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Abstract
Long-read RNA sequencing (RNA-seq) technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over short-read RNA-seq. We present LIQA to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read direct mRNA sequencing or cDNA sequencing data. LIQA incorporates base pair quality score and isoform-specific read length information in a survival model to assign different weights across reads, and uses an expectation-maximization algorithm for parameter estimation. We apply LIQA to long-read RNA-seq data from the Universal Human Reference, acute myeloid leukemia, and esophageal squamous epithelial cells and demonstrate its high accuracy in profiling alternative splicing events.
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Affiliation(s)
- Yu Hu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xuelian Chen
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jiang F Zhong
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Pradhan A, Mukkayyan N, Jakkala K, Ajitkumar P. Mycobacterial Populations Partly Change the Proportions of the Cells Undergoing Asymmetric/Symmetric Divisions in Response to Glycerol Levels in Growth Medium. Cells 2021; 10:1160. [PMID: 34064643 PMCID: PMC8151439 DOI: 10.3390/cells10051160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/18/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022] Open
Abstract
Twenty to thirty percent of the septating mycobacterial cells of the mid-log phase population showed highly deviated asymmetric constriction during division (ACD), while the remaining underwent symmetric constriction during division (SCD). The ACD produced short-sized cells (SCs) and normal/long-sized cells (NCs) as the sister-daughter cells, but with significant differential susceptibility to antibiotic/oxidative/nitrite stress. Here we report that, at 0.2% glycerol, formulated in the Middlebrook 7H9 medium, a significantly high proportion of the cells were divided by SCD. When the glycerol concentration decreased to 0.1% due to cell-growth/division, the ACD proportion gradually increased until the ACD:SCD ratio reached ~50:50. With further decrease in the glycerol levels, the SCD proportion increased with concomitant decrease in the ACD proportion. Maintenance of glycerol at 0.1%, through replenishment, held the ACD:SCD proportion at ~50:50. Transfer of the cells from one culture with a specific glycerol level to the supernatant from another culture, with a different glycerol level, made the cells change the ACD:SCD proportion to that of the culture from which the supernatant was taken. RT-qPCR data showed the possibility of diadenosine tetraphosphate phosphorylase (MSMEG_2932), phosphatidylinositol synthase (MSMEG_2933), and a Nudix family hydrolase (MSMEG_2936) involved in the ACD:SCD proportion-change in response to glycerol levels. We also discussed its physiological significance.
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Affiliation(s)
| | | | | | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India; (A.P.); (N.M.); (K.J.)
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53
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Abstract
RNA molecules can fold into complex two- and three-dimensional shapes that are critical for their function. Chemical probes have long been utilized to interrogate RNA structure and are now considered invaluable resources in the goal of relating structure to function. Recently, the power of deep sequencing and careful chemical probe design have merged, permitting researchers to obtain a holistic understanding of how RNA structure can be utilized to control RNA biology transcriptome-wide. Within this review, we outline the recent advancements in chemical probe design for interrogating RNA structures inside cells and discuss the recent advances in our understanding of RNA biology through the lens of chemical probing.
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Affiliation(s)
- Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chely M Garfio
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cellular Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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54
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Abstract
In this procedure, synthesis of cDNA is performed in the presence of saturating concentrations of all four dNTPs and trace amounts of a single radiolabeled dNTP. After subtraction hybridization, the enriched single-stranded cDNA is radiolabeled to high specific activity in a second synthetic reaction by extension of random oligonucleotide primers using the Klenow fragment of Escherichia coli DNA Pol I. Because the concentrations of dNTP in the first reaction are nonlimiting, both the amounts and size of cDNA generated are greater than those achieved in standard labeling protocols. The subtractive hybridization step can therefore be performed with higher efficiency. Because the resulting population of cDNA is not vulnerable to radiolytic cleavage, it can be stored indefinitely and radiolabeled to higher specific activity when needed. The protocol works best when the cDNA synthesized in the initial synthetic reaction is full length or close to it. For this reason, synthesis of cDNAs is primed by oligo(dT) rather than random hexanucleotide primers. In contrast, the subsequent radiolabeling reaction is primed by random oligonucleotides, yielding shorter DNA products whose size is ideal for hybridization.
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55
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DeKeyser JM, Thompson CH, George AL. Cryptic prokaryotic promoters explain instability of recombinant neuronal sodium channels in bacteria. J Biol Chem 2021; 296:100298. [PMID: 33460646 PMCID: PMC7948969 DOI: 10.1016/j.jbc.2021.100298] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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] [Received: 11/04/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 11/18/2022] Open
Abstract
Mutations in genes encoding the human-brain-expressed voltage-gated sodium (NaV) channels NaV1.1, NaV1.2, and NaV1.6 are associated with a variety of human diseases including epilepsy, autism spectrum disorder, familial migraine, and other neurodevelopmental disorders. A major obstacle hindering investigations of the functional consequences of brain NaV channel mutations is an unexplained instability of the corresponding recombinant complementary DNA (cDNA) when propagated in commonly used bacterial strains manifested by high spontaneous rates of mutation. Here, using a combination of in silico analysis, random and site-directed mutagenesis, we investigated the cause for instability of human NaV1.1 cDNA. We identified nucleotide sequences within the NaV1.1 coding region that resemble prokaryotic promoter-like elements, which are presumed to drive transcription of translationally toxic mRNAs in bacteria as the cause of the instability. We further demonstrated that mutations disrupting these elements mitigate the instability. Extending these observations, we generated full-length human NaV1.1, NaV1.2, and NaV1.6 plasmids using one or two introns that interrupt the latent reading frames along with a minimum number of silent nucleotide changes that achieved stable propagation in bacteria. Expression of the stabilized sequences in cultured mammalian cells resulted in functional NaV channels with properties that matched their parental constructs. Our findings explain a widely observed instability of recombinant neuronal human NaV channels, and we describe re-engineered plasmids that attenuate this problem.
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Affiliation(s)
- Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christopher H Thompson
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
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56
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Gu W, Yang Y, Ning C, Wang Y, Hu J, Zhang M, Kuang S, Sun Y, Li Y, Zhang Y, Sun J, Ying D, Xu S. Identification and characteristics of insulin-like growth factor system in the brain, liver, and gonad during development of a seasonal breeding teleost, Pampus argenteus. Gen Comp Endocrinol 2021; 300:113645. [PMID: 33058908 DOI: 10.1016/j.ygcen.2020.113645] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 05/11/2020] [Revised: 08/31/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Reproductive activity is closely related to the development and function of the brain and liver in teleosts, particularly in seasonal breeding teleosts. This study measured the involvement of the insulin-like growth factor (IGF) system in controlling the reproduction of the silver pomfret Pampus argenteus, a seasonal breeding tropical to temperate commercial fish. We cloned and characterized the cDNAs of igfs (igf2 and igf3) and igfrs (igf1ra, igf1rb, and igf2r) and examined their transcript levels in relation to seasonal reproduction. Phylogenetic analyses revealed that two types of IGFs (IGF-1 and IGF-2) and three types of IGFRs (IGF1RA, IGF1RB, and IGF2R) of the silver pomfret were clustered with those of teleosts; however, IGF-3 was a transmembrane protein different with the IGF-3 of other teleosts. The expression of IGF-3 was gonad-specific in the silver pomfret. The transcript levels of igf1 in the female brain were the highest, and the levels of igfrs in both sexes' brains increased during gametogenesis. Meanwhile, igfs and igfrs maintained high transcript levels in both sexes' liver and gonad during vitellogenesis and spermatogonia proliferation. We concluded that the development and activities of brain, liver, and gonad were related to the IGF system (IGFs and IGFRs). And the IGFs were mainly expressed in the liver. Nevertheless, gonadal development, especially vitellogenesis and spermatogonia proliferation, were related with IGFs in this species.
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Affiliation(s)
- Weiwei Gu
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Yang Yang
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China.
| | - Chao Ning
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Yajun Wang
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China.
| | - Jiabao Hu
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Man Zhang
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Siwen Kuang
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Yibo Sun
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Yaya Li
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Youyi Zhang
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Jiachu Sun
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
| | - Dongxu Ying
- Ningbo Xiangshangang Aquatic Product Introduction and Breeding Co. Ltd., Ningbo, China
| | - Shanliang Xu
- College of Marine Science, Ningbo University, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China
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Wang Y, Xiao X, Wang F, Yang Z, Yue J, Shi J, Ke F, Xie Z, Fan Y. An identified PfHMGB1 promotes microcystin-LR-induced liver injury of yellow catfish (Pelteobagrus fulvidraco). Ecotoxicol Environ Saf 2021; 207:111266. [PMID: 32919194 DOI: 10.1016/j.ecoenv.2020.111266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/21/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Microcystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of juvenile yellow catfish (Pelteobagrus fulvidraco) that were intraperitoneally injected with 50 μg/kg MC-LR. The PfHMGB1 mRNA level was highest in the liver and muscle among 11 tissues examined. The full-length cDNA sequence of PfHMGB1 was cloned and overexpressed in E. coli, and the purified protein rPfHMGB1 demonstrated DNA binding affinity. Endotoxin-free rPfHMGB1 (6-150 μg/mL) also showed dose-dependent hepatotoxicity and induced inflammatory gene expression of primary hepatocytes. PfHMGB1 antibody (anti-PfHMGB1) in vitro reduced MC-LR (30 and 50 μmol/L)-induced hepatotoxicity, suggesting PfHMGB1 is important in the toxic effects of MC-LR. In vivo study showed that MC-LR upregulated PfHMGB1 protein in the liver. The anti-PfHMGB1 blocked its counterpart and reduced ALT/AST activities after MC-LR exposure. Anti-PfHMGB1 partly neutralized MC-LR-induced hepatocyte disorganization, nucleus shrinkage, mitochondria, and rough endoplasmic reticula destruction. These findings suggest that PfHMGB1 promotes MC-LR-induced liver damage in the yellow catfish. HMGB1 may help protect catfish against widespread microcystin pollution.
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Affiliation(s)
- Yun Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Hubei Province, Wuhan, 430056, China; Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China.
| | - Xiaoxue Xiao
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
| | - Feijie Wang
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
| | - Zupeng Yang
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
| | - Jingkai Yue
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
| | - Jiale Shi
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
| | - Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhaohui Xie
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
| | - Yanru Fan
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, China
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McKelvey BA, Gilpatrick T, Wang Y, Timp W, Umbricht CB, Zeiger MA. Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines. Thyroid 2020; 30:1470-1481. [PMID: 32228178 PMCID: PMC7583328 DOI: 10.1089/thy.2020.0055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background: Telomerase reverse transcriptase (TERT) promoter mutations play a role in carcinogenesis and are found in both tumors and cancer cell lines. TERT promoter methylation, transcription factor binding, chromatin remodeling, and alternative splicing are also known to play an integral role in TERT regulation. Methods: Using nanopore Cas9 targeted sequencing, we characterized allele-specific methylation in thyroid cancer cell lines heterozygous for the TERT promoter mutation. Furthermore, using chromatin immunoprecipitation followed by Sanger sequencing, we probed allele-specific binding of the transcription factors GABPA (GA binding protein transcription factor subunit alpha) and MYC, as well as the chromatin marks H3K4me3 and H3K27me3. Finally, using coding single nucleotide polymorphisms and the long-read sequencing, we examined complementary DNA for monoallelic expression (MAE). Results: We found the mutant TERT promoter allele to be significantly less methylated than wild type, while more methylated in the gene body in heterozygous TERT mutant cell lines. We demonstrated that the transcriptional activators GABPA and MYC bind only to the mutant TERT allele. In addition, the activating and repressive chromatin marks H3K4me3 and H3K27me3, respectively, bind mutant and wild-type alleles exclusively. Finally, in heterozygous mutant cell lines, TERT exhibits MAE from the mutant allele only. Conclusions: In summary, by employing new long-read sequencing methods, we were able to definitively demonstrate allele-specific DNA methylation, histone modifications, transcription factor binding, and the resulting monoallelic transcription in cell lines with heterozygous TERT mutations.
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Affiliation(s)
- Brittany A. McKelvey
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Timothy Gilpatrick
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yongchun Wang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher B. Umbricht
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, and The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Martha A. Zeiger
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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59
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Faustino LC, Li CW, Stefan-Lifshitz M, Kim K, Clarke OB, Tomer Y. A Novel Mouse Model of Autoimmune Thyroiditis Induced by Immunization with Adenovirus Containing Full-Length Thyroglobulin cDNA: Implications to Genetic Studies of Thyroid Autoimmunity. Thyroid 2020; 30:1338-1345. [PMID: 32228171 PMCID: PMC7482114 DOI: 10.1089/thy.2019.0711] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background: Thyroglobulin (TG) is a key autoantigen in autoimmune thyroid diseases (AITD). Several single nucleotide polymorphisms (SNPs) in the TG locus were shown to be strongly associated with disease susceptibility in both humans and mice, and autoimmune response to TG is the earliest event in the development of thyroid autoimmunity in mice. The classical model of experimental autoimmune thyroiditis (EAT) is induced by immunizing mice with TG protein together with an adjuvant to break down immune tolerance. The classical EAT model has limited utility in genetic studies of TG since it does not allow testing the effects of TG sequence variants on the development of autoimmune thyroiditis. In this study, we have immunized CBA-J mice, an EAT-susceptible strain, with an adenovirus vector encoding the full-length human TG (hTG) to generate a model of EAT in which the TG sequence can be manipulated to test AITD-associated TG SNPs. Methods: We immunized CBA-J mice with hTG-expressing adenovirus following the well-recognized experimental autoimmune Graves' disease protocol that also uses an adenovirus vector to deliver the immunogen. Results: After hTG adenovirus immunizations, mice developed higher T cell proliferative and cytokine responses to hTG and TG2098 (a major T cell epitope in AITD) and higher titers of TG and thyroperoxidase autoantibodies compared with mice immunized with control LacZ-expressing adenovirus. The mice, however, did not develop thyroidal lymphocytic infiltration and hypothyroidism. Conclusions: Our data describe a novel murine model of autoimmune thyroiditis that does not require the use of adjuvants to break down tolerance and that will allow investigators to test the effects of hTG variants in the pathoetiology of Hashimoto's thyroiditis.
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Affiliation(s)
- Larissa C. Faustino
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Address correspondence to: Larissa C. Faustino, PhD, Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Cheuk W. Li
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Mihaela Stefan-Lifshitz
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kookjoo Kim
- Department of Anesthesiology and Columbia University, New York, New York, USA
- Department of Physiology, Columbia University, New York, New York, USA
| | - Oliver B. Clarke
- Department of Anesthesiology and Columbia University, New York, New York, USA
- Department of Physiology, Columbia University, New York, New York, USA
| | - Yaron Tomer
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
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60
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Sook Chung J, Christie A, Flynn E. Molecular cloning of crustacean hyperglycemic hormone (CHH) family members (CHH, molt-inhibiting hormone and mandibular organ-inhibiting hormone) and their expression levels in the Jonah crab, Cancer borealis. Gen Comp Endocrinol 2020; 295:113522. [PMID: 32492383 DOI: 10.1016/j.ygcen.2020.113522] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 05/14/2020] [Accepted: 05/22/2020] [Indexed: 11/15/2022]
Abstract
The crustacean hyperglycemic hormone (CHH) neuropeptide family has multiple functions in the regulation of hemolymph glucose levels, molting, ion, and water balance and reproduction. In crab species, three neuroendocrine tissues: the eyestalk ganglia (medulla terminalis X-organ and -sinus gland = ES), the pericardial organ (PO), and guts synthesize a tissue-specific isoforms of CHH neuropeptides. Recently the presence of the mandibular organ-inhibiting hormone (MOIH) was reported in the stomatogastric nervous system (STNS) that regulates the rhythmic muscle movements in esophagus, cardiac sac, gastric and pyloric ports of the foregut. In this study, we aimed to determine the presence of a tissue-specific CHH isoform in the Jonah crab, Cancer borealis using PCR with degenerate primers and 5', 3' rapid amplification of cDNA ends (RACE) in the ES. PO, and STNS. The analysis of CHH sequences shows that C. borealis has one type of CHH isoform, unlike other crab species. We also isolated the cDNA sequence of molt-inhibiting hormone (MIH) in the ES and MOIH in the ES and STNS. The presence of CHH, MOIH and MIH in the sinus gland of adult females and males is confirmed by using a dot-blot assay with the putative peaks collected from RP-HPLC and anti-Cancer sera for CHH, MIH, and MOIH. The present of crustacean female sex hormone (CFSH) in the sinus gland of adult females was examined with a dot-blot assay with anti-Callinectes CFSH serum. Levels of CHH, MOIH, and MIH in the sinus gland and their expressions in the eyestalk ganglia are estimated in the adult males, where CHH is the predominant form among these neuropeptides.
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Affiliation(s)
- J Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Columbus Center, Baltimore, MD 21202, USA.
| | - A Christie
- Pacific Biosciences Research Center, 1993 East-West Rd, Honolulu, HI 96822, USA.
| | - E Flynn
- George Washington University of School of Medicine, 2300 I St NW, Washington, DC 20052, USA
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Xu H, Meng X, Jia L, Wei Y, Sun B, Liang M. Tissue distribution of transcription for 29 lipid metabolism-related genes in Takifugu rubripes, a marine teleost storing lipid predominantly in liver. Fish Physiol Biochem 2020; 46:1603-1619. [PMID: 32415410 DOI: 10.1007/s10695-020-00815-7] [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] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
The tissue distribution pattern of lipid is highly diverse among different fish species. Tiger puffer has a special lipid storage pattern, storing lipid predominantly in liver. In order to better understand the lipid physiology in fish storing lipid in liver, the present study preliminarily investigated the tissue distribution of transcription for 29 lipid metabolism-related genes in tiger puffer, which are involved in lipogenesis, fatty acid oxidation, biosynthesis and hydrolysis of glycerides, lipid transport, and relevant transcription regulation. Samples of eight tissues, brain, eye, heart, spleen, liver, intestine, skin, and muscle, from fifteen juvenile tiger puffer were used in the qRT-PCR analysis. The intestine and brain had high transcription of lipogenic genes, whereas the liver and muscle had low expression levels. The intestine also had the highest transcription level of most apolipoproteins and lipid metabolism-related transcription factors. The transcription of fatty acid β-oxidation-related genes was low in the muscle. The peroxisomal fatty acid oxidation may dominate over mitochondrial β-oxidation in the liver and intestine of tiger puffer, and the MAG pathway probably predominates over the G3P pathway in re-acylation of absorbed lipids in the intestine. The intracellular glyceridases were highly transcribed in the brain, eye, and heart. In conclusion, in tiger puffer, the intestine could be a center of lipid metabolism whereas the liver is more likely a pure storage organ for lipid. The lipid metabolism in the muscle could also be inactive, possibly due to the very low level of intramuscular lipid.
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Affiliation(s)
- Houguo Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China
| | - Xiaoxue Meng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Linlin Jia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
| | - Yuliang Wei
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China
| | - Bo Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
| | - Mengqing Liang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
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Stone RA, Wei W, Sarfare S, McGeehan B, Engelhart KC, Khurana TS, Maguire MG, Iuvone PM, Nickla DL. Visual Image Quality Impacts Circadian Rhythm-Related Gene Expression in Retina and in Choroid: A Potential Mechanism for Ametropias. Invest Ophthalmol Vis Sci 2020; 61:13. [PMID: 32396635 PMCID: PMC7405616 DOI: 10.1167/iovs.61.5.13] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/22/2020] [Accepted: 03/21/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose Stimulated by evidence implicating diurnal/circadian rhythms and light in refractive development, we studied the expression over 24 hours of selected clock and circadian rhythm-related genes in retina/retinal pigment epithelium (RPE) and choroid of experimental ametropias in chicks. Methods Newly hatched chicks, entrained to a 12-hour light/dark cycle for 12 to 14 days, either experienced nonrestricted vision OU (i.e., in both eyes) or received an image-blurring diffuser or a minus 10-diopter (D) or a plus 10-D defocusing lens over one eye. Starting 1 day later and at 4-hour intervals for 24 hours, the retina/RPE and choroid were separately dissected. Without pooling, total RNA was extracted, converted to cDNA, and assayed by quantitative PCR for the expression of the following genes: Opn4m, Clock, Npas2, Per3, Cry1, Arntl, and Mtnr1a. Results The expression of each gene in retina/RPE and in choroid of eyes with nonrestricted vision OU varied over 24 hours, with equal levels OU for most genes and times. Altered visual input influenced gene expression in complex patterns that varied by gene, visual input, time, and eye, affecting experimental eyes with altered vision and also contralateral eyes with nonrestricted vision. Discussion Altering visual input in ways known to induce ametropias alters the retinal/RPE and choroidal expression of circadian rhythm-related genes, further linking circadian biology with eye growth regulation. While further investigations are needed, studying circadian processes may help understand refractive mechanisms and the increasing myopia prevalence in contemporary societies where lighting patterns can desynchronize endogenous rhythms from the natural environmental light/dark cycle.
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Affiliation(s)
- Richard A. Stone
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - Wenjie Wei
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - Shanta Sarfare
- Department of Bioscience, New England College of Optometry, Boston, Massachusetts, United States
| | - Brendan McGeehan
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - K. Cameron Engelhart
- Department of Bioscience, New England College of Optometry, Boston, Massachusetts, United States
| | - Tejvir S. Khurana
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - Maureen G. Maguire
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - P. Michael Iuvone
- Departments of Ophthalmology and Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Debora L. Nickla
- Department of Bioscience, New England College of Optometry, Boston, Massachusetts, United States
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63
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Suzuki S, Crane AM, Anirudhan V, Barillà C, Matthias N, Randell SH, Rab A, Sorscher EJ, Kerschner JL, Yin S, Harris A, Mendel M, Kim K, Zhang L, Conway A, Davis BR. Highly Efficient Gene Editing of Cystic Fibrosis Patient-Derived Airway Basal Cells Results in Functional CFTR Correction. Mol Ther 2020; 28:1684-1695. [PMID: 32402246 DOI: 10.1016/j.ymthe.2020.04.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 10/18/2019] [Revised: 04/01/2020] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
There is a strong rationale to consider future cell therapeutic approaches for cystic fibrosis (CF) in which autologous proximal airway basal stem cells, corrected for CFTR mutations, are transplanted into the patient's lungs. We assessed the possibility of editing the CFTR locus in these cells using zinc-finger nucleases and have pursued two approaches. The first, mutation-specific correction, is a footprint-free method replacing the CFTR mutation with corrected sequences. We have applied this approach for correction of ΔF508, demonstrating restoration of mature CFTR protein and function in air-liquid interface cultures established from bulk edited basal cells. The second is targeting integration of a partial CFTR cDNA within an intron of the endogenous CFTR gene, providing correction for all CFTR mutations downstream of the integration and exploiting the native CFTR promoter and chromatin architecture for physiologically relevant expression. Without selection, we observed highly efficient, site-specific targeted integration in basal cells carrying various CFTR mutations and demonstrated restored CFTR function at therapeutically relevant levels. Significantly, Omni-ATAC-seq analysis revealed minimal impact on the positions of open chromatin within the native CFTR locus. These results demonstrate efficient functional correction of CFTR and provide a platform for further ex vivo and in vivo editing.
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Affiliation(s)
- Shingo Suzuki
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ana M Crane
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Varada Anirudhan
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Cristina Barillà
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nadine Matthias
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Andras Rab
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Kenneth Kim
- Sangamo Therapeutics, Richmond, CA 94804, USA
| | - Lei Zhang
- Sangamo Therapeutics, Richmond, CA 94804, USA
| | | | - Brian R Davis
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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64
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Geffeney SL, Hanifin CT. Synthesizing and Expressing Native Ion Channels. Methods Mol Biol 2020; 2068:283-290. [PMID: 31576535 DOI: 10.1007/978-1-4939-9845-6_16] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthesizing and expressing ion channels in heterologous systems enable the characterization of the functional properties of these proteins. The cDNA that encodes ion channels can be amplified directly from mRNA or synthesized de novo in its entirety before cloning into an appropriate expression vector. Gibson assembly is a powerful tool that allows rapid cloning and integration of protein-coding cDNA into a variety of expression vectors. Here we describe a method in which the cDNA encoding a native snake ion channel (NaV 1.4) is synthesized in four equal-sized pieces (or blocks), and then assembled and ligated into an expression vector. Once in an appropriate expression vector, the assembled cDNA can be used for synthesis of mRNA, and the mRNA injected and expressed in Xenopus oocytes. This method has significant advantages over traditional rtPCR and ligation-based cloning including speed, cost, ease of codon optimization, and inclusion of silent restriction sites for Gibson-based mutagenesis.
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Affiliation(s)
- Shana L Geffeney
- Department of Biology, Utah State University-Uintah Basin, Vernal, UT, USA.
| | - Charles T Hanifin
- Department of Biology, Utah State University-Uintah Basin, Vernal, UT, USA.
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65
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Dueck ME, Lin R, Zayac A, Gallagher S, Chao AK, Jiang L, Datwani SS, Hung P, Stieglitz E. Precision cancer monitoring using a novel, fully integrated, microfluidic array partitioning digital PCR platform. Sci Rep 2019; 9:19606. [PMID: 31862911 PMCID: PMC6925289 DOI: 10.1038/s41598-019-55872-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2022] Open
Abstract
A novel digital PCR (dPCR) platform combining off-the-shelf reagents, a micro-molded plastic microfluidic consumable with a fully integrated single dPCR instrument was developed to address the needs for routine clinical diagnostics. This new platform offers a simplified workflow that enables: rapid time-to-answer; low potential for cross contamination; minimal sample waste; all within a single integrated instrument. Here we showcase the capability of this fully integrated platform to detect and quantify non-small cell lung carcinoma (NSCLC) rare genetic mutants (EGFR T790M) with precision cell-free DNA (cfDNA) standards. Next, we validated the platform with an established chronic myeloid leukemia (CML) fusion gene (BCR-ABL1) assay down to 0.01% mutant allele frequency to highlight the platform's utility for precision cancer monitoring. Thirdly, using a juvenile myelomonocytic leukemia (JMML) patient-specific assay we demonstrate the ability to precisely track an individual cancer patient's response to therapy and show the patient's achievement of complete molecular remission. These three applications highlight the flexibility and utility of this novel fully integrated dPCR platform that has the potential to transform personalized medicine for cancer recurrence monitoring.
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Affiliation(s)
| | | | | | | | - Alexander K Chao
- Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | | | | | | | - Elliot Stieglitz
- Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
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66
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Yang L, Zhang K, Bi S, Zhu JJ. Dual-Acceptor-Based Upconversion Luminescence Nanosensor with Enhanced Quenching Efficiency for in Situ Imaging and Quantification of MicroRNA in Living Cells. ACS Appl Mater Interfaces 2019; 11:38459-38466. [PMID: 31593426 DOI: 10.1021/acsami.9b12254] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Upconversion nanoparticles (UCNPs) have become competitive materials for bioanalysis, bioimaging, and early diagnosis of diseases, especially cancers. However, traditional upconversion luminescence (UCL) nanosensors are often challenged with complicated covalent modification and relatively poor stability. As efficient energy acceptors in the luminescence resonance energy-transfer (LRET) process, organic dyes exhibit unique advantages such as easy modification and stable property. Herein, a simple and universal bioplatform is constructed for in situ imaging and quantitation of intracellular microRNA-21 (miR-21) using dual-acceptor-based upconversion nanoprobes with enhanced quenching efficiency. In this assay, UCNPs with core-shell structures are synthesized, in which the emitting ions are confined in the shell to take the energy donors and acceptors in close proximity. The complementary DNA (cDNA) that can specifically recognize target miR-21 is labeled with organic dyes TAMRA and black hole quencher as dual acceptors and easily assembled on UCNPs via electrostatic adsorption. Compared with only one acceptor for LRET, two dyes quench more luminescence of UCNPs (>60%), which thus reduce the background and improve the sensitivity. With the enhanced quenching efficiency and simple assembly process, the proposed system is readily applied to in situ imaging of miR-21 in different cancer cells, which further achieves quantification of miR-21 in MCF-7 cells. Therefore, our proposed dual-acceptor-based upconversion nanoplatform opens up new opportunities for sensitive analysis of miRNA and provides potential applications in biomedical and clinical research.
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Affiliation(s)
- Lin Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Keying Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
- Anhui Key Laboratory of Spin Electron and Nanomaterials, School of Chemistry and Chemical Engineering , Suzhou University , Suzhou 234000 , Anhui , China
| | - Sai Bi
- Center for Marine Observation and Communications, Research Center for Intelligent and Wearable Technology, College of Chemistry and Chemical Engineering , Qingdao University , Qingdao 266071 , China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
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67
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Idrees M, Xu L, Song SH, Joo MD, Lee KL, Muhammad T, El Sheikh M, Sidrat T, Kong IK. PTPN11 (SHP2) Is Indispensable for Growth Factors and Cytokine Signal Transduction During Bovine Oocyte Maturation and Blastocyst Development. Cells 2019; 8:cells8101272. [PMID: 31635340 PMCID: PMC6830097 DOI: 10.3390/cells8101272] [Citation(s) in RCA: 20] [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] [Received: 09/06/2019] [Revised: 10/05/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
This study was aimed to investigate the role of SHP2 (Src-homology-2-containing phosphotyrosine phosphatase) in intricate signaling networks invoked by bovine oocyte to achieve maturation and blastocyst development. PTPN11 (Protein Tyrosine Phosphatase, non-receptor type 11) encoding protein SHP2, a positive transducer of RTKs (Receptor Tyrosine Kinases) and cytokine receptors, can play a significant role in bovine oocyte maturation and embryo development, but this phenomenon has not yet been explored. Here, we used different growth factors, cytokines, selective activator, and a specific inhibitor of SHP2 to ascertain its role in bovine oocyte developmental stages in vitro. We found that SHP2 became activated by growth factors and cytokines treatment and was highly involved in the activation of oocyte maturation and embryo development pathways. Activation of SHP2 triggered MAPK (mitogen-activated protein kinases) and PI3K/AKT (Phosphoinositide 3-kinase/Protein kinase B) signaling cascades, which is not only important for GVBD (germinal vesical breakdown) induction but also for maternal mRNA translation. Inhibition of phosphatase activity of SHP2 with PHPS1 (Phenylhydrazonopyrazolone sulfonate 1) reduced oocytes maturation as well as bovine blastocyst ICM (inner cell mass) volume. Supplementation of LIF (Leukemia Inhibitory Factor) to embryos showed an unconventional direct relation between p-SHP2 and p-STAT3 (Signal transducer and activator of transcription 3) for blastocyst ICM development. Other than growth factors and cytokines, cisplatin was used to activate SHP2. Cisplatin activated SHP2 modulate growth factors effect and combine treatment significantly enhanced quality and rate of developed blastocysts.
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Affiliation(s)
- Muhammad Idrees
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | - Lianguang Xu
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | - Seok-Hwan Song
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | - Myeong-Don Joo
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | | | - Tahir Muhammad
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | - Marwa El Sheikh
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | - Tabinda Sidrat
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
| | - Il-Keun Kong
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
- The King Kong Ltd., Daegu 43017, Korea.
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Gyeongnam Province, Korea.
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68
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Yang YL, Liang QZ, Xu SY, Mazing E, Xu GH, Peng L, Qin P, Wang B, Huang YW. Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone. Virology 2019; 536:110-118. [PMID: 31419711 PMCID: PMC7112019 DOI: 10.1016/j.virol.2019.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 05/30/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 01/08/2023]
Abstract
Swine enteric alphacoronavirus (SeACoV), also known as swine acute diarrhea syndrome coronavirus (SADS-CoV), belongs to the species Rhinolophus bat coronavirus HKU2. Herein, we report on the primary characterization of SeACoV in vitro. Four antibodies against the SeACoV spike, membrane, nucleocapsid and nonstructural protein 3 capable of reacting with viral antigens in SeACoV-infected Vero cells were generated. We established a DNA-launched SeACoV infectious clone based on the cell adapted passage-10 virus and rescued the recombinant virus with a unique genetic marker in cultured cells. Six subgenomic mRNAs containing the leader-body junction sites, including a bicistronic mRNA encoding the accessory NS7a and NS7b genes, were experimentally identified in SeACoV-infected cells. Cellular ultrastructural changes induced by SeACoV infection were visualized by electron microscopy. The availability of the SeACoV infectious clone and a panel of antibodies against different viral proteins will facilitate further studies on understanding the molecular mechanisms of SeACoV replication and pathogenesis.
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MESH Headings
- Alphacoronavirus/genetics
- Alphacoronavirus/metabolism
- Alphacoronavirus/pathogenicity
- Animals
- Antibodies, Viral/biosynthesis
- Antibodies, Viral/chemistry
- Antigens, Viral/chemistry
- Antigens, Viral/immunology
- Base Sequence
- Cell Membrane/ultrastructure
- Cell Membrane/virology
- Chiroptera
- Chlorocebus aethiops
- Clone Cells
- Coronavirus Infections/diagnosis
- Coronavirus Infections/veterinary
- Coronavirus Infections/virology
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Microscopy, Electron
- Nucleocapsid/chemistry
- Nucleocapsid/immunology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/immunology
- Rabbits
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Swine
- Swine Diseases/diagnosis
- Swine Diseases/virology
- Vero Cells
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/immunology
- Virus Replication
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Affiliation(s)
- Yong-Le Yang
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qi-Zhang Liang
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Shu-Ya Xu
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Evgeniia Mazing
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Guo-Han Xu
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Lei Peng
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Pan Qin
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Bin Wang
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yao-Wei Huang
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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69
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Xie Z, Wu S, Chen J, Zhu X, Zhou X, Hörtensteiner S, Ren G, Kuai B. The C-terminal cysteine-rich motif of NYE1/SGR1 is indispensable for its function in chlorophyll degradation in Arabidopsis. Plant Mol Biol 2019; 101:257-268. [PMID: 31302867 DOI: 10.1007/s11103-019-00902-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/09/2019] [Indexed: 05/08/2023]
Abstract
The C-terminal cysteine-rich motif of NYE1/SGR1 affects chlorophyll degradation likely by mediating its self-interaction and conformational change, and somehow altering its Mg-dechelating activity in response to the changing redox potential. During green organ senescence in plants, the most prominent phenomenon is the degreening caused by net chlorophyll (Chl) loss. NON-YELLOWING1/STAY-GREEN1 (NYE1/SGR1) was recently reported to be able to dechelates magnesium (Mg) from Chl a to initiate its degradation, but little is known about the domain/motif basis of its functionality. In this study, we carried out a protein truncation assay and identified a conserved cysteine-rich motif (CRM, P-X3-C-X3-C-X-C2-F-P-X5-P) at its C terminus, which is essential for its function. Genetic analysis showed that all four cysteines in the CRM were irreplaceable, and enzymatic assays demonstrated that the mutation of each of the four cysteines affected its Mg-dechelating activity. The CRM plays a critical role in the conformational change and self-interaction of NYE1 via the formation of inter- and intra-molecular disulfide bonds. Our results may provide insight into how NYE1 responds to rapid redox changes during leaf senescence and in response to various environmental stresses.
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Affiliation(s)
- Zuokun Xie
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Shengdong Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Junyi Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Xiaoyu Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Xin Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Stefan Hörtensteiner
- Institute of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China.
| | - Benke Kuai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China.
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70
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Readler JM, AlKahlout AS, Sharma P, Excoffon KJDA. Isoform specific editing of the coxsackievirus and adenovirus receptor. Virology 2019; 536:20-26. [PMID: 31394408 PMCID: PMC6733617 DOI: 10.1016/j.virol.2019.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 03/18/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
Abstract
The Coxsackievirus and adenovirus receptor (CAR) is both a viral receptor and cell adhesion protein. CAR has two transmembrane isoforms that localize distinctly in polarized epithelial cells. Whereas the seven exon-encoded isoform (CAREx7) exhibits basolateral localization, the eight exon-encoded isoform (CAREx8) can localize to the apical epithelial surface where it can mediate luminal adenovirus infection. To further understand the distinct biological functions of these two isoforms, CRISPR/Cas9 genomic editing was used to specifically delete the eighth exon of the CXADR gene in a Madine Darby Canine Kidney (MDCK) cell line with a stably integrated lentiviral doxycycline-inducible CAREx8 cDNA. The gene-edited clone demonstrated a significant reduction in adenovirus susceptibility when both partially and fully polarized, and doxycycline-induction of CAREx8 restored sensitivity to adenovirus. These data reinforce the importance of CAREx8 in apical adenovirus infection and provide a new model cell line to probe isoform specific biological functions of CAR.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/metabolism
- Animals
- Base Sequence
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coxsackie and Adenovirus Receptor-Like Membrane Protein/genetics
- Coxsackie and Adenovirus Receptor-Like Membrane Protein/metabolism
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Dogs
- Doxycycline/pharmacology
- Exons
- Gene Editing/methods
- Gene Expression Regulation, Viral
- Humans
- Madin Darby Canine Kidney Cells
- Promoter Regions, Genetic/drug effects
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- James M Readler
- Biomedical Sciences PhD Program, Wright State University, Dayton, OH, 45435, USA; Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, USA
| | - Amal S AlKahlout
- Department of Biological Sciences, Wright State University, Dayton, OH, 45435, USA
| | - Priyanka Sharma
- Department of Biological Sciences, Wright State University, Dayton, OH, 45435, USA
| | - Katherine J D A Excoffon
- Biomedical Sciences PhD Program, Wright State University, Dayton, OH, 45435, USA; Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, USA; Department of Biological Sciences, Wright State University, Dayton, OH, 45435, USA.
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71
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Campbell MLH, Peachey L, Callan L, Wathes DC, de Mestre AM. Cyclical cervical function in the mare involves remodelling of collagen content, which is correlated with modification of oestrogen receptor 1 abundance. Anim Reprod Sci 2019; 210:106192. [PMID: 31635778 DOI: 10.1016/j.anireprosci.2019.106192] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022]
Abstract
This study was conducted to elucidate mare cervical dilation mechanisms by testing two hypotheses: (i) the proportion of collagen staining in histological samples of mare cervices and (ii) the abundance of hormone receptors in the equine cervix differ with stage of the oestrous cycle and site within the cervix. Tissues and jugular vein blood samples were collected from 15 mares. Collagen content was assessed using Masson's Trichome staining. Receptor abundance was assessed using RT-PCR, qRT-PCR and immunohistochemistry. In sub-epithelial stroma, there was less collagen during the follicular than luteal phase, in the caudal- (P = 0.029), mid- (P = 0.0000) and cranial (P = 0.001) cervical tissue. In the deep stroma, there was less collagen staining during the follicular stage in the mid- (P = 0.004) and cranial- (P = 0.041) cervical regions. There were PTGER2, PTGER3, PGR and ESR1 mRNA transcripts in the cervix. A greater proportion of cells were positive for ESR1 protein during the follicular phase in sub-epithelial (P = 0.019) and deep (P = 0.013) stroma. The abundance of ESR1 in the epithelium was negatively correlated with collagen staining in sub-epithelial (P = 0.007) and deep (P = 0.005) stroma. The results of the study provide new information about the cervical biology of mares by increasing the knowledge about collagen content and the relationship between collagen content and ESR1 protein abundance during the oestrous cycle which indicates the ESR1 receptor is a candidate for involvement in control of cervical dilation.
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MESH Headings
- Animals
- Cervix Uteri/physiology
- Cloning, Molecular
- Collagen/physiology
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Estrogen Receptor beta/genetics
- Estrogen Receptor beta/metabolism
- Estrous Cycle/physiology
- Female
- Gene Expression Regulation/physiology
- Horses
- Labor Stage, First/physiology
- Luteinizing Hormone/genetics
- Luteinizing Hormone/metabolism
- Pregnancy
- Progesterone/metabolism
- RNA/genetics
- RNA/metabolism
- Receptors, FSH/genetics
- Receptors, FSH/metabolism
- Receptors, Prostaglandin E, EP2 Subtype/genetics
- Receptors, Prostaglandin E, EP2 Subtype/metabolism
- Receptors, Prostaglandin E, EP3 Subtype/genetics
- Receptors, Prostaglandin E, EP3 Subtype/metabolism
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Affiliation(s)
- M L H Campbell
- The Royal Veterinary College, Hawkshead Lane, North Mymms, Herts, AL9 7TA, UK; Department of Pathobiology and Population Sciences, UK.
| | - L Peachey
- The Royal Veterinary College, Hawkshead Lane, North Mymms, Herts, AL9 7TA, UK
| | - L Callan
- The Royal Veterinary College, Hawkshead Lane, North Mymms, Herts, AL9 7TA, UK
| | - D C Wathes
- The Royal Veterinary College, Hawkshead Lane, North Mymms, Herts, AL9 7TA, UK; Department of Pathobiology and Population Sciences, UK
| | - A M de Mestre
- The Royal Veterinary College, Hawkshead Lane, North Mymms, Herts, AL9 7TA, UK; Department of Comparative Biomedical Sciences, UK
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72
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Makii C, Ikeda Y, Oda K, Uehara Y, Nishijima A, Koso T, Kawata Y, Kashiyama T, Miyasaka A, Sone K, Tanikawa M, Tsuruga T, Mori-Uchino M, Nagasaka K, Matsumoto Y, Wada-Hiraike O, Kawana K, Hasegawa K, Fujiwara K, Aburatani H, Osuga Y, Fujii T. Anti-tumor activity of dual inhibition of phosphatidylinositol 3-kinase and MDM2 against clear cell ovarian carcinoma. Gynecol Oncol 2019; 155:331-339. [PMID: 31493899 DOI: 10.1016/j.ygyno.2019.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/07/2019] [Revised: 08/15/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022]
Abstract
INTRODUCTION PI3K pathway signaling has received attention as a molecular target in clear cell ovarian carcinoma (CCOC). MDM2 is one of the AKT effectors in the PI3K pathway, which binds to and degrades p53. In this study, we aimed to clarify the prognostic significance of PIK3CA and MDM2 expression, and potential therapeutic effect of a dual inhibition of the PI3K pathway and MDM2. MATERIALS AND METHODS cDNA expression was evaluated by using microarray data using 75 samples of CCOC. DS-7423 (dual inhibitor of pan-PI3K and mTOR) and RG7112 (MDM2 inhibitor) were used on CCOC cell lines to evaluate cell proliferation, expression level of MDM2 related proteins, and apoptosis by MTT assay, western blotting, and flow cytometry. DS-7423 (3 mg/kg) and/or RG7112 (50 mg/kg) were orally administrated every day for three weeks, and the anti-tumor effect was evaluated using tumor xenografts, along with immunohistochemistry. RESULTS Tumors with high expression of both PIK3CA and MDM2 showed significantly worse prognosis in expression array of 71 CCOCs (P = 0.013). Dual inhibition of the PI3K pathway by DS-7423 and MDM2 by RG7112 showed synergistic anti-proliferative effect in 4 CCOC cell lines without TP53 mutations. The combination therapy more robustly induced pro-apoptotic proteins (PUMA and cleaved PARP) with increase of sub G1 population and apoptotic cells, compared with either single agent alone. The combination therapy significantly reduced tumor volume in mice (P < 0.001 in OVISE, and P = 0.038 in RMG-I) without severe body weight loss. Immunohistochemistry from the xenograft tumors showed that the combination treatment significantly reduced vascularity and cell proliferation, with an increase of apoptotic cell death. CONCLUSION A combination therapy targeting the PI3K pathway and MDM2 might be a promising therapeutic strategy in CCOC.
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Affiliation(s)
- Chinami Makii
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Yuji Ikeda
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan; Current address; Department of Obstetrics and Gynecology, Nihon University, Tokyo, Japan
| | - Katsutoshi Oda
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan.
| | - Yuriko Uehara
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan; Division of Genome Science, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Akira Nishijima
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan; Division of Genome Science, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takahiro Koso
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan; Division of Genome Science, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yoshiko Kawata
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Tomoko Kashiyama
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Aki Miyasaka
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Tetsushi Tsuruga
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Mayuyo Mori-Uchino
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Kazunori Nagasaka
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Yoko Matsumoto
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Kei Kawana
- Department of Obstetrics and Gynecology, Nihon University, Tokyo, Japan
| | - Kosei Hasegawa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Keiichi Fujiwara
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Hiroyuki Aburatani
- Division of Genome Science, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Japan
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73
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Covaleda-Cortés G, Hernández M, Trejo SA, Mansur M, Rodríguez-Calado S, García-Pardo J, Lorenzo J, Vendrell J, Chávez MÁ, Alonso-Del-Rivero M, Avilés FX. Characterization, Recombinant Production and Structure-Function Analysis of NvCI, A Picomolar Metallocarboxypeptidase Inhibitor from the Marine Snail Nerita versicolor. Mar Drugs 2019; 17:md17090511. [PMID: 31470614 PMCID: PMC6780499 DOI: 10.3390/md17090511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 08/08/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/05/2023] Open
Abstract
A very powerful proteinaceous inhibitor of metallocarboxypeptidases has been isolated from the marine snail Nerita versicolor and characterized in depth. The most abundant of four, very similar isoforms, NvCla, was taken as reference and N-terminally sequenced to obtain a 372-nucleotide band coding for the protein cDNA. The mature protein contains 53 residues and three disulphide bonds. NvCIa and the other isoforms show an exceptionally high inhibitory capacity of around 1.8 pM for human Carboxypeptidase A1 (hCPA1) and for other A-like members of the M14 CPA subfamily, whereas a twofold decrease in inhibitory potency is observed for carboxypeptidase B-like members as hCPB and hTAFIa. A recombinant form, rNvCI, was produced in high yield and HPLC, mass spectrometry and spectroscopic analyses by CD and NMR indicated its homogeneous, compact and thermally resistant nature. Using antibodies raised with rNvCI and histochemical analyses, a preferential distribution of the inhibitor in the surface regions of the animal body was observed, particularly nearby the open entrance of the shell and gut, suggesting its involvement in biological defense mechanisms. The properties of this strong, small and stable inhibitor of metallocarboxypeptidases envisage potentialities for its direct applicability, as well as leading or minimized forms, in biotechnological/biomedical uses.
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Affiliation(s)
- Giovanni Covaleda-Cortés
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Martha Hernández
- Faculty of Forestry Science, Biotechnology Center, Universidad de Concepción, Victoria 631, Barrio Universitario, 2407 Concepción, Chile
| | - Sebastián Alejandro Trejo
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Manuel Mansur
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Sergi Rodríguez-Calado
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Javier García-Pardo
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Julia Lorenzo
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
| | - Josep Vendrell
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - María Ángeles Chávez
- Center for Protein Research, Faculty of Biology, Universidad de la Habana, 10400 La Habana, Cuba
| | - Maday Alonso-Del-Rivero
- Center for Protein Research, Faculty of Biology, Universidad de la Habana, 10400 La Habana, Cuba.
| | - Francesc Xavier Avilés
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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74
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Chen L, Li W, Li Y, Feng X, Du K, Wang G, Zhao L. Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE. Plant Mol Biol 2019; 100:647-658. [PMID: 31154655 DOI: 10.1007/s11103-019-00886-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/13/2019] [Accepted: 05/24/2019] [Indexed: 05/28/2023]
Abstract
Found a trans-splicing of PHYTOENE SYNTHASE 1 alters tomato fruit color by map-based cloning, functional complementation and RACE providing an insight into fruit color development. Color is an important fruit quality trait and a major determinant of the economic value of tomato (Solanum lycopersicum). Fruit color inheritance in a yellow-fruited cherry tomato (cv. No. 22), named yellow-fruited tomato 2 (yft2), was shown to be controlled by a single recessive gene, YFT2. The YFT2 gene was mapped in a 95.7 kb region on chromosome 3, and the candidate gene, PHYTOENE SYNTHASE 1 (PSY1), was confirmed by functional complementation analysis. Constitutive over expression of PSY1 in yft2 increased the accumulation of carotenoids and resulted in a red fruit color, while no causal mutation was detected in the YFT2 allele of yft2, compared with red-fruited SL1995 cherry tomato or cultivated variety (cv. M82). Expression of YFT2 3' region in yft2 was significantly lower than in SL1995, and further studies revealed a difference in YFT2 post-transcriptional processing in yft2 compared with SL1995 and cv. M82, resulting in a longer YFT2 transcript. The alternatively trans-spliced allele of YFT2 in yft2 is predicted to encode a novel LT-YFT2 protein of 432 amino acid (AA) residues, compared to the 412 AA YFT2 protein of SL1995. The trans-spliced event also resulted in significantly down regulated expression of YFT2 in yft2 tomato, and the YFT2 allele suppressed expression of the downstream genes involved in the carotenoid biosynthesis pathway and carotenoids synthesis by a mechanism of the feed-forward regulation. In conclusion, we found that trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development.
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Affiliation(s)
- Lulu Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenzhen Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yongpeng Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuechao Feng
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Keyu Du
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ge Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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75
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Zhou X, Du J, Liu Y, Yang C, Lai J. Functional characterization of DiMMS21, a SUMO ligase from Desmodium intortum. Plant Physiol Biochem 2019; 141:206-214. [PMID: 31176880 DOI: 10.1016/j.plaphy.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/24/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
SUMOylation is an important protein modification that regulates the properties of substrate proteins in a variety of cellular processes. SUMOylation is catalyzed via a cascade of enzymes and is usually stimulated by SUMO E3 ligases. However, the molecular functions and regulatory mechanisms of SUMOylation in forage crops are unknown. Here, we isolated and functionally characterized DiMMS21, a homolog of the Arabidopsis thaliana SUMO ligase AtMMS21, from the forage legume Desmodium intortum. DiMMS21 is expressed ubiquitously in various D. intortum organs and its encoded protein is found in the cytoplasm and nucleus. Bioinformatics analysis indicated that DiMMS21 contains a conserved SP-RING domain that is required for its activity. Biochemical evidence supports the notion that this protein is a functional SUMO ligase. When expressed in an Arabidopsis mms21 mutant, DiMMS21 completely rescued the defects in root, leaf, and silique development. The results from cotyledon greening and marker gene expression suggested that DiMMS21 can only partially complements the role of AtMMS21 in abscisic acid (ABA) responses. In summary, we characterized the molecular features of DiMMS21 and uncovered potential roles of this SUMO ligase in development and ABA responses, increasing our understanding on the function of SUMOylation in forage crops.
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Affiliation(s)
- Xuan Zhou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jinju Du
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Yiyang Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China; College of Life Science, Shandong Normal University, Jinan, 250014, China; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
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76
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Lee GW, Chung MS, Lee SS, Chung BY, Lee S. Transcriptome-guided identification and functional characterization of key terpene synthases involved in constitutive and methyl jasmonate-inducible volatile terpene formation in Eremochloa ophiuroides (Munro) Hack. Plant Physiol Biochem 2019; 141:193-201. [PMID: 31174036 DOI: 10.1016/j.plaphy.2019.05.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/20/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Centipedegrass (Eremochloa ophiuroides [Munro] Hack.) is a warm-season turfgrass, widely planted in residential lawns and recreational fields. Here, we uncovered three major terpenes released from the shoots of Eo: (E)-β-ocimene (6%), α-muurolene (87.8%), and eremophilene (6.2%). Methyl jasmonate (MeJA) treatment increased the emission of monoterpenes, including (E)- and (Z)-β-ocimene, limonene, and myrcene, as well as sesquiterpene blends of (E)-caryophyllene, α-copaene, (+)-cyclosativene, and α-farnesene. RNA sequencing analysis predicted 14 putative Eo terpene synthase (EoTPS) genes, and two full-length EoTPS were successfully amplified: Eo7816 (1722 bp) and Eo6039 (1701 bp). Phylogenetic analysis revealed that Eo7816 and Eo6039 belonged to the clades of TPS-b and TPS-a, respectively. The Arabidopsis transgenic plants overexpressing Eo7816 exclusively released (E)-β-ocimene (96%) with (Z)-β-ocimene and myrcene. In contrast, Eo6039-overexpressing Arabidopsis plants emitted significant amounts of α-muurolene (69.4%) and eremophilene (21.8%). Together, we demonstrated that the two TPSs play roles in producing major volatile terpenes in Eo.
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Affiliation(s)
- Gun Woong Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Moon-Soo Chung
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Seung Sik Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Byung Yeoup Chung
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sungbeom Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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77
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Jia Y, Dai J, Zhang L, Xia H. Effect of Exogenous Zinc on MsrB1 Expression and Protein Oxidation in Human Lens Epithelial Cells. Biol Trace Elem Res 2019; 190:60-64. [PMID: 30306419 DOI: 10.1007/s12011-018-1543-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 06/15/2018] [Accepted: 10/04/2018] [Indexed: 11/30/2022]
Abstract
Aging has been related to zinc deficiency, resulting in protein oxidation and age-related decline of methionine sulfoxide reductase (Msr) activity. This study was designed to investigate the levels of methionine sulfoxide reductase B1 (MsrB1) mRNA and oxidized proteins in human lens epithelial (hLE) cells after treatment with exogenous zinc. The role of exogenous zinc in regulation of MsrB1 gene expression and protein oxidation in hLE cells was studied by MTT assay, oxidized protein measurement kit, and real-time PCR. The results showed that hLE cell viability was significantly decreased by MsrB1 gene knockdown or peroxynitrite (ONOO-) treatment, while it was significantly increased after treatment with exogenous zinc (P < 0.05). Protein carbonyl content in hLE cell by MsrB1 gene knockdown or ONOO- treatment was significantly decreased after treatment with ZnSO4 (P < 0.01). And exogenous zinc could increase the level of MsrB1 in hLE cell under normal (P < 0.001) and oxidative stress (P < 0.01) conditions. In conclusion, exogenous zinc could protect hLE cells against MsrB1 gene knockdown or ONOO--induced cell death by upregulation of MsrB1 involved in the elimination of reactive oxygen species (ROS) and oxidized proteins.
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Affiliation(s)
- Yi Jia
- Department of Chemical Biology, School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China.
| | - Jie Dai
- Department of Chemical Biology, School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Liangliang Zhang
- Department of Chemical Biology, School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Huan Xia
- Department of Chemical Biology, School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
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78
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Kim KS, Kim MA, Sohn YC. Molecular characterization, expression analysis, and functional properties of multiple 5-hydroxytryptamine receptors in Pacific abalone (Haliotis discus hannai). Gen Comp Endocrinol 2019; 276:52-59. [PMID: 30849410 DOI: 10.1016/j.ygcen.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 10/01/2018] [Revised: 02/12/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
Neurotransmitters such as serotonin (5-hydroxytryptamine; 5-HT) in the central nervous system regulate diverse physiological functions, including reproduction, feeding, learning, and memory, in diverse animal phyla. 5-HT and the 5-HT1 subtype receptor play important roles in sexual maturation and in the initiation of gamete release in mollusks. However, little is known about the involvement of other 5-HT receptor subfamilies in the reproduction process. In the present study, we identified the cDNAs encoding eight subtypes of 5-HT receptors from the ganglia tissues of the Pacific abalone Haliotis discus hannai (Mollusca; Gastropoda; Haliotidae), and examined the gonadal expression of the transcripts of 5-HT receptors. A phylogenetic analysis indicated that the molluskan 5-HT receptors are largely classified into four major clades: 5-HT1/5/7, 5-HT2, 5-HT4, and 5-HT6. Among the H. discus hannai (Hdh) 5-HT1-7 transcripts, Hdh5-HT1B, 4A, 4B, and 6 were the major subtypes detected in the mature ovary. Estradiol-17β injection into the pedal sinus induced the downregulation of 5-HT4B and upregulation of 5-HT6 transcripts in the ovary of mature abalone within 72 h. In HEK293 cells overexpressing Hdh5-HT1B, forskolin-stimulated cAMP response element luciferase (CRE-Luc) reporter activity was inhibited by 5-HT in a dose-dependent manner, whereas serum response element luciferase (SRE-Luc) activity was not affected. In Hdh5-HT4A-expressing HEK293 cells, forskolin-stimulated CRE-Luc and SRE-Luc reporter activities were both marginally increased by treatment with a high dose of 5-HT. Our results provide new insights into the roles of 5-HT through diverse G protein-coupled 5-HT receptors in the reproductive process of mollusks.
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Affiliation(s)
- Kyeong Seop Kim
- Department of Marine Molecular Biosciences, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung, Gangwon 25457, Republic of Korea
| | - Mi Ae Kim
- East Coast Life Sciences Institute, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung, Gangwon 25457, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Molecular Biosciences, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung, Gangwon 25457, Republic of Korea.
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Li M, Li X, Chen X, Chen J. De novo synthesis of the complete genome of coxsackievirus A10 based on Golden Gate cloning combined with promoter reconstruction. Plasmid 2019; 103:17-24. [PMID: 30928703 DOI: 10.1016/j.plasmid.2019.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 11/09/2018] [Revised: 03/09/2019] [Accepted: 03/09/2019] [Indexed: 11/22/2022]
Abstract
In the present study, a donor plasmid derived from pUC19 and two recipient plasmids, which had been modified from the donor plasmid and contained the red fluorescence protein gene mCherry as a reporter gene downstream of the hybrid tac promoter with the -35 region deletion mutation, were constructed. The complete genome sequence of coxsackievirus A10 downstream of the T7 promoter was divided into 7 fragments and synthesized by overlap extension PCR and the DNAworks program. Using the Golden Gate cloning strategy, the 7 fragments were then cloned into the donor plasmid and transferred to the recipient plasmid upstream of the deletion mutation tac promoter in a defined order and orientation without any deletions or insertions at the junction sites. Because the -35 region of the tac promoter was introduced into the 3' end of the last fragment during construction, the hybrid promoter was reconstructed to promote expression of mCherry, which facilitated the selection of colonies with the complete genome of coxsackievirus A10 to generate an infectious cDNA clone via reverse genetic engineering.
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Affiliation(s)
- Meng Li
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China.
| | - Xinguo Li
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China
| | - Xiaoqi Chen
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China
| | - Jing Chen
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China
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80
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Wang JD, Chen LF, Lin DJ, Zhang JS, Zhao JH, Xiao D, Wang R, Wang R, Gao SJ. Molecular cloning, characterization and functional analysis of GluCl from the oriental armyworm, Mythimna separata Walker. Pestic Biochem Physiol 2019; 156:56-62. [PMID: 31027581 DOI: 10.1016/j.pestbp.2019.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/23/2019] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Glutamate-gated chloride channels (GluCls) mediate inhibitory synaptic transmission in invertebrate nervous systems, and only one GluCl gene has been found in insects. Therefore, insect GluCls are one of the major targets of insecticides including avermectins. In the present study, a 1347 bp full-length cDNA encoding a 449-amino acid protein (named MsGluCl, GenBank ID: MK336885) was cloned from the oriental armyworm, Mythimna separata, and characterized two alternative splicing variants of MsGluCl. The protein shares 76.9-98.6% identity with other insect GluCl isoforms. Spatial and temporal expression analysis revealed that MsGluCl was highly expressed in the 3rd instar and adult head. Dietary ingestion of dsMsGluCl significantly reduced the mRNA level of MsGluCl and decreased abamectin mortality. Thus, our results reveal that MsGluCl could be the molecular target of abamectin and provide the basis for further understanding the resistance mechanism to abamectin in arthropods.
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Affiliation(s)
- Jin-da Wang
- National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University, Fuzhou 350002, China.
| | - Li-Fei Chen
- National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Dong-Jiang Lin
- National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Jia-Song Zhang
- National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Ji-Han Zhao
- National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Da Xiao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ran Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Rong Wang
- College of Forestry, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - San-Ji Gao
- National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University, Fuzhou 350002, China
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81
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Yuan LJ, Peng C, Liu BH, Feng JB, Qiu GF. Identification and Characterization of a Luteinizing Hormone Receptor (LHR) Homolog from the Chinese Mitten Crab Eriocheir sinensis. Int J Mol Sci 2019; 20:ijms20071736. [PMID: 30965614 PMCID: PMC6480239 DOI: 10.3390/ijms20071736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 03/06/2019] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 02/06/2023] Open
Abstract
Luteinizing hormone (LH), a pituitary gonadotropin, coupled with LH receptor (LHR) is essential for the regulation of the gonadal maturation in vertebrates. Although LH homolog has been detected by immunocytochemical analysis, and its possible role in ovarian maturation was revealed in decapod crustacean, so far there is no molecular evidence for the existence of LHR. In this study, we cloned a novel LHR homolog (named EsLHR) from the Chinese mitten crab Eriocheir sinensis. The complete sequence of the EsLHR cDNA was 2775bp, encoding a protein of 924 amino acids, sharing 71% amino acids identity with the ant Zootermopsis nevadensis LHR. EsLHR expression was found to be high in the ovary, while low in testis, gill, brain, and heart, and no expression in the thoracic ganglion, eye stalk, muscle, and hepatopancreas. Quantitative PCR revealed that the expression level of EsLHR mRNA was significantly higher in the ovaries in previtellogenic (Pvt), late vitellogenic (Lvt), and germinal vesicle breakdown (GVBD) stages than that in the vitellogenic (Mvt) and early vitellogenic (Evt) stages (P < 0.05), and, the highest and the lowest expression were in Lvt, and Evt, respectively. The strong signal was mainly localized in the ooplasm of Pvt oocyte as detected by in situ hybridization. The crab GnRH homolog can significantly induce the expression of EsLHR mRNA at 36 hours post injection in vivo (P < 0.01), suggesting that EsLHR may be involved in regulating ovarian development through GnRH signaling pathway in the mitten crab.
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Affiliation(s)
- Li-Juan Yuan
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Chao Peng
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Bi-Hai Liu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Jiang-Bin Feng
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Gao-Feng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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82
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Li XY, Guo F, Ma SY, Zhu MY, Pan WH, Bian HW. Regulation of flowering time via miR172-mediated APETALA2-like expression in ornamental gloxinia (Sinningia speciosa). J Zhejiang Univ Sci B 2019; 20:322-331. [PMID: 30932377 PMCID: PMC6454313 DOI: 10.1631/jzus.b1800003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 01/03/2018] [Accepted: 06/19/2018] [Indexed: 01/14/2023]
Abstract
We investigated the microRNA172 (miR172)-mediated regulatory network for the perception of changes in external and endogenous signals to identify a universally applicable floral regulation system in ornamental plants, manipulation of which could be economically beneficial. Transgenic gloxinia plants, in which miR172 was either overexpressed or suppressed, were generated using Agrobacterium-mediated transformation. They were used to study the effect of altering the expression of this miRNA on time of flowering and to identify its mRNA target. Early or late flowering was observed in transgenic plants in which miR172 was overexpressed or suppressed, respectively. A full-length complementary DNA (cDNA) of gloxinia (Sinningia speciosa) APETALA2-like (SsAP2-like) was identified as a target of miR172. The altered expression levels of miR172 caused up- or down-regulation of SsAP2-like during flower development, which affected the time of flowering. Quantitative real-time reverse transcription PCR analysis of different gloxinia tissues revealed that the accumulation of SsAP2-like was negatively correlated with the expression of miR172a, whereas the expression pattern of miR172a was negatively correlated with that of miR156a. Our results suggest that transgenic manipulation of miR172 could be used as a universal strategy for regulating time of flowering in ornamental plants.
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Affiliation(s)
- Xiao-yan Li
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sheng-yun Ma
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mu-yuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei-huai Pan
- College of Life Sciences, Shaoxing University, Shaoxing 312000, China
| | - Hong-wu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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83
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John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Sci Adv 2019; 5:eaav1110. [PMID: 31032404 PMCID: PMC6482013 DOI: 10.1126/sciadv.aav1110] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/07/2019] [Indexed: 05/30/2023]
Abstract
Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
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Affiliation(s)
- Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Yameng Lu
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sylke Wohlrab
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gurjeet S. Kohli
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Felix C. Mark
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Sarah Farhat
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marius Felder
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Stephan Frickenhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Hochschule Bremerhaven, Bremerhaven, Germany
| | - Laure Guillou
- CNRS, UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 6, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
| | - Patrick J. Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Betina M. Porcel
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Klaus Valentin
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gernot Glöckner
- Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
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84
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O'Neill BT, Bhardwaj G, Penniman CM, Krumpoch MT, Suarez Beltran PA, Klaus K, Poro K, Li M, Pan H, Dreyfuss JM, Nair KS, Kahn CR. FoxO Transcription Factors Are Critical Regulators of Diabetes-Related Muscle Atrophy. Diabetes 2019; 68:556-570. [PMID: 30523026 PMCID: PMC6385751 DOI: 10.2337/db18-0416] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/21/2018] [Indexed: 12/25/2022]
Abstract
Insulin deficiency and uncontrolled diabetes lead to a catabolic state with decreased muscle strength, contributing to disease-related morbidity. FoxO transcription factors are suppressed by insulin and thus are key mediators of insulin action. To study their role in diabetic muscle wasting, we created mice with muscle-specific triple knockout of FoxO1/3/4 and induced diabetes in these M-FoxO-TKO mice with streptozotocin (STZ). Muscle mass and myofiber area were decreased 20-30% in STZ-Diabetes mice due to increased ubiquitin-proteasome degradation and autophagy alterations, characterized by increased LC3-containing vesicles, and elevated levels of phosphorylated ULK1 and LC3-II. Both the muscle loss and markers of increased degradation/autophagy were completely prevented in STZ FoxO-TKO mice. Transcriptomic analyses revealed FoxO-dependent increases in ubiquitin-mediated proteolysis pathways in STZ-Diabetes, including regulation of Fbxo32 (Atrogin1), Trim63 (MuRF1), Bnip3L, and Gabarapl. These same genes were increased 1.4- to 3.3-fold in muscle from humans with type 1 diabetes after short-term insulin deprivation. Thus, FoxO-regulated genes play a rate-limiting role in increased protein degradation and muscle atrophy in insulin-deficient diabetes.
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Affiliation(s)
- Brian T O'Neill
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Gourav Bhardwaj
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Christie M Penniman
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Megan T Krumpoch
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Pablo A Suarez Beltran
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Katherine Klaus
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, MN
| | - Kennedy Poro
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Mengyao Li
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Hui Pan
- Bioinformatics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA
- Department of Biomedical Engineering, Boston University, Boston, MA
| | - Jonathan M Dreyfuss
- Bioinformatics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA
- Department of Biomedical Engineering, Boston University, Boston, MA
| | - K Sreekumaran Nair
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, MN
| | - C Ronald Kahn
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
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85
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Wang T, Lin P, Guo S, Wang Y, Zhang Z, Feng J. Molecular characterization and expression analysis of signal transducer and activator of transcription 1 (STAT1) in Japanese eel Anguilla japonica. Fish Shellfish Immunol 2019; 86:956-964. [PMID: 30590158 DOI: 10.1016/j.fsi.2018.12.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/05/2018] [Revised: 12/20/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Signal transducer and activator of transcription 1 (STAT1) is one of critical signal transduction proteins of interferon (IFN) pathway and the structure and function of this protein have been well identified in mammals, but the information about the STAT1 is still limited in teleost fishes. In the present study, the full-length cDNA sequence of STAT1 (AjSTAT1) in Japanese eel (Anguilla japonica) was identified and characterized. Multiple alignment of the amino acid sequence showed that the AjSTAT1 protein has the typical conserved domains including the amino-terminal, coiled-coil, DNA-binding, linker, Src homology 2 (SH2), transcriptional activation domains (TAD). Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed a broad expression for AjSTAT1 in a wide range of tissues, with the predominant expression in liver, followed by the spleen, intestine, gills, skin, kidney, and the very low expression in heart and muscle. The AjSTAT1 expressions in liver, spleen and kidney were significantly induced following injection with LPS, the viral mimic poly I:C, and Aeromonas hydrophila infection. In vitro, the AjSTAT1 transcripts of Japanese eel liver cells were significantly enhanced by the treatment of poly I:C or the stimulation of the high concentration of Aeromonas hydrophila (1 × 107 cfu/mL and 1 × 108 cfu/mL). Subcellular localization showed that in the natural state AjSTAT1was uniformly distributed in the cytoplasm, but AjSTAT1 was found to aggregated in the cytoplasm as well as partly in the nucleus after the stimulation of LPS and poly I:C. These results collectively suggested AjSTAT1 is an important transcription factor possibly involved in Japanese eel defense against viral and bacterial infection.
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Affiliation(s)
- Tingting Wang
- College of Fisheries, Jimei University, Xiamen, 361021, Fujian Province, China; Engineer Research Center of Eel Modern Industry Technology, Ministry of Education, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, China
| | - Peng Lin
- College of Fisheries, Jimei University, Xiamen, 361021, Fujian Province, China; Engineer Research Center of Eel Modern Industry Technology, Ministry of Education, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, China
| | - Songlin Guo
- College of Fisheries, Jimei University, Xiamen, 361021, Fujian Province, China; Engineer Research Center of Eel Modern Industry Technology, Ministry of Education, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, China
| | - Yilei Wang
- College of Fisheries, Jimei University, Xiamen, 361021, Fujian Province, China; Engineer Research Center of Eel Modern Industry Technology, Ministry of Education, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianjun Feng
- College of Fisheries, Jimei University, Xiamen, 361021, Fujian Province, China; Engineer Research Center of Eel Modern Industry Technology, Ministry of Education, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, China.
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86
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Jia ZQ, Sheng CW, Tang T, Liu D, Leviticus K, Zhao CQ, Chang XL. Identification of the ionotropic GABA receptor-like subunits from the striped stem borer, Chilo suppressalis Walker (Lepidoptera: Pyralidae). Pestic Biochem Physiol 2019; 155:36-44. [PMID: 30857625 DOI: 10.1016/j.pestbp.2019.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 10/22/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Ionotropic γ-aminobutyric acid (GABA) receptors (GABARs) mediate rapid inhibitory neurotransmission in both vertebrates and invertebrates, and are important molecular targets of insecticides. However, components of insect GABARs remain elusive. In addition to CsRDL1 and CsRDL2, the complementary DNAs (cDNAs) of another two GABA receptor-like subunits, CsLCCH3 and Cs8916, were identified from the rice striped stem borer, Chilo suppressalis Walker in the present study. Both CsLCCH3 and Cs8916 subunits shared common structural features, such as a highly-conserved Cys-loop structure, six distinct regions involved in ligand binding (loops A-F), and four transmembrane domains (TM 1-4). Transcript analysis demonstrated that the relative mRNA expression levels of both CsLCCH3 and Cs8916 subunits were the highest in the ventral nerve cord. Regarding developmental stage, transcript levels of both subunits were highest in eggs. Injections of double-stranded RNAs (dsRNAs), including dsRDL1, dsRDL2, dsLCCH3, or ds8916, significantly reduced mRNA abundance after 24 and 48 h. However, no observable effects on the development of C. suppressalis were observed. Injection of dsRDL1 or dsRDL2 did significantly reduce the mortality of C. suppressalis treated with fluralaner. Our results indicated that CsRDLs mediated the susceptibility of C. suppressalis to fluralaner, whereas CsLCCH3 and CsL8916 did not. The current investigation enhances our knowledge of Lepidopteran GABARs and offers a molecular basis for the development of novel insecticides to control C. suppressalis.
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Affiliation(s)
- Zhong-Qiang Jia
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng-Wang Sheng
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Tang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Liu
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Kipchoge Leviticus
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Chun-Qing Zhao
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiao-Li Chang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai Engineering Research Centre of Low-carbon Agriculture, Shanghai 201403, China.
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87
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Abstract
In the last few years single-cell RNA sequencing (scRNA-seq) has enabled the investigation of cellular heterogeneity at the transcriptional level, the characterization of rare cell types as well as the detailed analysis of the stochastic nature of gene expression. A large number of methods have been developed, varying in their throughput, sensitivity, and scalability. A major distinction is whether they profile only 5'- or 3'-terminal part of the transcripts or allow for the characterization of the entire length of the transcripts. Among the latter, Smart-seq2 is still considered the "gold standard" due to its sensitivity, precision, lower cost, scalability and for being easy to set up on automated platforms. In this chapter I describe how to efficiently generate sequencing-ready libraries, highlight common issues and pitfalls, and offer solutions for generating high-quality data.
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Affiliation(s)
- Simone Picelli
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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88
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Okada S, Ueda H, Noda Y, Suzuki T. Transcriptome-wide identification of A-to-I RNA editing sites using ICE-seq. Methods 2018; 156:66-78. [PMID: 30578846 DOI: 10.1016/j.ymeth.2018.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023] Open
Abstract
In A-to-I RNA editing, adenosine is converted to inosine in double-stranded regions of RNAs. Inosine, an abundant epitranscriptomic mark, contributes to a wide range of biological processes by regulating gene expression post-transcriptionally. To understand the effect of A-to-I RNA editing on regulation of the epitranscriptome, accurate mapping of inosines is necessary. To this end, we established a biochemical method called inosine chemical erasing sequencing (ICE-seq) that enables unbiased and reliable identification of A-to-I RNA editing sites throughout the transcriptome. Here, we describe our updated protocol for ICE-seq in the human transcriptome.
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Affiliation(s)
- Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Ueda
- Biological Data Science Division, Research Center for Advanced Science and Technology (RCAST), University of Tokyo, Tokyo 153-8904, Japan
| | - Yuta Noda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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89
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Tuo DC, Yan P, Zhao GY, Li XY, Zhou P, Shen WT. Two agroinfection-compatible fluorescent protein-tagged infectious cDNA clones of papaya leaf distortion mosaic virus facilitate the tracking of virus infection. Acta Virol 2018; 62:202-207. [PMID: 29895162 DOI: 10.4149/av_2018_213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Papaya leaf distortion mosaic virus (PLDMV, the genus Potyvirus) is an emerging threat to papaya production. Here, agroinfection-compatible fluorescent protein-tagged PLDMV infectious cDNA clones driven by the Cauliflower mosaic virus 35S promoter were successfully constructed using one-step Gibson assembly. The clones were directly transformed into Agrobacterium tumefaciens to prevent potential problems such as plasmid instability during propagation in Escherichia coli. Ninety-five percent of papaya seedlings infected with PLDMV-GFP or PLDMV-mCherry developed systemic symptoms typical of those caused by wild-type PLDMV. Green and mCherry red fluorescence was observed in leaves, stems, and roots of infected papaya plants. The fluorescent protein-tagged agroinfectious PLDMV cDNA clones were stable in papaya for more than 90 days and during six serial passages at 30-day intervals. The availability of these infectious clones will contribute to research on PLDMV-host interactions and can be applied in the papaya breeding program for PLDMV resistance.
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90
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Zhang HC, Ma KX, Yang YJ, Shi CY, Chen GW, Liu DZ. Molecular cloning, characterization, expression and enzyme activity of catalase from planarian Dugesia japonica in response to environmental pollutants. Ecotoxicol Environ Saf 2018; 165:88-95. [PMID: 30193168 DOI: 10.1016/j.ecoenv.2018.08.083] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 04/18/2018] [Revised: 06/30/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
Catalase (CAT) is an important antioxidant enzyme that protects aerobic organisms against oxidative damage by degrading hydrogen peroxide to oxygen and water. CAT mRNAs have been cloned from many species and employed as useful biomarkers of oxidative stress. In the present study, we cloned the cDNA sequence of CAT gene from freshwater planarian Dugesia japonica (designated as DjCAT) by means of RACE method. Sequence analysis and multiple alignment jointly showed that the full-length cDNA sequence consists of 1734 nucleotides, encoding 506 amino acids. Three catalytic amino acid residues of His71, Asn144 and Tyr354, two CAT family signature sequences of a proximal active site signature (60FDRERIPERVVHAKGGGA77) and a heme-ligand signature motif (350RLFSYRDTQ358) are highly conserved, suggesting that the DjCAT belongs to the NADPH and heme-binding CAT family and has similar functions. In addition, the transcriptional level of CAT gene and activity of CAT enzyme upon acute exposure of environmental pollutants glyphosate and 1-decyl-3-methylimidazolium bromide ([C10mim]Br) were investigated systematically. The variation of CAT mRNA expression in D. japonica was quantified by real-time PCR and the results indicated that it was up-regulated after exposure to glyphosate or [C10mim]Br with a dose-dependent manner but not linearly. Even though the variation trend of CAT activity upon glyphosate stress was not monotonously increased and inconsistent with that after [C10mim]Br exposure on day 1 and 3 sampling time, with the duration prolonged to day 5 they both presented a dose-dependent increase and the differences achieved extreme significance in all treated groups compared to the control. These findings suggested that DjCAT plays an important role in antioxidant defense in D. japonica, and the mRNA expression of CAT would also be used as an effective biomarker to monitor the pollution in aquatic environment just like its corresponding enzyme.
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Affiliation(s)
- He-Cai Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ke-Xue Ma
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yu-Juan Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Chang-Ying Shi
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guang-Wen Chen
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
| | - De-Zeng Liu
- Institute of Natural Resources, Heilongjiang Academy of Science, Harbin 150031, China
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91
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Katsarou M, Stratikos E, Chroni A. Thermodynamic destabilization and aggregation propensity as the mechanism behind the association of apoE3 mutants and lipoprotein glomerulopathy. J Lipid Res 2018; 59:2339-2348. [PMID: 30309894 PMCID: PMC6277168 DOI: 10.1194/jlr.m088732] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 07/25/2018] [Revised: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
Lipoprotein glomerulopathy (LPG) is a rare renal disease, characterized by lipoprotein thrombi in glomerular capillaries. A series of apoE mutations have been associated with LPG development. We previously showed that three mutants based on apoE3 sequence, in which an arginine was substituted by proline, are thermodynamically destabilized and aggregation-prone. To examine whether other LPG-associated apoE3 mutations induce similar effects, we characterized three nonproline LPG-associated apoE3 mutations, namely, R25C (apoEKyoto), R114C (apoETsukuba), and A152D (apoELasVegas). All three apoE3 variants are found to have significantly reduced helical content and to be thermodynamically destabilized, both in lipid-free and lipoprotein-associated form, and to expose a larger portion of hydrophobic surface to the solvent compared with WT apoE3. Furthermore, all three apoE3 variants are aggregation-prone, as shown by dynamic light-scattering measurements and by their enhanced capacity to bind the amyloid probe thioflavin T. Overall, our data suggest that the LPG-associated apoE3 mutations R25C, R114C, and A152D induce protein misfolding, which may contribute to protein aggregation in glomerular capillaries. The similar effects of both LPG-associated proline and nonproline mutations on apoE3 structure suggest that the thermodynamic destabilization and enhanced aggregation of apoE3 may constitute a common underlying mechanism behind the pathogenesis of LPG.
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Affiliation(s)
- Maria Katsarou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos," Agia Paraskevi, Athens 15341, Greece
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety (INRaSTES), National Centre for Scientific Research "Demokritos," Agia Paraskevi, Athens 15341, Greece
| | - Angeliki Chroni
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos," Agia Paraskevi, Athens 15341, Greece
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92
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Yang LT, Liu JW, Wu YM, Qi YP, Wang JL, Lai NW, Ye X, Chen LS. Proteome profile analysis of boron-induced alleviation of aluminum-toxicity in Citrus grandis roots. Ecotoxicol Environ Saf 2018; 162:488-498. [PMID: 30015195 DOI: 10.1016/j.ecoenv.2018.07.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 01/26/2018] [Revised: 07/02/2018] [Accepted: 07/08/2018] [Indexed: 05/25/2023]
Abstract
Aluminum (Al)-toxicity and boron (B)-deficiency are two major factors limiting crop production in tropical and subtropical areas. Elevating B supply can alleviate the Al-induced inhibition of growth in Citrus grandis. Seedlings of C. grandis were irrigated for 18 weeks with nutrient solutions containing two B levels (2.5 and 20 μM H3BO3) and two Al levels (0 and 1.2 mM AlCl3·6H2O). By using 2-dimensional electrophoresis (2-DE) based MALDI-TOF/TOF-MS method, this study successfully identified and quantified sixty-one differentially abundant proteins in Citrus roots in response to B-Al interactions. The mechanisms underlying the B-induced alleviation of Al-toxicity unveiled by 2-DE technique could be summarized as follows: a) remodeling of cell wall by reducing the synthesis of lignin (sugar ATP Binding Cassette (ABC) transporter ATPase and cinnamyl alcohol dehydrogenase) and increasing the modification of cell wall (UDP-forming); b) enhancing the abundances of proteasomes and turnover of dysfunctional proteins (proteasome or protease); c) increasing the abundance of stress response proteins, such as alcohol dehydrogenase, S-adenosylmethionine synthetase (SAMS) and glycosyl hydrolase; d) reinforcing cellular biological regulation and signal transduction (calreticulin-1). For the first time, some proteins, such as cell division protein 48 (CDC48), calreticulin and phospholipase, which might be involved in the downstream signaling of Al in Citrus plants, were successfully identified.
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Affiliation(s)
- Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing-Wen Liu
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Agricultural Bureau of Tianmen City, Tianmen 431700, China
| | - Yan-Mei Wu
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Jin-Ling Wang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ning-Wei Lai
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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93
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Abstract
Hirudo nipponia (known as Shui Zhi in Chinese) is a well-known Chinese medicine with numerous active ingredients in its body, especially in its saliva. This native Chinese blood-sucking leech has been used for therapeutic purposes since before 100 AD. Modern Chinese physicians use it for a wide range of diseases. Genomic data and molecular information about the pharmacologically active substances produced by this medicinal leech are presently unavailable despite this organism’s medicinal importance. In this study, we performed transcriptome profiling of the salivary glands of medicinal leech H. nipponia using the Illumina platform. In total, 84,657,362 clean reads were assembled into 50,535 unigenes. The obtained unigenes were compared to public databases. Furthermore, a unigene sequence similarity search and comparisons with the whole transcriptome of medical leech were performed to identify potential proteins. Finally, more than 21 genes were predicted to be involved in anticoagulatory, antithrombotic, antibacterial, anti-inflammatory and antitumor processes, which might play important roles in the treatment of various diseases. This study is the first analysis of a sialotranscriptome in H. nipponia. The transcriptome profile will shed light on its genetic background and provide a useful tool to deepen our understanding of the medical value of H. nipponia.
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Affiliation(s)
- Zenghui Lu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Ping Shi
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Huajian You
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Yanqi Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Shijiang Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
- * E-mail:
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94
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Saccà E, Corazzin M, Giannico F, Fabro C, Mason F, Spanghero M. Effect of dietary nitrogen level and source on mRNA expression of urea transporters in the rumen epithelium of fattening bulls. Arch Anim Nutr 2018; 72:341-350. [PMID: 30183395 DOI: 10.1080/1745039x.2018.1507977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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] [Indexed: 12/27/2022]
Abstract
This paper aims to study the effect of the dietary treatments on mRNA expression of urea transporter B (UT-B) and some aquaporins (AQP) in rumen epithelium of Italian Simmental young bulls. Eighty animals allocated to 16 pens were fed from about 500 to 650 kg body weight with four experimental diets, which resulted from the combination of two crude protein levels (125 and 110 g/kg dry matter, diets M and L, respectively) and two nitrogen sources (soybean meal (SBM) or SBM partly replaced by an isonitrogenous mixture of corn and urea; diets -U and +U, respectively). At slaughtering samples of blood and rumen epithelium were collected from six bulls for each diet. Blood samples were analysed for haematological parameters and quantitative PCR was carried out on the mRNA extracted from the rumen epithelium samples. The bulls fed diets M had lower plasma concentrations of aspartate aminotransferase than those receiving diets L (78.9 vs. 88.3 U/l, p = 0.04). Plasma urea was higher (p = 0.03) for diets M and lower for diets +U (2.0 vs. 2.5 and 1.73 vs. 2.00 mmol/l, respectively, in M and L diets, p = 0.04). The effect of dietary treatments on rumen UT expression were limited to AQP3, which was down regulated (p = 0.01) in diets +U. Finally, a high positive correlation (R2 = 0.871) between the expressions of AQP7 and AQP10 was found. In conclusion, the AQP3 appears very responsive to dietary treatments and therefore it is a candidate to be further studied in rumen metabolism experiments. The close relationship between mRNA expression of AQP7 and AQP10 indicates a similar function of these two proteins.
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Affiliation(s)
- Elena Saccà
- a Department of Agricultural, Food, Environmental and Animal Sciences , University of Udine , Udine (UD) , Italy
| | - Mirco Corazzin
- a Department of Agricultural, Food, Environmental and Animal Sciences , University of Udine , Udine (UD) , Italy
| | - Francesco Giannico
- b Department of Agricultural and Environmental Sciences , University of Bari , Bari (BA) , Italy
| | - Carla Fabro
- a Department of Agricultural, Food, Environmental and Animal Sciences , University of Udine , Udine (UD) , Italy
| | - Federico Mason
- a Department of Agricultural, Food, Environmental and Animal Sciences , University of Udine , Udine (UD) , Italy
| | - Mauro Spanghero
- a Department of Agricultural, Food, Environmental and Animal Sciences , University of Udine , Udine (UD) , Italy
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95
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Okitsu N, Matsui K, Horikawa M, Sugahara K, Tanaka Y. Identification and Characterization of Novel Nemophila menziesii Flavone Glucosyltransferases that Catalyze Biosynthesis of Flavone 7,4'-O-Diglucoside, a Key Component of Blue Metalloanthocyanins. Plant Cell Physiol 2018; 59:2075-2085. [PMID: 29986079 DOI: 10.1093/pcp/pcy129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/02/2018] [Indexed: 05/23/2023]
Abstract
The brilliant blue color of the Nemophila menziesii flower is derived from metalloanthocyanin, which consists of anthocyanin {petunidin 3-O-[6-O-(trans-p-coumaroyl)-β-glucoside]-5-O-[6-O-(malonyl)-β-glucoside]}, flavone [apigenin 7-O-β-glucoside-4'-O-(6-O-malonyl)-O-β-glucoside] and metal ions (Mg2+, Fe3+). Although the two glucosyl moieties at the apigenin 7-O and 4'-O positions are essential for metalloanthocyanin formation, the mechanism of glucosylation has not yet been clarified. In this study, we used crude protein extract prepared from N. menziesii petals to determine that apigenin is sequentially glucosylated by the catalysis of UDP-glucose:flavone 4'-O-glucosyltrasferase (F4'GT) and UDP-glucose:flavone 4'-O-glucoside 7-O-glucosyltransferase (F4'G7GT). We identified 150 contigs exhibiting homology with a UDP-glucose-dependent GT in the N. menziesii petal transcriptome and isolated 24 putative full-length GT cDNAs which were then subjected to functional analysis. Two GT cDNAs, NmF4'GT and NmF4'G7GT, which are highly expressed during the early stages of petal development and rarely in leaves, were shown to encode F4'GT and F4'G7GT activities, respectively. Biochemical characterization of the recombinant enzymes revealed that NmF4'GT specifically catalyzed 4'-glucosylation of flavonoids and that NmF4'G7GT specifically catalyzed 7-glucosylation of flavone 4'-O-glucosides and flavones. Apigenin 7,4'-O-diglucoside was efficiently synthesized from apigenin in the presence of recombinant NmF4'GT and NmF4'G7GT. Transgenic tobacco BY-2 cells expressing NmF4'GT and NmF4'G7GT converted apigenin into apigenin 7,4'-O-diglucoside, confirming their activities in vivo. Based on these results, we conclude that these two GTs act co-ordinately to catalyze apigenin 7,4'-O-diglucoside biosynthesis in N. menziesii.
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Affiliation(s)
- Naoko Okitsu
- Research Institute, Suntory Global Innovation Center Ltd, 8-1-1 Seikadai, Seika-cho, Soraku-Gun, Kyoto, Japan
| | - Keisuke Matsui
- Research Institute, Suntory Global Innovation Center Ltd, 8-1-1 Seikadai, Seika-cho, Soraku-Gun, Kyoto, Japan
| | - Manabu Horikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-Gun, Kyoto, Japan
| | - Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-Gun, Kyoto, Japan
| | - Yoshikazu Tanaka
- Research Institute, Suntory Global Innovation Center Ltd, 8-1-1 Seikadai, Seika-cho, Soraku-Gun, Kyoto, Japan
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96
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Jarugula S, Gowda S, Dawson WO, Naidu RA. Development of infectious cDNA clones of Grapevine leafroll-associated virus 3 and analyses of the 5' non-translated region for replication and virion formation. Virology 2018; 523:89-99. [PMID: 30103103 DOI: 10.1016/j.virol.2018.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 05/16/2018] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 01/28/2023]
Abstract
Infectious cDNA clones were developed for Grapevine leafroll-associated virus 3 (GLRaV-3, genus Ampelovirus, family Closteroviridae). In vitro RNA transcripts generated from cDNA clones showed replication via the production of 3'-coterminal subgenomic (sg) mRNAs in Nicotiana benthamiana protoplasts. The detection of sgRNAs and the recovery of progeny recombinant virions from N. benthamiana leaves agroinfiltrated with full-length cDNA clones confirmed RNA replication and virion formation. The 5' non-translated region (5' NTR) of GLRaV-3 was exchangeable between genetic variants and complement the corresponding cognate RNA functions in trans. Mutational analysis of the 5' NTR in minireplicon cDNA clones showed that the conserved 40 nucleotides at the 5'-terminus were indispensable for replication, compared to downstream variable portion of the 5' NTR. Some of the functional mutations in the 5' NTR were tolerated in full-length cDNA clones and produced sgRNAs and virions in N. benthamiana leaves, whereas other mutations affected replication and virion formation.
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Affiliation(s)
- Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, WA 99350, United States
| | - Siddarame Gowda
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - William O Dawson
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, WA 99350, United States.
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97
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Zhang Y, Carrion SA, Zhang Y, Zhang X, Zinski AL, Michal JJ, Jiang Z. Alternative polyadenylation analysis in animals and plants: newly developed strategies for profiling, processing and validation. Int J Biol Sci 2018; 14:1709-1714. [PMID: 30416385 PMCID: PMC6216028 DOI: 10.7150/ijbs.27168] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 05/08/2018] [Accepted: 08/05/2018] [Indexed: 12/25/2022] Open
Abstract
Alternative polyadenylation is an essential RNA processing event that contributes significantly to regulation of transcriptome diversity and functional dynamics in both animals and plants. Here we review newly developed next generation sequencing methods for genome-wide profiling of alternative polyadenylation (APA) sites, bioinformatics pipelines for data processing and both wet and dry laboratory approaches for APA validation. The library construction methods LITE-Seq (Low-Input 3'-Terminal sequencing) and PAC-seq (PolyA Click sequencing) tag polyA+ cDNA, while BAT-seq (BArcoded, three-prime specific sequencing) and PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3'End Retrieval by CrossLinking ImmunoPrecipitation) enrich polyA+ RNA. Interestingly, only WTTS-seq (Whole Transcriptome Termini Site sequencing) targets both polyA+ RNA and polyA+ cDNA. Varieties of bioinformatics pipelines are well established to pursue read quality control, mapping, clustering, characterization and pathway analysis. The RHAPA (RNase H alternative polyadenylation assay) and 3'RACE-seq (3' rapid amplification of cDNA end sequencing) methods directly validate APA sites, while WTSS-seq (whole transcriptome start site sequencing), RNA-seq (RNA sequencing) and public APA databases can serve as indirect validation methods. We hope that these tools, pipelines and resources trigger huge waves of interest in the research community to investigate APA events underlying physiological, pathological and psychological changes and thus understand the information transfer events from genome to phenome relevant to economically important traits in both animals and plants.
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Affiliation(s)
| | | | | | | | | | | | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620
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98
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Shen Y, Shao Y, Cui Y, Zhao X, Zhang W, Li C. Novel C-type lectin from razor clam Sinonovacula constricta agglutinates bacteria and erythrocytes in a Ca 2+-dependent manner. Dev Comp Immunol 2018; 86:9-16. [PMID: 29723812 DOI: 10.1016/j.dci.2018.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/07/2018] [Revised: 04/19/2018] [Accepted: 04/21/2018] [Indexed: 06/08/2023]
Abstract
Among its other physiological roles, C-type lectins functioned as pattern recognition receptors (PRR) in innate immunity received much attention. In the present study, a novel C-type lectin was identified and characterized from the invertebrate razor clam Sinonovacula constrict and designated as ScCTL. The complete cDNA sequence of ScCTL was 828 bp in length and coded a secreted polypeptide of 158 amino acids with a typical CRD domain. Multiple sequence alignments combined with phylogenetic analysis both collectively confirmed that ScCTL was a novel member belong to lectin family. Spatial expression distribution analysis revealed that ScCTL was extensively expressed in all of the examined tissues, and the highest expression was detected in the hepatopancreas. After 1 × 107 CFU/mL Vibrio parahaemolyticus challenge by immersion infection, the ScCTL transcript in hepatopancreas and gill were markedly upregulated and arrived the maximum levels at 24 or 12 h after challenge, respectively. Recombinant ScCTL could agglutinate not only all tested bacteria but sheep and mouse erythrocyte in the presence of Ca2+. All of our studies suggested that ScCTL performed important roles in protecting cells from pathogenic infection in S. constrict.
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Affiliation(s)
- Yaoyao Shen
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yi Cui
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Xuelin Zhao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
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99
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Gismondi E. Identification of molt-inhibiting hormone and ecdysteroid receptor cDNA sequences in Gammarus pulex, and variations after endocrine disruptor exposures. Ecotoxicol Environ Saf 2018; 158:9-17. [PMID: 29656166 DOI: 10.1016/j.ecoenv.2018.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 02/07/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
In amphipods, growth, development and reproduction are mediated by the molt, which is a hormonally controlled process and which, therefore, could be impacted by endocrine disruption compounds (EDC). The molt process is controlled by both X-organ (XO) and Y-organ (YO) through a variety of hormones and receptors including the molt-inhibiting hormone (MIH) and the ecdysteroid receptor (EcR). However, although many studies were devoted to characterize MIH and EcR in crustaceans, only few works evaluated their variations under EDCs exposures. Consequently, the present work aimed to characterize MIH and EcR genes of the amphipod Gammarus pulex, as well as to study their relative expression variations after exposure to four EDCs, proved in vertebrates: ethinylestradiol (estrogen), 4-hydroxytamoxifen (anti-estrogen), 17α-methyltestosterone (androgen) and cyproterone acetate (anti-androgen). PCR amplification allowed to obtain 204 bp length and 255 bp length fragments, encoding for partial sequences of 68 amino acids and 85 amino acids, which correspond to EcR and MIH, respectively, and which are highly conserved in crustacean species. Results highlighted MIH and EcR expressions mainly in G. pulex head, which is the localization of XO and YO. Moreover, irrespective of the EDC exposure, increases of MIH and EcR relative expressions were observed, as it was observed after the exposure to 20-hydroxyecdysone (20HE), the natural molt hormone, used as positive control. Therefore, it appeared that tested EDCs behaved like 20HE, suggesting that their effects could occur through the ecdysteroids pathways, and so impact the molt process of G. pulex on the long term. Finally, the present study is a first step in the possibility of using MIH and EcR relative expressions as biomarkers of exposure for EDCs risk assessment. However additional studies must first be carried out to better characterize and understand their variations, and also better predicted consequences for the exposed amphipods.
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Affiliation(s)
- Eric Gismondi
- University of Liège, Laboratory of Animal Ecology and Ecotoxicology (LEAE) - Freshwater and Oceanic Sciences Unit of Research (FOCUS), Chemistry Institute, Bât. B6C, 11 allée du 6 Août, B-4000 Sart-Tilman, Belgium.
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Diniz MRV, Paiva ALB, Guerra-Duarte C, Nishiyama MY, Mudadu MA, de Oliveira U, Borges MH, Yates JR, Junqueira-de-Azevedo IDL. An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches. PLoS One 2018; 13:e0200628. [PMID: 30067761 PMCID: PMC6070231 DOI: 10.1371/journal.pone.0200628] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 12/06/2017] [Accepted: 06/29/2018] [Indexed: 01/23/2023] Open
Abstract
Phoneutria nigriventer is one of the largest existing true spiders and one of the few considered medically relevant. Its venom contains several neurotoxic peptides that act on different ion channels and chemical receptors of vertebrates and invertebrates. Some of these venom toxins have been shown as promising models for pharmaceutical or biotechnological use. However, the large diversity and the predominance of low molecular weight toxins in this venom have hampered the identification and deep investigation of the less abundant toxins and the proteins with high molecular weight. Here, we combined conventional and next-generation cDNA sequencing with Multidimensional Protein Identification Technology (MudPIT), to obtain an in-depth panorama of the composition of P. nigriventer spider venom. The results from these three approaches showed that cysteine-rich peptide toxins are the most abundant components in this venom and most of them contain the Inhibitor Cysteine Knot (ICK) structural motif. Ninety-eight sequences corresponding to cysteine-rich peptide toxins were identified by the three methodologies and many of them were considered as putative novel toxins, due to the low similarity to previously described toxins. Furthermore, using next-generation sequencing we identified families of several other classes of toxins, including CAPs (Cysteine Rich Secretory Protein-CRiSP, antigen 5 and Pathogenesis-Related 1-PR-1), serine proteinases, TCTPs (translationally controlled tumor proteins), proteinase inhibitors, metalloproteinases and hyaluronidases, which have been poorly described for this venom. This study provides an overview of the molecular diversity of P. nigriventer venom, revealing several novel components and providing a better basis to understand its toxicity and pharmacological activities.
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MESH Headings
- Amino Acid Sequence
- Animals
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- High-Throughput Nucleotide Sequencing
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Peptides/metabolism
- Proteomics
- Sequence Alignment
- Sequence Analysis, DNA
- Spider Venoms/metabolism
- Spiders/genetics
- Spiders/metabolism
- Toxins, Biological/genetics
- Toxins, Biological/metabolism
- Transcriptome
- Tumor Protein, Translationally-Controlled 1
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Affiliation(s)
- Marcelo R. V. Diniz
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ana L. B. Paiva
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Clara Guerra-Duarte
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Milton Y. Nishiyama
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Ursula de Oliveira
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | - Márcia H. Borges
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - John R. Yates
- Department of Chemical Physiology and Molecular and Cellular Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
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