scholarly journals A viral toolbox for conditional and transneuronal gene expression in zebrafish

2021 ◽  
Author(s):  
Chie Satou ◽  
Rachael L. Neve ◽  
Hassana K. Oyibo ◽  
Estelle Arn Bouldoires ◽  
Takuma Mori ◽  
...  
Keyword(s):  
Gene Expression ◽  
Herpes Simplex ◽  
Gene Transfer ◽  
Retrograde Tracing ◽  
Structure And Function ◽  
Herpes Simplex Viruses ◽  
Neuronal Circuitry ◽  
Systems Neuroscience ◽  
Efficient Gene ◽  
And Function

AbstractZebrafish are an important model in systems neuroscience but a key limitation is the lack of viral tools to interrogate the structure and function of neuronal circuitry. We developed methods for efficient gene transfer and retrograde tracing by herpes simplex viruses (HSV1), for conditional HSV1-mediated gene expression using the Gal4/UAS system, and for transneuronal tracing by rabies viruses. This toolbox creates new opportunities to visualize and manipulate specific sets of neurons through the combination of genetic and viral approaches in zebrafish.

Neural system-enriched gene expression: relationship to biological pathways and neurological diseases

2004 ◽  
Vol 18 (2) ◽  
pp. 167-183 ◽  
Author(s):  
Jianhua Zhang ◽  
Amy Moseley ◽  
Anil G. Jegga ◽  
Ashima Gupta ◽  
David P. Witte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Intracellular Signaling ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene List ◽  
Structure And Function ◽  
System Structure ◽  
Psychiatric Disease ◽  
And Function

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

scholarly journals The essential activities of the bacterial sigma factor

2017 ◽  
Vol 63 (2) ◽  
pp. 89-99 ◽  
Author(s):  
Maria C. Davis ◽  
Christopher A. Kesthely ◽  
Emily A. Franklin ◽  
Shawn R. MacLellan
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Rna Synthesis ◽  
Gene Expression Regulation ◽  
Structure And Function ◽  
Structural Studies ◽  
General Transcription Factors ◽  
Transcription Process ◽  
Promoter Dna ◽  
And Function

Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.

Structure and Function of Ion Pumps Studied by Atomic Force Microscopy and Gene-transfer Experiments Using Chimeric Na+/K+- and Ca2+ ATPases

1994 ◽  
pp. 264-275
Author(s):  
Kunio Takeyasu ◽  
Jose K. Paul ◽  
Mehdi Ganjeizadeh ◽  
M. Victor Lemas ◽  
Shusheng Wang ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Gene Transfer ◽  
Structure And Function ◽  
Ion Pumps ◽  
Force Microscopy ◽  
Atomic Force ◽  
And Function

scholarly journals Renal ischemia alters expression of mitochondria-related genes and impairs mitochondrial structure and function in swine scattered tubular-like cells

2020 ◽  
Vol 319 (1) ◽  
pp. F19-F28 ◽  
Author(s):  
Rahele A. Farahani ◽  
Xiang-Yang Zhu ◽  
Hui Tang ◽  
Kyra L. Jordan ◽  
Lilach O. Lerman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Structural Damage ◽  
Nuclear Dna ◽  
Mitochondrial Genes ◽  
Structure And Function ◽  
Mitochondrial Damage ◽  
Renal Ischemia ◽  
Gene Gain ◽  
Mitochondrial Structure ◽  
And Function

Scattered tubular-like cells (STCs) are dedifferentiated surviving tubular epithelial cells that repair neighboring injured cells. Experimental renal artery stenosis (RAS) impairs STC reparative potency by inducing mitochondrial injury, but the exact mechanisms of mitochondrial damage remain unknown. We hypothesized that RAS alters expression of mitochondria-related genes, contributing to mitochondrial structural damage and dysfunction in swine STCs. CD24+/CD133+ STCs were isolated from pig kidneys after 10 wk of RAS or sham ( n = 3 each). mRNA sequencing was performed, and nuclear DNA (nDNA)-encoded mitochondrial genes and mitochondrial DNA (mtDNA)-encoded genes were identified. Mitochondrial structure, ATP generation, biogenesis, and expression of mitochondria-associated microRNAs were also assessed. There were 96 nDNA-encoded mitochondrial genes upregulated and 12 mtDNA-encoded genes downregulated in RAS-STCs versus normal STCs. Functional analysis revealed that nDNA-encoded and mtDNA-encoded differentially expressed genes were primarily implicated in mitochondrial respiration and ATP synthesis. Mitochondria from RAS STCs were swollen and showed cristae remodeling and loss and decreased ATP production. Immunoreactivity of the mitochondrial biogenesis marker peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α and expression of the mitochondria-associated microRNAs miR-15a, miR-181a, miR-196a, and miR-296-3p, which target several mtDNA genes, were higher in RAS-STCs compared with normal STCs, suggesting a potential modulation of mitochondria-related gene expression. These results demonstrate that RAS induces an imbalance in mtDNA- and nDNA-mitochondrial gene expression, impairing mitochondrial structure and function in swine STCs. These observations support development of gene gain- and loss-of-function strategies to ameliorate mitochondrial damage and preserve the reparative potency of STCs in patients with renal ischemia.

Assessment of Structure and Function Over a 3-year Period after Gene Transfer in RPE65−/− dogs

2005 ◽  
Vol 111 (1) ◽  
pp. 39-48 ◽  
Author(s):  
Kristina Narfström ◽  
Vaegan ◽  
Martin Katz ◽  
Ragnheidur Bragadottir ◽  
Elizabeth P. Rakoczy ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Structure And Function ◽  
And Function

Human surfactant protein B: structure, function, regulation, and genetic disease

1995 ◽  
Vol 75 (4) ◽  
pp. 749-757 ◽  
Author(s):  
J. A. Whitsett ◽  
L. M. Nogee ◽  
T. E. Weaver ◽  
A. D. Horowitz
Keyword(s):  
Gene Expression ◽  
Surfactant Protein ◽  
Structure And Function ◽  
Respiratory Epithelial Cell ◽  
Surfactant Protein B ◽  
Cell Gene Expression ◽  
Surfactant Phospholipids ◽  
And Function ◽  
Respiratory Epithelial ◽  
Cell Gene

Elucidation of the structure and function of the hydrophobic surfactant protein (SP-B) and the SP-B gene has provided critical insight into surfactant homeostasis and control of respiratory epithelial cell gene expression. Surfactant protein B, in concert with surfactant protein A (SP-A), surfactant protein C (SP-C), and surfactant phospholipids, contributes to the structure and function of surfactant particles, determining surface activities and pathways by which surfactant phospholipids and proteins are processed, routed, packaged, and secreted from lamellar bodies by type II epithelial cells. After secretion, SP-B plays an essential role in determining the structure of tubular myelin, the stability and rapidity of spreading, and the recycling of surfactant phospholipids. The biochemical and structural signals underlying the homeostasis of alveolar surfactant are likely mediated by interactions between the surfactant proteins and phospholipids producing discrete structural forms that vary in size, aproprotein, and phospholipid content. Distinctions in structure, protein, and size are likely to determine the function of surfactant particles, their catabolism, or recycling by alveolar macrophages and airway epithelial cells. Analysis of the genetic controls governing the SP-B gene has led to the definition of DNA-protein interactions that determine respiratory epithelial cell gene expression in general. The important role of SP-B in lung function was defined by the study of a lethal neonatal respiratory disease, hereditary SP-B deficiency, caused by mutations in the human SP-B gene.

scholarly journals Ruthenium-caged antisense morpholinos for regulating gene expression in zebrafish embryos

2015 ◽  
Vol 6 (4) ◽  
pp. 2342-2346 ◽  
Author(s):  
Julianne C. Griepenburg ◽  
Teresa L. Rapp ◽  
Patrick J. Carroll ◽  
James Eberwine ◽  
Ivan J. Dmochowski
Keyword(s):  
Gene Expression ◽  
Visible Light ◽  
Control Structure ◽  
Structure And Function ◽  
Zebrafish Embryos ◽  
And Function

Ruthenium photolinkers provide a versatile method of using visible light to control structure and function of biopolymers.

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