Methods: We analyzed KRAS codon 12 sequence variants in 106 lung cancer surgical specimens. We conducted a PNA-PCR reaction that suppresses wild-type KRAS amplification and genotyped the product with a set of OCEAN reactions carried out in fluorescence microplate format. The isothermal OCEAN assay enabled a 3-way DNA junction to form between the specific target nucleic acid, a fluorescently labeled “amplifier”, and an “anchor”. The amplifier-anchor contact contains the recognition site for a restriction enzyme. Digestion produces a cleaved amplifier and generation of a fluorescent signal. The cleaved amplifier dissociates from the 3-way DNA junction, allowing a new amplifier to bind and propagate the reaction. Results: The system detected and genotyped KRAS sequence variants down to ∼0.3% variant-to-wild-type alleles. PNA-PCR/OCEAN had a concordance rate with PNA-PCR/sequencing of 93% to 98%, depending on the exact implementation. Concordance rate with restriction endonuclease-mediated selective-PCR/sequencing was 89%. Conclusion: OCEAN is a practical and low-cost novel technology for sequence-specific signal generation. Reliable analysis of KRAS sequence alterations in human specimens circumvents the requirement for sequencing. Application is expected in genotyping KRAS codon 12 sequence variants in surgical specimens or in bodily fluids, as well as single-base variations and sequence alterations in other genes.


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