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Methods in Molecular Biology (Clifton,... 2022Proteins are typically not expressed homogeneously in all cells of a complex organism. Within cells, proteins can dynamically change locations, be transported to their...
Proteins are typically not expressed homogeneously in all cells of a complex organism. Within cells, proteins can dynamically change locations, be transported to their destinations, or be degraded upon external signals. Thus, revealing the cellular and subcellular localizations as well as the temporal dynamics of a protein provides important insights into the possible function of the studied protein. Tagging a protein of interest with a genetically encoded fluorophore enables us to follow its expression dynamics in the living organism. Here, we summarize the genetic resources available for tagged Drosophila proteins that assist in studying protein expression and dynamics. We also review the various techniques used in the past and at present to tag a protein of interest with a genetically encoded fluorophore. Comparing the pros and cons of the various techniques guides the reader to judge the suitable applications possible with these tagged proteins in Drosophila.
Topics: Animals; CRISPR-Cas Systems; Drosophila; Drosophila Proteins; Fluorescent Dyes
PubMed: 35980582
DOI: 10.1007/978-1-0716-2541-5_12 -
The Journal of Biological Chemistry Nov 2019Previous work with the classic T4 endonuclease V digestion of DNA from irradiated cells followed by Southern hybridization led to the conclusion that lacks...
Previous work with the classic T4 endonuclease V digestion of DNA from irradiated cells followed by Southern hybridization led to the conclusion that lacks transcription-coupled repair (TCR). This conclusion was reinforced by the Genome Project, which revealed that lacks Cockayne syndrome WD repeat protein (CSA), CSB, or UV-stimulated scaffold protein A (UVSSA) homologs, whose orthologs are present in eukaryotes ranging from to humans that carry out TCR. A recently developed excision assay and the excision repair-sequencing (XR-Seq) method have enabled genome-wide analysis of nucleotide excision repair in various organisms at single-nucleotide resolution and in a strand-specific manner. Using these methods, we have discovered that S2 cells carry out robust TCR comparable with that observed in mammalian cells. Our findings provide critical new insights into the mechanisms of TCR among various different species.
Topics: Animals; DNA Damage; DNA Repair; DNA Repair Enzymes; Drosophila Proteins; Drosophila melanogaster
PubMed: 31624146
DOI: 10.1074/jbc.AC119.011448 -
Current Biology : CB Jun 2015Schimizzi and Longmore summarise what we know about Ajuba LIM-domain proteins and their various subcellular roles.
Schimizzi and Longmore summarise what we know about Ajuba LIM-domain proteins and their various subcellular roles.
Topics: Animals; Drosophila Proteins; LIM Domain Proteins; Signal Transduction
PubMed: 26035782
DOI: 10.1016/j.cub.2015.02.034 -
Genetics Sep 2020Key discoveries in have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable... (Review)
Review
Key discoveries in have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable -regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these -regulatory elements operate in development and disease.
Topics: Animals; Drosophila Proteins; Drosophila melanogaster; Enhancer Elements, Genetic; Genetic Techniques; Transcription Factors; Transcriptional Activation
PubMed: 32878914
DOI: 10.1534/genetics.120.301370 -
Current Opinion in Neurobiology Apr 2022The representation of contextual information peripheral to a salient stimulus is central to an animal's ability to correctly interpret and flexibly respond to that... (Review)
Review
The representation of contextual information peripheral to a salient stimulus is central to an animal's ability to correctly interpret and flexibly respond to that stimulus. While the computations and circuits underlying the context-dependent modulation of stimulus-response pairings have typically been studied in vertebrates, the genetic tractability, numeric simplification, and well-characterized connectivity patterns of the Drosophila melanogaster brain have facilitated circuit-level insights into contextual processing. Recent studies in flies reveal the neuronal mechanisms that create flexible context-dependent behavioral responses to sensory events in conditions of predation threat, feeding regulation, and social interaction.
Topics: Animals; Behavior, Animal; Brain; Drosophila; Drosophila Proteins; Drosophila melanogaster
PubMed: 35286864
DOI: 10.1016/j.conb.2022.02.003 -
Current Biology : CB Oct 2017Fukaya and Levine explain the basic features of the genetic phenomenon of transvection, a special class of genetic complementation of mutant alleles on homologous...
Fukaya and Levine explain the basic features of the genetic phenomenon of transvection, a special class of genetic complementation of mutant alleles on homologous chromosomes.
Topics: Alleles; Animals; Drosophila Proteins; Drosophila melanogaster; Gene Expression
PubMed: 29017034
DOI: 10.1016/j.cub.2017.08.001 -
Glia Jan 2019Glial cells constitute without any dispute an essential element in providing an efficiently operating nervous system. Work in many labs over the last decades has... (Review)
Review
Glial cells constitute without any dispute an essential element in providing an efficiently operating nervous system. Work in many labs over the last decades has demonstrated that neuronal function, from action potential generation to its propagation, from eliciting synaptic responses to the subsequent postsynaptic integration, is evolutionarily highly conserved. Likewise, the biology of glial cells appears conserved in its core elements and therefore, a deeper understanding of glial cells is expected to benefit from analyzing model organisms such as Drosophila melanogaster. Drosophila is particularly well suited for studying glial biology since in the fly nervous system only a limited number of glial cells exists, which can be individually identified based on position and a set of molecular markers. In combination with the well-known genetic tool box an unprecedented level of analysis is feasible, that not only can help to identify novel molecules and principles governing glial cell function but also will help to better understand glial functions first identified in the mammalian nervous system. Here we review the current knowledge on Drosophila glia to spark interest in using this system to analyze complex glial traits in the future.
Topics: Animals; Cell Differentiation; Drosophila; Drosophila Proteins; Drosophila melanogaster; Models, Animal; Neuroglia; Neurons
PubMed: 30443934
DOI: 10.1002/glia.23459 -
Proteomics Oct 2014Centromeres are chromosomal regions crucial for correct chromosome segregation during mitosis and meiosis. They are epigenetically defined by centromeric proteins such...
Centromeres are chromosomal regions crucial for correct chromosome segregation during mitosis and meiosis. They are epigenetically defined by centromeric proteins such as the centromere-specific histone H3-variant centromere protein A (CENP-A). In humans, 16 additional proteins have been described to be constitutively associated with centromeres throughout the cell cycle, known as the constitutive centromere-associated network (CCAN). In contrast, only one additional constitutive centromeric protein is known in Drosophila melanogaster (D.mel), the conserved CCAN member CENP-C. To gain further insights into D.mel centromere composition and biology, we analyzed affinity-purified chromatin prepared from D.mel cell lines expressing green fluorescent protein tagged histone three variants by MS. In addition to already-known centromeric proteins, we identified novel factors that were repeatedly enriched in affinity purification-MS experiments. We analyzed the cellular localization of selected candidates by immunocytochemistry and confirmed localization to the centromere and other genomic regions for ten factors. Furthermore, RNA interference mediated depletion of CG2051, CG14480, and hyperplastic discs, three of our strongest candidates, leads to elevated mitotic defects. Knockdowns of these candidates neither impair the localization of several known kinetochore proteins nor CENP-A(CID) loading, suggesting their involvement in alternative pathways that contribute to proper centromere function. In summary, we provide a comprehensive analysis of the proteomic composition of Drosophila centromeres. All MS data have been deposited in the ProteomeXchange with identifier PXD000758 (http://proteomecentral.proteomexchange.org/dataset/PXD000758).
Topics: Animals; Cell Line; Centromere; Chromatin; Chromosomal Proteins, Non-Histone; Drosophila Proteins; Drosophila melanogaster; Gene Knockdown Techniques; Kinetochores; Microscopy, Fluorescence
PubMed: 24841622
DOI: 10.1002/pmic.201400052 -
International Journal of Molecular... Jul 2022Memories are lasting representations over time of associations between stimuli or events. In general, the relatively slow consolidation of memories requires protein... (Review)
Review
Memories are lasting representations over time of associations between stimuli or events. In general, the relatively slow consolidation of memories requires protein synthesis with a known exception being the so-called Anesthesia Resistant Memory (ARM) in Drosophila. This protein synthesis-independent memory type survives amnestic shocks after a short, sensitive window post training, and can also emerge after repeated cycles of training in a negatively reinforced olfactory conditioning task, without rest between cycles (massed conditioning-MC). We discussed operational and molecular mechanisms that mediate ARM and differentiate it from protein synthesis-dependent long-term memory (LTM) in Drosophila. Based on the notion that ARM is unlikely to specifically characterize Drosophila, we examined protein synthesis and MC-elicited memories in other species and based on intraspecies shared molecular components and proposed potential relationships of ARM with established memory types in Drosophila and vertebrates.
Topics: Anesthesia; Animals; Drosophila; Drosophila Proteins; Drosophila melanogaster; Memory; Memory, Long-Term
PubMed: 35955662
DOI: 10.3390/ijms23158527 -
Genetics Nov 2020The Genetics Society of America's (GSA's) Edward Novitski Prize recognizes a single experimental accomplishment or a body of work in which an exceptional level of... (Review)
Review
The Genetics Society of America's (GSA's) Edward Novitski Prize recognizes a single experimental accomplishment or a body of work in which an exceptional level of creativity, and intellectual ingenuity, has been used to design and execute scientific experiments to solve a difficult problem in genetics. The 2020 recipient is Welcome W. Bender of Harvard Medical School, recognizing his creativity and ingenuity in revealing the molecular nature and regulation of the bithorax gene complex.
Topics: Awards and Prizes; Drosophila Proteins; Genetics; History, 20th Century; History, 21st Century; Homeodomain Proteins; Societies, Scientific; Transcription Factors
PubMed: 33158983
DOI: 10.1534/genetics.120.303708