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Han B, Yue F, Zhang X, Xu K, Zhang Z, Sun Z, Mu L, Li X. Genetically engineering of Saccharomyces cerevisiae for enhanced oral delivery vaccine vehicle. Fish Shellfish Immunol 2024; 146:109425. [PMID: 38316348 DOI: 10.1016/j.fsi.2024.109425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 01/24/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
As a series of our previous studies reported, recombinant yeast can be the oral vaccines to deliver designed protein and DNA, as well as functional shRNA, into dendritic cells (DCs) in mice for specific immune regulation. Here, we report the further optimization of oral yeast-based vaccine from two aspects (yeast characteristics and recombinant DNA constitution) to improve the effect of immune regulation. After screening four genes in negative regulation of glucan synthesis in yeast (MNN9, GUP1, PBS2 and EXG1), this research combined HDR-based genome editing technology with Cre-loxP technology to acquire 15 gene-knockout strains without drug resistance-gene to exclude biosafety risks; afterward, oral feeding experiments were performed on the mice using 15 oral recombinant yeast-based vaccines constructed by the gene-knockout strains harboring pCMV-MSTN plasmid to screen the target strain with more effective inducing mstn-specific antibody which in turn increasing weight gain effect. And subsequently based on the selected gene-knockout strain, the recombinant DNA in the oral recombinant yeast-based vaccine is optimized via a combination of protein fusion expression (OVA-MSTN) and interfering RNA technology (shRNA-IL21), comparison in terms of both weight gain effect and antibody titer revealed that the selected gene-knockout strain (GUP1ΔEXG1Δ) combined with specific recombinant DNA (pCMV-OVA-MSTN-shIL2) had a better effect of the vaccine. This study provides a useful reference to the subsequent construction of a more efficient oral recombinant yeast-based vaccine in the food and pharmaceutical industry.
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Affiliation(s)
- Baoquan Han
- Department of Urology, Shenzhen University General Hospital, Shenzhen, 518055, China; College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Feng Yue
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Kun Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Zhongyi Sun
- Department of Urology, Shenzhen University General Hospital, Shenzhen, 518055, China.
| | - Lu Mu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoyu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
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2
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Steward RA, Pruisscher P, Roberts KT, Wheat CW. Genetic constraints in genes exhibiting splicing plasticity in facultative diapause. Heredity (Edinb) 2024; 132:142-155. [PMID: 38291272 PMCID: PMC10923799 DOI: 10.1038/s41437-024-00669-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.
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Affiliation(s)
- Rachel A Steward
- Zoology Department, Stockholm University, Stockholm, Sweden.
- Biology Department, Lund University, Lund, Sweden.
| | - Peter Pruisscher
- Zoology Department, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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3
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Abstract
The "rediscovery" 11β-hydroxyandrostenedione (11OHA4) placed the spotlight on this unique adrenal-derived hormone with researchers and clinicians once again focusing on the steroid's presence in endocrine pathology. Little was known about the steroid other than its chemical characterisation and that a mitochondrial cytochrome P450 enzyme catalysed the 11β-hydroxylation of 11OHA4. The fact that neither the biosynthesis nor metabolism of 11OHA4 had been fully characterised presented an ideal opportunity to investigate the metabolic pathways. In addition, methodologies and analytical tools have improved vastly since 11OHA4 was first identified in the 1950s. Cell models, recombinant DNA technology and steroid quantification using liquid chromatography mass spectrometry have greatly facilitated investigations in the field of steroidogenesis. Evident from the structure is that 11OHA4 can be metabolised by hydroxysteroid dehydrogenases and reductases acting on the C4/C5 double bond and on functional moieties at specific carbons on the cyclopentane-perhydro-phenanthrene backbone of the steroid. In this chapter, the biosynthesis and metabolism of 11OHA4 is followed using two strategies that complement each another; (i) human cell models either transiently transfected with recombinant DNA or expressing endogenous steroidogenic enzymes and (ii) steroid identification and quantification using high resolution mass spectrometry. These methodologies have proven invaluable in the determination of 11OHA4's metabolic route. Both strategies are presented with the focus on the accurate identification and quantification of steroids using UHPLC-MS/MS and UPC2-MS/MS. The protocols described in this chapter lay a sound foundation which can aid the researcher and be adapted and implement in future studies.
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Affiliation(s)
- Amanda C Swart
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa; Department of Chemistry, Stellenbosch University, Stellenbosch, South Africa.
| | - Desmaré van Rooyen
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Therina du Toit
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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4
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Bhatnagar A, Krick K, Karisetty BC, Armour EM, Heller EA, Elefant F. Tip60's Novel RNA-Binding Function Modulates Alternative Splicing of Pre-mRNA Targets Implicated in Alzheimer's Disease. J Neurosci 2023; 43:2398-2423. [PMID: 36849418 PMCID: PMC10072303 DOI: 10.1523/jneurosci.2331-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
The severity of Alzheimer's disease (AD) progression involves a complex interplay of genetics, age, and environmental factors orchestrated by histone acetyltransferase (HAT)-mediated neuroepigenetic mechanisms. While disruption of Tip60 HAT action in neural gene control is implicated in AD, alternative mechanisms underlying Tip60 function remain unexplored. Here, we report a novel RNA binding function for Tip60 in addition to its HAT function. We show that Tip60 preferentially interacts with pre-mRNAs emanating from its chromatin neural gene targets in the Drosophila brain and this RNA binding function is conserved in human hippocampus and disrupted in Drosophila brains that model AD pathology and in AD patient hippocampus of either sex. Since RNA splicing occurs co-transcriptionally and alternative splicing (AS) defects are implicated in AD, we investigated whether Tip60-RNA targeting modulates splicing decisions and whether this function is altered in AD. Replicate multivariate analysis of transcript splicing (rMATS) analysis of RNA-Seq datasets from wild-type and AD fly brains revealed a multitude of mammalian-like AS defects. Strikingly, over half of these altered RNAs are identified as bona-fide Tip60-RNA targets that are enriched for in the AD-gene curated database, with some of these AS alterations prevented against by increasing Tip60 in the fly brain. Further, human orthologs of several Tip60-modulated splicing genes in Drosophila are well characterized aberrantly spliced genes in human AD brains, implicating disruption of Tip60's splicing function in AD pathogenesis. Our results support a novel RNA interaction and splicing regulatory function for Tip60 that may underly AS impairments that hallmark AD etiology.SIGNIFICANCE STATEMENT Alzheimer's disease (AD) has recently emerged as a hotbed for RNA alternative splicing (AS) defects that alter protein function in the brain yet causes remain unclear. Although recent findings suggest convergence of epigenetics with co-transcriptional AS, whether epigenetic dysregulation in AD pathology underlies AS defects remains unknown. Here, we identify a novel RNA interaction and splicing regulatory function for Tip60 histone acetyltransferase (HAT) that is disrupted in Drosophila brains modeling AD pathology and in human AD hippocampus. Importantly, mammalian orthologs of several Tip60-modulated splicing genes in Drosophila are well characterized aberrantly spliced genes in human AD brain. We propose that Tip60-mediated AS modulation is a conserved critical posttranscriptional step that may underlie AS defects now characterized as hallmarks of AD.
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Affiliation(s)
- Akanksha Bhatnagar
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104
| | - Keegan Krick
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | - Ellen M Armour
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Felice Elefant
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104
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Pellagatti A, Boultwood J. Splicing factor mutations in the myelodysplastic syndromes: Role of key aberrantly spliced genes in disease pathophysiology and treatment. Adv Biol Regul 2023; 87:100920. [PMID: 36216757 DOI: 10.1016/j.jbior.2022.100920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 03/01/2023]
Abstract
Mutations of splicing factor genes (including SF3B1, SRSF2, U2AF1 and ZRSR2) occur in more than half of all patients with myelodysplastic syndromes (MDS), a heterogeneous group of myeloid neoplasms. Splicing factor mutations lead to aberrant pre-mRNA splicing of many genes, some of which have been shown in functional studies to impact on hematopoiesis and to contribute to the MDS phenotype. This clearly demonstrates that impaired spliceosome function plays an important role in MDS pathophysiology. Recent studies that harnessed the power of induced pluripotent stem cell (iPSC) and CRISPR/Cas9 gene editing technologies to generate new iPSC-based models of splicing factor mutant MDS, have further illuminated the role of key downstream target genes. The aberrantly spliced genes and the dysregulated pathways associated with splicing factor mutations in MDS represent potential new therapeutic targets. Emerging data has shown that IRAK4 is aberrantly spliced in SF3B1 and U2AF1 mutant MDS, leading to hyperactivation of NF-κB signaling. Pharmacological inhibition of IRAK4 has shown efficacy in pre-clinical studies and in MDS clinical trials, with higher response rates in patients with splicing factor mutations. Our increasing knowledge of the effects of splicing factor mutations in MDS is leading to the development of new treatments that may benefit patients harboring these mutations.
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Affiliation(s)
- Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
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Vasilev N. Medicinal Plants: Guests and Hosts in the Heterologous Expression of High-Value Products. Planta Med 2022; 88:1175-1189. [PMID: 34521134 DOI: 10.1055/a-1576-4148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Medicinal plants play an important dual role in the context of the heterologous expression of high-value pharmaceutical products. On the one hand, the classical biochemical and modern omics approaches allowed for the discovery of various genes encoding biosynthetic pathways in medicinal plants. Recombinant DNA technology enabled introducing these genes and regulatory elements into host organisms and enhancing the heterologous production of the corresponding secondary metabolites. On the other hand, the transient expression of foreign DNA in plants facilitated the production of numerous proteins of pharmaceutical importance. This review summarizes several success stories of the engineering of plant metabolic pathways in heterologous hosts. Likewise, a few examples of recombinant protein expression in plants for therapeutic purposes are also highlighted. Therefore, the importance of medicinal plants has grown immensely as sources for valuable products of low and high molecular weight. The next step ahead for bioengineering is to achieve more success stories of industrial-scale production of secondary plant metabolites in microbial systems and to fully exploit plant cell factories' commercial potential for recombinant proteins.
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Affiliation(s)
- Nikolay Vasilev
- TU Dortmund University, Biochemical and Chemical Engineering, Technical Biochemistry, Dortmund, Germany
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7
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Liu Z, Kang K, Ka-Ming Chan F. Generation of recombinant vaccinia virus and analysis of virus-induced cell death. STAR Protoc 2021; 2:100871. [PMID: 34661172 PMCID: PMC8503571 DOI: 10.1016/j.xpro.2021.100871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Vaccinia virus is a large double-stranded DNA virus that is widely used to express foreign genes from different origins. We generated recombinant vaccinia virus that expresses a viral inhibitor to examine its effect on virus-induced necroptosis. We provide a detailed protocol to describe the generation of recombinant vaccinia virus, validation of protein expression, and determination of necroptosis using live cell imaging. This approach can be adapted to examine the effect of other cell death regulators on virus-induced cell death. For complete details on the use and execution of this protocol, please refer to Liu et al. (2021).
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Affiliation(s)
- Zhijun Liu
- Department of Immunology, Duke University School of Medicine, DUMC 3010, Durham, NC 27710, USA
| | - Kidong Kang
- Department of Immunology, Duke University School of Medicine, DUMC 3010, Durham, NC 27710, USA
| | - Francis Ka-Ming Chan
- Department of Immunology, Duke University School of Medicine, DUMC 3010, Durham, NC 27710, USA
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Salafutdinov II, Gazizov IM, Gatina DK, Mullin RI, Bogov AA, Islamov RR, Kiassov AP, Masgutov RF, Rizvanov AA. Influence of Recombinant Codon-Optimized Plasmid DNA Encoding VEGF and FGF2 on Co-Induction of Angiogenesis. Cells 2021; 10:cells10020432. [PMID: 33670607 PMCID: PMC7922559 DOI: 10.3390/cells10020432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Over the past few decades, several methods have been proposed to stimulate skin wound healing. The most promising of these are gene therapy and stem cell therapy. Our present experiments have combined several approaches utilizing human umbilical cord blood mononuclear cells using cell therapy, and direct gene therapy using genetic constructs to accelerate complete healing of skin wounds in rats. Studies have shown that the transplantation of transfected cells stopped proliferative processes in regenerating wounds earlier than the transplantation of untransfected cells. The use of direct gene therapy using the VEGF and FGF2 genes stimulates the revascularization of the rat cutaneous wound. Abstract Several methods for the stimulation of skin wound repair have been proposed over the last few decades. The most promising among them are gene and stem cell therapy. Our present experiments combined several approaches via the application of human umbilical cord blood mononuclear cells (hUCB-MC) that were transfected with pBud-VEGF165-FGF2 plasmid (gene-cell therapy) and direct gene therapy using pBud-VEGF165-FGF2 plasmid to enhance healing of full thickness skin wounds in rats. The dual expression cassette plasmid pBud-VEGF165-FGF2 encodes both VEGF and FGF2 therapeutic genes, expressing pro-angiogenic growth factors. Our results showed that, with two weeks post-transplantation, some transplanted cells still retained expression of the stem cell and hematopoietic markers C-kit and CD34. Other transplanted cells were found among keratinocytes, hair follicle cells, endothelial cells, and in the derma. PCNA expression studies revealed that transplantation of transfected cells terminated proliferative processes in regenerating wounds earlier than transplantation of untransfected cells. In the direct gene therapy group, four days post-operatively, the processes of flap revascularization, while using Easy LDI Microcirculation Camera, was higher than in control wounded skin. We concluded that hUCB-MC can be used for the treatment of skin wounds and transfection these cells with VEGF and FGF2 genes enhances their regenerative abilities. We also concluded that the application of pBud-VEGF165-FGF2 plasmids is efficient for the direct gene therapy of skin wounds by stimulation of wound revascularization.
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Affiliation(s)
- Ilnur I. Salafutdinov
- Research Laboratory Omics Technology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia;
- OpenLab “Gene and Cell Technologies”, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (A.P.K.); (R.F.M.)
- Correspondence: (I.I.S.); (A.A.R.)
| | - Ilnaz M. Gazizov
- Department of Human Anatomy, Kazan State Medical University, 420012 Kazan, Russia;
| | - Dilara K. Gatina
- Research Laboratory Omics Technology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia;
- OpenLab “Gene and Cell Technologies”, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (A.P.K.); (R.F.M.)
| | - Ruslan I. Mullin
- Department of Orthopaedics, Republic Clinical Hospital, 420064 Kazan, Russia; (R.I.M.); (A.A.B.)
| | - Alexey A. Bogov
- Department of Orthopaedics, Republic Clinical Hospital, 420064 Kazan, Russia; (R.I.M.); (A.A.B.)
| | - Rustem R. Islamov
- Department of Medical Biology and Genetics, Kazan State Medical University, 420012 Kazan, Russia;
| | - Andrey P. Kiassov
- OpenLab “Gene and Cell Technologies”, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (A.P.K.); (R.F.M.)
- Morphology and General Pathology Department, Institute of Fundamental Medicine and Biology, Federal University, 420008 Kazan, Russia
| | - Ruslan F. Masgutov
- OpenLab “Gene and Cell Technologies”, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (A.P.K.); (R.F.M.)
- Department of Orthopaedics, Republic Clinical Hospital, 420064 Kazan, Russia; (R.I.M.); (A.A.B.)
| | - Albert A. Rizvanov
- Research Laboratory Omics Technology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia;
- OpenLab “Gene and Cell Technologies”, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (A.P.K.); (R.F.M.)
- Correspondence: (I.I.S.); (A.A.R.)
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9
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Mivelaz M, Fierz B. Observing protein interaction dynamics to chemically defined chromatin fibers by colocalization single-molecule fluorescence microscopy. Methods 2020; 184:112-124. [PMID: 32004546 DOI: 10.1016/j.ymeth.2020.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/15/2020] [Accepted: 01/26/2020] [Indexed: 02/04/2023] Open
Abstract
In eukaryotic cells, the genome is packaged into chromatin and exists in different states, ranging from open euchromatic regions to highly condensed heterochromatic regions. Chromatin states are highly dynamic and are organized by an interplay of histone post-translational modifications and effector proteins, both of which are central in the regulation of gene expression. For this, chromatin effector proteins must first search the nucleus for their targets, before binding and performing their role. A key question is how chromatin effector proteins search, interact with and alter the different chromatin environments. Here we present a modular fluorescence based in vitro workflow to directly observe dynamic interactions of effector proteins with defined chromatin fibres, replicating different chromatin states. We discuss the design and creation of chromatin assemblies, the synthesis of modified histones, the fabrication of microchannels and the approach to data acquisition and analysis. All of this with the aim to better understand the complex in vivo relationship between chromatin structure and gene expression.
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Affiliation(s)
- Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne, SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne, SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland.
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10
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Fitz-James MH, Tong P, Pidoux AL, Ozadam H, Yang L, White SA, Dekker J, Allshire RC. Large domains of heterochromatin direct the formation of short mitotic chromosome loops. eLife 2020; 9:e57212. [PMID: 32915140 PMCID: PMC7515631 DOI: 10.7554/elife.57212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
During mitosis chromosomes reorganise into highly compact, rod-shaped forms, thought to consist of consecutive chromatin loops around a central protein scaffold. Condensin complexes are involved in chromatin compaction, but the contribution of other chromatin proteins, DNA sequence and histone modifications is less understood. A large region of fission yeast DNA inserted into a mouse chromosome was previously observed to adopt a mitotic organisation distinct from that of surrounding mouse DNA. Here, we show that a similar distinct structure is common to a large subset of insertion events in both mouse and human cells and is coincident with the presence of high levels of heterochromatic H3 lysine nine trimethylation (H3K9me3). Hi-C and microscopy indicate that the heterochromatinised fission yeast DNA is organised into smaller chromatin loops than flanking euchromatic mouse chromatin. We conclude that heterochromatin alters chromatin loop size, thus contributing to the distinct appearance of heterochromatin on mitotic chromosomes.
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Affiliation(s)
- Maximilian H Fitz-James
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Pin Tong
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Liyan Yang
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Sharon A White
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Robin C Allshire
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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11
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Trump BD, Galaitsi SE, Appleton E, Bleijs DA, Florin M, Gollihar JD, Hamilton RA, Kuiken T, Lentzos F, Mampuys R, Merad M, Novossiolova T, Oye K, Perkins E, Garcia‐Reyero N, Rhodes C, Linkov I. Building biosecurity for synthetic biology. Mol Syst Biol 2020; 16:e9723. [PMID: 32692486 PMCID: PMC7373080 DOI: 10.15252/msb.20209723] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The fast-paced field of synthetic biology is fundamentally changing the global biosecurity framework. Current biosecurity regulations and strategies are based on previous governance paradigms for pathogen-oriented security, recombinant DNA research, and broader concerns related to genetically modified organisms (GMOs). Many scholarly discussions and biosecurity practitioners are therefore concerned that synthetic biology outpaces established biosafety and biosecurity measures to prevent deliberate and malicious or inadvertent and accidental misuse of synthetic biology's processes or products. This commentary proposes three strategies to improve biosecurity: Security must be treated as an investment in the future applicability of the technology; social scientists and policy makers should be engaged early in technology development and forecasting; and coordination among global stakeholders is necessary to ensure acceptable levels of risk.
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Affiliation(s)
- Benjamin D Trump
- US Army Corps of Engineers, Engineer Research and Development CenterVicksburgMSUSA
| | - SE Galaitsi
- US Army Corps of Engineers, Engineer Research and Development CenterVicksburgMSUSA
| | | | - Diederik A Bleijs
- Biosecurity OfficeNetherlands National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Marie‐Valentine Florin
- International Risk Governance CenterÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | | | - R Alexander Hamilton
- United Nations Interregional Crime and Justice Research Institute (UNICRI)TurinItaly
| | - Todd Kuiken
- Genetic Engineering & Society Center at North Carolina State UniversityRaleighNCUSA
| | | | - Ruth Mampuys
- Netherlands Commission on Genetic Modification (COGEM)BilthovenThe Netherlands
| | - Myriam Merad
- French National Centre for Scientific ResearchParisFrance
| | | | - Kenneth Oye
- International Risk Governance CenterÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Massachusetts Institute of TechnologyCambridgeMAUSA
| | - Edward Perkins
- US Army Corps of Engineers, Engineer Research and Development CenterVicksburgMSUSA
| | | | | | - Igor Linkov
- US Army Corps of Engineers, Engineer Research and Development CenterVicksburgMSUSA
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Urbino C, Regragui ZF, Granier M, Peterschmitt M. Fitness advantage of inter-species TYLCV recombinants induced by beneficial intra-genomic interactions rather than by specific mutations. Virology 2020; 542:20-27. [PMID: 31957662 DOI: 10.1016/j.virol.2020.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 11/19/2022]
Abstract
Tomato yellow leaf curl virus (TYLCV) and its related viruses are prone to recombination. It was reported that random homologous recombination between 20% diverging TYLCV related species is rarely deleterious and may be associated with a fitness advantage. Indeed, TYLCV-IS76, a recombinant between the 20% divergent TYLCV and tomato yellow leaf curl Sardinia virus (TYLCSV), exhibited a higher fitness than that of parental viruses. As this typical fitness advantage was observed with TYLCV-IS76 representatives of different pedigrees, it was thought that it is induced by beneficial intra-genomic interactions rather than by specific mutations. This hypothesis was further supported with TYLCV-IS141, a TYLCV recombinant with a short TYLCSV inherited fragment of around 141 nts, slightly longer than that of TYLCV-IS76. Indeed, the typical fitness advantage was detected irrespective of the position of the recombination breakpoint (loci 76 or 141) and the sequences of the TYLCV and TYLCSV inherited fragments.
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Affiliation(s)
- Cica Urbino
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Zohra Fatima Regragui
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Martine Granier
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Michel Peterschmitt
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
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13
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Van Skike ND, Minkah NK, Hogan CH, Wu G, Benziger PT, Oldenburg DG, Kara M, Kim-Holzapfel DM, White DW, Tibbetts SA, French JB, Krug LT. Viral FGARAT ORF75A promotes early events in lytic infection and gammaherpesvirus pathogenesis in mice. PLoS Pathog 2018; 14:e1006843. [PMID: 29390024 PMCID: PMC5811070 DOI: 10.1371/journal.ppat.1006843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 02/13/2018] [Accepted: 12/27/2017] [Indexed: 12/19/2022] Open
Abstract
Gammaherpesviruses encode proteins with homology to the cellular purine metabolic enzyme formyl-glycinamide-phosphoribosyl-amidotransferase (FGARAT), but the role of these viral FGARATs (vFGARATs) in the pathogenesis of a natural host has not been investigated. We report a novel role for the ORF75A vFGARAT of murine gammaherpesvirus 68 (MHV68) in infectious virion production and colonization of mice. MHV68 mutants with premature stop codons in orf75A exhibited a log reduction in acute replication in the lungs after intranasal infection, which preceded a defect in colonization of multiple host reservoirs including the mediastinal lymph nodes, peripheral blood mononuclear cells, and the spleen. Intraperitoneal infection rescued splenic latency, but not reactivation. The 75A.stop virus also exhibited defective replication in primary fibroblast and macrophage cells. Viruses produced in the absence of ORF75A were characterized by an increase in the ratio of particles to PFU. In the next round of infection this led to the alteration of early events in lytic replication including the deposition of the ORF75C tegument protein, the accelerated kinetics of viral gene expression, and induction of TNFα release and cell death. Infecting cells to deliver equivalent genomes revealed that ORF75A was required for initiating early events in infection. In contrast with the numerous phenotypes observed in the absence of ORF75A, ORF75B was dispensable for replication and pathogenesis. These studies reveal that murine rhadinovirus vFGARAT family members ORF75A and ORF75C have evolved to perform divergent functions that promote replication and colonization of the host. Gammaherpesviruses are infectious agents that cause cancer. The study of viral genes unique to this subfamily may offer insight into the strategies that these viruses use to persist in the host and drive disease. The vFGARATs are a family of viral proteins found only in gammaherpesviruses, and are critical for replication in cell culture. Here we report that a rhadinovirus of rodents requires a previously uncharacterized vFGARAT family member, ORF75A, to support viral growth and persistence in mice. In addition, viruses lacking ORF75A are defective in the production of infectious viral particles. Thus, duplications and functional divergence of the various vFGARATs in the rhadinovirus lineage have likely been driven by selective pressures to disseminate within and colonize the host. Identification of the shared host processes that are targeted by the diverse family of vFGARATs may reveal novel targets for therapeutic agents to prevent life-long infections by these oncogenic viruses.
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Affiliation(s)
- Nick D. Van Skike
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nana K. Minkah
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Chad H. Hogan
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
- Graduate Program of Genetics, Stony Brook University, Stony Brook, New York, United States of America
| | - Gary Wu
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Peter T. Benziger
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | | | - Mehmet Kara
- Department of Molecular Genetics and Microbiology and UF Shands Cancer Center, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Deborah M. Kim-Holzapfel
- Departments of Chemistry and of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Douglas W. White
- Gundersen Health System, La Crosse, Wisconsin, United States of America
| | - Scott A. Tibbetts
- Department of Molecular Genetics and Microbiology and UF Shands Cancer Center, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Jarrod B. French
- Departments of Chemistry and of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Laurie T. Krug
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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14
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Treat BR, Bidula SM, Ramachandran S, St Leger AJ, Hendricks RL, Kinchington PR. Influence of an immunodominant herpes simplex virus type 1 CD8+ T cell epitope on the target hierarchy and function of subdominant CD8+ T cells. PLoS Pathog 2017; 13:e1006732. [PMID: 29206240 PMCID: PMC5736228 DOI: 10.1371/journal.ppat.1006732] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 12/19/2017] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) latency in sensory ganglia such as trigeminal ganglia (TG) is associated with a persistent immune infiltrate that includes effector memory CD8+ T cells that can influence HSV-1 reactivation. In C57BL/6 mice, HSV-1 induces a highly skewed CD8+ T cell repertoire, in which half of CD8+ T cells (gB-CD8s) recognize a single epitope on glycoprotein B (gB498-505), while the remainder (non-gB-CD8s) recognize, in varying proportions, 19 subdominant epitopes on 12 viral proteins. The gB-CD8s remain functional in TG throughout latency, while non-gB-CD8s exhibit varying degrees of functional compromise. To understand how dominance hierarchies relate to CD8+ T cell function during latency, we characterized the TG-associated CD8+ T cells following corneal infection with a recombinant HSV-1 lacking the immunodominant gB498-505 epitope (S1L). S1L induced a numerically equivalent CD8+ T cell infiltrate in the TG that was HSV-specific, but lacked specificity for gB498-505. Instead, there was a general increase of non-gB-CD8s with specific subdominant epitopes arising to codominance. In a latent S1L infection, non-gB-CD8s in the TG showed a hierarchy targeting different epitopes at latency compared to at acute times, and these cells retained an increased functionality at latency. In a latent S1L infection, these non-gB-CD8s also display an equivalent ability to block HSV reactivation in ex vivo ganglionic cultures compared to TG infected with wild type HSV-1. These data indicate that loss of the immunodominant gB498-505 epitope alters the dominance hierarchy and reduces functional compromise of CD8+ T cells specific for subdominant HSV-1 epitopes during viral latency.
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Affiliation(s)
- Benjamin R. Treat
- Molecular Virology and Microbiology Graduate Program, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sarah M. Bidula
- Molecular Virology and Microbiology Graduate Program, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Srividya Ramachandran
- Molecular Virology and Microbiology Graduate Program, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anthony J. St Leger
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Immunology Graduate Program, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert L. Hendricks
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, Pittsburgh, Pennsylvania, United States of America
| | - Paul R. Kinchington
- Molecular Virology and Microbiology Graduate Program, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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15
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Abstract
BACKGROUND Developing innovative drugs with potent efficacy, specificity, and high safety remains an ongoing task in antitumor therapy development. In the last few years, peptide drugs have become attractive agents in cancer therapy. HM-3, mainly with antiangiogenic effect, and AP25, with an additional antiproliferative effect, are two peptides designed in our laboratory targeting αvβ3 and α5β1 integrins, respectively. The low molecular weight of the two peptides renders their recombinant expression very difficult, and the complicated structure of AP25 makes its chemical synthesis restricted, which presents a big challenge for its development. METHODS Bifunctional peptides designed by the ligation of HM-3 and AP25, using linkers with different flexibility, were prepared using recombinant DNA technology in Escherichia coli. The fusion peptides were expressed in a modified auto-induction medium based on a mixture of glucose, glycerol, and lactose as carbon substrates and NH4+ as nitrogen source without any amino acid or other elements. Subsequently, the antiangiogenic, antiproliferative, and cell adhesion assays were conducted to evaluate the bioactivity of the two fusion peptides. RESULTS The peptides were successfully expressed in a soluble form without any induction, which allows the culture to reach higher cell density before protein expression occurs. Human umbilical vein endothelial cell migration assay and chick embryo chorioallantoic membrane assay showed, at low doses, a significantly increased antiangiogenic effect (>75%) of the purified products compared with the single molecules. Meanwhile, MTT assay confirmed their enhanced antitumor activity against gastric cancer cell line MGC-803; however, no significant effect was observed on hepatoma HepG2 cells and no cytotoxicity on normal human lens epithelial cell SRA01/04 and human epithelial esophageal cells. CONCLUSION Bifunctional molecules with antiangiogenic and antiproliferative effects were obtained by using this technique, which presents an alternative for small peptide production, instead of the conventional chemical method. The increased molecular weight facilitates the peptide expression with a simultaneous improvement in their stability and biological activity.
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Affiliation(s)
- Sarra Setrerrahmane
- The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing, Jiangsu
| | - Jian Yu
- The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing, Jiangsu
| | - Jingchao Hao
- The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing, Jiangsu
- College of Pharmacy & the Provincial Key Laboratory of Natural Drug and Pharmacology, Kunming, Yunnan
| | - Heng Zheng
- State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, Jiangsu, People’s Republic of China
| | - Hanmei Xu
- The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing, Jiangsu
- State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, Jiangsu, People’s Republic of China
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16
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El Naofal M, Kim A, Yon HY, Baity M, Ming Z, Bui-Griffith J, Tang Z, Robinson M, Grubbs EG, Cote GJ, Hu P. Role of CDKN2C Fluorescence In Situ Hybridization in the Management of Medullary Thyroid Carcinoma. Ann Clin Lab Sci 2017; 47:523-528. [PMID: 29066476 PMCID: PMC7057027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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.
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Affiliation(s)
- Maha El Naofal
- School of Health Professions Program in Diagnostic Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adriel Kim
- School of Health Professions Program in Diagnostic Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Yi Yon
- School of Health Professions Program in Diagnostic Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed Baity
- School of Health Professions Program in Diagnostic Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhao Ming
- Program in Cytogenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacquelin Bui-Griffith
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenya Tang
- Department of Clinical Cytogenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa Robinson
- Department of Clinical Cytogenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth G Grubbs
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gilbert J Cote
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter Hu
- School of Health Professions Program in Diagnostic Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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17
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Tsuboi K, Nagatomo T, Gohno T, Higuchi T, Sasaki S, Fujiki N, Kurosumi M, Takei H, Yamaguchi Y, Niwa T, Hayashi SI. Single CpG site methylation controls estrogen receptor gene transcription and correlates with hormone therapy resistance. J Steroid Biochem Mol Biol 2017; 171:209-217. [PMID: 28412323 DOI: 10.1016/j.jsbmb.2017.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/14/2017] [Accepted: 04/06/2017] [Indexed: 12/19/2022]
Abstract
Hormone therapy is the most effective treatment for patients with estrogen receptor α-positive breast cancers. However, although resistance occurs during treatment in some cases and often reflects changed estrogen receptor α status, the relationship between changes in estrogen receptor α expression and resistance to therapy are poorly understood. In this study, we identified a mechanism for altered estrogen receptor α expression during disease progression and acquired hormone therapy resistance in aromatase inhibitor-resistant breast cancer cell lines. Subsequently, we investigated promoter switching and DNA methylation status of the estrogen receptor α promoter, and found marked changes of methylation at a single CpG site (CpG4) in resistant cells. In addition, luciferase reporter assays showed reduced transcriptional activity from this methylated CpG site. This CpG region was also completely conserved among species, suggesting that it acts as a methylation-sensitive Ets-2 transcription factor binding site, as confirmed using chromatin immunoprecipitation assays. In estrogen receptor α-positive tumors, CpG4 methylation levels were inversely correlated with estrogen receptor α expression status, suggesting that single CpG site plays an important role in the regulation of estrogen receptor α transcription.
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Affiliation(s)
- Kouki Tsuboi
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Takamasa Nagatomo
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Tatsuyuki Gohno
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Toru Higuchi
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Shunta Sasaki
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Natsu Fujiki
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Masafumi Kurosumi
- Department of Pathology, Saitama Cancer Center, Ina-machi, Saitama, 362-0806, Japan
| | - Hiroyuki Takei
- Division of Breast Surgery, Saitama Cancer Center, Ina-machi, Saitama, 362-0806, Japan
| | - Yuri Yamaguchi
- Resarch Institute for Clinical Oncology, Saitama Cancer Center, Ina-machi, Saitama, 362-0806, Japan
| | - Toshifumi Niwa
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan
| | - Shin-Ichi Hayashi
- Department of Molecular and Functional Dynamics, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan.
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18
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Abstract
When some scientists hear the word “bioethics,” they break out in intellectual hives. They shouldn’t. Good bioethics is about enabling science to move forward. Bioethics pushes scientists to acknowledge that they operate not within a vacuum but within a society in which diverse perspectives and values must be engaged. Bioethicists give voice to those divergent perspectives and provide a framework to facilitate informed and inclusive discussions that spur progress, rather than stall it. The field is needed to advance cutting-edge biomedical research in domains in which the benefits to be had are enormous, such as genome editing, but ethical concerns persist.
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Affiliation(s)
- Carolyn P. Neuhaus
- Division of Medical Ethics, NYU School of Medicine, New York, New York, United States of America
- * E-mail:
| | - Arthur L. Caplan
- Division of Medical Ethics, NYU School of Medicine, New York, New York, United States of America
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19
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Abstract
Adeno-associated virus (AAV) has become a vector of choice for the treatment of a variety of genetic diseases that require safe and long-term delivery of a missing protein. Muscle-directed gene transfer for delivery of protective antibodies against AIDS viruses and other pathogens has been used experimentally in mice and monkeys. Here we examined a number of variations to AAV vector design for the ability to produce authentic immunoglobulin G (IgG) molecules. Expression of rhesus IgG from a single single-stranded AAV (ssAAV) vector (one vector approach) was compared to expression from two self-complementary AAV (scAAV) vectors, one for heavy chain and one for light chain (two vector approach). Both the one vector and the two vector approaches yielded considerable levels of expressed full-length IgG. A number of modifications to the ssAAV expression system were then examined for their ability to increase the efficiency of IgG expression. Inclusion of a furin cleavage sequence with a linker peptide just upstream of the 2A self-cleaving sequence from foot-and-mouth disease virus (F2A) increased IgG expression approximately 2 fold. Inclusion of these sequences also helped to ensure a proper sequence at the C-terminal end of the heavy chain. Inclusion of the post-transcriptional regulatory element from woodchuck hepatitis virus (WPRE) further increased IgG expression 1.5–2.0 fold. IgG1 versions of the two rhesus IgGs that were examined consistently expressed better than the IgG2 forms. In contrast to what has been reported for AAV2-mediated expression of other proteins, introduction of capsid mutations Y445F and Y731F did not increase ssAAV1-mediated expression of IgG as determined by transduction experiments in cell culture. Our findings provide a rational basis for AAV vector design for expression of authentic IgG.
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Affiliation(s)
- Sebastian P. Fuchs
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - José M. Martinez-Navio
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Guangping Gao
- Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ronald C. Desrosiers
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- * E-mail:
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20
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Benoit RM, Ostermeier C, Geiser M, Li JSZ, Widmer H, Auer M. Seamless Insert-Plasmid Assembly at High Efficiency and Low Cost. PLoS One 2016; 11:e0153158. [PMID: 27073895 PMCID: PMC4830597 DOI: 10.1371/journal.pone.0153158] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/16/2016] [Indexed: 01/28/2023] Open
Abstract
Seamless cloning methods, such as co-transformation cloning, sequence- and ligation-independent cloning (SLIC) or the Gibson assembly, are essential tools for the precise construction of plasmids. The efficiency of co-transformation cloning is however low and the Gibson assembly reagents are expensive. With the aim to improve the robustness of seamless cloning experiments while keeping costs low, we examined the importance of complementary single-stranded DNA ends for co-transformation cloning and the influence of single-stranded gaps in circular plasmids on SLIC cloning efficiency. Most importantly, our data show that single-stranded gaps in double-stranded plasmids, which occur in typical SLIC protocols, can drastically decrease the efficiency at which the DNA transforms competent E. coli bacteria. Accordingly, filling-in of single-stranded gaps using DNA polymerase resulted in increased transformation efficiency. Ligation of the remaining nicks did not lead to a further increase in transformation efficiency. These findings demonstrate that highly efficient insert-plasmid assembly can be achieved by using only T5 exonuclease and Phusion DNA polymerase, without Taq DNA ligase from the original Gibson protocol, which significantly reduces the cost of the reactions. We successfully used this modified Gibson assembly protocol with two short insert-plasmid overlap regions, each counting only 15 nucleotides.
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Affiliation(s)
- Roger M. Benoit
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
- * E-mail: (MA); (RMB)
| | | | - Martin Geiser
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Julia Su Zhou Li
- The Kellog School of Science and Technology, The Scripps Research Institute, La Jolla, United States of America
| | - Hans Widmer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Manfred Auer
- University of Edinburgh, School of Biological Sciences (CSE) and School of Biomedical Sciences (CMVM), Edinburgh, United Kingdom
- * E-mail: (MA); (RMB)
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21
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Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC. A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation. Biochem J 2015; 467:91-102. [PMID: 25793418 DOI: 10.1042/bj20141063] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Guanine quadruplex structures (GQSs) play important roles in the regulation of gene expression and cellular processes. Recent studies provide strong evidence for the formation and function of DNA and RNA GQSs in human cells. However, whether GQSs form and are functional in plants remains essentially unexplored. On the basis of circular dichroism (CD)-detected titration, UV-detected melting, in-line probing (ILP) and reporter gene assay studies, we report the first example of a plant RNA GQS that inhibits translation. This GQS is located within the 5'-UTR of the ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED (ATR) mRNA of Arabidopsis thaliana (mouse-ear cress). We show that this GQS is highly stable and is thermodynamically favoured over a competing hairpin structure in the 5'-UTR at physiological K⁺ and Mg²⁺ concentrations. Results from ILP reveal the secondary structure of the RNA and support formation of the GQS in vitro in the context of the complete 5'-UTR. Transient reporter gene assays performed in living plants reveal that the GQS inhibits translation but not transcription, implicating this GQS as a translational repressor in vivo. Our results provide the first complete demonstration of the formation and function of a regulatory RNA GQS in plants and open new avenues to explore potential functional roles of GQS in the plant kingdom.
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Affiliation(s)
- Chun Kit Kwok
- *Department of Chemistry, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Yiliang Ding
- *Department of Chemistry, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Saima Shahid
- †Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Sarah M Assmann
- †Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Philip C Bevilacqua
- *Department of Chemistry, Pennsylvania State University, University Park, PA 16802, U.S.A
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22
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Tokareva O, Michalczechen-Lacerda VA, Rech EL, Kaplan DL. Recombinant DNA production of spider silk proteins. Microb Biotechnol 2013; 6:651-63. [PMID: 24119078 PMCID: PMC3815454 DOI: 10.1111/1751-7915.12081] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/27/2022] Open
Abstract
Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks.
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Affiliation(s)
- Olena Tokareva
- Department of Biomedical Engineering, Tufts UniversityMedford, MA, 02155, USA
| | - Valquíria A Michalczechen-Lacerda
- Department of Cell Biology, Campus Universitario Darcy Ribeiro, Institute of Biology, University of BrasiliaBrasilia, DF, 70910-900, Brazil
| | - Elíbio L Rech
- Embrapa Genetics Resources and Biotechnology, Biotechnology UnitParque Estação Biológica PqEB W5 Norte, Brasilia, 70770-900, DF, Brazil
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts UniversityMedford, MA, 02155, USA
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23
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Rudd BD, Venturi V, Smith NL, Nzingha K, Goldberg EL, Li G, Nikolich-Zugich J, Davenport MP. Acute neonatal infections 'lock-in' a suboptimal CD8+ T cell repertoire with impaired recall responses. PLoS Pathog 2013; 9:e1003572. [PMID: 24068921 PMCID: PMC3771883 DOI: 10.1371/journal.ppat.1003572] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/07/2013] [Indexed: 11/28/2022] Open
Abstract
Microbial infection during various stages of human development produces widely different clinical outcomes, yet the links between age-related changes in the immune compartment and functional immunity remain unclear. The ability of the immune system to respond to specific antigens and mediate protection in early life is closely correlated with the level of diversification of lymphocyte antigen receptors. We have previously shown that the neonatal primary CD8+ T cell response to replication competent virus is significantly constricted compared to the adult response. In the present study, we have analyzed the subsequent formation of neonatal memory CD8+ T cells and their response to secondary infectious challenge. In particular, we asked whether the less diverse CD8+ T cell clonotypes that are elicited by neonatal vaccination with replication competent virus are ‘locked-in’ to the adult memory T cell, and thus may compromise the strength of adult immunity. Here we report that neonatal memory CD8+ T cells mediate poor recall responses compared to adults and are comprised of a repertoire of lower avidity T cells. During a later infectious challenge the neonatal memory CD8+ T cells compete poorly with the fully diverse repertoire of naïve adult CD8+ T cells and are outgrown by the adult primary response. This has important implications for the timing of vaccination in early life. Newborns typically have a heightened sensitivity to infectious diseases, the reasons for which are not yet well understood. One contributing factor is the limited diversity of lymphocyte receptors early in life to recognize antigen and control infection. We have previously shown that antigen-specific CD8+ T cell repertoires are significantly constricted in neonates compared with adults. In this study, we addressed the question of whether the developmental stage of the host at the time of vaccination influences the composition of the memory CD8+ T cell repertoire and its ability to mount a robust response to subsequent infections. We observed that the antigen-specific T cell repertoires elicited in the context of an acute neonatal infection, that are less diverse and comprised of lower-avidity T cells, are partially ‘locked-in’ to the adult memory T cell repertoire. However, in the face of a secondary infectious challenge, naïve adult T cells outcompete the lower avidity neonatal memory T cells and raise the diversity of the overall CD8+ T cell response. These results have potential implications for the design of vaccines to be administered in early life.
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MESH Headings
- Aging
- Animals
- Animals, Newborn
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/pathology
- DNA, Recombinant/metabolism
- Herpes Simplex/immunology
- Herpes Simplex/prevention & control
- Herpes Simplex/virology
- Herpesvirus 1, Human/genetics
- Herpesvirus 1, Human/immunology
- Herpesvirus 1, Human/metabolism
- Immune System/growth & development
- Immune System/immunology
- Immune System/pathology
- Immunologic Deficiency Syndromes/etiology
- Immunologic Deficiency Syndromes/immunology
- Immunologic Deficiency Syndromes/metabolism
- Immunologic Deficiency Syndromes/pathology
- Immunologic Memory
- Listeria monocytogenes/genetics
- Listeria monocytogenes/immunology
- Listeria monocytogenes/metabolism
- Listeria monocytogenes/pathogenicity
- Listeriosis/immunology
- Listeriosis/microbiology
- Listeriosis/physiopathology
- Listeriosis/prevention & control
- Mice, Inbred Strains
- Models, Immunological
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Specific Pathogen-Free Organisms
- Vaccines, Attenuated/adverse effects
- Vaccines, Attenuated/immunology
- Vaccinia/immunology
- Vaccinia/prevention & control
- Vaccinia/virology
- Vaccinia virus/genetics
- Vaccinia virus/immunology
- Vaccinia virus/metabolism
- Virulence
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Affiliation(s)
- Brian D. Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (BDR); (JNZ); (MPD)
| | - Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
| | - Norah L. Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, United States of America
| | - Kito Nzingha
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, United States of America
| | - Emily L. Goldberg
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Arizona, and the BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Gang Li
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Arizona, and the BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Janko Nikolich-Zugich
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Arizona, and the BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (BDR); (JNZ); (MPD)
| | - Miles P. Davenport
- Complex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
- * E-mail: (BDR); (JNZ); (MPD)
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24
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Bao S, Zhu L, Zhuang Q, Wang L, Xu PX, Itoh K, Holzman IR, Lin J. Distribution dynamics of recombinant Lactobacillus in the gastrointestinal tract of neonatal rats. PLoS One 2013; 8:e60007. [PMID: 23544119 PMCID: PMC3609735 DOI: 10.1371/journal.pone.0060007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/19/2013] [Indexed: 11/19/2022] Open
Abstract
One approach to deliver therapeutic agents, especially proteins, to the gastro-intestinal (GI) tract is to use commensal bacteria as a carrier. Genus Lactobacillus is an attractive candidate for use in this approach. However, a system for expressing exogenous proteins at a high level has been lacking in Lactobacillus. Moreover, it will be necessary to introduce the recombinant Lactobacillus into the GI tract, ideally by oral administration. Whether orally administered Lactobacillus can reach and reside in the GI tract has not been explored in neonates. In this study, we have examined these issues in neonatal rats. To achieve a high level of protein expression in Lactobacillus, we tested the impact of three promoters and two backbones on protein expression levels using mRFP1, a red fluorescent protein, as a reporter. We found that a combination of an L-lactate dehydrogenase (ldhL) promoter of Lactobacillus sakei with a backbone from pLEM415 yielded the highest level of reporter expression. When this construct was used to transform Lactobacillus casei, Lactobacillus delbrueckii and Lactobacillus acidophilus, high levels of mRFP1 were detected in all these species and colonies of transformed Lactobacillus appeared pink under visible light. To test whether orally administered Lactobacillus can be retained in the GI tract of neonates, we fed the recombinant Lactobacillus casei to neonatal rats. We found that about 3% of the bacteria were retained in the GI tract of the rats at 24 h after oral feeding with more recombinant Lactobacillus in the stomach and small intestine than in the cecum and colon. No mortality was observed throughout this study with Lactobacillus. In contrast, all neonatal rats died within 24 hours after fed with transformed E. coli. Taken together, our results indicate that Lactobacillus has the potential to be used as a vehicle for the delivery of therapeutic agents to neonates.
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Affiliation(s)
- Sujin Bao
- Saint James School of Medicine, Bonaire, The Netherlands Antilles
- Yuying Children’s Hospital, Wenzhou Medical College, Wenzhou, China
| | - Libin Zhu
- Yuying Children’s Hospital, Wenzhou Medical College, Wenzhou, China
| | - Qiang Zhuang
- The First Affiliated Hospital, Wenzhou Medical College, Wenzhou, China
| | - Lucia Wang
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Pin-Xian Xu
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Keiji Itoh
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ian R. Holzman
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jing Lin
- Yuying Children’s Hospital, Wenzhou Medical College, Wenzhou, China
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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25
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Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 2013; 31:230-2. [PMID: 23360966 DOI: 10.1038/nbt.2507] [Citation(s) in RCA: 1395] [Impact Index Per Article: 126.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/14/2013] [Indexed: 11/10/2022]
Abstract
We employ the CRISPR-Cas system of Streptococcus pyogenes as programmable RNA-guided endonucleases (RGENs) to cleave DNA in a targeted manner for genome editing in human cells. We show that complexes of the Cas9 protein and artificial chimeric RNAs efficiently cleave two genomic sites and induce indels with frequencies of up to 33%.
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Affiliation(s)
- Seung Woo Cho
- National Creative Research Initiatives Center for Genome Engineering, Seoul National University, Seoul, South Korea
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26
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Cohen SN. Stanley N. Cohen - an interview by Judy Peng. Biotechnol J 2012; 7:1430. [PMID: 23139234 DOI: 10.1002/biot.201200359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Biotechnology Journal talks to Prof. Stanley Cohen after his plenary lecture at the International Biotechnology Symposium, Sept 2012, in Daegu, Korea.
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27
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Jiang X, Yang J, Zhang H, Zou H, Wang C, Xian M. In vitro assembly of multiple DNA fragments using successive hybridization. PLoS One 2012; 7:e30267. [PMID: 22291927 PMCID: PMC3266897 DOI: 10.1371/journal.pone.0030267] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 12/12/2011] [Indexed: 11/25/2022] Open
Abstract
Construction of recombinant DNA from multiple fragments is widely required in molecular biology, especially for synthetic biology purposes. Here we describe a new method, successive hybridization assembling (SHA) which can rapidly do this in a single reaction in vitro. In SHA, DNA fragments are prepared to overlap one after another, so after simple denaturation-renaturation treatment they hybridize in a successive manner and thereby assemble into a recombinant molecule. In contrast to traditional methods, SHA eliminates the need for restriction enzymes, DNA ligases and recombinases, and is sequence-independent. We first demonstrated its feasibility by constructing plasmids from 4, 6 and 8 fragments with high efficiencies, and then applied it to constructing a customized vector and two artificial pathways. As SHA is robust, easy to use and can tolerate repeat sequences, we expect it to be a powerful tool in synthetic biology.
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Affiliation(s)
- Xinglin Jiang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jianming Yang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Haibo Zhang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Huibin Zou
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Cong Wang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Mo Xian
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
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28
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Abstract
We describe here a method for sequence- and ligation-independent cloning (SLIC). SLIC uses an exonuclease, T4 DNA polymerase, to generate single-stranded DNA overhangs in insert and vector sequences. These fragments are then assembled in vitro and transformed into Escherichia coli to generate recombinant DNA of interest. SLIC inserts can also be generated by incomplete PCR (iPCR) or mixed PCR. As many as five inserts can be assembled in one reaction simultaneously with great efficiency using SLIC. SLIC circumvents sequence constraints for recombinant DNA using standard restriction enzyme-mediated cloning and previous ligation-independent cloning methods and provides a new approach for the efficient generation of recombinant DNA.
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Affiliation(s)
- Mamie Z Li
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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29
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Abstract
The baculovirus-insect cell system is effective in the production of large quantities of biologically active recombinant proteins. The secretory production of an antibody Fab fragment in lepidopteran insect cells infected with a recombinant baculovirus that contains both the heavy-chain (Hc; Fd fragment) and light-chain (Lc) genes of the Fab fragment is described in this chapter. The recombinant baculovirus can be generated rapidly and efficiently through site-specific transposon-mediated insertion of foreign genes into a baculovirus genome called a bacmid in Escherichia coli. Factors influencing the Fab fragment production are discussed.
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Affiliation(s)
- Takanori Furuta
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
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30
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Abstract
Recombineering is a recombination-based highly efficient method of genetic engineering. It can be used to manipulate the bacterial chromosomal DNA as well as any episomal DNA. Recombineering can be used to insert selectable or nonselectable DNA fragments and subclone DNA fragments without the use of restriction enzymes and also to make precise alterations including single nucleotide changes in the DNA. Here we describe a galactokinase (galK)-based two-step method to generate point mutations in the bacterial artificial chromosome (BAC) insert using the recombineering technology. It takes advantage of the ability to select and also counterselect for the presence of galK.
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Affiliation(s)
- Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
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31
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Zhang YL, Zhang WQ, Wang QB, Ding SY, Lv R, Meng L. [Construction of recombinant shuttle plasmid pIMP1-eHER2/neu and screening and identification of its stable Clostridium sporogenes transformants]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2011; 27:1184-1187. [PMID: 22078443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
AIM To construct recombinant clostridium sporogenes modified with the extracellular domain of human oncogene HER2/neu, to lay a foundation for further study of its antitumor effect. METHODS The extracellular domain (ECD) of HER2/neu gene was attached to the downstream of promoter and signal sequence of clostridia endo-1, 4-glucanase (eglAp) by SOE-PCR to construct fusion gene eglAp-HER2/neu, which was then inserted into E.coli-clostridia shuttle plasmid pIMP1 to construct recombinant plasmid pIMP1-eHER2/neu. The recombinant plasmid was firstly transformed into E.coli DH5α.Then the correct construct was identified and introduced into C. sporogenes by electroporation. Positive clones were selected by erythromycin resistance, bacteria PCR were used for verification. RESULTS Restriction map and sequencing result showed that the sequence and ORF of fusion gene eglAp-HER2/neu in recombinant plasmid pIMP1-eHER2/neu was correct. Bacteria PCR results indicated that the recombinant plasmid pIMP1-eHER2/neu was successfully transformed into C.sporogenes. After more than 20 passages under antibiotic pressure, C.sporogenes transformants could stably carry the recombinant plasmid pIMP1-eHER2/neu. CONCLUSION Stable C.sporogenes transformants with the recombinant plasmid pIMP1-eHER2/neu are successfully acquired, which laid a foundation for further anti-tumor study.
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Affiliation(s)
- Yan-li Zhang
- Qingdao University Medical College, Qingdao, China.
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32
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Dean DM, Wilder JA. The "Frankenplasmid" lab: an investigative exercise for teaching recombinant DNA methods. Biochem Mol Biol Educ 2011; 39:367-374. [PMID: 21948510 DOI: 10.1002/bmb.20531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/27/2011] [Indexed: 05/31/2023]
Abstract
We describe an investigative laboratory module designed to give college undergraduates strong practical and theoretical experience with recombinant DNA methods within 3 weeks. After deducing restriction enzyme maps for two different plasmids, students ligate the plasmids together in the same reaction, transform E. coli with this mixture of ligated DNA, and plate the cells on media that specifically select for hybrid plasmids. The main goal of the assignment is for students to deduce the gene map of one hybrid "Frankenplasmid" using the LacZ phenotype of its transformants, PCR, and restriction mapping. Our protocol results in a number of possible outcomes, meaning that students are mapping truly unknown plasmids. The open-ended nature of this assignment results in an effective module that teaches recombinant DNA procedures while engaging students with its investigative approach, increasing complexity, and puzzle-like quality. Moreover, the modular design of the activity allows it to be adapted to a more limited schedule, introductory courses, or more advanced courses.
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Affiliation(s)
- Derek M Dean
- Department of Biology, Williams College, Williamstown, Massachusetts 01267, USA.
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33
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Huang YW, Fang Y, Meng XJ. Identification and characterization of a porcine monocytic cell line supporting porcine reproductive and respiratory syndrome virus (PRRSV) replication and progeny virion production by using an improved DNA-launched PRRSV reverse genetics system. Virus Res 2009; 145:1-8. [PMID: 19505514 DOI: 10.1016/j.virusres.2009.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 05/26/2009] [Accepted: 05/28/2009] [Indexed: 11/17/2022]
Abstract
In this study, an improved DNA-launched (plasmid DNA transfection-based) reverse genetics system with reduced cost and labor was developed for porcine reproductive and respiratory syndrome virus (PRRSV) by introduction of ribozyme elements at both termini of the viral genomic cDNA that were placed under the control of a eukaryotic hybrid promoter. The rescue efficacy of PRRSV with this system was approximately 10-50-fold higher than the in vitro-transcribed RNA-based system and the traditional DNA-launched system without the engineered ribozyme elements, as determined by reporter GFP level in transfected cells and the peak titer of the recovery virus. By using this new reverse genetics system, we identified and characterized a porcine monocytic cell line, 3D4/31, capable of supporting PRRSV replication, progeny virion production, and attachment on the cell surface. The establishment of this improved reverse genetic system and the identification of a porcine monocytic cell line supporting PRRSV replication will aid future studies of host-virus interaction of PRRSV.
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Affiliation(s)
- Y W Huang
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0342, USA
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34
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Narvaiza I, Linfesty DC, Greener BN, Hakata Y, Pintel DJ, Logue E, Landau NR, Weitzman MD. Deaminase-independent inhibition of parvoviruses by the APOBEC3A cytidine deaminase. PLoS Pathog 2009; 5:e1000439. [PMID: 19461882 PMCID: PMC2678267 DOI: 10.1371/journal.ppat.1000439] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 04/22/2009] [Indexed: 12/17/2022] Open
Abstract
The APOBEC3 proteins form a multigene family of cytidine deaminases with inhibitory activity against viruses and retrotransposons. In contrast to APOBEC3G (A3G), APOBEC3A (A3A) has no effect on lentiviruses but dramatically inhibits replication of the parvovirus adeno-associated virus (AAV). To study the contribution of deaminase activity to the antiviral activity of A3A, we performed a comprehensive mutational analysis of A3A. By mutation of non-conserved residues, we found that regions outside of the catalytic active site contribute to both deaminase and antiviral activities. Using A3A point mutants and A3A/A3G chimeras, we show that deaminase activity is not required for inhibition of recombinant AAV production. We also found that deaminase-deficient A3A mutants block replication of both wild-type AAV and the autonomous parvovirus minute virus of mice (MVM). In addition, we identify specific residues of A3A that confer activity against AAV when substituted into A3G. In summary, our results demonstrate that deaminase activity is not necessary for the antiviral activity of A3A against parvoviruses. The APOBEC3 proteins constitute a family of seven cytidine deaminases. Cytidine deaminases are editing enzymes able to remove the amine group from cytidine in single-strand DNA (ssDNA) and RNA, converting it to uracil. APOBEC3 proteins have potent antiviral activity against retroviruses, retrotransposons, and DNA viruses. APOBEC3 generated high interest because of the ability of APOBEC3G (A3G) to inhibit HIV. APOBEC3A (A3A) is a member of the family that inhibits the human parvovirus adeno-associated virus (AAV) and the retrotransposon LINE-1. Parvoviruses are simple ssDNA viruses that do not require a retrotranscription step for their replication. In contrast to A3G, which is predominantly cytoplasmic, A3A is located in both the nucleus and cytoplasm. In addition, A3A consists of a single cytidine deaminase catalytic domain, whereas A3G has two. The dependence of the antiviral function on deaminase activity is controversial. In this study, we identify numerous A3A residues required for deaminase and antiviral activities. We show that A3A not only inhibits AAV but also the minute virus of mice (MVM). Importantly, we demonstrate that A3A does not require its deaminase activity to block the replication of both parvoviruses. Thus, exploiting the simplicity of parvoviruses together with the single-domain cytidine deaminase A3A, we are able to demonstrate that cytidine deaminase activity is not required for APOBEC3 mediated viral inhibition.
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Affiliation(s)
- Iñigo Narvaiza
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Daniel C. Linfesty
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Benjamin N. Greener
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Yoshiyuki Hakata
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, University of Missouri–Columbia, School of Medicine, Life Sciences Center, Columbia, Missouri, United States of America
| | - Eric Logue
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Nathaniel R. Landau
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Matthew D. Weitzman
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- * E-mail:
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35
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Scull MA, Gillim-Ross L, Santos C, Roberts KL, Bordonali E, Subbarao K, Barclay WS, Pickles RJ. Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. PLoS Pathog 2009; 5:e1000424. [PMID: 19436701 PMCID: PMC2673688 DOI: 10.1371/journal.ppat.1000424] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 04/10/2009] [Indexed: 11/19/2022] Open
Abstract
Transmission of avian influenza viruses from bird to human is a rare event even though avian influenza viruses infect the ciliated epithelium of human airways in vitro and ex vivo. Using an in vitro model of human ciliated airway epithelium (HAE), we demonstrate that while human and avian influenza viruses efficiently infect at temperatures of the human distal airways (37 degrees C), avian, but not human, influenza viruses are restricted for infection at the cooler temperatures of the human proximal airways (32 degrees C). These data support the hypothesis that avian influenza viruses, ordinarily adapted to the temperature of the avian enteric tract (40 degrees C), rarely infect humans, in part due to differences in host airway regional temperatures. Previously, a critical residue at position 627 in the avian influenza virus polymerase subunit, PB2, was identified as conferring temperature-dependency in mammalian cells. Here, we use reverse genetics to show that avianization of residue 627 attenuates a human virus, but does not account for the different infection between 32 degrees C and 37 degrees C. To determine the mechanism of temperature restriction of avian influenza viruses in HAE at 32 degrees C, we generated recombinant human influenza viruses in either the A/Victoria/3/75 (H3N2) or A/PR/8/34 (H1N1) genetic background that contained avian or avian-like glycoproteins. Two of these viruses, A/Victoria/3/75 with L226Q and S228G mutations in hemagglutinin (HA) and neuraminidase (NA) from A/Chick/Italy/1347/99 and A/PR/8/34 containing the H7 and N1 from A/Chick/Italy/1347/99, exhibited temperature restriction approaching that of wholly avian influenza viruses. These data suggest that influenza viruses bearing avian or avian-like surface glycoproteins have a reduced capacity to establish productive infection at the temperature of the human proximal airways. This temperature restriction may limit zoonotic transmission of avian influenza viruses and suggests that adaptation of avian influenza viruses to efficient infection at 32 degrees C may represent a critical evolutionary step enabling human-to-human transmission.
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Affiliation(s)
- Margaret A Scull
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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36
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Ribeyre C, Lopes J, Boulé JB, Piazza A, Guédin A, Zakian VA, Mergny JL, Nicolas A. The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo. PLoS Genet 2009; 5:e1000475. [PMID: 19424434 PMCID: PMC2673046 DOI: 10.1371/journal.pgen.1000475] [Citation(s) in RCA: 282] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 04/08/2009] [Indexed: 12/02/2022] Open
Abstract
In budding yeast, the Pif1 DNA helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. Here, we provide evidence for a new Pif1 function by demonstrating that its absence promotes genetic instability of alleles of the G-rich human minisatellite CEB1 inserted in the Saccharomyces cerevisiae genome, but not of other tandem repeats. Inactivation of other DNA helicases, including Sgs1, had no effect on CEB1 stability. In vitro, we show that CEB1 repeats formed stable G-quadruplex (G4) secondary structures and the Pif1 protein unwinds these structures more efficiently than regular B-DNA. Finally, synthetic CEB1 arrays in which we mutated the potential G4-forming sequences were no longer destabilized in pif1Δ cells. Hence, we conclude that CEB1 instability in pif1Δ cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences. Changes in the primary DNA sequence are a major source of pathologies and cancers. The hereditary information also resides in secondary DNA structures, a layer of genetic information that remains poorly understood. Biophysical and structural studies have long established that, in vitro, the DNA molecule can adopt diverse structures different from the canonical Watson-Crick conformations. However, for a long time their existence in vivo has been regarded with a certain skepticism and their functional role elusive. One example is the G-quadruplex structure, which involves G-quartets that form between four DNA strands. Here, using in vitro and in vivo assays in the yeast S. cerevisiae, we reveal the unexpected role of the Pif1 helicase in maintaining the stability of the human CEB1 G-rich tandem repeat array. By site-directed mutagenesis, we show that the genomic instability of CEB1 repeats in absence of Pif1 and is directly dependent on the ability of CEB1 to form G-quadruplex structures. We show that Pif1 is very efficient in vitro in processing G-quadruplex structures formed by CEB1. We propose that Pif1 maintains CEB1 repeats by its ability to resolve G-quadruplex structures, thus providing circumstantial evidence of their formation in vivo.
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Affiliation(s)
- Cyril Ribeyre
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Judith Lopes
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Jean-Baptiste Boulé
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Aurèle Piazza
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Aurore Guédin
- Laboratoire de Biophysique, Museum National d'Histoire Naturelle USM 503, INSERM U565, CNRS UMR5153, Paris, France
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jean-Louis Mergny
- Laboratoire de Biophysique, Museum National d'Histoire Naturelle USM 503, INSERM U565, CNRS UMR5153, Paris, France
| | - Alain Nicolas
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
- * E-mail:
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Zhao P, Ma D, Yan S, Shao N, Zhang J, Bi Z, Dai J, Ji M, Ji C. Towards a Novel Vaccine against Human Cytomegalovirus Based on a Chimeric Ad5F35 Adenovirus Vector Expressing the Immunodominant Antigenic Domain 1 Epitope. Intervirology 2009; 52:35-42. [PMID: 19372702 DOI: 10.1159/000212989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 03/04/2009] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ping Zhao
- Department of Hematology, Qilu Hospital, Shandong University, Jinan, PR China
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Li MN, Zheng GH, Wang L, Xiao W, Fu XH, Le YQ, Ren DM. Evaluation of the effectiveness and safety of the thermo-treatment process to dispose of recombinant DNA waste from biological research laboratories. Sci Total Environ 2009; 407:791-797. [PMID: 18849060 DOI: 10.1016/j.scitotenv.2008.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 07/18/2008] [Accepted: 08/06/2008] [Indexed: 05/26/2023]
Abstract
The discharge of recombinant DNA waste from biological laboratories into the eco-system may be one of the pathways resulting in horizontal gene transfer or "gene pollution". Heating at 100 degrees C for 5-10 min is a common method for treating recombinant DNA waste in biological research laboratories in China. In this study, we evaluated the effectiveness and the safety of the thermo-treatment method in the disposal of recombinant DNA waste. Quantitative PCR, plasmid transformation and electrophoresis technology were used to evaluate the decay/denaturation efficiency during the thermo-treatment process of recombinant plasmid, pET-28b. Results showed that prolonging thermo-treatment time could improve decay efficiency of the plasmid, and its decay half-life was 2.7-4.0 min during the thermo-treatment at 100 degrees C. However, after 30 min of thermo-treatment some transforming activity remained. Higher ionic strength could protect recombinant plasmid from decay during the treatment process. These results indicate that thermo-treatment at 100 degrees C cannot decay and inactivate pET-28b completely. In addition, preliminary results showed that thermo-treated recombinant plasmids were not degraded completely in a short period when they were discharged into an aquatic environment. This implies that when thermo-treated recombinant DNAs are discharged into the eco-system, they may have enough time to re-nature and transform, thus resulting in gene diffusion.
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Affiliation(s)
- Meng-Nan Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Zhang L, Zhong Q, Bao L, Zhang Y, Gao L, Huang B, Zhang HD. Rv0901 from Mycobacterium tuberculosis, a possible novel virulent gene proved through the recombinant Mycobacterium smegmatis. Jpn J Infect Dis 2009; 62:26-31. [PMID: 19168955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The function of protein-coding gene Rv0901 of Mycobacterium tuberculosis, which belongs to the cell wall and cell processes category, is not yet clear. To explore its features, we amplified this gene from the H37Rv genome, and His-tagged Rv0901 protein was expressed and purified. Also, a recombinant plasmid bearing Rv0901 was constructed and electroporated into a virulent Mycobacterium smegmatis, using shuttle expression vector pMV261. Transformants were induced to express a predicted protein of Rv0901, identified by SDS-PAGE. Rv0901 protein and recombinant M. smegmatis were used to expose mammalian cells. In addition we studied the effect of protein or recombinant M. smegmatis on cells and in animals with regard to survival ratio, apoptosis ratio, quantum of nitric oxide, and gamma interferon. Together, gene function, protein function, and animal test results suggest that Rv0901 has some relationship with the virulence and immunogenicity of M. tuberculosis.
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Affiliation(s)
- Le Zhang
- West China Center of Medical Sciences, Sichuan University, Sichuan, China
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Xiao S, Wang J, Jiang J, Cao X, Wu G, Zhao H. Characterization of Fyn signaling on the age-dependent immuno-modulation on traumatic rats. Brain Res 2008; 1255:162-9. [PMID: 19109931 DOI: 10.1016/j.brainres.2008.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 12/01/2008] [Accepted: 12/02/2008] [Indexed: 11/19/2022]
Abstract
Traumatic stress is well characterized to develop immuno-depression in our previous report. Here, we provide evidence that adult and aged rats showed similar decrease in lymphocyte proliferation and natural killer (NK) cell activity. However, compared with beginning recovering from traumatic stress after 3 day and fully recovered by 7 day in adult rats, aged rats begin the recovery phage later than 3 day and do not fully recovered by 7 day. In parallel, Fyn expression in cerebral cortex was augmented with the highest level at 3 day of trauma in both age groups of rats, although aged rats exhibited lower level than the younger cohorts. Immune consequences were consequently modified by intracerebroventricular (i.c.v.) injection of Fyn antibody or recombinant adenovirus expressing active Fyn. Finally, the increase in Fyn expression was converged on ERK1/2 (extracellular signal regulated kinase 1/2) activation. Taken together, the data indicated that immunological processes in response to traumatic stress was age dependent, Fyn-ERK1/2 signal pathway was required to convey the recovery signals.
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Affiliation(s)
- Sheng Xiao
- Department of Integrative Medicine and Neurobiology, National Key Lab of Medical Neurobiology, Institute of Brain Research Sciences, Fudan University, 138# Yixueyuan Rd. Box 291, Shanghai, 200032, PR China
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Xiong F, Zhang C, Zheng H, Xiao S, Yu M, Xu Y, Liu Z, Zhou C. [Construction of recombinant plasmid pVAX1-microdystrophin and preliminary study on the treatment to Duchenne muscular dystrophy]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2008; 25:624-628. [PMID: 19065517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
OBJECTIVE To construct the recombinant plasmid containing human microdystrophin cDNA, and study the microdystrophin expression in vivo and in vitro. METHODS Microdystrophin cDNA was obtained from recombinant plasmid pBSK-MICRO digested with restrictive endonuclease Not I, the product was inserted into plasmid pVAX1, resulting in pAMICDYS. And then 3T3 cells were transfected with pAMICDYS. Forty-eight hours after transfection, the expression of the microdystrophin was detected by reverse transcription-polymerase chain reaction (RT-PCR) and immunocytochemistry. Finally, TA muscles of mdx mice were injected with the recombinant plasmid pAMICDYS through i.m. and the pathological change of TA was evaluated by histology, and the expression of microdystrophin in mdx TA was detected by immunohistochemical analysis. RESULTS The recombinant plasmid containing human microdystrophin cDNA was constructed successfully. The recombinant plasmid was proved to be able to express microdystrophin protein both in vivo and in vitro. Moreover, treatment of the TA of mdx mice with the recombinant plasmid could decrease the number of centrally nucleated myofibers. CONCLUSION Recombinant plasmid containing the microdystrophin gene was constructed successfully, and it could express microdystrophin protein both in vivo and in vitro. It provides basis for further study on microdystrophin as a target gene to treat Duchenne muscular dystrophy (DMD) by electrotransfer, i.v, arterial injection and combining with other exogenous gene to enhance microdystrophin expression.
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Affiliation(s)
- Fu Xiong
- Department of Medical Genetics, Southern Medical University, Guangzhou, Guangdong, 510515 P. R. China
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Affiliation(s)
- Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. kevin.hms.harvard.edu
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Ondrej V, Lukásová E, Krejcí J, Kozubek S. Intranuclear trafficking of plasmid DNA is mediated by nuclear polymeric proteins lamins and actin. Acta Biochim Pol 2008; 55:307-315. [PMID: 18560607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 05/19/2008] [Accepted: 06/03/2008] [Indexed: 05/26/2023]
Abstract
Functions of nuclear polymeric proteins such as lamin A/C and actin in transport of plasmid DNA were studied. The results show that the lamina plays an important role in plasmid DNA's entry into the cell nucleus from the cytoplasm. Selective disruption of lamin A/C led to a halt in plasmid DNA transport through the nuclear envelope. Inside the nucleus, plasmid DNA was frequently localized at sites with impaired genome integrity, such as DNA double-strand breaks (DSBs), occurring spontaneously or induced by ionizing radiation. Polymeric actin obviously participates in nuclear transport of plasmid DNA, since inhibition of actin polymerization by latrunculin B disturbed plasmid transport inside the cell nucleus. In addition, precluding of actin polymerization inhibited plasmid co-localization with newly induced DSBs. These findings indicate the crucial role of polymeric actin in intranuclear plasmid transport.
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Affiliation(s)
- Vladan Ondrej
- Laboratory of Molecular Cytology and Cytometry, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Ye H, Hill J, Kauffman J, Gryniewicz C, Han X. Detection of protein modifications and counterfeit protein pharmaceuticals using isotope tags for relative and absolute quantification and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry: studies of insulins. Anal Biochem 2008; 379:182-91. [PMID: 18489896 DOI: 10.1016/j.ab.2008.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 04/24/2008] [Accepted: 04/24/2008] [Indexed: 11/15/2022]
Abstract
Isotope tags for relative and absolute quantification (iTRAQ) reagent coupled with matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) mass spectrometric analysis has been evaluated as both a qualitative and quantitative method for the detection of modifications to active pharmaceutical ingredients derived from recombinant DNA technologies and as a method to detect counterfeit drug products. Five types of insulin (human, bovine, porcine, Lispro, and Lantus) were used as model products in the study because of their minor variations in amino acid sequence. Several experiments were conducted in which each insulin variant was separately digested with Glu-C, and the digestate was labeled with one of four different iTRAQ reagents. All digestates were then combined for desalting and MALDI-TOF/TOF mass spectrometric analysis. When the digestion procedure was optimized, the insulin sequence coverage was 100%. Five different types of insulin were readily differentiated, including human insulin (P28K29) and Lispro insulin (K28P29), which differ only by the interchange of two contiguous residues. Moreover, quantitative analyses show that the results obtained from the iTRAQ method agree well with those determined by other conventional methods. Collectively, the iTRAQ method can be used as a qualitative and quantitative technique for the detection of protein modification and counterfeiting.
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Affiliation(s)
- Hongping Ye
- US Food and Drug Administration, Center for Drug Evaluation and Research, Division of Pharmaceutical Analysis, St. Louis, MO 63101, USA.
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Su WJ, Wu Y, Wu HL, Zhu SY, Wang WB. Expression of Bombyx mori nucleopolyhedrovirus ORF76 in permissive and non-permissive cell lines by a novel Bac-to-Bac/BmNPV baculovirus expression system. Pol J Microbiol 2008; 57:271-274. [PMID: 19275039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Open reading frame 76 of Bombyx mori nucleopolyhedrovirus (BmNPV), designated as Bm76, is a gene whose function is completely unknown. With EGFP fused to the 3' terminal of Bm76 as the reporter gene and BmNPV bacmid as the expression vector, a recombinant bacmid was successfully constructed expressing Bm76-EGFP fusion protein under the control of polyhedrin promoter in Bombyx mori cells (Bm cells), BmNPV's permissive cell line, laying the foundation for rescue experiment of Bm76 deletion mutant. Moreover, the supernatant from Bm cells transfected with the recombinant bacmid was used to infect Trichoplusia Ni cells (Tn cells), BmNPV's non-permissive cell line. Unexpectedly, the expression of Bm76-EGFP fusion protein in some Tn cells was detected, implying that viral DNA was replicated in these cells. The causes are being studied for the inability of BmNPV to produce enough viable budded viruses in Tn cells despite of viral DNA replication.
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Affiliation(s)
- Wu-Jie Su
- Institute of Life Sciences, JiangSu University, Xuefu Road 301, Zhenjiang 212013, PR China
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Uehara A, Yamamoto Y, Watanabe A, Aburatani H, Komiyama M. Construction of chimera protein by using artificial restriction DNA cutter. ACTA ACUST UNITED AC 2007:279-80. [PMID: 17150742 DOI: 10.1093/nass/49.1.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have already developed artificial restriction DNA cutter (ARCUT), which can hydrolyze double-stranded DNA site-selectively, by using Ce(IV)/EDTA in combination with two pseudo-complementary peptide nucleic acids (pcPNAs). Here, ARCUT was used to prepare a chimera protein. The gene for WW-domain containing oxidoreductase (WWOX) was clipped off by ARCUT just before its stop codon, and ligated with the gene for enhanced green fluorescent protein (EGFP). Conventional PCR for insertion of restriction enzyme site is never required.
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Affiliation(s)
- Akihiko Uehara
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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McLenachan S, Sarsero JP, Ioannou PA. Flow-cytometric analysis of mouse embryonic stem cell lipofection using small and large DNA constructs. Genomics 2007; 89:708-20. [PMID: 17449222 DOI: 10.1016/j.ygeno.2007.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 02/06/2007] [Accepted: 02/06/2007] [Indexed: 11/28/2022]
Abstract
Using the lipofection reagent LipofectAMINE 2000 we have examined the delivery of plasmid DNA (5-200 kb) to mouse embryonic stem (mES) cells by flow cytometry. To follow the physical uptake of lipoplexes we labeled DNA molecules with the fluorescent dye TOTO-1. In parallel, expression of an EGFP reporter cassette in constructs of different sizes was used as a measure of nuclear delivery. The cellular uptake of DNA lipoplexes is dependent on the uptake competence of mES cells, but it is largely independent of DNA size. In contrast, nuclear delivery was reduced with increasing plasmid size. In addition, linear DNA is transfected with lower efficiency than circular DNA. Inefficient cytoplasmic trafficking appears to be the main limitation in the nonviral delivery of large DNA constructs to the nucleus of mES cells. Overcoming this limitation should greatly facilitate functional studies with large genomic fragments in embryonic stem cells.
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Affiliation(s)
- Samuel McLenachan
- Murdoch Childrens Research Institute, Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
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Pignatta D, Kumar P, Turina M, Dandekar A, Falk BW. Quantitative analysis of efficient endogenous gene silencing in Nicotiana benthamiana plants using tomato bushy stunt virus vectors that retain the capsid protein gene. Mol Plant Microbe Interact 2007; 20:609-18. [PMID: 17555269 DOI: 10.1094/mpmi-20-6-0609] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Tomato bushy stunt virus (TBSV) coat protein (CP) replacement vectors have been used previously to silence transgenes (e.g., the green fluorescent protein gene) but have not been effective for silencing endogenous plant genes. New TBSV vectors which retained the CP gene were developed by engineering an XhoI restriction site in three positions (3f, CEB, and CEA) of the pTBSV-100 infectious clone. Magnesium chelatase (ChlH) and phytoene desaturase (PDS) were chosen as targets for endogenous gene silencing. Initial experiments using CP replacement vectors with a 230-bp sense or antisense ChlH insert gave a silencing phenotype prominent only in the first new leaves above those inoculated. No silencing phenotype was apparent beyond these leaves whereas, for PDS, no silencing phenotype was observed. When plants were inoculated with the XhoI insert vectors containing ChlH and PDS sequences, plants showed a silencing phenotype extensively throughout the challenged plant, indicating an improved ability for virus movement and silencing in Nicotiana benthamiana host plants. Silencing efficiencies were quantified using realtime reverse-transcription polymerase chain reaction, indicating specific silencing effects of each individual silencing vector. Only one recombinant vector (pPD-3f5), where the XhoI insert was at the 3' end of the CP gene, failed to give effective silencing. Here, we show that our new CP-retaining TBSV vectors (CEA-CEB) form typical TBSV virions, retain silencing inserts of variable lengths (110 to 260 nucleotides), and can systemically silence endogenous genes in N. benthamiana.
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Affiliation(s)
- Daniela Pignatta
- Dipartimento di Scienze e Tecnologie Agroambientali, Bologna, Italy
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Ramessar K, Peremarti A, Gómez-Galera S, Naqvi S, Moralejo M, Muñoz P, Capell T, Christou P. Biosafety and risk assessment framework for selectable marker genes in transgenic crop plants: a case of the science not supporting the politics. Transgenic Res 2007; 16:261-80. [PMID: 17436060 DOI: 10.1007/s11248-007-9083-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 02/05/2007] [Indexed: 11/25/2022]
Abstract
Selectable marker gene systems are vital for the development of transgenic crops. Since the creation of the first transgenic plants in the early 1980s and their subsequent commercialization worldwide over almost an entire decade, antibiotic and herbicide resistance selectable marker gene systems have been an integral feature of plant genetic modification. Without them, creating transgenic crops is not feasible on purely economic and practical terms. These systems allow the relatively straightforward identification and selection of plants that have stably incorporated not only the marker genes but also genes of interest, for example herbicide tolerance and pest resistance. Bacterial antibiotic resistance genes are also crucial in molecular biology manipulations in the laboratory. An unprecedented debate has accompanied the development and commercialization of transgenic crops. Divergent policies and their implementation in the European Union on one hand and the rest of the world on the other (industrialized and developing countries alike), have resulted in disputes with serious consequences on agricultural policy, world trade and food security. A lot of research effort has been directed towards the development of marker-free transformation or systems to remove selectable markers. Such research has been in a large part motivated by perceived problems with antibiotic resistance selectable markers; however, it is not justified from a safety point of view. The aim of this review is to discuss in some detail the currently available scientific evidence that overwhelmingly argues for the safety of these marker gene systems. Our conclusion, supported by numerous studies, most of which are commissioned by some of the very parties that have taken a position against the use of antibiotic selectable marker gene systems, is that there is no scientific basis to argue against the use and presence of selectable marker genes as a class in transgenic plants.
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Affiliation(s)
- Koreen Ramessar
- Departament de Produccio Vegetal i Ciencia Forestal, Universitat de Lleida, Av. Alcalde Rovira Roure, 191, Lleida 25198, Spain
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Ulasov IV, Tyler MA, Han Y, Glasgow JN, Lesniak MS. Novel recombinant adenoviral vector that targets the interleukin-13 receptor alpha2 chain permits effective gene transfer to malignant glioma. Hum Gene Ther 2007; 18:118-29. [PMID: 17328684 DOI: 10.1089/hum.2006.146] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transduction of malignant glioma with adenovirus serotype 5 (Ad5) vectors is limited by the low levels of coxsackievirus and adenovirus receptor (CAR) on tumor cells. However, malignant brain tumors have been found to overexpress a glioma-associated receptor, interleukin-13 receptor alpha2 chain (IL-13Ralpha2), a marker of both glial transformation and tumor grade. To selectively target Ad5 to IL-13Ralpha2, we constructed a replication-deficient adenoviral vector that possesses an IL-13 ligand presented by a T4 phage fibritin shaft, and designated the new virus LU-13. Western blot and sequence analyses confirmed proper trimerization and ligand presentation by the T4 fibritin shaft. Confocal microscopy analysis of primary glioma suspensions incubated with viral recombinants showed that LU-13 colocalized with IL-13Ralpha2. Luciferase transduction assays conducted in both primary and passaged glioma cell cultures exhibited at least 10-fold enhanced gene transduction. Moreover, the virus preferentially bound to glioma cells, as documented by increased adenoviral E4 DNA copy number. In vitro competition assays performed with anti-human IL-13 monoclonal antibody confirmed significant attenuation of LU-13 transduction. These results were further confirmed in vivo, where LU-13 showed a 300-fold increase in transgene expression. In summary, we describe here the development of a novel and targeted adenoviral vector that binds IL-13Ralpha2. Our findings confirm the ability of LU-13 to bind IL-13Ralpha2 and increase transgene expression, making it an attractive gene therapy vector for the treatment of malignant glioma in a clinical setting.
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Affiliation(s)
- Ilya V Ulasov
- Division of Neurosurgery, University of Chicago, Chicago, IL 60637, USA
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