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Ghanei-Motlagh R, Hernández-Orts JS, Fast MD, Whyte SK, El-Matbouli M, Saleh M. Morphological and molecular characterization of Stomachicola muraenesocis Yamaguti, 1934 (Digenea: Hemiuridae) from the daggertooth pike conger Muraenesox cinereus (Forsskål). Parasitology 2024; 151:24-44. [PMID: 37953070 PMCID: PMC10941220 DOI: 10.1017/s0031182023001063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023]
Abstract
Hemiurid digeneans conspecific with Stomachicola muraenesocis Yamaguti, 1934 (the type species of the genus Stomachicola Yamaguti, 1934) were collected from the stomach of the daggertooth pike conger Muraenesox cinereus (Forsskål) off the Persian Gulf of Iran. This study aimed to provide a detailed characterization of Stom. muraenesocis, including measurements, illustrations and scanning electron microscopy (s.e.m.) representations. Comparisons with the original and previous descriptions revealed morphological and metrical variations in several features (i.e. body size and shape, arrangement of reproductive organs, soma to ecsoma length ratio, position of genital opening, number of vitelline tubules and extension of uterine coils) between Stom. muraenesocis from different hosts and localities. This study presents the first molecular sequence data associated with the small (18S) and large (28S) subunit nuclear ribosomal RNA genes (rDNA) for Stom. muraenesocis. Phylogenetic analyses of the 18S dataset placed Stom. muraenesocis as sister lineage to a clade formed of a group of species of Lecithaster Lühe, 1901 (Lecithasteridae Odhner, 1905). In contrast, phylogenetic analyses based on the 28S consistently recovered a sister relationship between Stom. muraenesocis and representatives of the Hemiuridae Looss, 1899. Further comprehensive phylogenetically based classification in light of morphology and taxonomic history of the Hemiuridae and Lecithasteridae is required to infer phylogenetic affinities and historical biogeography of Stomachicola. A comprehensive list of previously reported species of Stomachicola together with their associated hosts, localities and morphometric data is provided.
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Affiliation(s)
- Reza Ghanei-Motlagh
- Division of Fish Health, University of Veterinary Medicine, Vienna, Austria
- Hoplite Research Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Jesús S. Hernández-Orts
- Natural History Museum, London, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Mark D. Fast
- Hoplite Research Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Shona K. Whyte
- Hoplite Research Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | | | - Mona Saleh
- Division of Fish Health, University of Veterinary Medicine, Vienna, Austria
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Lax G, Keeling PJ. Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid. J Eukaryot Microbiol 2023; 70:e12991. [PMID: 37424051 DOI: 10.1111/jeu.12991] [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: 04/05/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data, and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several "orphan" taxa remain without any molecular data whatsoever. Dolium sedentarium is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch of euglenids, the Petalomonadida. We report the first molecular sequencing data for Dolium using single-cell transcriptomics, adding another small piece in the puzzle of euglenid evolution. Both SSU rDNA and multigene phylogenies confirm it as a solitary branch within Petalomonadida.
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Affiliation(s)
- Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Lang D, Wang X, Liu C, Geng W, Irwin DM, Chen S, Li C, Yu L, Xiao H. Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla. Sci China Life Sci 2022; 66:1170-1182. [PMID: 36443512 DOI: 10.1007/s11427-022-2195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022]
Abstract
RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease (RNase) A superfamily, a gene family that is widely used as a model for molecular evolutionary studies. Here, we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this clade. Unexpectedly, RNase9 experienced an evolutionary scenario of "birth and death" in Ruminantia, and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues (epididymis, vas deferens or prostate). This expression pattern combined with the estimate that these genes duplicated during the middle Eocene, a time when Ruminantia become a successful lineage, suggests that the RNase9 gene duplication might have been advantageous for promoting sperm motility and male fertility as an adaptation to climate seasonality changes of this period. In contrast, all RNase9 genes were lost in the Cetacean lineage, which might be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environment and a balance to the demands of ocean resources. This study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla, providing new insights into the evolution of the RNaseA superfamily and molecular mechanisms for organismal adaptations to the environment.
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Affiliation(s)
- Datian Lang
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- Biodiversity Research Center of Wumeng Mountain, Department of Agronomy and Life Science, Zhaotong University, Zhaotong, 657000, China
| | - Xiaoping Wang
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Chunbing Liu
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Weihang Geng
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Li Yu
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
| | - Heng Xiao
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
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Mazrouee S, Hallmark CJ, Mora R, Del Vecchio N, Carrasco Hernandez R, Carr M, McNeese M, Fujimoto K, Wertheim JO. Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection. Sci Rep 2022; 12:19230. [PMID: 36357480 PMCID: PMC9648870 DOI: 10.1038/s41598-022-21924-8] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Detection of viral transmission clusters using molecular epidemiology is critical to the response pillar of the Ending the HIV Epidemic initiative. Here, we studied whether inference with an incomplete dataset would influence the accuracy of the reconstructed molecular transmission network. We analyzed viral sequence data available from ~ 13,000 individuals with diagnosed HIV (2012-2019) from Houston Health Department surveillance data with 53% completeness (n = 6852 individuals with sequences). We extracted random subsamples and compared the resulting reconstructed networks versus the full-size network. Increasing simulated completeness was associated with an increase in the number of detected clusters. We also subsampled based on the network node influence in the transmission of the virus where we measured Expected Force (ExF) for each node in the network. We simulated the removal of nodes with the highest and then lowest ExF from the full dataset and discovered that 4.7% and 60% of priority clusters were detected respectively. These results highlight the non-uniform impact of capturing high influence nodes in identifying transmission clusters. Although increasing sequence reporting completeness is the way to fully detect HIV transmission patterns, reaching high completeness has remained challenging in the real world. Hence, we suggest taking a network science approach to enhance performance of molecular cluster detection, augmented by node influence information.
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Affiliation(s)
- Sepideh Mazrouee
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
| | | | | | | | - Rocio Carrasco Hernandez
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, México
| | | | | | - Kayo Fujimoto
- Department of Health Promotion and Behavioral Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, USA
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Oteng'o AO, Won BY, Cho TO. Proposal for the Sungminiaceae fam. nov. (Ralfsiales, Phaeophyceae) for Sungminia gen. nov. with three new species based on molecular and morphological analyses. J Phycol 2022; 58:719-728. [PMID: 35852925 PMCID: PMC9804423 DOI: 10.1111/jpy.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Based on morphological and molecular analyses, five families have been recognized within the crustose brown algal order Ralfsiales. Our morphological and molecular sequence data were used to assess the establishment and phylogenetic relationship of Sungminia gen. nov. Phylogenies based on rbcL and concatenated rbcL and COI-5P genes support the recognition of Sungminia composed of three distinct lineages, Sungminia gladiata sp. nov., S. pyriformis sp. nov., and S. asiatica sp. nov. We consider that the Sungminia group is clearly distinct at the family level and propose to place Sungminia in a new family, the Sungminiaceae fam. Nov. Our phylogenetic analyses show that the Sungminiaceae forms a strongly supported monophyletic clade with probable sister relationship to the Mesosporaceae. The Sungminiaceae is characterized by perithallial erect filaments moderately adhered, the rod-shaped perithallial erect filaments, plurangia terminated with single sterile cell, and unangia terminally inserted on 1-2 celled stalk that is lateral-basal or sessile to a paraphysis.
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Affiliation(s)
- Antony O. Oteng'o
- Department of Life ScienceChosun UniversityGwangju61452Republic of Korea
- Department of Integrative Biological Sciences and BK21 FOUR Educational Research Group for Age‐associated Disorder Control TechnologyChosun UniversityGwangju61452Republic of Korea
| | - Boo Y. Won
- Department of Life ScienceChosun UniversityGwangju61452Republic of Korea
| | - Tae O. Cho
- Department of Life ScienceChosun UniversityGwangju61452Republic of Korea
- Department of Integrative Biological Sciences and BK21 FOUR Educational Research Group for Age‐associated Disorder Control TechnologyChosun UniversityGwangju61452Republic of Korea
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Chen C, Nadeau S, Topolsky I, Beerenwinkel N, Stadler T. Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example. Epidemics 2022; 39:100576. [PMID: 35605437 PMCID: PMC9107180 DOI: 10.1016/j.epidem.2022.100576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022] Open
Abstract
The SARS-CoV-2 pandemic led to a huge increase in global pathogen genome sequencing efforts, and the resulting data are becoming increasingly important to detect variants of concern, monitor outbreaks, and quantify transmission dynamics. However, this rapid up-scaling in data generation brought with it many IT infrastructure challenges. In this paper, we report about developing an improved system for genomic epidemiology. We (i) highlight key challenges that were exacerbated by the pandemic situation, (ii) provide data infrastructure design principles to address them, and (iii) give an implementation example developed by the Swiss SARS-CoV-2 Sequencing Consortium (S3C) in response to the COVID-19 pandemic. Finally, we discuss remaining challenges to data infrastructure for genomic epidemiology. Improving these infrastructures will help better detect, monitor, and respond to future public health threats.
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Affiliation(s)
- Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, CH 4058, Switzerland; Swiss Institute of Bioinformatics, Lausanne, CH 1015, Switzerland.
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Jurkute N, D'Esposito F, Robson AG, Pitceathly RDS, Cordeiro F, Raymond FL, Moore AT, Michaelides M, Yu-Wai-Man P, Webster AR, Arno G. SSBP1-Disease Update: Expanding the Genetic and Clinical Spectrum, Reporting Variable Penetrance and Confirming Recessive Inheritance. Invest Ophthalmol Vis Sci 2021; 62:12. [PMID: 34905022 PMCID: PMC8684315 DOI: 10.1167/iovs.62.15.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 09/14/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose To report novel genotypes and expand the phenotype spectrum of SSBP1-disease and explore potential disease mechanism. Methods Five families with previously unsolved optic atrophy and retinal dystrophy underwent whole genome sequencing as part of the National Institute for Health Research BioResource Rare-Diseases and the UK's 100,000 Genomes Project. In silico analysis and protein modelling was performed on the identified variants. Deep phenotyping including retinal imaging and International Society for Clinical Electrophysiology of Vision standard visual electrophysiology was performed. Results Seven individuals from five unrelated families with bilateral optic atrophy and/or retinal dystrophy with extraocular signs and symptoms in some are described. In total, 6 SSBP1 variants were identified including the previously unreported variants: c.151A>G, p.(Lys51Glu), c.335G>A p.(Gly112Glu), and c.380G>A, p.(Arg127Gln). One individual was found to carry biallelic variants (c.380G>A p.(Arg127Gln); c.394A>G p.(Ile132Val)) associated with likely autosomal recessive SSBP1-disease. In silico analysis predicted all variants to be pathogenic and Three-dimensional protein modelling suggested possible disease mechanisms via decreased single-stranded DNA binding affinity or impaired higher structure formation. Conclusions SSBP1 is essential for mitochondrial DNA replication and maintenance, with defects leading to a spectrum of disease that includes optic atrophy and/or retinal dystrophy, occurring with or without extraocular features. This study provides evidence of intrafamilial variability and confirms the existence of an autosomal recessive inheritance in SSBP1-disease consequent upon a previously unreported genotype.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Fabiana D'Esposito
- Imperial College Ophthalmic Research Unit, Western Eye Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, Federico II University, Naples, Italy
| | - Anthony G. Robson
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Robert D. S. Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Francesca Cordeiro
- Imperial College Ophthalmic Research Unit, Western Eye Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - F. Lucy Raymond
- NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Anthony T. Moore
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Patrick Yu-Wai-Man
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Andrew R. Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - for the Genomics England Research Consortium
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Imperial College Ophthalmic Research Unit, Western Eye Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, Federico II University, Naples, Italy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom
- NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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Liu Y, Wang Y, Zhou S, Yan M, Tang Q, Zhang J. Structure and chain conformation of bioactive β-D-glucan purified from water extracts of Ganoderma lucidum unbroken spores. Int J Biol Macromol 2021; 180:484-493. [PMID: 33689774 DOI: 10.1016/j.ijbiomac.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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] [Received: 12/25/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/25/2023]
Abstract
Two polysaccharide fractions (GLSB50 and GLSB70) with total sugar content of 82.07 wt% and 53.79 wt%, respectively, were obtained from the water extracts of unbroken Ganoderma lucidum spores by sequential ethanol precipitation treatment. Compared with GLSB70, GLSB50 exhibited better activity on stimulation of humoral immune responses in immunosuppressed mice. A novel β-D-glucan (GLSB50A-III-1) with weight average molecular weight (Mw) of 1.93 × 105 g/mol was purified from GLSB50 through chromatography separation. The exponent α value of Mark-Houwink-Sakurada equation was calculated to be 0.13, indicating that GLSB50A-III-1 presented globular spheres conformation in aqueous solution. Structural analysis showed that GLSB50A-III-1 mainly consisted of (1 → 3), (1 → 4), (1 → 6)-linked β-d-glucose residues in the backbone, with two single β-D-Glcp attached at O-6 of β-(1 → 3) and β-(1 → 4)-linked residues separately as side chains. The repeat unit of GLSB50A-III-1 was deduced as follows.
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Affiliation(s)
- Yanfang Liu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, National Engineering Research Center of Edible Fungi, National R&D Center for Edible Fungi Processing, Shanghai 201403, China
| | - Yatao Wang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, National Engineering Research Center of Edible Fungi, National R&D Center for Edible Fungi Processing, Shanghai 201403, China
| | - Shuai Zhou
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, National Engineering Research Center of Edible Fungi, National R&D Center for Edible Fungi Processing, Shanghai 201403, China.
| | - Mengqiu Yan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, National Engineering Research Center of Edible Fungi, National R&D Center for Edible Fungi Processing, Shanghai 201403, China
| | - Qingjiu Tang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, National Engineering Research Center of Edible Fungi, National R&D Center for Edible Fungi Processing, Shanghai 201403, China.
| | - Jingsong Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, National Engineering Research Center of Edible Fungi, National R&D Center for Edible Fungi Processing, Shanghai 201403, China.
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Abstract
alpha-crystallin, the major protein of the mammalian lens in most species, is an aggregate assembled from two polypeptides, each with a molecular weight around 20,000 Da. It is polydisperse and can be isolated in a variety of forms, including spherical particles with molecular weights ranging upwards from about 200 kDa. Sequence comparisons reveal that it is a member of the small heat shock protein (shsp) family. These proteins are aggregates assembled from polypeptides of 10 to 25 kDa that share a common central domain of about 90 residues (the 'alpha-crystallin domain') with variable N- and C-terminal extensions. alpha-crystallin has been intensively studied for more than 50 years but its three-dimensional structure remains unknown because it has not been possible to obtain crystals for X-ray studies and it is too large for NMR measurements. Structural information has been derived from a variety of solution studies. Because of the protein's polydispersity, interpretation of data has been difficult. This led to different viewpoints and vigorous debate on its structure and properties. Recently, the crystal structures of two closely-related small heat shock proteins have been determined. These have provided some insight into the structure of a-crystallin and explanations of previous observations. Like many other heat shock proteins, alpha-crystallin exhibits chaperone-like properties, including the ability to prevent the precipitation of denatured proteins and to increase cellular tolerance to stress. It has been suggested that these functions are important for the maintenance of lens transparency and the prevention of cataract.
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Affiliation(s)
- Robert C Augusteyn
- Vision Cooperative Research Centre, University of NSW, Sydney, Australia
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Gouy M, Tannier E, Comte N, Parsons DP. Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation. Methods Mol Biol 2021; 2231:241-260. [PMID: 33289897 DOI: 10.1007/978-1-0716-1036-7_15] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present Seaview version 5, a multiplatform program to perform multiple alignment and phylogenetic tree building from molecular sequence data. Seaview provides network access to sequence databases, alignment with arbitrary algorithm, parsimony, distance and maximum likelihood tree building with PhyML, and display, printing, and copy-to-clipboard or to SVG files of rooted or unrooted, binary or multifurcating phylogenetic trees. While Seaview is primarily a program providing a graphical user interface to guide the user into performing desired analyses, Seaview possesses also a command-line mode adequate for user-provided scripts. Seaview version 5 introduces the ability to reconcile a gene tree with a reference species tree and use this reconciliation to root and rearrange the gene tree. Seaview is freely available at http://doua.prabi.fr/software/seaview .
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Affiliation(s)
- Manolo Gouy
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France.
| | - Eric Tannier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
- INRIA Grenoble-Rhône-Alpes, Montbonnot, France
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Pandey B, Tyagi C, Prajapati GK, Mishra AK, Hashem A, Alqarawi AA, Abd_Allah EF, Mohanta TK. Analysis of mutations of defensin protein using accelerated molecular dynamics simulations. PLoS One 2020; 15:e0241679. [PMID: 33253167 PMCID: PMC7703945 DOI: 10.1371/journal.pone.0241679] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022] Open
Abstract
Plant defensins possess diverse biological functions that include antifungal and antibacterial activities and α-amylase and trypsin inhibitory properties. Two mutations, G9R and V39R, were confirmed to increase the antifungal activity of Raphanus sativus antifungal protein 2 (RsAFP2). Accelerated Molecular Dynamics (aMD) were carried out to examine the conformational changes present in these RsAFP2 mutants, and its two closest homologs compared to the wild-type protein. Specifically, the root mean square fluctuation values for the eight cysteine amino acids involved in the four disulfide bonds were low in the V39R mutant compared to the wild-type. Additionally, analysis of the free energy change revealed that G9R and V39R mutations exert a neutral and stabilizing effect on RsAFP2 conformation, and this is supported by the observed lower total energy of mutants compared to the wild-type, suggesting that enhanced stability of the mutants. However, MD simulations to a longer time scale would aid in capturing more conformational state of the wild-type and mutants defensin protein. Furthermore, the aMD simulations on fungal mimic membranes with RsAFP2 and its mutants and homologs showed that the mutant proteins caused higher deformation and water diffusion than the native RsAFP2, especially the V39R mutant. The mutant variants seem to interact by specifically targeting the POPC and POPI lipids amongst others. This work highlights the stabilizing effect of mutations at the 9th and 39th positions of RsAFP2 and their increased membrane deformation activity.
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Affiliation(s)
- Bharati Pandey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gopal Kumar Prajapati
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (AKM); , (TKM)
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Abdulaziz A. Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (AKM); , (TKM)
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12
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Ambler J, Diallo AA, Dearden PK, Wilcox P, Hudson M, Tiffin N. Including Digital Sequence Data in the Nagoya Protocol Can Promote Data Sharing. Trends Biotechnol 2020; 39:116-125. [PMID: 32654776 DOI: 10.1016/j.tibtech.2020.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023]
Abstract
The Nagoya Protocol (NP), a legal framework under the Convention on Biological Diversity (CBD), formalises fair and equitable sharing of benefits arising from biological diversity. It encompasses biological samples and associated indigenous knowledge, with equitable return of benefits to those providing samples. Recent proposals that the use of digital sequence information (DSI) derived from samples should also require benefit-sharing under the NP have raised concerns that this might hamper research progress. Here, we propose that formalised benefit-sharing for biological data use can increase willingness to participate in research and share data, by ensuring equitable collaboration between sample providers and researchers, and preventing exploitative practices. Three case studies demonstrate how equitable benefit-sharing agreements might build long-term collaborations, furthering research for global benefits.
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Affiliation(s)
- Jon Ambler
- Computational Biology Division, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
| | | | - Peter K Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Phil Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Maui Hudson
- Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | - Nicki Tiffin
- Computational Biology Division, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa; Centre for Infectious Disease Epidemiology Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.
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13
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Sisco MC, Silva MG, Lopez B, Arguelles C, Mendonça-Lima L, de Waard JH, Duarte RS, Suffys PN. Newly sequenced genomes of four Bacillus Calmette Guerin vaccines. Mem Inst Oswaldo Cruz 2020; 115:e190401. [PMID: 32401897 PMCID: PMC7212995 DOI: 10.1590/0074-02760190401] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
Abstract
Bacillus Calmette Guerin (BCG) vaccines comprise a family of related strains. Whole genome sequencing has allowed the better characterisation of the differences between many of the BCG vaccines. As sequencing technologies improve, updating of publicly available sequence data becomes common practice. We hereby announce the draft genome of four commonly used BCG vaccines in Brazil, Argentina and Venezuela.
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Affiliation(s)
- Maria Carolina Sisco
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Médica, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada às Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Marlei Gomés Silva
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Médica, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas, Buenos Aires, Argentina
| | - Claudia Arguelles
- Instituto Nacional de Producción de Biológicos Carlos G Malbrán, Buenos Aires, Argentina
| | - Leila Mendonça-Lima
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil
| | - Jacobus H de Waard
- Servicio Autónomo Instituto de Biomedicina Dr Jacinto Convit, Caracas, Venezuela
- One Health Research Group, Universidad de Las Américas, Facultad de Ciencias de la Salud, Quito, Ecuador
| | - Rafael Silva Duarte
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Médica, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada às Micobactérias, Rio de Janeiro, RJ, Brasil
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14
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Abstract
Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Motoaki Seki
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Christian R Landry
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada.
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
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15
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Guo S, Wang Y, Bilal M, Hu H, Wang W, Zhang X. Microbial Synthesis of Antibacterial Phenazine-1,6-dicarboxylic Acid and the Role of PhzG in Pseudomonas chlororaphis GP72AN. J Agric Food Chem 2020; 68:2373-2380. [PMID: 32013409 DOI: 10.1021/acs.jafc.9b07657] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pseudomonas chlororaphis have been demonstrated to be environmentally friendly biocontrol strains, and most of them can produce phenazine compounds. Phenazine-1,6-dicarboxylic acid (PDC), with a potential antibacterial activity, is generally found in Streptomyces but not in Pseudomonas. The present study aimed to explore the feasibility of PDC synthesis and the function of PhzG in Pseudomonas. A PDC producer was constructed by replacing phzG in P. chlororaphis with lphzG from Streptomyces lomondensis. Through gene deletion, common start codon changing, gene silence, and in vitro assay, our result revealed that the yield of PDC in P. chlororaphis is associated with the relative expression of phzG to phzA and phzB. In addition, it is found that PDC can be spontaneously synthesized without PhzG. This study provides an efficient way for PDC production and promotes a better understanding of PhzG function in PDC biosynthesis. Moreover, this study gives an alternative opportunity for developing new antibacterial biopesticides.
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Affiliation(s)
- Shuqi Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yining Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
- National Experimental Teaching Center for Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
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16
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Abstract
Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must include structural representation as an indispensable component. Mathematical representations that simplify the biomolecular structural complexity and reduce ML dimensionality have emerged as a prime winner in D3R Grand Challenges. This review is devoted to the recent advances in developing low-dimensional and scalable mathematical representations of biomolecules in our laboratory. We discuss three classes of mathematical approaches, including algebraic topology, differential geometry, and graph theory. We elucidate how the physical and biological challenges have guided the evolution and development of these mathematical apparatuses for massive and diverse biomolecular data. We focus the performance analysis on protein-ligand binding predictions in this review although these methods have had tremendous success in many other applications, such as protein classification, virtual screening, and the predictions of solubility, solvation free energies, toxicity, partition coefficients, protein folding stability changes upon mutation, etc.
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Affiliation(s)
- Duc Duy Nguyen
- Department of Mathematics, Michigan State University, MI 48824, USA.
| | - Zixuan Cang
- Department of Mathematics, Michigan State University, MI 48824, USA.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA. and Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA and Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
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17
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Zou D, Min Y, Liu Y, Wei X, Wang J. Identification of a Spermidine Synthase Gene from Soybean by Recombinant Expression, Transcriptional Verification, and Sequence Analysis. J Agric Food Chem 2020; 68:2366-2372. [PMID: 32017555 DOI: 10.1021/acs.jafc.9b07443] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spermidine possesses multiple healthy functions, and soybeans contain the most abundant spermidine. In this study, spermidine contents of soybeans from different varieties and production regions in China were evaluated, and a spermidine synthase gene (speE) was identified by recombinant expression, transcriptional verification, and sequence analysis. Spermidine contents of soybean samples from 18 varieties ranged 72.38-228.82 mg/kg, and those from 19 production regions ranged 134.64-242.32 mg/kg. The highest-spermidine sample GZ was used to clone four predicted speE genes. Expressing the gene speE5 improved the spermidine titer by 54% in Bacillus amyloliquefaciens, confirming that speE5 was involved in spermidine synthesis. Transcriptional verification was performed through a soybean germination model. Germination for 48 h led to a onefold increase of spermidine in samples SHX and HB, and corresponding speE5 transcriptional levels were improved by 26-fold and 18-fold, respectively, further verifying the function of speE5. Finally, the sequences of the speE5 gene and deduced amino acids were analyzed, and the conserved sites and catalysis mechanisms were presented. This study identified an active spermidine synthase gene from soybean for the first time, which provided an important gene resource for genetic breeding of spermidine-rich soybean or microbial cell factory.
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Affiliation(s)
- Dian Zou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology and Business University (BTBU) , Beijing 100048 , China
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Yu Min
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology and Business University (BTBU) , Beijing 100048 , China
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Yingli Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology and Business University (BTBU) , Beijing 100048 , China
| | - Xuetuan Wei
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology and Business University (BTBU) , Beijing 100048 , China
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Jing Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing Technology and Business University (BTBU) , Beijing 100048 , China
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18
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Abstract
The IPD-MHC Database represents the official repository for non-human major histocompatibility complex (MHC) sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. IPD-MHC gathers allelic MHC class I and class II sequences from classical and non-classical MHC loci from various non-human animals including pets, farmed and experimental model animals. So far, Atlantic salmon and rainbow trout are the only teleost fish species with MHC class I and class II sequences present. For the remaining teleost or ray-finned species, data on alleles originating from given classical locus is scarce hampering their inclusion in the database. However, a fast expansion of sequenced genomes opens for identification of classical loci where high-throughput sequencing (HTS) will enable typing of allelic variants in a variety of new teleost or ray-finned species. HTS also opens for large-scale studies of salmonid MHC diversity challenging the current database nomenclature and analysis tools. Here we establish an Illumina approach to identify allelic MHC diversity in Atlantic salmon, using animals from an endangered wild population, and alter the salmonid MHC nomenclature to accommodate the expected sequence expansions.
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Affiliation(s)
- Arvind Y M Sundaram
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Åse Helen Garseth
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway
| | - Giuseppe Maccari
- The Pirbright Institute, Woking, UK
- Anthony Nolan Research Institute, London, UK
| | - Unni Grimholt
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway.
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19
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Csávás M, Eszenyi D, Mező E, Lázár L, Debreczeni N, Tóth M, Somsák L, Borbás A. Stereoselective Synthesis of Carbon-Sulfur-Bridged Glycomimetics by Photoinitiated Thiol-Ene Coupling Reactions. Int J Mol Sci 2020; 21:ijms21020573. [PMID: 31963149 PMCID: PMC7013897 DOI: 10.3390/ijms21020573] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
Oligosaccharides and glycoconjugates are abundant in all living organisms, taking part in a multitude of biological processes. The application of natural O-glycosides in biological studies and drug development is limited by their sensitivity to enzymatic hydrolysis. This issue made it necessary to design hydrolytically stable carbohydrate mimetics, where sulfur, carbon, or longer interglycosidic connections comprising two or three atoms replace the glycosidic oxygen. However, the formation of the interglycosidic linkages between the sugar residues in high diastereoslectivity poses a major challenge. Here, we report on stereoselective synthesis of carbon-sulfur-bridged disaccharide mimetics by the free radical addition of carbohydrate thiols onto the exo-cyclic double bond of unsaturated sugars. A systematic study on UV-light initiated radical mediated hydrothiolation reactions of enoses bearing an exocyclic double bond at C1, C2, C3, C4, C5, and C6 positions of the pyranosyl ring with various sugar thiols was performed. The effect of temperature and structural variations of the alkenes and thiols on the efficacy and stereoselectivity of the reactions was systematically studied and optimized. The reactions proceeded with high efficacy and, in most cases, with complete diastereoselectivity producing a broad array of disaccharide mimetics coupling through an equatorially oriented methylensulfide bridge.
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Affiliation(s)
- Magdolna Csávás
- Department of Pharmaceutical Chemistry University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (M.C.); (D.E.); (E.M.); (N.D.)
| | - Dániel Eszenyi
- Department of Pharmaceutical Chemistry University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (M.C.); (D.E.); (E.M.); (N.D.)
| | - Erika Mező
- Department of Pharmaceutical Chemistry University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (M.C.); (D.E.); (E.M.); (N.D.)
| | - László Lázár
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (L.L.); (M.T.); (L.S.)
| | - Nóra Debreczeni
- Department of Pharmaceutical Chemistry University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (M.C.); (D.E.); (E.M.); (N.D.)
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Marietta Tóth
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (L.L.); (M.T.); (L.S.)
| | - László Somsák
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (L.L.); (M.T.); (L.S.)
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (M.C.); (D.E.); (E.M.); (N.D.)
- Correspondence: ; Tel.: +36-52-512900-22472
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20
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Abstract
Synthetic peptides representing different areas of the CEA molecule were used as immunogens for the development of anti-CEA antibodies. Both polyclonal and monoclonal antibodies were generated using peptides composed of CEA amino acid positions 99–128 and 585–613, respectively. One MAb, designated CP4, generated using the CEA peptide 99–128, was chosen for a more detailed analysis of reactivity. MAb CP4 reacts in solid phase RIAs with CEA peptide 99–128 immunogen and purified native CEA. CP4 did not react with purified non- specific cross reacting antigen (NCA), even though there were two single amino acid differences between NCA and CEA in the 29 amino acid peptide. The affinity constants of CP4 for the CEA peptide 99–128 and native CEA are 4.07 × 109M−1and 5.75 × 108M−1, respectively. When CP4 was reacted with purified CEA in Western blotting experiments, the Mr 180,000 glycoprotein characteristic of CEA was detected, but CP4 reacted to various size entities in tumor cell extracts. The results of liquid competition RIAs showed that the epitope that MAb CP4 recognized on native CEA is not available for binding when CEA is in solution. Physical (adsorption to a solid matrix) or chemical (deglycosylation or formalin-fixation) alteration of CEA is required for binding of CP4 to CEA. MAb CP4 reacted approximately 1,000-fold greater to deglycosylated CEA than native CEA. Immunohistochemical studies using formalin-fixed paraffin-embedded tissue sections demonstrated that, among carcinomas, CP4 reacts selectively with colorectal carcinomas, while normal colon is negative. Although stomach carcinoma is negative, dysplastic lesions and areas of intestinal metaplasia are reactive. Two of 7 normal stomach tissues showed focal cytoplasmic reactivity of the surface epithelium. CP4, therefore, appears to react with an epitope with highly restricted expression in colorectal carcinoma. These studies demonstrate the complexities in dealing with an anti-peptide MAb with reactivity to an epitope which is accessible only under certain conditions.
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Affiliation(s)
- P Horan Hand
- Laboratory of Tumor Immunology and Biology, National Cancer Institute, Bethesda, MD
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21
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Pallegar P, Peña-Castillo L, Langille E, Gomelsky M, Lang AS. Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus. J Bacteriol 2020; 202:e00554-19. [PMID: 31659012 PMCID: PMC6941535 DOI: 10.1128/jb.00554-19] [Citation(s) in RCA: 8] [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: 08/28/2019] [Accepted: 10/19/2019] [Indexed: 02/08/2023] Open
Abstract
Gene transfer agents (GTAs) are bacteriophage-like particles produced by several bacterial and archaeal lineages that contain small pieces of the producing cells' genomes that can be transferred to other cells in a process similar to transduction. One well-studied GTA is RcGTA, produced by the alphaproteobacterium Rhodobacter capsulatus RcGTA gene expression is regulated by several cellular regulatory systems, including the CckA-ChpT-CtrA phosphorelay. The transcription of multiple other regulator-encoding genes is affected by the response regulator CtrA, including genes encoding putative enzymes involved in the synthesis and hydrolysis of the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). To investigate whether c-di-GMP signaling plays a role in RcGTA production, we disrupted the CtrA-affected genes potentially involved in this process. We found that disruption of four of these genes affected RcGTA gene expression and production. We performed site-directed mutagenesis of key catalytic residues in the GGDEF and EAL domains responsible for diguanylate cyclase (DGC) and c-di-GMP phosphodiesterase (PDE) activities and analyzed the functions of the wild-type and mutant proteins. We also measured RcGTA production in R. capsulatus strains where intracellular levels of c-di-GMP were altered by the expression of either a heterologous DGC or a heterologous PDE. This adds c-di-GMP signaling to the collection of cellular regulatory systems controlling gene transfer in this bacterium. Furthermore, the heterologous gene expression and the four gene disruptions had similar effects on R. capsulatus flagellar motility as found for gene transfer, and we conclude that c-di-GMP inhibits both RcGTA production and flagellar motility in R. capsulatusIMPORTANCE Gene transfer agents (GTAs) are virus-like particles that move cellular DNA between cells. In the alphaproteobacterium Rhodobacter capsulatus, GTA production is affected by the activities of multiple cellular regulatory systems, to which we have now added signaling via the second messenger dinucleotide molecule bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). Similar to the CtrA phosphorelay, c-di-GMP also affects R. capsulatus flagellar motility in addition to GTA production, with lower levels of intracellular c-di-GMP favoring increased flagellar motility and gene transfer. These findings further illustrate the interconnection of GTA production with global systems of regulation in R. capsulatus, providing additional support for the notion that the production of GTAs has been maintained in this and related bacteria because it provides a benefit to the producing organisms.
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Affiliation(s)
- Purvikalyan Pallegar
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Evan Langille
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour 2020. [PMID: 31599058 DOI: 10.1101/489088] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 05/13/2023]
Abstract
Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | | | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Wen X Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Gui T Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Allred LK, Sealey Voyksner JA, Voyksner RD. Evaluation of Qualitative and Quantitative Immunoassays To Detect Barley Contamination in Gluten-Free Beer with Confirmation Using LC/MS/MS. J AOAC Int 2019; 97:1615-25. [PMID: 25313640 DOI: 10.5740/jaoacint.14-058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
To meet the need for the detection and quantitation of barley gluten in beer, qualitative screening and quantitative immunoassays based on the monoclonal antigluten antibody 401/21 (Skerritt) were validated in a single laboratory. Sample replicates were tested at each stage of beer production using multiple yeast strains and methods of end-stage protein removal. Quantitation was performed using barley-specific standards based on barley flour extracts. Immunoassay results were confirmed using LC/MS/MS for barley-specific peptides. The LOD for the qualitative screening test was 5 mg/L barley gluten. Recovery for the barley-spiked worts ranged from 81 to 128% in the quantitative ELISA assay; the LOD was <1 mg/L, and the LOQ was 5 mg/L. Both screening and confirmation methods were found to be fit for the purposes of detection of low levels of barley gluten in beer.
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Ma L, Ng TK, Chen H, Brelén ME, Lai TYY, Ho M, Tam POS, Young AL, Chen W, Tham CC, Pang CP, Chen LJ. Identification and characterization of a novel promoter variant in placental growth factor for neovascular age-related macular degeneration. Exp Eye Res 2019; 187:107748. [PMID: 31377148 DOI: 10.1016/j.exer.2019.107748] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 06/20/2019] [Accepted: 07/26/2019] [Indexed: 02/05/2023]
Abstract
PURPOSE Intronic variants in the placental growth factor (PGF) gene have been associated with neovascular age-related macular degeneration (AMD). This study is to discover and characterize rare variants in the PGF gene for neovascular AMD. METHODS The promoter region, coding sequences and splicing regions of the PGF gene were sequenced in a Hong Kong southern Chinese cohort of 235 neovascular AMD patients and 435 controls. A detected 18 base-pair deletion variant in the promoter region of PGF was analyzed in a Shantou southern Chinese cohort of 189 neovascular AMD patients and 846 controls. The transcription activity of this disease-associated promoter variant was determined in human ARPE-19 cells by promoter-luciferase analysis. RESULTS A novel 18-base-pair deletion mutation in the promoter region of PGF was identified in 3 (1.28%) patients and 1 (0.23%) control subject (OR = 5.61; 95% CI 0.58-54.26) in the Hong Kong cohort, and in 2 (1.06%) patients and 2 (0.24%) controls (OR = 4.51; 95% CI: 0.63-32.25) in the Shantou cohort. In the combined southern Chinese sample, this deletion had a significant association with neovascular AMD (P = 0.026; OR = 5.08, 95% CI: 1.21-21.36). The 18-base-pair deletion was predicted to alter the transcription factor binding sites in the PGF promoter, and higher luciferase expression was detected in ARPE-19 cells transfected with the deletion variant plasmid than those transfected with wild type plasmid (P = 0.0002). CONCLUSIONS This study identified a rare, functional promoter variant in the PGF gene that increases PGF transcription activity and confers a 5-fold risk to neovascular AMD.
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Affiliation(s)
- Li Ma
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tsz Kin Ng
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China; Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China; Shantou University Medical College, Shantou, Guangdong, China
| | - Haoyu Chen
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Marten E Brelén
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Timothy Y Y Lai
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mary Ho
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Pancy O S Tam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Alvin L Young
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China; Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Weiqi Chen
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Clement C Tham
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China; Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China; Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.
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Martins L, de Almeida AB, Dos Santos EJL, Foster BL, Machado RA, Kantovitz KR, Coletta RD, Nociti FH. A novel combination of biallelic ALPL mutations associated with adult hypophosphatasia: A phenotype-genotype association and computational analysis study. Bone 2019; 125:128-139. [PMID: 31077853 DOI: 10.1016/j.bone.2019.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 01/29/2019] [Revised: 04/28/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023]
Abstract
Hypophosphatasia (HPP) is an inherited metabolic disorder that causes defective skeletal and dental mineralization. HPP exhibits a markedly heterogeneous range of clinical manifestations caused by dysfunction of the tissue-nonspecific isozyme of alkaline phosphatase (TNSALP), resulting from loss-of-function mutations in the ALPL gene. HPP has been associated with predominantly missense mutations in ALPL, and a number of compound heterozygous genotypes have been identified. Here, we describe a case of a subject with adult-onset HPP caused by a novel combination of missense mutations p.Gly473Ser and p.Ala487Val, resulting in chronic musculoskeletal pain, myopathy, persistent fatigue, vomiting, and an uncommon dental phenotype of short-rooted permanent teeth. Pedigree and biochemical analysis indicated that severity of symptoms was correlated with levels of residual ALP activity, and co-segregated with the p.Gly473Ser missense mutation. Bioinformatic analysis to predict the structural and functional impact of each of the point mutations in the TNSALP molecule, and its potential contribution to the clinical symptoms, revealed that the affected Gly473 residue is localized in the homodimer interface and predicted to have a dominant negative effect. The affected Ala487 residue was predicted to bind to Tyr479, which is closely located the N-terminal α-helix of TNSALP monomer 2, suggesting that both changes may impair dimer stability and catalytic functions. In conclusion, these findings assist in defining genotype-phenotype associations for HPP, and further define specific sites within the TNSALP molecule potentially related to neuromuscular manifestations in adult HPP, allowing for a better understanding of HPP pathophysiology.
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Affiliation(s)
- Luciane Martins
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Amanda Bandeira de Almeida
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Elis Janaína Lira Dos Santos
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Brian L Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Renato Assis Machado
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Kamila Rosamilia Kantovitz
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil; Department of Dental Materials, São Leopoldo Mandic School of Dentistry and Research Center, Campinas, SP, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil.
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Park YS, Kim S, Park DG, Kim DH, Yoon KW, Shin W, Han K. Comparison of library construction kits for mRNA sequencing in the Illumina platform. Genes Genomics 2019; 41:1233-1240. [PMID: 31350733 DOI: 10.1007/s13258-019-00853-3] [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: 05/07/2019] [Accepted: 07/15/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND The emergence of next-generation sequencing (NGS) technologies has made a tremendous contribution to the deciphering and significance of transcriptome analysis in biological fields. Since the advent of NGS technology in 2007, Illumina, Inc. has provided one of the most widely used sequencing platforms for NGS analysis. OBJECTIVE Although reagents and protocols provided by Illumina are adequately performed in transcriptome sequencing, recently, alternative reagents and protocols which are relatively cost effective are accessible. However, the kits derived from various manufacturers have advantages and disadvantages when researchers carry out the transcriptome library construction. METHODS We compared them using a variety of protocols to produce Illumina-compatible libraries based on transcriptome. Three different mRNA sequencing kits were selected for this study: TruSeq® RNA Sample Preparation V2 (Illumina, Inc., USA), Universal Plus mRNA-Seq (NuGEN, Ltd., UK), and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England BioLabs, Ltd., USA). We compared them focusing on cost, experimental time, and data output. RESULTS The quality and quantity of sequencing data obtained through the NGS technique were strongly influenced by the type of the sequencing library kits. It suggests that for transcriptome studies, researchers should select a suitable library construction kit according to the goal and resources of experiments. CONCLUSION The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.
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Affiliation(s)
- Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea
| | - Songmi Kim
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Dong-Guk Park
- Department of Surgery, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Kyeong-Wook Yoon
- Department of Neurosurgery, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Wonseok Shin
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
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Perego RA, Cairoli R, Cornacchini G, Bianchi C, Corizzato M, Tresoldi E, Morra E. The Role of Quantitative Polymerase Chain Reaction in the Management of Follicular Lymphoma Patients. Tumori 2019; 91:59-66. [PMID: 15850006 DOI: 10.1177/030089160509100111] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aims and backgroundIn order to increase the prognostic significance of polymerase chain reaction (PCR) data it has been suggested that quantitative PCR can be used to measure tumor burden. However, this option has not yet been definitely supported or refuted in patients with follicular lymphoma (FL). We decided to evaluate whether knowledge of the quantitative level of minimal residual disease and its variations can be of use in the management of FL patients.MethodsWe used qualitative and competitive PCR to study 11 patients with refractory or relapsed FL harboring the t(14;18) translocation who underwent autologous (nine patients) or allogeneic (two patients) stem cell transplantation (SCT). Competitive PCR was performed with a multiple competitor carrying specific sequences including Bcl2/lgH MBR and mcr, and the β-globin gene.ResultsAfter a median post-SCT follow-up of 44 months (range, 12-62), overall survival was 91% and disease-free survival 82%. The quantitative PCR data showed that: 1) effective chemotherapy before SCT substantially (1-2 log) reduced the tumor burden in the bone marrow (BM); 2) the increase in rearranged DNA detected in BM was associated with disease progression and relapse; 3) a PCR-negative autograft seemed to lead to lasting molecular remission even when it was performed in patients with a low level of BM infiltration before transplant; and 4) allo-SCT made and maintained the BM PCR negative even in the presence of a greater tumor burden before SCT. Six of the nine patients having CR after SCT (four auto and two allo) are in continuous molecular remission.ConclusionsIn FL patients qualitative and quantitative PCR may provide data that can be helpful for the prognostic evaluation of tumor progression and the early detection of impending relapse by highlighting biological features such as the quality of the infused material, the tumor burden at transplant, and the behavior of tumor cells after transplant.
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Affiliation(s)
- Roberto A Perego
- Department of Experimental and Environmental Medicine and Medical Biotechnologies, School of Medicine, Milano-Bicocca University, Monza, Milan, Italy.
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Anderson JA, Brustkern S, Cong B, Deege L, Delaney B, Hong B, Lawit S, Mathesius C, Schmidt J, Wu J, Zhang J, Zimmermann C. Evaluation of the History of Safe Use of the Maize ZMM28 Protein. J Agric Food Chem 2019; 67:7466-7474. [PMID: 31184886 DOI: 10.1021/acs.jafc.9b00391] [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] [Indexed: 06/09/2023]
Abstract
The ZMM28 protein encoded by the zmm28 gene is endogenous to maize. DP202216 maize was genetically modified to increase and extend expression of the zmm28 gene relative to native zmm28 gene expression, resulting in plants with enhanced grain yield potential. Evaluation of the history of safe use (HOSU) is one component of the safety assessment framework for a newly expressed protein in a GM crop. The deduced amino acid sequence of the introduced ZMM28 protein in DP202216 maize is identical to the ZMM28 protein in nonmodified conventional maize. The ZMM28 protein has also been found in selected varieties of sweet corn kernels, and closely related proteins are found in other commonly consumed food crops. Concentrations of the ZMM28 protein in event DP202216 maize, conventional maize, and sweet corn are reported. This information supports, in part, the evaluation of HOSU, which can be leveraged in the safety assessment of the ZMM28 protein. Additional studies will be considered in the food and feed safety assessment of the DP202216 maize event.
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Affiliation(s)
- Jennifer A Anderson
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Sarah Brustkern
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Bin Cong
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Lora Deege
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Bryan Delaney
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Bonnie Hong
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Shai Lawit
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Carey Mathesius
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Jean Schmidt
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Jingrui Wu
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - John Zhang
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Cindi Zimmermann
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
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Erster O, Rubinstein MG, Menasherow S, Ivanova E, Venter E, Šekler M, Kolarevic M, Stram Y. Importance of the lumpy skin disease virus (LSDV) LSDV126 gene in differential diagnosis and epidemiology and its possible involvement in attenuation. Arch Virol 2019; 164:2285-2295. [PMID: 31250104 DOI: 10.1007/s00705-019-04327-5] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/24/2019] [Indexed: 12/19/2022]
Abstract
Examination of lumpy skin disease virus (LSDV) isolates from different geographic regions and times revealed that assays developed in our laboratory for differentiating between virulent Israeli viruses and Neethling vaccine virus (NVV) are generally useful in most, if not all, endemic areas in which NVV-based vaccines are used. Recently it was revealed that the LSDV126 gene of field isolates contains a duplicated region of 27 bp (9 aa), while the vaccine viruses have only one copy. Phylogenetic analysis of a 532-bp segment carrying the LSDV126 gene and whole virus genome sequences revealed that LSDV isolates formed two groups: virulent and vaccine viruses. In this analysis, all of the capripox viruses that lack the ability to efficiently infect cattle were found to carry only one copy of the 27-bp fragment, suggesting that the LSDV126 gene plays an important role in the ability of capripox viruses to infect cattle. In silico analysis of potential antigenic sites in LSDV126 revealed that LSDV126 variants with only one copy of the repeat lack a potentially important antigenic epitope, supporting its possible significance in cattle infection. This study provides new information about the nature of the LSDV126 gene and its possible role in the life cycle of LSDV.
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Affiliation(s)
- Oran Erster
- Kimron Veterinary Institute, P.O. Box 12, 50250, Beit Dagan, Israel
| | | | | | | | - Estelle Venter
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
- College of Public Health, Medical and Veterinary Sciences, Discipline Veterinary Science, James Cook University, Townsville, Australia
| | - Milanko Šekler
- Veterinary Specialist Institute "Kraljevo", Žička 34, Kraljevo, 36000, Republic of Serbia
| | - Mišo Kolarevic
- Veterinary Specialist Institute "Kraljevo", Žička 34, Kraljevo, 36000, Republic of Serbia
| | - Yehuda Stram
- Kimron Veterinary Institute, P.O. Box 12, 50250, Beit Dagan, Israel.
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Alvarez-Quinto RA, Lockhart BEL, Olszewski N. Complete genome sequence of a previously undescribed badnavirus occurring in Polyscias fruticosa L. (Ming aralia). Arch Virol 2019; 164:2371-2374. [PMID: 31165927 DOI: 10.1007/s00705-019-04307-9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/06/2019] [Indexed: 11/26/2022]
Abstract
A previously undescribed badnavirus was identified in plants of Polyscias fruticosa (Ming aralia) showing symptoms of mild mosaic and leaf senescence. Characteristic bacilliform virions of the Polyscias badnavirus averaging 30 × 120 nm in size were observed by transmission electron microscopy in partially purified leaf tissue extracts from symptomatic but not asymptomatic plants collected in the USA and Nigeria. The isolate from the USA was complete sequenced. The genome is 7592 bp in length and contains three open reading frames with an arrangement similar to that of other members of the genus Badnavirus. The largest open reading frame (ORF3) encodes a putative polyprotein, with predicted domains including zinc finger, aspartic protease, reverse transcriptase (RT) and RNase H, in that order. The USA and Nigeria isolates of the virus had a high level (98%) of nucleotide sequence identity in the RT+RNase H region. Within the genus Badnavirus, these viruses were most closely related to schefflera ringspot virus (SRV), sharing 63% identity at the nucleotide level. Based on the ICTV species demarcation criteria for the genus Badnavirus (more than 20% nucleotide sequence divergence in the RT+RNase H region), the Polyscias virus is proposed to be a new member of the genus, and the name polyscias mosaic virus (PoMV) is proposed. The complete genome sequence was deposited in the NCBI GenBank database under accession no. MH475918.
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Affiliation(s)
- R A Alvarez-Quinto
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
| | - B E L Lockhart
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - N Olszewski
- Department of Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA
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Chen C, Su L, Xu F, Xia Y, Wu J. Improved Thermostability of Maltooligosyltrehalose Synthase from Arthrobacter ramosus by Directed Evolution and Site-Directed Mutagenesis. J Agric Food Chem 2019; 67:5587-5595. [PMID: 31016980 DOI: 10.1021/acs.jafc.9b01123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Maltooligosyltrehalose synthase (MTSase) is a key enzyme in trehalose production. MTSase from Arthrobacter ramosus has poor thermostability, limiting its industrial use. In this study, mutant G415P was obtained by directed evolution and S361R/S444E was subsequently generated based on a structure analysis of the region around G415. The t1/2 of G415P and S361R/S444E at 60 °C increased by 3.0- and 3.2-fold, respectively, compared with the wild-type enzyme. A triple mutant (G415P/S361R/S444E) was obtained through a combination of the above mutants, and its t1/2 significantly increased by 19.7-fold. Kinetic and thermodynamic stability results showed that the T50 and Tm values of the triple mutant increased by 7.1 and 7.3 °C, respectively, compared with those of the wild-type enzyme. When the triple mutant was used in trehalose production, the yield reached 71.6%, higher than the 70.3% achieved with the wild-type. Thus, the mutant has a potential application for industrial trehalose production.
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Ziko L, Adel M, Malash MN, Siam R. Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival. Mar Drugs 2019; 17:md17050273. [PMID: 31071993 PMCID: PMC6562949 DOI: 10.3390/md17050273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 03/25/2019] [Revised: 04/12/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea brine pools. Shotgun sequence assembly and secondary metabolite analysis shell (antiSMASH) screening unraveled 2751 Red Sea brine SMGCs, pertaining to 28 classes. Predicted categorization of the SMGC products included those (1) commonly abundant in microbes (saccharides, fatty acids, aryl polyenes, acyl-homoserine lactones), (2) with antibacterial and/or anticancer effects (terpenes, ribosomal peptides, non-ribosomal peptides, polyketides, phosphonates) and (3) with miscellaneous roles conferring adaptation to the environment/special structure/unknown function (polyunsaturated fatty acids, ectoine, ladderane, others). Saccharide (80.49%) and putative (7.46%) SMGCs were the most abundant. Selected Red Sea brine pool sites had distinct SMGC profiles, e.g., for bacteriocins and ectoine. Top promising candidates, SMs with pharmaceutical applications, were addressed. Prolific SM-producing phyla (Proteobacteria, Actinobacteria, Cyanobacteria), were ubiquitously detected. Sites harboring the largest numbers of bacterial and archaeal phyla, had the most SMGCs. Our results suggest that the Red Sea brine niche constitutes a rich biological mine, with the predicted SMs aiding extremophile survival and adaptation.
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Affiliation(s)
- Laila Ziko
- Graduate Program of Biotechnology, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
| | - Mustafa Adel
- Graduate Program of Biotechnology, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
| | - Mohamed N Malash
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
- Microbiology and Immunology Department, Faculty of Pharmacy, Ahram Canadian University, Giza 12581, Egypt.
| | - Rania Siam
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
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Zeng J, Bi B, Zhang F, Cheng G, Vuong Thi MD, Zhang G. Cu/ZnSOD always responded stronger and rapider than MnSOD in Lymantria dispar larvae under the avermectin stress. Pestic Biochem Physiol 2019; 156:72-79. [PMID: 31027583 DOI: 10.1016/j.pestbp.2019.02.010] [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: 11/02/2018] [Revised: 02/03/2019] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Metalloenzyme SODs play important roles in insects dealing with environmental stress. Here, we cloned the Cu/ZnSOD (LdCZS) and MnSOD (LdMS) mRNA of Lymantria dispar by rapid amplification of cDNA ends (RACE). Afterwards their expression patterns were detected by quantitative real-time polymerase chain reaction (qPCR) after bioinformatic analysis. We found that both LdCZS and LdMS were widely detected in all gypsy moth larvae and all five tissues that we analyzed, and both of them were up-regulated after larvae were fed with avermectin of sublethal concentration and LC10. The LdCZS expression value are always higher than LdMS after treating with avermectin of sublethal concentrations. In addition, temporal expression profile in avermectin treated larvae showed that LdCZS expressed highest at 2nd hour, and LdMS expressed highest at 6th hour. The cuticulas transcribed LdCZS and LdMS significantly higher than heads, fat bodies, Malpighian tubes, and midguts after spraying avermectin of sublethal concentration. These results suggested that both Cu/ZnSOD and MnSOD are important antioxidant enzymes in L. dispar defensing against pesticide stress, and LdCZS always responded rapider and stronger than LdMS.
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Affiliation(s)
- JianYong Zeng
- School of Forest, Northeast Forestry University, Harbin 150040, China.
| | - Bing Bi
- School of Forest, Northeast Forestry University, Harbin 150040, China
| | - FangMing Zhang
- School of Forest, Northeast Forestry University, Harbin 150040, China.
| | - Gong Cheng
- Jilin Kunyun Biological Technology Co., Ltd, 138000, China
| | - Minh Dien Vuong Thi
- School of Forest, Northeast Forestry University, Harbin 150040, China; Vietnam Academy of Agricultural Sciences, Hanoi 100803, Viet Nam
| | - GuoCai Zhang
- School of Forest, Northeast Forestry University, Harbin 150040, China.
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Hawkes TR, Langford MP, Viner R, Blain RE, Callaghan FM, Mackay EA, Hogg BV, Singh S, Dale RP. Characterization of 4-hydroxyphenylpyruvate dioxygenases, inhibition by herbicides and engineering for herbicide tolerance in crops. Pestic Biochem Physiol 2019; 156:9-28. [PMID: 31027586 DOI: 10.1016/j.pestbp.2019.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 11/06/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
4-Hydroxyphenylpyruvate dioxgenase (HPPD) enzymes from rat and from several plants contained only about a single inhibitor-binding active site per dimer which matched the content of iron in the purified Arabidopsis thaliana and Avena sativa enzymes. The dimeric HPPDs were about 10 fold more catalytically active than the tetrameric P. fluorescens enzyme with kcat/KmHPP values ranging from 0.8 to 2.5 s-1 μM-1. Most were also highly sensitive to herbicides with, for example, Ki values for mesotrione ranging from 25 to 100 pM. Curiously HPPDs from cool climate grasses were much less herbicide-sensitive. When likewise expressed in Nicotinia tabacum, Avena sativa HPPD, Ki value of 11 nM for mesotrione, conferred far greater tolerance to mesotrione (CallistoTM) than did any of the more sensitive HPPDs. Targeted mutagenesis of the Avena HPPD led to the discovery of 4 mutations imparting improved inherent tolerance, defined as the ratio of Ki to KmHPP, by about 16 fold without any loss of catalytic activity. The Nicotinia line with the highest expression of this quadruple mutant exhibited substantial resistance even up to a 3 kg/ha post-emergence application of mesotrione. The maximum observed expression level of heterologous plant HPPDs in tobacco was ca. 0.35% of the total soluble protein whereas the endogenous tobacco HPPD constituted only ca. 0.00075%. At such high expression even HPPDs with impaired catalytic activity could be effective. A quintuple mutant Avena sativa HPPD conferred substantial tolerance across a broad range of HPPD herbicide chemistries despite being only ca. 5 % as catalytically active as the wild type enzyme. Testing various wild type and mutant HPPDs in tobacco revealed that tolerance to field rates of herbicide generally requires about two order of magnitude increases in both inherent herbicide tolerance and expression relative to endogenous levels. This double hurdle may explain why target-site based resistance to HPPD-inhibiting herbicides has been slow to evolve in weeds.
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Affiliation(s)
- Tim R Hawkes
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Michael P Langford
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Russell Viner
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Rachael E Blain
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Fiona M Callaghan
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Elaine A Mackay
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Bridget V Hogg
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Shradha Singh
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom
| | - Richard P Dale
- Syngenta Ltd., Jealott's Hill Research Centre, Bracknell RG426EY, United Kingdom.
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Mei XJ, Li MS, Yang Y, Liu M, Mao HY, Zhang ML, Cao MJ, Liu GM. Reducing Allergenicity to Arginine Kinase from Mud Crab Using Site-Directed Mutagenesis and Peptide Aptamers. J Agric Food Chem 2019; 67:4958-4966. [PMID: 30966750 DOI: 10.1021/acs.jafc.9b00608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The mud crab ( Scylla paramamosain) is widely consumed but can cause a severe food allergic reaction. To reduce allergenicity to arginine kinase (AK), site-directed mutagenesis was used to destroy disulfide bonds or mutate critical amino acids of conformational epitopes. Three hypoallergenic mutant AKs (mAK1, mAK2, and mAK3) were generated, with the immunoreactivity decreasing by 54.2, 40.1, and 71.4%, respectively. In comparison to recombinant AK (rAK), the structure of mAKs was clearly changed. Additionally, antisense peptides were designed on the basis of linear epitopes and pepsin-cutting sites of AK. Five peptide aptamers were screened by molecular docking and then analyzed by the immunoglobulin E inhibition enzyme-linked immunosorbent assay and human Laboratory of Allergic Diseases 2 mast cell degranulation assay. The peptide aptamers could significantly inhibit allergenicity of rAK and mAKs, and the inhibitory effect of peptide aptamer 3 was slightly better than the others. These results provide synergistic methods to reduce allergenicity to AK, which could be applied to other shellfish allergens.
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Affiliation(s)
- Xue-Jiao Mei
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , People's Republic of China
| | - Meng-Si Li
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , People's Republic of China
| | - Yang Yang
- College of Environment and Public Health , Xiamen Huaxia University , Xiamen , Fujian 361024 , People's Republic of China
| | - Meng Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , People's Republic of China
| | - Hai-Yan Mao
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , People's Republic of China
| | - Ming-Li Zhang
- Xiamen Medical College Affiliated Second Hospital , Xiamen , Fujian 361021 , People's Republic of China
| | - Min-Jie Cao
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , People's Republic of China
| | - Guang-Ming Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , People's Republic of China
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Pozzi C, Lopresti L, Tassone G, Mangani S. Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS). Molecules 2019; 24:molecules24081638. [PMID: 31027295 PMCID: PMC6514825 DOI: 10.3390/molecules24081638] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/10/2023] Open
Abstract
In cells, thymidylate synthases provide the only de novo source of 2′-deoxythymidine-5′-monophosphate (dTMP), required for DNA synthesis. The activity of these enzymes is pivotal for cell survival and proliferation. Two main families of thymidylate synthases have been identified in bacteria, folate-dependent thymidylate synthase (TS) and flavin-dependent TS (FDTS). TS and FDTS are highly divergent enzymes, characterized by exclusive catalytic mechanisms, involving different sets of cofactors. TS and FDTS mechanisms of action have been recently revised, providing new perspectives for the development of antibacterial drugs targeting these enzymes. Nonetheless, some catalytic details still remain elusive. For bacterial TSs, half-site reactivity is still an open debate and the recent evidences are somehow controversial. Furthermore, different behaviors have been identified among bacterial TSs, compromising the definition of common mechanisms. Moreover, the redox reaction responsible for the regeneration of reduced flavin in FDTSs is not completely clarified. This review describes the recent advances in the structural and functional characterization of bacterial TSs and FDTSs and the current understanding of their mechanisms of action. Furthermore, the recent progresses in the development of inhibitors targeting TS and FDTS in human pathogenic bacteria are summarized.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Ludovica Lopresti
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
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Tian Z, Li Y, Xing Y, Li R, Liu J. Structural Insights into Two Representative Conformations of the Complex Formed by Grapholita molesta (Busck) Pheromone Binding Protein 2 and Z-8-Dodecenyl Acetate. J Agric Food Chem 2019; 67:4425-4434. [PMID: 30945860 DOI: 10.1021/acs.jafc.9b00052] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Grapholita molesta is a notorious fruit borer globally, causing severe damage to fruit production. To control the pest, one commonly used mean is pheromone-mediated management. As an important sex pheromone, Z-8-dodecenyl acetate (Z8-12: Ac), is often coformulated with other active ingredients to regulate the behavior of G. molesta. To uncover its interactions with G. molesta pheromone binding protein 2 (GmolPBP2) is used to help develop insect attractants. During 200 ns molecular dynamics simulations, two representative conformations of the GmolPBP2-Z8-12: Ac complex are selected. Conformation II at the time of 14-106 ns is dominantly maintained by the hydrophobic interactions and hydrogen bond. In Conformation I, which lasts from 106 to 200 ns, the hydrophobic interactions are enhanced while the hydrogen bond is quite weakened, due to the formation of a more sophisticated hydrophobic binding pocket and the enlargement of hydrogen bond distance. Taking the two conformations as a whole, the affinity between GmolPBP2 and Z8-12: Ac is crucially determined by three hot-spots including Phe11, Trp36, and Ile51. These results would provide a basis for the discovery, optimization, and design of leading compounds potentially active to attract G. molesta.
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Affiliation(s)
- Zhen Tian
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , China
- College of Horticulture and Plant Protection , Yangzhou University , Wenhui East Road, No. 48 , Yangzhou , Jiangsu Province 225009 , China
| | - Yue Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Yijia Xing
- College of Horticulture and Plant Protection , Yangzhou University , Wenhui East Road, No. 48 , Yangzhou , Jiangsu Province 225009 , China
| | - Ruichi Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , China
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Abstract
Clinical studies in human volunteers are an essential part of drug development. These studies are designed to account for possible differences between the effects of pharmaceutical products in pre-clinical studies and in humans. However, the tragic outcome of the recent Phase 1 clinical trial on TGN1412 casts considerable doubt over the relevance of this traditional drug development paradigm to the testing of therapeutic agents for human use. The role of alternatives to animal testing is considered, and a series of recommendations are made, which could ensure that clinical trials are well informed and based on the most relevant scientific information.
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Affiliation(s)
- Nirmala Bhogal
- FRAME, 96-98 North Sherwood Street, Nottingham, NG1 4EE, UK.
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Tang B, Tai S, Dai W, Zhang C. Expression and Functional Analysis of Two Odorant-Binding Proteins from Bradysia odoriphaga (Diptera: Sciaridae). J Agric Food Chem 2019; 67:3565-3574. [PMID: 30866622 DOI: 10.1021/acs.jafc.9b00568] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Two OBP genes, BodoOBP1 and BodoOBP2, were cloned from Bradysia odoriphaga, a major agricultural pest of Chinese chives. The amino acid sequence alignment of both BodoOBPs showed high similarity. Fluorescence competitive binding assays revealed that both BodoOBPs have a moderate binding affinity to dipropyl trisulfide. Tissue expression profiles indicated that both BodoOBPs are antennae-specific and more abundant in the male antennae than in the female antennae. Developmental expression profile analysis indicated that expression levels of both BodoOBPs were higher in the male adult stage than in the other developmental stages. Both BodoOBPs also showed differential expression in pre- and postmating adults. RNAi assays indicated that ability of dsOBPs-treated males to detect females was significantly reduced compared to controls. Attraction of plant volatile dipropyl trisulfide to dsOBPs-treated adults was also significantly lower than in the control. Our findings indicate that both BodoOBPs are involved in host-seeking behavior and in detecting sex pheromones.
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Affiliation(s)
- Bowen Tang
- Key Laboratory of Plant Protection Resources and Pest Integrated Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , P. R. China
| | - Shulei Tai
- Key Laboratory of Plant Protection Resources and Pest Integrated Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , P. R. China
| | - Wu Dai
- Key Laboratory of Plant Protection Resources and Pest Integrated Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , P. R. China
| | - Chunni Zhang
- Key Laboratory of Plant Protection Resources and Pest Integrated Management of the Ministry of Education, College of Plant Protection , Northwest A&F University , Yangling , Shaanxi 712100 , P. R. China
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Shan Y, Shu C, He K, Cheng X, Geng L, Xiang W, Zhang J. Characterization of a Novel Insecticidal Protein Cry9Cb1 from Bacillus thuringiensis. J Agric Food Chem 2019; 67:3781-3788. [PMID: 30865469 DOI: 10.1021/acs.jafc.9b00385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 05/26/2023]
Abstract
In recent decades, there have been increasing reports of insect resistance in Bacillus thuringiensis (Bt) crops. Alternative use of Cry toxins, with high insecticidal activity and different mechanisms of action, may be an important strategy to manage this resistance. Cry9 protein, with high toxicity to the lepidopteran pests and no cross-resistance with commercial Cry1 proteins, is a valuable relevant resource. A novel insecticidal protein, MP1489, subsequently named as Cry9Cb1, with 88% amino acid sequence identity with Cry9Ca1, was identified from Bt strain SP663; it exhibited high insecticidal activity against Plutella xylostella, Ostrinia furnacalis, and Chilo suppressalis and no cross-resistance with Cry1Fa in Ostrinia furnacalis. Its minimal active fragments against Plutella xylostella and Ostrinia furnacalis were identified to be 72T-657V and 68D-655A, respectively; food-safety assessment showed no sequence homology with any known allergen and rapid degradation and inactivation by both heat and the gastrointestinal environment. Therefore, Cry9Cb1 is proposed to have a brilliant prospect as an insecticidal protein in agriculture.
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Affiliation(s)
- Yueming Shan
- School of Life Science , Northeast Agricultural University , Harbin 150030 , People's Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Kanglai He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Xue Cheng
- School of Life Science , Northeast Agricultural University , Harbin 150030 , People's Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Lili Geng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Wensheng Xiang
- School of Life Science , Northeast Agricultural University , Harbin 150030 , People's Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
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Zhang L, Shang J, Jia Q, Li K, Yang H, Liu H, Tang Z, Chang X, Zhang M, Wang W, Yang W. Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes. Arch Virol 2019; 164:1037-1048. [PMID: 30747339 DOI: 10.1007/s00705-019-04165-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/11/2019] [Indexed: 01/14/2023]
Abstract
Soybean mosaic virus (SMV) is one of the major pathogens causing serious soybean losses. Little is known about the genetic structure and evolutionary biology of the SMV population in southwestern China. In this study, 29 SMV isolates were obtained from Sichuan Province, and the genomic regions encoding the first protein (P1) and coat protein (CP) were sequenced. Combined with SMV isolates from the southeastern and northeastern regions of China, the genetic and molecular evolution of SMV was studied. Recombination analysis revealed that intraspecific and interspecific recombination had occurred in the SMV population. A phylogenetic tree based on the P1 gene reflected the geographic origin of the non-interspecific recombinant SMV (SMV-NI), while a tree based on the CP gene did not. Though frequent gene flow of the SMV-NI populations was found between the southeastern and northeastern populations, the southwestern population was relatively independent. Genetic differentiation was significant between the SMV interspecific recombinant (SMV-RI) and the non-interspecific recombinant (SMV-NI) populations. It was interesting to note that there was an almost identical recombination breakpoint in SMV-RI and Watermelon mosaic virus (WMV). Population dynamics showed that SMV-RI might be in an expanding state, while the SMV-NI population is relatively stable.
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Affiliation(s)
- Lei Zhang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Shang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Qi Jia
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Li
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, China
| | - Hui Yang
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanhuan Liu
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongqin Tang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoli Chang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Zhang
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenming Wang
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenyu Yang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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Kempaiah Nagappa L, Satha P, Govindaraju T, Balaram H. Phosphoglycolate phosphatase is a metabolic proofreading enzyme essential for cellular function in Plasmodium berghei. J Biol Chem 2019; 294:4997-5007. [PMID: 30700551 PMCID: PMC6442027 DOI: 10.1074/jbc.ac118.007143] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/28/2019] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum (Pf) 4-nitrophenylphosphatase has been shown previously to be involved in vitamin B1 metabolism. Here, conducting a BLASTp search, we found that 4-nitrophenylphosphatase from Pf has significant homology with phosphoglycolate phosphatase (PGP) from mouse, human, and yeast, prompting us to reinvestigate the biochemical properties of the Plasmodium enzyme. Because the recombinant PfPGP enzyme is insoluble, we performed an extended substrate screen and extensive biochemical characterization of the recombinantly expressed and purified homolog from Plasmodium berghei (Pb), leading to the identification of 2-phosphoglycolate and 2-phospho-L-lactate as the relevant physiological substrates of PbPGP. 2-Phosphoglycolate is generated during repair of damaged DNA ends, 2-phospho-L-lactate is a product of pyruvate kinase side reaction, and both potently inhibit two key glycolytic enzymes, triosephosphate isomerase and phosphofructokinase. Hence, PGP-mediated clearance of these toxic metabolites is vital for cell survival and functioning. Our results differ significantly from those in a previous study, wherein the PfPGP enzyme has been inferred to act on 2-phospho-D-lactate and not on the L isomer. Apart from resolving the substrate specificity conflict through direct in vitro enzyme assays, we conducted PGP gene knockout studies in P. berghei, confirming that this conserved metabolic proofreading enzyme is essential in Plasmodium In summary, our findings establish PbPGP as an essential enzyme for normal physiological function in P. berghei and suggest that drugs that specifically inhibit Plasmodium PGP may hold promise for use in anti-malarial therapies.
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Affiliation(s)
| | - Pardhasaradhi Satha
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
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Shen W, Feng J, Liu Z, Diao D, Liu CH, Kong X. Identification of the membrane-spanning domain of glycoprotein 45 in bovine immunodeficiency virus. Acta Virol 2019; 62:294-303. [PMID: 30160145 DOI: 10.4149/av_2018_223] [Citation(s) in RCA: 0] [Impact Index Per Article: 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
The membrane-spanning domain (MSD) of the transmembrane subunit (TM) anchors the envelope glycoprotein (Env) on the lipid bilayer of the host cell membrane and virions. Its functions include membrane fusion efficiency and intracellular trafficking of the lentivirus envelope protein. Our study aimed to determine the MSD of bovine immunodeficiency virus (BIV) glycoprotein 45 (gp45) and reveal structural characteristics of the BIV Env protein. We have predicted the region of the BIV MSD and obtained the sequence using bioinformatics software. Various kinds of assays, including analogy analysis, fluorescence microscopy, and dye-transfer-based assays, were carried out to validate the prediction. The results, for the first time, show that the BIV MSD is located at the D170 to M191 amino acids of gp45, and the identified MSD divides gp45 into the extracellular domain (ED), MSD and cytoplasmic domain (CT). We further found that the BIV MSD had a similar structure and function as the HIV MSD using amino acid sequence alignment and fluorescence microscopy. Additionally, the dye-transfer-based assay demonstrates that deletion of the BIV MSD efficiently decreases cell-cell fusion. Based on the identification of the MSD, a "snorkeling" model, in which the flanking charged amino acid residues are buried in the lipid bilayer while their side chains interact with polar head groups, was proposed for the BIV MSD. Ultimately, we further improved the primary structure of the BIV envelope glycoprotein.
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Yang Y, Liu M, Zhang W, Cao Y, Li C, Wang W. Identification and Characterization of Two New 1- O-Acyl-glucose-ester Forming Glucosyltransferases from Erigeron breviscapus. J Agric Food Chem 2019; 67:2848-2855. [PMID: 30821967 DOI: 10.1021/acs.jafc.8b07215] [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] [Indexed: 06/09/2023]
Abstract
Two versatile UDP-glucosyltransferases, UGT75L25 and UGT75X1, were isolated from Erigeron breviscapus. The enzymes display high sequence identity to flavonoid 7- O-glucosyltransferase from Malus species and cluster to the phylogenetic group L of plant glucosyltransferases, also involved in the formation of hydroxycinnamoyl glucose esters, which are used as bifunctional donors in the glucosylation or acylation of anthocyanins. The enzymes, functionally expressed in Escherichia coli, exhibit broad substrate specificity toward 21 structurally diverse types of phenolic acids, including (hydroxy)cinnamates, vanillic acid, 3-hydroxycoumarin, and 7-hydroxyflavonoids. The catalytic characteristics of UGT75L25 and UGT75X1 were exploited to generate the corresponding acyl-glucose-esters or glucosides with high efficiency. These findings demonstrate the significant potential of acyl-glucose-esters in the further enzymatic synthesis of bioactive anthocyanins.
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Affiliation(s)
- Yan Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoplés Republic of China, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Minzhi Liu
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoplés Republic of China, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Wenxuan Zhang
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoplés Republic of China, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Yunsong Cao
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoplés Republic of China, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Changkun Li
- Beijing Branch , Shimadzu (China) Co., Ltd. , Beijing 100020 , China
| | - Wei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoplés Republic of China, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
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Liu X, Wang D, Pan C, Feng E, Fan H, Li M, Zhu L, Tong Y, Wang H. Genome sequence of Bacillus anthracis typing phage AP631. Arch Virol 2019; 164:917-921. [PMID: 30666457 PMCID: PMC6394722 DOI: 10.1007/s00705-018-04135-3] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/02/2018] [Indexed: 11/25/2022]
Abstract
AP631, a virulent bacteriophage of Bacillus anthracis, is widely used in China to identify anthrax bacteria. In this study, we report the complete AP631 phage genome sequence as well as comparative genomic analysis with other bacteriophages of B. cereus and related species. The double-stranded circular DNA genome of phage AP631 was 39,549 bp in length with 35.01% G + C content. The phage genome contained 56 putative protein-coding genes but no rRNA or tRNA genes. Comparative phylogenetic analysis of the phage major capsid proteins and terminase large subunits showed that phage AP631 belongs to the B. cereus sensu lato phage clade II. Comparative genomic analysis revealed a high degree of sequence similarity between phage AP631 and B. anthracis phages Wbeta, Gamma, Cherry, and Fah, as well as three AP631-specific genes bearing no significant similarity to those of other phages.
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Affiliation(s)
- Xiankai Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Chao Pan
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Erling Feng
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Hang Fan
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Manli Li
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Li Zhu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China.
| | - Hengliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China.
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Endo K, Kobayashi K, Wang HT, Chu HA, Shen JR, Wada H. Site-directed mutagenesis of two amino acid residues in cytochrome b 559 α subunit that interact with a phosphatidylglycerol molecule (PG772) induces quinone-dependent inhibition of photosystem II activity. Photosynth Res 2019; 139:267-279. [PMID: 30039358 DOI: 10.1007/s11120-018-0555-3] [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: 03/07/2018] [Accepted: 07/07/2018] [Indexed: 06/08/2023]
Abstract
X-ray crystallographic analysis (1.9-Å resolution) of the cyanobacterial photosystem II (PSII) dimer showed the presence of five phosphatidylglycerol (PG) molecules per reaction center. One of the PG molecules, PG772, is located in the vicinity of the QB-binding site. To investigate the role of PG772 in PSII, we performed site-directed mutagenesis in the cytochrome (Cyt) b559 α subunit of Synechocystis sp. PCC 6803 to change two amino acids, Thr-5 and Ser-11, which interact with PG772. The photosynthetic activity of intact cells was slightly lower in all mutants than that of cells in the control strain; however, the oxygen-evolving PSII activity was decreased markedly in cells of mutants, as measured using artificial quinones (such as p-benzoquinone). Furthermore, electron transport from QA to QB was inhibited in mutants incubated with quinones, particularly under high-intensity light conditions. Lipid analysis of purified PSII showed approximately one PG molecule per reaction center, presumably PG772, was lost in the PSII dimer from the T5A and S11A mutants compared with that in the PSII dimer from the control strain. In addition, protein analysis of monomer and dimer showed decreased levels of PsbV and PsbU extrinsic proteins in the PSII monomer purified from T5A and S11A mutants. These results suggest that site-directed mutagenesis of Thr-5 and Ser-11, which presumably causes the loss of PG772, induces quinone-dependent inhibition of PSII activity under high-intensity light conditions and destabilizes the binding of extrinsic proteins to PSII.
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Affiliation(s)
- Kaichiro Endo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Koichi Kobayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Hsing-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan, Republic of China
| | - Hsiu-An Chu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan, Republic of China
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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Xu Z, Chen H, Wang Z, Fan F, Shi P, Tu M, Du M. Isolation and Characterization of Peptides from Mytilus edulis with Osteogenic Activity in Mouse MC3T3-E1 Preosteoblast Cells. J Agric Food Chem 2019; 67:1572-1584. [PMID: 30614690 DOI: 10.1021/acs.jafc.8b06530] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Seafood provides a range of health benefits because of its high protein levels. In this study, a novel peptide, YPRKDETGAERT, was identified from NHA-2 of Mytilus edulis by capillary-electrophoresis electrospray ionization-quadrupole-time of flight (CESI-Q-TOF). Peptide YPRKDETGAERT showed the highest affinity among all the peptides, with -CDOCKER energy values of 204.482 kcal/mol on one integrin (PDB: 3VI4 ) and 210.16 kcal/mol on another integrin (PDB: 1L5G ). The secondary mass spectrogram at the m/ z of peptide YPRKDETGAERT was 1422.53 Da, which was determined by CESI-Q-TOF. Peptide YPRKDETGAERT induced an increase of 28.27 ± 3.66% in mouse-MC3T3-E1-preosteoblast-cell growth. The alkaline-phosphatase activity of peptide YPRKDETGAERT was 2.79 ± 0.07 mU, which was an increase of 21.25% compared with that of the control. These results provide theoretical and practical insights for the preparation and application of osteogenic peptides in the functional-foods industry.
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Affiliation(s)
- Zhe Xu
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , China
| | - Hui Chen
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , China
| | - Zhenyu Wang
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , China
| | - Fengjiao Fan
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin 150001 , China
| | - Pujie Shi
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin 150001 , China
| | - Maolin Tu
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin 150001 , China
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , China
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Wang W, Hu C, Li XR, Wang XQ, Yang XQ. CpGSTd3 is a lambda-Cyhalothrin Metabolizing Glutathione S-Transferase from Cydia pomonella (L.). J Agric Food Chem 2019; 67:1165-1172. [PMID: 30638381 DOI: 10.1021/acs.jafc.8b05432] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 06/09/2023]
Abstract
Little is known about the role of specific delta GST genes in the detoxification of lambda-cyhalothrin in the global quarantine fruit pest codling moth, Cydia pomonella (L.). Real-time quantitative PCR shows that CpGSTd3 was ubiquitously expressed at all developmental stages and is most abundant in the larval stage and lowest in the egg stage; the mRNA level of CpGSTd3 is higher in the midgut and Malpighian tubules of fourth-instar larvae and abdomens of adults than in other tissues. Exposure of fourth-instar larvae to an LD10 dosage of lambda-cyhalothrin significantly induced the transcript of CpGSTd3 at 3 h, but the mRNA level was down-regulated after 12 h of treatment. Recombinant CpGSTd3 expressed in Escherichia coli was able to catalyze the conjugation of 1-chloro-2,4-dinitrobenzene (CDNB) and with an IC50 value of 0.65 mM for lambda-cyhalothrin. Metabolism assays indicate that recombinant CpGSTd3 could metabolize lambda-cyhalothrin. These results suggest that CpGSTd3 is probably a lambda-cyhalothrin metabolizing GST in C. pomonella.
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Affiliation(s)
- Wei Wang
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , Liaoning , China
- Key Laboratory of Economical and Applied Entomology of Liaoning Province , Shenyang 110866 , Liaoning , China
| | - Chao Hu
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , Liaoning , China
- Key Laboratory of Economical and Applied Entomology of Liaoning Province , Shenyang 110866 , Liaoning , China
| | - Xin-Ru Li
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , Liaoning , China
- Key Laboratory of Economical and Applied Entomology of Liaoning Province , Shenyang 110866 , Liaoning , China
| | - Xiao-Qi Wang
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , Liaoning , China
- Key Laboratory of Economical and Applied Entomology of Liaoning Province , Shenyang 110866 , Liaoning , China
| | - Xue-Qing Yang
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , Liaoning , China
- Key Laboratory of Economical and Applied Entomology of Liaoning Province , Shenyang 110866 , Liaoning , China
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Gallego M, Mora L, Hayes M, Reig M, Toldrá F. Peptides with Potential Cardioprotective Effects Derived from Dry-Cured Ham Byproducts. J Agric Food Chem 2019; 67:1115-1126. [PMID: 30648392 DOI: 10.1021/acs.jafc.8b05888] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interest in using food byproducts as a source of bioactive peptides has increased significantly in the recent years. The goal of this work was to determine the presence and stability of peptides showing angiotensin I-converting enzyme (ACE-I), endothelin-converting enzyme (ECE), dipeptidyl peptidase-IV (DPP-IV), and platelet-activating factor-acetylhydrolase (PAF-AH) inhibitory activity derived from dry-cured ham bones, which could exert cardiovascular health benefits. ACE-I and DPP-IV inhibitory peptides were stable against heating typically used in Mediterranean household cooking methods and also to in vitro digestion. PAF-AH inhibitory activity significantly increased following simulated gastrointestinal digestion whereas ECE inhibitory significantly decreased ( P < 0.05). The mass spectrometry analysis revealed a notable degradation of hemoglobin-derived peptides after simulated digestion, and the release of a large number of dipeptides that may have contributed to the observed bioactivities. These results suggest that natural peptides from Spanish dry-cured ham bones could contribute to a positive impact on cardiovascular health.
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Affiliation(s)
- Marta Gallego
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Avenue Agustín Escardino 7 , 46980 Paterna (Valencia) , Spain
| | - Leticia Mora
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Avenue Agustín Escardino 7 , 46980 Paterna (Valencia) , Spain
| | - Maria Hayes
- Teagasc , The Irish Agricultural and Food Development Authority, Food BioSciences Department , Ashtown, Dublin 15, Ireland
| | - Milagro Reig
- Instituto de Ingeniería de Alimentos para el Desarrollo , Universitat Politècnica de Valencia , Camino de Vera s/n , 46022 Valencia , Spain
| | - Fidel Toldrá
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Avenue Agustín Escardino 7 , 46980 Paterna (Valencia) , Spain
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Dong XB, Liu Y, Feng X, Shi D, Bian YB, Ibrahim SA, Huang W. Purification and Characterization of a Cadmium-Binding Protein from Lentinula edodes. J Agric Food Chem 2019; 67:1261-1268. [PMID: 30623660 DOI: 10.1021/acs.jafc.8b05924] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Many organisms possess the ability to produce metal-binding proteins to absorb cadmium. Metallothioneins, an important family of cysteine-rich metal-binding proteins, have been isolated and well characterized. However, Lentinula edodes may have a different type of cadmium-binding protein that contains fewer cysteine residues. In the present study, we purified a cadmium-binding protein from L. edodes (LECBP) by gel filtration and anion exchange chromatography and then identified LECBP by LC-MS/MS. We found LECBP to be a novel cadmium-binding protein, which contained 220 amino acid residues but no cysteine residue. LECBP had a high binding affinity for Cd(II) with a Kd value of 97.3 μM. The percentages of α-helix, β-sheet, β-turn, and random coil in LECBP were 15.7%, 39.4%, 8.0%, and 37.1%, respectively. In addition, high temperatures and an acidic environment influenced the conformation of LECBP. Our results will thus provide a new perspective to understand the mechanism of cadmium accumulation in L. edodes.
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Affiliation(s)
| | | | - Xi Feng
- Department of Nutrition, Food Science and Packaging , California State University , San Jose , California 95192 , United States
| | - Defang Shi
- Research Institute of Agricultural Products Processing and Nuclear-Agricultural Technology , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , China
| | | | - Salam A Ibrahim
- Department of Family and Consumer Sciences , North Carolina A&T State University , 171 Carver Hall , Greensboro , North Carolina 27411 , United States
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