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1.
Behav Brain Res ; 460: 114781, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38043677

ABSTRACT

Parkinson's disease (PD) is a common neurodegenerative movement disorder, characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta and the accumulation of aggregated alpha synuclein (aSyn). The disease often presents with early prodromal non-motor symptoms and later motor symptoms. Diagnosing PD based purely on motor symptoms is often too late for successful intervention, as a significant neuronal loss has already occurred. Furthermore, the lower prevalence of PD in females is not well understood, highlighting the need for a better understanding of the interaction between sex and aSyn, the crucial protein for PD pathogenesis. Here, we conducted a comprehensive phenotyping study in 1- to 5-month-old mice overexpressing human aSyn gene (SNCA) in a bacterial artificial chromosome (BAC-SNCA). We demonstrate a SNCA gene-dose-dependent increase of human aSyn and phosphorylated aSyn, as well as a decrease in tyrosine hydroxylase expression in BAC-SNCA mice, with more pronounced effects in male mice. Phosphorylated aSyn was already found in the dorsal motor nucleus of the vagus nerve of 2-month-old mice. This was time-wise associated with significant gait altrations in BAC-SNCA mice as early as 1 and 3 months of age using CatWalk gait analysis. Furthermore, anxiety-related behavioral tests revealed an increase in anxiety levels in male BAC-SNCA mice. Finally, 5-month-old male BAC-SNCA mice exhibited a SNCA gene-dose-dependent elevation in energy expenditure in automated home-cage monitoring. For the first time, these findings describe early-onset, sex- and gene-dose-dependent, aSyn-mediated disturbances in BAC-SNCA mice, providing a model for sex-differences, early-onset neuropathology, and prodromal symptoms of PD.


Subject(s)
Neurodegenerative Diseases , Parkinson Disease , alpha-Synuclein , Animals , Female , Humans , Male , Mice , alpha-Synuclein/genetics , alpha-Synuclein/metabolism , Chromosomes, Artificial, Bacterial/metabolism , Dopaminergic Neurons/metabolism , Mice, Transgenic , Neurodegenerative Diseases/metabolism , Parkinson Disease/metabolism , Vagus Nerve/metabolism
2.
Genomics ; 114(4): 110411, 2022 07.
Article in English | MEDLINE | ID: mdl-35716824

ABSTRACT

Gene duplications increase genetic and phenotypic diversity and occur in complex genomic regions that are still difficult to sequence and assemble. PHD Finger Protein 7 (PHF7) acts during spermiogenesis for histone-to-histone protamine exchange and is a determinant of male fertility in Drosophila and the mouse. We aimed to explore and characterise in the chicken genome the expanding family of the numerous orthologues of the unique mouse Phf7 gene (highly expressed in the testis), observing the fact that this information is unclear and/or variable according to the versions of databases. We validated nine primer pairs by in silico PCR for their use in screening the chicken bacterial artificial chromosome (BAC) library to produce BAC-derived probes to detect and localise PHF7-like loci by fluorescence in situ hybridisation (FISH). We selected nine BAC that highlighted nine chromosomal regions for a total of 10 distinct PHF7-like loci on five Gallus gallus chromosomes: Chr1 (three loci), Chr2 (two loci), Chr12 (one locus), Chr19 (one locus) and ChrZ (three loci). We sequenced the corresponding BAC by using high-performance PacBio technology. After assembly, we performed annotation with the FGENESH program: there were a total of 116 peptides, including 39 PHF7-like proteins identified by BLASTP. These proteins share a common exon-intron core structure of 8-11 exons. Phylogeny revealed that the duplications occurred first between chromosomal regions and then inside each region. There are other duplicated genes in the identified BAC sequences, suggesting that these genomic regions exhibit a high rate of tandem duplication. We showed that the PHF7 gene, which is highly expressed in the rooster testis, is a highly duplicated gene family in the chicken genome, and this phenomenon probably concerns other bird species.


Subject(s)
Chickens , Testis , Animals , Chickens/genetics , Chickens/metabolism , Chromosomes, Artificial, Bacterial/metabolism , Gene Duplication , Genome , Histones/metabolism , Male , Mice , PHD Zinc Fingers , Testis/metabolism
3.
Neuron ; 110(7): 1173-1192.e7, 2022 04 06.
Article in English | MEDLINE | ID: mdl-35114102

ABSTRACT

In Huntington's disease (HD), the uninterrupted CAG repeat length, but not the polyglutamine length, predicts disease onset. However, the underlying pathobiology remains unclear. Here, we developed bacterial artificial chromosome (BAC) transgenic mice expressing human mutant huntingtin (mHTT) with uninterrupted, and somatically unstable, CAG repeats that exhibit progressive disease-related phenotypes. Unlike prior mHTT transgenic models with stable, CAA-interrupted, polyglutamine-encoding repeats, BAC-CAG mice show robust striatum-selective nuclear inclusions and transcriptional dysregulation resembling those in murine huntingtin knockin models and HD patients. Importantly, the striatal transcriptionopathy in HD models is significantly correlated with their uninterrupted CAG repeat length but not polyglutamine length. Finally, among the pathogenic entities originating from mHTT genomic transgenes and only present or enriched in the uninterrupted CAG repeat model, somatic CAG repeat instability and nuclear mHTT aggregation are best correlated with early-onset striatum-selective molecular pathogenesis and locomotor and sleep deficits, while repeat RNA-associated pathologies and repeat-associated non-AUG (RAN) translation may play less selective or late pathogenic roles, respectively.


Subject(s)
Huntington Disease , Nerve Tissue Proteins , Animals , Chromosomes, Artificial, Bacterial/genetics , Chromosomes, Artificial, Bacterial/metabolism , Disease Models, Animal , Humans , Huntingtin Protein/genetics , Huntington Disease/genetics , Huntington Disease/pathology , Mice , Mice, Transgenic , Nerve Tissue Proteins/genetics , Neurons/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Trinucleotide Repeat Expansion/genetics
4.
Cells ; 10(10)2021 10 14.
Article in English | MEDLINE | ID: mdl-34685731

ABSTRACT

TWIK-1 is the first identified member of the two-pore domain potassium (K2P) channels that are involved in neuronal excitability and astrocytic passive conductance in the brain. Despite the physiological roles of TWIK-1, there is still a lack of information on the basic expression patterns of TWIK-1 proteins in the brain. Here, using a modified bacterial artificial chromosome (BAC), we generated a transgenic mouse (Tg mouse) line expressing green fluorescent protein (GFP) under the control of the TWIK-1 promoter (TWIK-1 BAC-GFP Tg mice). We confirmed that nearly all GFP-producing cells co-expressed endogenous TWIK-1 in the brain of TWIK-1 BAC-GFP Tg mice. GFP signals were highly expressed in various brain areas, including the dentate gyrus (DG), lateral entorhinal cortex (LEC), and cerebellum (Cb). In addition, we found that GFP signals were highly expressed in immature granule cells in the DG. Finally, our TWIK-1 BAC-GFP Tg mice mimic the upregulation of TWIK-1 mRNA expression in the hippocampus following the injection of kainic acid (KA). Our data clearly showed that TWIK-1 BAC-GFP Tg mice are a useful animal model for studying the mechanisms regulating TWIK-1 gene expression and the physiological roles of TWIK-1 channels in the brain.


Subject(s)
Chromosomes, Artificial, Bacterial/metabolism , Green Fluorescent Proteins/metabolism , Potassium Channels, Tandem Pore Domain/genetics , Animals , Cerebellum/metabolism , Dentate Gyrus/metabolism , Entorhinal Cortex/metabolism , Kainic Acid , Mice, Transgenic , Models, Animal , Neuroglia/metabolism , Neurons/metabolism , Reproducibility of Results , Up-Regulation
5.
Cell Rep ; 36(11): 109700, 2021 09 14.
Article in English | MEDLINE | ID: mdl-34525356

ABSTRACT

The power of Drosophila melanogaster as a model system relies on tractable germline genetic manipulations. Despite Drosophila's expansive genetics toolbox, such manipulations are still accomplished one change at a time and depend predominantly on phenotypic screening. We describe a drug-based genetic platform consisting of four selection and two counterselection markers, eliminating the need to screen for modified progeny. These markers work reliably individually or in combination to produce specific genetic outcomes. We demonstrate three example applications of multiplexed drug-based genetics by generating (1) transgenic animals, expressing both components of binary overexpression systems in a single transgenesis step; (2) dual selectable and counterselectable balancer chromosomes; and (3) selectable, fluorescently tagged P[acman] bacterial artificial chromosome (BAC) strains. We perform immunoprecipitation followed by proteomic analysis on one tagged BAC line, demonstrating our platform's applicability to biological discovery. Lastly, we provide a plasmid library resource to facilitate custom transgene design and technology transfer to other model systems.


Subject(s)
Drosophila/genetics , Genetic Techniques , Animals , Animals, Genetically Modified/genetics , Animals, Genetically Modified/metabolism , Chromosomes, Artificial, Bacterial/genetics , Chromosomes, Artificial, Bacterial/metabolism , Drosophila/metabolism , Drug Resistance/drug effects , Drug Resistance/genetics , Female , Ganciclovir/analogs & derivatives , Ganciclovir/pharmacology , Gentamicins/pharmacology , Male , Transgenes/genetics
6.
Dis Model Mech ; 14(8)2021 08 01.
Article in English | MEDLINE | ID: mdl-34350953

ABSTRACT

People of recent sub-Saharan African ancestry develop kidney failure much more frequently than other groups. A large fraction of this disparity is due to two coding sequence variants in the APOL1 gene. Inheriting two copies of these APOL1 risk variants, known as G1 and G2, causes high rates of focal segmental glomerulosclerosis (FSGS), HIV-associated nephropathy and hypertension-associated end-stage kidney disease. Disease risk follows a recessive mode of inheritance, which is puzzling given the considerable data that G1 and G2 are toxic gain-of-function variants. We developed coisogenic bacterial artificial chromosome (BAC) transgenic mice harboring either the wild-type (G0), G1 or G2 forms of human APOL1. Expression of interferon gamma (IFN-γ) via plasmid tail vein injection results in upregulation of APOL1 protein levels together with robust induction of heavy proteinuria and glomerulosclerosis in G1/G1 and G2/G2 but not G0/G0 mice. The disease phenotype was greater in G2/G2 mice. Neither heterozygous (G1/G0 or G2/G0) risk variant mice nor hemizygous (G1/-, G2/-) mice had significant kidney injury in response to IFN-γ, although the heterozygous mice had a greater proteinuric response than the hemizygous mice, suggesting that the lack of significant disease in humans heterozygous for G1 or G2 is not due to G0 rescue of G1 or G2 toxicity. Studies using additional mice (multicopy G2 and a non-isogenic G0 mouse) supported the notion that disease is largely a function of the level of risk variant APOL1 expression. Together, these findings shed light on the recessive nature of APOL1-nephropathy and present an important model for future studies.


Subject(s)
AIDS-Associated Nephropathy , Apolipoprotein L1 , Animals , Apolipoprotein L1/genetics , Apolipoprotein L1/metabolism , Chromosomes, Artificial, Bacterial/metabolism , Gain of Function Mutation , Genetic Predisposition to Disease , Humans , Mice , Mice, Transgenic
7.
Purinergic Signal ; 17(3): 449-465, 2021 09.
Article in English | MEDLINE | ID: mdl-34050505

ABSTRACT

Extracellular purines are important signaling molecules involved in numerous physiological and pathological processes via the activation of P2 receptors. Information about the spatial and temporal P2 receptor (P2R) expression and its regulation remains crucial for the understanding of the role of P2Rs in health and disease. To identify cells carrying P2X2Rs in situ, we have generated BAC transgenic mice that express the P2X2R subunits as fluorescent fusion protein (P2X2-TagRFP). In addition, we generated a BAC P2Y1R TagRFP reporter mouse expressing a TagRFP reporter for the P2RY1 gene expression. We demonstrate expression of the P2X2R in a subset of DRG neurons, the brain stem, the hippocampus, as well as on Purkinje neurons of the cerebellum. However, the weak fluorescence intensity in our P2X2R-TagRFP mouse precluded tracking of living cells. Our P2Y1R reporter mice confirmed the widespread expression of the P2RY1 gene in the CNS and indicate for the first time P2RY1 gene expression in mouse Purkinje cells, which so far has only been described in rats and humans. Our P2R transgenic models have advanced the understanding of purinergic transmission, but BAC transgenic models appeared not always to be straightforward and permanent reliable. We noticed a loss of fluorescence intensity, which depended on the number of progeny generations. These problems are discussed and may help to provide more successful animal models, even if in future more versatile and adaptable nuclease-mediated genome-editing techniques will be the methods of choice.


Subject(s)
Chromosomes, Artificial, Bacterial/genetics , Receptors, Purinergic P2X2/biosynthesis , Receptors, Purinergic P2X2/genetics , Receptors, Purinergic P2Y1/biosynthesis , Receptors, Purinergic P2Y1/genetics , Animals , Cells, Cultured , Chromosomes, Artificial, Bacterial/metabolism , Female , Ganglia, Spinal/metabolism , Gene Expression , HEK293 Cells , Humans , Mice , Mice, Inbred C57BL , Mice, Transgenic , Xenopus laevis
8.
J Vis Exp ; (169)2021 03 04.
Article in English | MEDLINE | ID: mdl-33749670

ABSTRACT

The genome is associated with several structures inside cell nuclei, in order to regulate its activity and anchor it in specific locations. These structures are collectively known as the nucleoskeleton and include the nuclear lamina, the nucleoli, and nuclear bodies. Although many variants of fluorescence in situ hybridization (FISH) exist to study the genome and its organization, these are often limited by resolution and provide insufficient information on the genome's association with nuclear structures. The DNA halo method uses high salt concentrations and nonionic detergents to generate DNA loops that remain anchored to structures within nuclei through attachment regions within the genome. Here, soluble nuclear proteins, such as histones, lipids, and DNA not tightly bound to the nuclear matrix, are extracted. This leads to the formation of a halo of unattached DNA surrounding a residual nucleus which itself contains DNA closely associated with internal nuclear structures and extraction-resistant proteins. These extended DNA strands enable increased resolution and can facilitate physical mapping. In combination with FISH, this method has the added advantage of studying genomic interactions with all the structures that the genome is anchored by. This technique, termed HALO-FISH, is highly versatile whereby DNA halos can be coupled with nucleic acid probes to reveal gene loci, whole chromosomes, alpha satellite, telomeres and even RNA. This technique provides an insight into nuclear organization and function in normal cells and in disease progression such as with cancer.


Subject(s)
Chromosomes/metabolism , DNA/metabolism , Genetic Loci , In Situ Hybridization, Fluorescence , Telomere/metabolism , Cell Nucleus/metabolism , Cells, Cultured , Chromosomes, Artificial, Bacterial/metabolism , Dermis/cytology , Fibroblasts/metabolism , Humans , Image Processing, Computer-Assisted
9.
Virus Res ; 297: 198393, 2021 05.
Article in English | MEDLINE | ID: mdl-33727092

ABSTRACT

Duck enteritis virus (DEV) can cause an acute, contagious and lethal disease of many species of waterfowl. An infectious bacterial artificial chromosome clone of DEV vaccine strain pE1 (pDEV-EF1) has been constructed in our previous study. Based on pE1, a recombinant mutated clone pDL (pVP26CFP-gCRFP), which carries a red fluorescent protein (mRFP) gene fused to the viral envelope protein gC in combination with a cyan fluorescent protein (CFP) gene fused to the viral capsid VP26, was constructed by two-step Red/ET recombination and the recombinant virus rDL (rVP26CFP-gCRFP) was rescued from chicken embryo fibroblasts (CEFs) by calcium phosphate transfection. Western blot analysis revealed that VP26-CFP and gC-mRFP were both expressed in fusion forms in rDL-infected CEFs, and subcellular localization study showed that gC-mRFP was mainly localized in whole cell at 36, 48 h post infection (p.i.); and then mostly migrated to the cytoplasm after 60 h.p.i., ; whereas VP26-CFP was localized in the nucleus in all stages of virus infection. Additionally, viral particles at different stages of morphogenesis (A capsids, B capsids, C capsids) were observed in virus-infected cells by transmission electron microscopy, indicating that exogenous gene insertion has no effect on virus assembly. This study has laid a foundation for visually studying localization, transportation of DEV capsid proteins and envelope glycoproteins as well as virus assembly, virion movement and virus-cell interaction.


Subject(s)
Capsid , Enteritis , Animals , Capsid/metabolism , Capsid Proteins/genetics , Capsid Proteins/metabolism , Chick Embryo , Chickens , Chromosomes, Artificial, Bacterial/metabolism , Ducks
10.
Genesis ; 59(3): e23409, 2021 03.
Article in English | MEDLINE | ID: mdl-33484096

ABSTRACT

Mutations in the osteopetrotic transmembrane protein 1 (Ostm1) gene are responsible for the most severe form of autosomal recessive osteopetrosis both in humans and in the gray lethal (gl/gl) mouse. This defect leads to increased bone mass with bone marrow occlusion and hematopoietic defects. To establish the expression profile of the mouse Ostm1 protein in vivo, homologous recombination in bacteria was designed to generate a V5-Ostm1 bacterial artificial chromosome (BAC) that was subsequently integrated in the mouse genome. Tissue expression of the transgene V5-Ostm1 RNA and protein in transgenic mice follow the endogenous expression profile. Immunohistochemistry analysis demonstrated expression in neuronal populations from central and peripheral nervous system and defined a unique cellular expression pattern. Importantly, together with appropriate protein post-translational modification, in vivo rescue of the osteopetrotic bone gl/gl phenotype in BAC V5-Ostm1 gl/gl mice is consistent with the expression of a fully functional and active protein. These mice represent a unique tool to unravel novel Ostm1 functions in individual tissue and neuronal cell populations and the V5-Ostm1 transgene represents an easy visual marker to monitor the expression of Ostm1 in vitro and in vivo.


Subject(s)
Chromosomes, Artificial, Bacterial/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Osteopetrosis/genetics , Osteopetrosis/metabolism , Animals , Disease Models, Animal , Mice , Mice, Inbred C57BL , Mice, Transgenic , Mutation , Phenotype , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
11.
Mol Brain ; 13(1): 118, 2020 08 28.
Article in English | MEDLINE | ID: mdl-32859226

ABSTRACT

Repressor element 1-silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) is a transcription repressor and its expression is regulated by the Wnt pathway through ß-catenin. Metabotropic glutamate receptor 5 (mGluR5) signaling plays a key role in controlling neuronal gene expression. Interestingly, REST/NRSF nuclear translocation and signaling, as well as mGluR5 signaling are altered in the presence of mutant huntingtin. It remains unclear whether mGluR5 can modulate Wnt and REST/NRSF signaling under physiological conditions and whether this modulation is altered in Huntington's disease (HD). Using primary corticostriatal neurons derived from wild type mouse embryos, we find that targeting mGluR5 using the agonist, DHPG, or the negative allosteric modulator, CTEP, modulates REST/NRSF expression by regulating the assembly of N-cadherin/ ß-catenin complex in a Src kinase-dependent manner. We have validated our in vitro findings in vivo using two HD mouse models. Specifically, we show that pharmacological inhibition of mGluR5 in zQ175 mice and genetic ablation of mGluR5 in BACHD mice corrected the pathological activation of Src and rescued REST/NRSF-dependent signaling. Together, our data provide evidence that mGluR5 regulates REST/NRSF expression via the Wnt pathway and highlight the contribution of impaired REST/ NRSF signaling to HD pathology.


Subject(s)
Cadherins/metabolism , Huntington Disease/metabolism , Receptor, Metabotropic Glutamate 5/metabolism , Repressor Proteins/metabolism , Signal Transduction , beta Catenin/metabolism , Animals , Cells, Cultured , Chromosomes, Artificial, Bacterial/metabolism , Gene Deletion , Imidazoles/pharmacology , Male , Mice , Models, Biological , Neurons/metabolism , Phosphorylation , Protein Binding , Pyridines/pharmacology , Synaptosomal-Associated Protein 25/metabolism , src-Family Kinases/metabolism
12.
Sci Rep ; 10(1): 5658, 2020 03 27.
Article in English | MEDLINE | ID: mdl-32221415

ABSTRACT

Duck plague virus (DPV), a member of the alphaherpesviruses subfamily, causes massive ducks death and results in a devastating hit to duck industries in China. It is of great significance for us to analyze the functions of DPV genes for controlling the outbreak of duck plague. Thus, glycoproteins E (gE) of DPV, which requires viral cell-to-cell spreading and the final envelopment in herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), was chosen herein. The gE mutant virus BAC-CHv-ΔgE was constructed by using a markerless two-step Red recombination system implemented on the DPV genome cloned into a bacterial artificial chromosome (BAC). Viral plaques on duck embryo fibroblast (DEF) cells of BAC-CHv-ΔgE were on average approximately 60% smaller than those produced by BAC-CHv virus. Viral replication kinetics showed that BAC-CHv-ΔgE grew to lower titers than BAC-CHv virus did in DEF cells. Electron microscopy confirmed that deleting of DPV gE resulted in a large number of capsids accumulating around vesicles and very few of them could bud into vesicles. The drastic inhibition of virion formation in the absence of the DPV gE indicated that it played an important role in virion morphogenesis before the final envelopment of intracytoplasmic nucleocapsids.


Subject(s)
Alphaherpesvirinae/metabolism , Capsid/metabolism , Cytoplasm/metabolism , Cytoplasmic Vesicles/metabolism , Ducks/metabolism , Viral Structural Proteins/metabolism , Virion/metabolism , Animals , Cell Line , Chromosomes, Artificial, Bacterial/metabolism , Cytoplasm/virology , Cytoplasmic Vesicles/virology , Ducks/virology , Glycoproteins/metabolism , Herpesvirus 1, Human/metabolism , Herpesvirus 1, Suid/metabolism , Mardivirus/metabolism , Virus Assembly/physiology , Virus Replication/physiology
13.
J Biotechnol ; 305: 43-50, 2019 Nov 10.
Article in English | MEDLINE | ID: mdl-31505217

ABSTRACT

In metabolic engineering and synthetic biology, the number of genes expressed to achieve better production and pathway regulation in each strain is steadily increasing. The method of choice for expression in Escherichia coli is usually one or several multi-copy plasmids. Meanwhile, the industry standard for long-term, robust production is chromosomal integration of the desired genes. Despite recent advances, genetic manipulation of the bacterial chromosome remains more time consuming than plasmid construction. To allow screening of different metabolic engineering strategies at a level closer to industry while maintaining the molecular-biology advantages of plasmid-based expression, we have investigated the single-copy bacterial artificial chromosome (BAC) as a development tool for metabolic engineering. Using (R)-3-hydroxybutyrate as a model product, we show that BAC can outperform multi-copy plasmids in terms of yield, productivity and specific growth rate, with respective increases of 12%, 18%, and 5%. We both show that gene expression by the BAC simplifies pathway optimization and that the phenotype of pathway expression from BAC is very close to that of chromosomal expression. From these results, we conclude that the BAC can provide a simple platform for performing pathway design and optimization.


Subject(s)
Chromosomes, Artificial, Bacterial/genetics , Escherichia coli/genetics , Metabolic Engineering/methods , Chromosomes, Artificial, Bacterial/metabolism , Escherichia coli/metabolism , Hydroxybutyrates/metabolism , Plasmids/genetics , Plasmids/metabolism , Synthetic Biology
14.
Elife ; 72018 11 30.
Article in English | MEDLINE | ID: mdl-30499775

ABSTRACT

Vertebrate pelvic reduction is a classic example of repeated evolution. Recurrent loss of pelvic appendages in sticklebacks has previously been linked to natural mutations in a pelvic enhancer that maps upstream of Pitx1. The sequence of this upstream PelA enhancer is not conserved to mammals, so we have surveyed a large region surrounding the mouse Pitx1 gene for other possible hind limb control sequences. Here we identify a new pelvic enhancer, PelB, that maps downstream rather than upstream of Pitx1. PelB drives expression in the posterior portion of the developing hind limb, and deleting the sequence from mice alters the size of several hind limb structures. PelB sequences are broadly conserved from fish to mammals. A wild stickleback population lacking the pelvis has an insertion/deletion mutation that disrupts the structure and function of PelB, suggesting that changes in this ancient enhancer contribute to evolutionary modification of pelvic appendages in nature.


Subject(s)
Biological Evolution , Enhancer Elements, Genetic , Paired Box Transcription Factors/genetics , Pelvis/growth & development , Vertebrates/growth & development , Vertebrates/genetics , Animals , Base Sequence , Chromosomes, Artificial, Bacterial/metabolism , Conserved Sequence , Fishes/embryology , Gene Expression Regulation, Developmental , Genetic Loci , Genome , Hindlimb/growth & development , Lizards/embryology , Mice , Paired Box Transcription Factors/metabolism , Sequence Deletion
15.
Genome Biol ; 19(1): 117, 2018 08 15.
Article in English | MEDLINE | ID: mdl-30111345

ABSTRACT

BACKGROUND: Alternative RNA processing plays an essential role in shaping cell identity and connectivity in the central nervous system. This is believed to involve differential regulation of RNA processing in various cell types. However, in vivo study of cell type-specific post-transcriptional regulation has been a challenge. Here, we describe a sensitive and stringent method combining genetics and CLIP (crosslinking and immunoprecipitation) to globally identify regulatory interactions between NOVA and RNA in the mouse spinal cord motoneurons. RESULTS: We developed a means of undertaking motoneuron-specific CLIP to explore motoneuron-specific protein-RNA interactions relative to studies of the whole spinal cord in mouse. This allowed us to pinpoint differential RNA regulation specific to motoneurons, revealing a major role for NOVA in regulating cytoskeleton interactions in motoneurons. In particular, NOVA specifically promotes the palmitoylated isoform of the cytoskeleton protein Septin 8 in motoneurons, which enhances dendritic arborization. CONCLUSIONS: Our study demonstrates that cell type-specific RNA regulation is important for fine tuning motoneuron physiology and highlights the value of defining RNA processing regulation at single cell type resolution.


Subject(s)
Cross-Linking Reagents/metabolism , Cytoskeleton/metabolism , Immunoprecipitation , Motor Neurons/metabolism , Nerve Tissue Proteins/metabolism , RNA-Binding Proteins/metabolism , Alternative Splicing/genetics , Amino Acid Sequence , Animals , COS Cells , Chlorocebus aethiops , Chromosomes, Artificial, Bacterial/metabolism , Dendrites/metabolism , Exons/genetics , Lipoylation , Mice , Mice, Transgenic , NIH 3T3 Cells , Nerve Tissue Proteins/chemistry , Neuro-Oncological Ventral Antigen , Pseudopodia/metabolism , RNA/metabolism , RNA-Binding Proteins/chemistry , Septins/metabolism , Transcriptome/genetics
16.
Arch Virol ; 163(3): 599-607, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29149435

ABSTRACT

Equine herpesvirus type 1 (EHV-1) UL11 is a 74-amino-acid tegument protein encoded by ORF51 of the EHV-1 genome. EHV-1 UL11 was previously reported by other researchers using the RacL22 and RacH strains to be nonessential for viral replication in cultured cells. Here, we constructed UL11 mutant viruses including a UL11 null mutant and three C-terminal truncated mutants, for further characterization of EHV-1 UL11 using bacterial artificial chromosome (BAC) technology based on the neuropathogenic strain Ab4p. EHV-1 Ab4p UL11 was localized to juxtanuclear and Golgi regions as reported by other researchers. We found that no progeny viruses were produced by transfection of fetal equine kidney cells and rabbit kidney (RK-13) cells with the UL11 null mutant and truncation mutant BAC DNAs. However, mutant viruses were generated after transfection of RK13-UL11 cells constitutively expressing EHV-1 UL11 with the mutant BAC DNAs. In conclusion, UL11 of EHV-1 Ab4p is essential for replication in cultured cells.


Subject(s)
Epithelial Cells/virology , Herpesvirus 1, Equid/genetics , Herpesvirus 1, Equid/pathogenicity , Open Reading Frames , Viral Structural Proteins/genetics , Virus Replication , Animals , Base Sequence , Cell Line , Cell Nucleus/ultrastructure , Cell Nucleus/virology , Chromosomes, Artificial, Bacterial/chemistry , Chromosomes, Artificial, Bacterial/metabolism , Epithelial Cells/ultrastructure , Gene Expression , Golgi Apparatus/ultrastructure , Golgi Apparatus/virology , Herpesvirus 1, Equid/growth & development , Herpesvirus 1, Equid/metabolism , Horses , Kidney/cytology , Kidney/virology , Mutation , Rabbits , Viral Structural Proteins/metabolism , Virulence
17.
BMC Biotechnol ; 17(1): 81, 2017 Nov 14.
Article in English | MEDLINE | ID: mdl-29137618

ABSTRACT

BACKGROUND: Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. METHODS: The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments. The first PCR yields linear DNA fragments and is followed by a second asymmetric (one primer) PCR and subsequent annealing that inserts overlapping overhangs at both sides of each DNA fragment. The overlapping overhangs of the neighboring DNA fragments annealed and the nick was sealed by T4 DNA ligase, followed by bacterial transformation to yield the desired plasmids. RESULTS: We characterized the capability and limitations of new developed AFEAP cloning and demonstrated its application to assemble DNA with varying scenarios. Under the optimized conditions, AFEAP cloning allows assembly of an 8 kb plasmid from 1-13 fragments with high accuracy (between 80 and 100%), and 8.0, 11.6, 19.6, 28, and 35.6 kb plasmids from five fragments at 91.67, 91.67, 88.33, 86.33, and 81.67% fidelity, respectively. AFEAP cloning also is capable to construct bacterial artificial chromosome (BAC, 200 kb) with a fidelity of 46.7%. CONCLUSIONS: AFEAP cloning provides a powerful, efficient, seamless, and sequence-independent DNA assembly tool for multiple fragments up to 13 and large DNA up to 200 kb that expands synthetic biologist's toolbox.


Subject(s)
Cloning, Molecular/methods , DNA/metabolism , Polymerase Chain Reaction/methods , Synthetic Biology/methods , Chromosomes, Artificial, Bacterial/chemistry , Chromosomes, Artificial, Bacterial/genetics , Chromosomes, Artificial, Bacterial/metabolism , DNA/chemistry , DNA/genetics , Plasmids/genetics
18.
Ann Clin Lab Sci ; 47(5): 523-528, 2017 Sep.
Article in English | MEDLINE | ID: mdl-29066476

ABSTRACT

Medullary thyroid carcinoma (MTC), an aggressive form of thyroid cancer, occurs sporadically in approximately 75% of MTCs. RET and RAS mutations play a role in about 40% and 15%, respectively, of sporadic MTCs and are predominant drivers in MTC pathways. These mutations are some of the most comprehensively described and screened for in MTC patients; however, in recent studies, other mutations in the CDKN2C gene (p18) have been implicated in the tumorigenesis of MTC. Comparative genomic hybridization analysis revealed that approximately 40% of sporadic MTC samples have loss of CDKN2C at chromosome 1p32 in addition to frequent losses of CDKN2D (p19) at chromosome 19p13. However, no feasible routine method had been established to detect loss of heterozygosity (LOH) of CDKN2C and CD-KN2D The aim of this study is to assess the feasibility of using Fluorescence in situ Hybridization (FISH) to screen MTC patients for CDKN2C and CDKN2D deletions. We subjected 5 formalin-fixed, paraffin-embedded (FFPE) MTC samples with defined RET/RAS mutations to dual-color FISH assays to detect loss of CDKN2C and/or CDKN2D We prepared spectrum orange probes using the bacterial artificial chromosomes RP11-779F9 for CDKN2C (p18) and RP11-177J4 for CDKN2D (p19) and prepared spectrum green control probes to the 1q25.2 and 19q11 regions (RP11-1146A3 and RP11-942P7, respectively). Nine FFPE normal thyroid tissue samples were used to establish the cutoff values for the FISH signal patterns. Of the five FFPE MTC samples, four and one yielded a positive significant result for CDKNN2C loss and CDKN2D loss, respectively. The results of a Clinical Laboratory Improvement Amendments validation with a CDKN2C/CKS1B probe set for CDKN2C (p18) loss of heterozygosity were 100% concordant with the FISH results obtained in this study. Thus, FISH is a fast and reliable diagnostic or prognostic indicator of gene loss in MTC.


Subject(s)
Carcinoma, Neuroendocrine/genetics , Cyclin-Dependent Kinase Inhibitor p18/genetics , Cytogenetic Analysis/methods , Neoplasm Proteins/genetics , Thyroid Gland/metabolism , Thyroid Neoplasms/genetics , Cancer Care Facilities , Carcinoma, Neuroendocrine/diagnosis , Carcinoma, Neuroendocrine/metabolism , Carcinoma, Neuroendocrine/pathology , Chromosomes, Artificial, Bacterial/metabolism , Cyclin-Dependent Kinase Inhibitor p18/metabolism , Cyclin-Dependent Kinase Inhibitor p19/genetics , Cyclin-Dependent Kinase Inhibitor p19/metabolism , DNA, Complementary/metabolism , DNA, Recombinant/metabolism , Feasibility Studies , Gene Deletion , Humans , In Situ Hybridization, Fluorescence , Loss of Heterozygosity , Neoplasm Proteins/metabolism , Prognosis , Recombinant Proteins/metabolism , Reproducibility of Results , Texas , Thyroid Gland/pathology , Thyroid Neoplasms/diagnosis , Thyroid Neoplasms/metabolism , Thyroid Neoplasms/pathology , Time Factors
19.
Mol Brain ; 10(1): 42, 2017 09 02.
Article in English | MEDLINE | ID: mdl-28865483

ABSTRACT

Deep brain stimulation in thalamic regions has been proposed as a treatment for epilepsy. The electrical current excites thalamocortical activity which is controlled by γ-aminobutyric acid (GABA)ergic interneurons in the reticular thalamic nucleus (nRT). Previous studies showed that enhancing GABAergic inhibitory strength in the nRT reduces the duration and power of seizures, indicating that the thalamus plays an important role in modulating cortical seizures. The aim of the present study was to apply optogenetics to study the role of the nRT in modulating cortical seizures. We used PV-ChR2-EYFP transgenic mice from Jackson Laboratories, in which only Channelrhodopsin-2 (ChR2) is expressed in parvalbumin-expressing interneurons. Cortical seizure-like activity was induced by electrical stimulation of the corpus callosum after applying 4-aminopyridine. ChR2 expression was abundant in the nRT and cerebellum in PV-ChR2-EYFP transgenic mice. Light stimulation in the nRT caused burst firing in regions of the thalamus and nRT in vitro. Multi-unit activity increased during high-frequency (100 and 50 Hz) light stimulation in the S1 region and thalamus in vivo. Corpus callosum stimulation-induced seizure-like activity was effectively suppressed by high-frequency (100 Hz) and long-duration (10 s) light stimulation. The suppressive effects were reversed by applying a GABAB receptor antagonist but not a GABAA receptor antagonist in the cortex. The results indicated that light stimulation affected thalamocortical relay neurons by activating ChR2-expression neurons in the nRT. High-frequency and long-duration light stimulation was more effective in suppressing cortical seizure-like activity. GABAB receptors may participate in suppressing seizure-like activity.


Subject(s)
Cerebral Cortex/pathology , Channelrhodopsins/metabolism , Chromosomes, Artificial, Bacterial/metabolism , Optogenetics , Parvalbumins/metabolism , Photic Stimulation , Seizures/pathology , Thalamus/pathology , Animals , Bacterial Proteins/metabolism , Electric Stimulation , Luminescent Proteins/metabolism , Mice, Transgenic , Movement , Reproducibility of Results , gamma-Aminobutyric Acid/pharmacology
20.
Proc Natl Acad Sci U S A ; 114(23): 6104-6109, 2017 06 06.
Article in English | MEDLINE | ID: mdl-28533400

ABSTRACT

Human cytomegalovirus (HCMV) strains that have been passaged in vitro rapidly acquire mutations that impact viral growth. These laboratory-adapted strains of HCMV generally exhibit restricted tropism, produce high levels of cell-free virus, and develop susceptibility to natural killer cells. To permit experimentation with a virus that retained a clinically relevant phenotype, we reconstructed a wild-type (WT) HCMV genome using bacterial artificial chromosome technology. Like clinical virus, this genome proved to be unstable in cell culture; however, propagation of intact virus was achieved by placing the RL13 and UL128 genes under conditional expression. In this study, we show that WT-HCMV produces extremely low titers of cell-free virus but can efficiently infect fibroblasts, epithelial, monocyte-derived dendritic, and Langerhans cells via direct cell-cell transmission. This process of cell-cell transfer required the UL128 locus, but not the RL13 gene, and was significantly less vulnerable to the disruptive effects of IFN, cellular restriction factors, and neutralizing antibodies compared with cell-free entry. Resistance to neutralizing antibodies was dependent on high-level expression of the pentameric gH/gL/gpUL128-131A complex, a feature of WT but not passaged strains of HCMV.


Subject(s)
Cell Culture Techniques/methods , Cytomegalovirus/genetics , Cytomegalovirus/metabolism , Antibodies, Neutralizing , Cell Line , Cells, Cultured , Chromosomes, Artificial, Bacterial/metabolism , Cytomegalovirus/pathogenicity , Cytomegalovirus Infections/immunology , Cytomegalovirus Infections/metabolism , Fibroblasts/metabolism , Humans , Membrane Glycoproteins/metabolism , Mutation , Phenotype , Tropism/immunology , Viral Envelope Proteins/metabolism , Virus Internalization , Virus Replication/immunology
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